Heudiconv missed on fmri scan

hcp4715 · February 12, 2019, 11:11pm

Dear all,

I am new to heudicov, I followed the tutorial by Stanford Center for Reproducible Neuroscience (http://reproducibility.stanford.edu/bids-tutorial-series-part-2a/) to convert my own dataset. It seems that there is no error, but obviously one resting scan was not converted.

Information of my system: ubuntu 18.04 (dual boot with window 10), wiht the latest docker version of heudiconv.

Appreciate any comments and suggestions, because I read the tutorial carefully and could’t find which part was wrong

Below is part of dicominfor.tsv ('cause I can only upload one image)

dim1	dim2	dim3	dim4	TR	TE	protocol_name
512	512	3	1	0.0086	4	localizer
72	84	60	480	1	29	resting1_mb4_TR_1000
72	84	60	217	1	29	fmri_Tag1_mb4_TR_1000_fam
72	84	60	496	1	29	fmri_Tag1_mb4_TR_1000
72	84	60	480	1	29	resting2_mb4_TR_1000
320	320	224	1	1.9	2.54	t1_mpr_ns_sag_p2_iso08
448	448	45	1	6.1	79	t2_tse_tra_448_p2_3mm
64	64	100	1	1.03	7.35	gre_field_mapping
64	64	50	1	1.03	7.35	gre_field_mapping
128	128	4680	1	9.1	85	ep2d_diff_mddw_64_p2_b=1000
128	128	72	1	9.1	85	ep2d_diff_mddw_64_p2_b=1000

Below is the screen shot of the func folder, as you can see, only one run of resting there, but the dicom data have two runs.

Here is the code in my heuristic.py

import os


def create_key(template, outtype=('nii.gz',), annotation_classes=None):
    if template is None or not template:
        raise ValueError('Template must be a valid format string')
    return template, outtype, annotation_classes


def infotodict(seqinfo):
    """Heuristic evaluator for determining which runs belong where
    """
    t1w        = create_key('sub-{subject}/{session}/anat/sub-{subject}_T1w')
    t2w        = create_key('sub-{subject}/{session}/anat/sub-{subject}_T2w')
    func_fam   = create_key('sub-{subject}/{session}/func/sub-{subject}_{session}_task-fam_bold')
    func_task  = create_key('sub-{subject}/{session}/func/sub-{subject}_{session}_task-exp_bold')
    func_rest  = create_key('sub-{subject}/{session}/func/sub-{subject}_{session}_task-rest_run-{item:01d}_bold')
    fmap_mag   = create_key('sub-{subject}/{session}/fmap/sub-{subject}_{session}_magnitude')
    fmap_phase = create_key('sub-{subject}/{session}/fmap/sub-{subject}_{session}_phasediff')
    dwi        = create_key('sub-{subject}/{session}/dwi/sub-{subject}_{session}_run-{item:01d}_dwi')

    # data = create_key('run{item:03d}')
    info = {t1w: [], t2w: [], func_fam: [], func_task: [], func_rest: [], fmap_mag: [], fmap_phase:[], dwi: []}
    last_run = len(seqinfo)

    for s in seqinfo:
        """
        The namedtuple `s` contains the following fields:
        """
	# define T1w
        if (s.dim1 == 320) and (s.dim2 == 320) and ('t1_mpr' in s.protocol_name):
            info[t1w] = [s.series_id]
	# define T2w
        if (s.dim1 == 448) and (s.dim2 == 448) and ('t2_tse' in s.protocol_name):
            info[t2w] = [s.series_id]
	# define functional familiarization 
        if (s.dim1 == 72) and (s.dim4 == 217) and ('fmri' in s.protocol_name):
            info[func_fam] = [s.series_id]
	# define functional task
        if (s.dim1 == 72) and (s.dim4 == 496) and ('fmri' in s.protocol_name):
            info[func_task] = [s.series_id]
	# define functional resting
        if (s.dim1 == 72) and (s.dim2 == 84) and ('resting' in s.protocol_name):
            info[func_rest] = [s.series_id]
	# define field map (magnitude)
        if (s.dim3 == 100) and (s.dim4 == 1) and ('gre_field_mapping' in s.protocol_name):
            info[fmap_mag] = [s.series_id]
	# define field map (phasic)
        if (s.dim3 == 50) and (s.dim4 == 1) and ('gre_field_mapping' in s.protocol_name):
            info[fmap_phase] = [s.series_id]
	# define DTI
        if (s.dim1 == 128) and (s.dim4 == 1) and ('diff' in s.protocol_name):
            info[dwi].append(s.series_id)

    return info

Below are the code and output when I run heudiconv:
hcp4715@hcp4715-Precision-5510:~$ sudo docker run --rm -it -v /media/hcp4715/USB1/Data/RepDopa/BIDS_test:/base nipy/heudiconv:latest -d /base/Dicom/sub-{subject}/ses-{session}// -o /base/Nifti/ -f /base/Nifti/code/heuristic.py -s 001 -ss 01 -c dcm2niix -b --overwrite --minmeta
INFO: Running heudiconv version 0.5.4.dev1
INFO: Need to process 1 study sessions
INFO: PROCESSING STARTS: {‘subject’: ‘001’, ‘outdir’: ‘/base/Nifti/’, ‘session’: ‘01’}
INFO: Processing 6854 dicoms
INFO: Will not reuse existing conversion table files because heuristic has changed
INFO: Analyzing 6854 dicoms
INFO: Generated sequence info with 11 entries
INFO: Doing conversion using dcm2niix
INFO: Converting /base/Nifti/sub-001/ses-01/anat/sub-001_ses-01_T1w (224 DICOMs) -> /base/Nifti/sub-001/ses-01/anat . Converter: dcm2niix . Output types: (‘nii.gz’,)
190212-23:03:28,7 nipype.workflow INFO:
[Node] Setting-up “convert” in “/tmp/dcm2niixjbel5e38/convert”.
INFO: [Node] Setting-up “convert” in “/tmp/dcm2niixjbel5e38/convert”.
190212-23:03:28,95 nipype.workflow INFO:
[Node] Running “convert” (“nipype.interfaces.dcm2nii.Dcm2niix”), a CommandLine Interface with command:
dcm2niix -b y -z y -x n -t n -m n -f anat -o . -s n -v n /tmp/dcm2niixjbel5e38/convert
INFO: [Node] Running “convert” (“nipype.interfaces.dcm2nii.Dcm2niix”), a CommandLine Interface with command:
dcm2niix -b y -z y -x n -t n -m n -f anat -o . -s n -v n /tmp/dcm2niixjbel5e38/convert
190212-23:03:28,311 nipype.interface INFO:
stdout 2019-02-12T23:03:28.311461:Chris Rorden’s dcm2niiX version v1.0.20180622 GCC6.3.0 (64-bit Linux)
INFO: stdout 2019-02-12T23:03:28.311461:Chris Rorden’s dcm2niiX version v1.0.20180622 GCC6.3.0 (64-bit Linux)
190212-23:03:28,311 nipype.interface INFO:
stdout 2019-02-12T23:03:28.311461:Found 224 DICOM file(s)
INFO: stdout 2019-02-12T23:03:28.311461:Found 224 DICOM file(s)
190212-23:03:28,311 nipype.interface INFO:
stdout 2019-02-12T23:03:28.311461:Convert 224 DICOM as ./anat (320x320x224x1)
INFO: stdout 2019-02-12T23:03:28.311461:Convert 224 DICOM as ./anat (320x320x224x1)
190212-23:03:29,95 nipype.interface INFO:
stdout 2019-02-12T23:03:29.095953:compress: “/usr/bin/pigz” -n -f -6 “./anat.nii”
INFO: stdout 2019-02-12T23:03:29.095953:compress: “/usr/bin/pigz” -n -f -6 “./anat.nii”
190212-23:03:29,96 nipype.interface INFO:
stdout 2019-02-12T23:03:29.095953:Conversion required 0.955019 seconds (0.295855 for core code).
INFO: stdout 2019-02-12T23:03:29.095953:Conversion required 0.955019 seconds (0.295855 for core code).
190212-23:03:29,125 nipype.workflow INFO:
[Node] Finished “convert”.
INFO: [Node] Finished “convert”.
190212-23:03:29,412 nipype.workflow INFO:
[Node] Setting-up “embedder” in “/tmp/embedmetaruuj143z/embedder”.
INFO: [Node] Setting-up “embedder” in “/tmp/embedmetaruuj143z/embedder”.
190212-23:03:29,450 nipype.workflow INFO:
[Node] Running “embedder” (“nipype.interfaces.utility.wrappers.Function”)
INFO: [Node] Running “embedder” (“nipype.interfaces.utility.wrappers.Function”)
190212-23:03:29,456 nipype.workflow INFO:
[Node] Finished “embedder”.
INFO: [Node] Finished “embedder”.
INFO: Post-treating /base/Nifti/sub-001/ses-01/anat/sub-001_ses-01_T1w.json file
INFO: Converting /base/Nifti/sub-001/ses-01/anat/sub-001_ses-01_T2w (45 DICOMs) -> /base/Nifti/sub-001/ses-01/anat . Converter: dcm2niix . Output types: (‘nii.gz’,)
190212-23:03:29,461 nipype.workflow INFO:
[Node] Setting-up “convert” in “/tmp/dcm2niixz9rsujso/convert”.
INFO: [Node] Setting-up “convert” in “/tmp/dcm2niixz9rsujso/convert”.
190212-23:03:29,481 nipype.workflow INFO:
[Node] Running “convert” (“nipype.interfaces.dcm2nii.Dcm2niix”), a CommandLine Interface with command:
dcm2niix -b y -z y -x n -t n -m n -f anat -o . -s n -v n /tmp/dcm2niixz9rsujso/convert
INFO: [Node] Running “convert” (“nipype.interfaces.dcm2nii.Dcm2niix”), a CommandLine Interface with command:
dcm2niix -b y -z y -x n -t n -m n -f anat -o . -s n -v n /tmp/dcm2niixz9rsujso/convert
190212-23:03:29,534 nipype.interface INFO:
stdout 2019-02-12T23:03:29.534329:Chris Rorden’s dcm2niiX version v1.0.20180622 GCC6.3.0 (64-bit Linux)
INFO: stdout 2019-02-12T23:03:29.534329:Chris Rorden’s dcm2niiX version v1.0.20180622 GCC6.3.0 (64-bit Linux)
190212-23:03:29,534 nipype.interface INFO:
stdout 2019-02-12T23:03:29.534329:Found 45 DICOM file(s)
INFO: stdout 2019-02-12T23:03:29.534329:Found 45 DICOM file(s)
190212-23:03:29,534 nipype.interface INFO:
stdout 2019-02-12T23:03:29.534329:Convert 45 DICOM as ./anat (448x448x45x1)
INFO: stdout 2019-02-12T23:03:29.534329:Convert 45 DICOM as ./anat (448x448x45x1)
190212-23:03:29,784 nipype.interface INFO:
stdout 2019-02-12T23:03:29.784202:compress: “/usr/bin/pigz” -n -f -6 “./anat.nii”
INFO: stdout 2019-02-12T23:03:29.784202:compress: “/usr/bin/pigz” -n -f -6 “./anat.nii”
190212-23:03:29,784 nipype.interface INFO:
stdout 2019-02-12T23:03:29.784202:Conversion required 0.292782 seconds (0.048126 for core code).
INFO: stdout 2019-02-12T23:03:29.784202:Conversion required 0.292782 seconds (0.048126 for core code).
190212-23:03:29,801 nipype.workflow INFO:
[Node] Finished “convert”.
INFO: [Node] Finished “convert”.
190212-23:03:30,43 nipype.workflow INFO:
[Node] Setting-up “embedder” in “/tmp/embedmetasqe8g9j9/embedder”.
INFO: [Node] Setting-up “embedder” in “/tmp/embedmetasqe8g9j9/embedder”.
190212-23:03:30,53 nipype.workflow INFO:
[Node] Running “embedder” (“nipype.interfaces.utility.wrappers.Function”)
INFO: [Node] Running “embedder” (“nipype.interfaces.utility.wrappers.Function”)
190212-23:03:30,57 nipype.workflow INFO:
[Node] Finished “embedder”.
INFO: [Node] Finished “embedder”.
INFO: Post-treating /base/Nifti/sub-001/ses-01/anat/sub-001_ses-01_T2w.json file
INFO: Converting /base/Nifti/sub-001/ses-01/func/sub-001_ses-01_task-fam_bold (217 DICOMs) -> /base/Nifti/sub-001/ses-01/func . Converter: dcm2niix . Output types: (‘nii.gz’,)
190212-23:03:30,66 nipype.workflow INFO:
[Node] Setting-up “convert” in “/tmp/dcm2niixwo8mij39/convert”.
INFO: [Node] Setting-up “convert” in “/tmp/dcm2niixwo8mij39/convert”.
190212-23:03:30,151 nipype.workflow INFO:
[Node] Running “convert” (“nipype.interfaces.dcm2nii.Dcm2niix”), a CommandLine Interface with command:
dcm2niix -b y -z y -x n -t n -m n -f func -o . -s n -v n /tmp/dcm2niixwo8mij39/convert
INFO: [Node] Running “convert” (“nipype.interfaces.dcm2nii.Dcm2niix”), a CommandLine Interface with command:
dcm2niix -b y -z y -x n -t n -m n -f func -o . -s n -v n /tmp/dcm2niixwo8mij39/convert
190212-23:03:30,413 nipype.interface INFO:
stdout 2019-02-12T23:03:30.413450:Chris Rorden’s dcm2niiX version v1.0.20180622 GCC6.3.0 (64-bit Linux)
INFO: stdout 2019-02-12T23:03:30.413450:Chris Rorden’s dcm2niiX version v1.0.20180622 GCC6.3.0 (64-bit Linux)
190212-23:03:30,413 nipype.interface INFO:
stdout 2019-02-12T23:03:30.413450:Found 217 DICOM file(s)
INFO: stdout 2019-02-12T23:03:30.413450:Found 217 DICOM file(s)
190212-23:03:30,413 nipype.interface INFO:
stdout 2019-02-12T23:03:30.413450:slices stacked despite varying acquisition numbers (if this is not desired please recompile)
INFO: stdout 2019-02-12T23:03:30.413450:slices stacked despite varying acquisition numbers (if this is not desired please recompile)
190212-23:03:30,414 nipype.interface INFO:
stdout 2019-02-12T23:03:30.413450:Convert 217 DICOM as ./func (84x72x60x217)
INFO: stdout 2019-02-12T23:03:30.413450:Convert 217 DICOM as ./func (84x72x60x217)
190212-23:03:32,700 nipype.interface INFO:
stdout 2019-02-12T23:03:32.700203:compress: “/usr/bin/pigz” -n -f -6 “./func.nii”
INFO: stdout 2019-02-12T23:03:32.700203:compress: “/usr/bin/pigz” -n -f -6 “./func.nii”
190212-23:03:32,700 nipype.interface INFO:
stdout 2019-02-12T23:03:32.700203:Conversion required 2.539633 seconds (0.319509 for core code).
INFO: stdout 2019-02-12T23:03:32.700203:Conversion required 2.539633 seconds (0.319509 for core code).
190212-23:03:32,728 nipype.workflow INFO:
[Node] Finished “convert”.
INFO: [Node] Finished “convert”.
190212-23:03:33,359 nipype.workflow INFO:
[Node] Setting-up “embedder” in “/tmp/embedmetah7drbdhx/embedder”.
INFO: [Node] Setting-up “embedder” in “/tmp/embedmetah7drbdhx/embedder”.
190212-23:03:33,391 nipype.workflow INFO:
[Node] Running “embedder” (“nipype.interfaces.utility.wrappers.Function”)
INFO: [Node] Running “embedder” (“nipype.interfaces.utility.wrappers.Function”)
190212-23:03:33,397 nipype.workflow INFO:
[Node] Finished “embedder”.
INFO: [Node] Finished “embedder”.
INFO: Post-treating /base/Nifti/sub-001/ses-01/func/sub-001_ses-01_task-fam_bold.json file
INFO: Converting /base/Nifti/sub-001/ses-01/func/sub-001_ses-01_task-exp_bold (496 DICOMs) -> /base/Nifti/sub-001/ses-01/func . Converter: dcm2niix . Output types: (‘nii.gz’,)
190212-23:03:33,415 nipype.workflow INFO:
[Node] Setting-up “convert” in “/tmp/dcm2niixhsbjkjop/convert”.
INFO: [Node] Setting-up “convert” in “/tmp/dcm2niixhsbjkjop/convert”.
190212-23:03:33,599 nipype.workflow INFO:
[Node] Running “convert” (“nipype.interfaces.dcm2nii.Dcm2niix”), a CommandLine Interface with command:
dcm2niix -b y -z y -x n -t n -m n -f func -o . -s n -v n /tmp/dcm2niixhsbjkjop/convert
INFO: [Node] Running “convert” (“nipype.interfaces.dcm2nii.Dcm2niix”), a CommandLine Interface with command:
dcm2niix -b y -z y -x n -t n -m n -f func -o . -s n -v n /tmp/dcm2niixhsbjkjop/convert
190212-23:03:34,169 nipype.interface INFO:
stdout 2019-02-12T23:03:34.168945:Chris Rorden’s dcm2niiX version v1.0.20180622 GCC6.3.0 (64-bit Linux)
INFO: stdout 2019-02-12T23:03:34.168945:Chris Rorden’s dcm2niiX version v1.0.20180622 GCC6.3.0 (64-bit Linux)
190212-23:03:34,169 nipype.interface INFO:
stdout 2019-02-12T23:03:34.168945:Found 496 DICOM file(s)
INFO: stdout 2019-02-12T23:03:34.168945:Found 496 DICOM file(s)
190212-23:03:34,169 nipype.interface INFO:
stdout 2019-02-12T23:03:34.168945:slices stacked despite varying acquisition numbers (if this is not desired please recompile)
INFO: stdout 2019-02-12T23:03:34.168945:slices stacked despite varying acquisition numbers (if this is not desired please recompile)
190212-23:03:34,169 nipype.interface INFO:
stdout 2019-02-12T23:03:34.168945:Convert 496 DICOM as ./func (84x72x60x496)
INFO: stdout 2019-02-12T23:03:34.168945:Convert 496 DICOM as ./func (84x72x60x496)
190212-23:03:39,405 nipype.interface INFO:
stdout 2019-02-12T23:03:39.405333:compress: “/usr/bin/pigz” -n -f -6 “./func.nii”
INFO: stdout 2019-02-12T23:03:39.405333:compress: “/usr/bin/pigz” -n -f -6 “./func.nii”
190212-23:03:39,405 nipype.interface INFO:
stdout 2019-02-12T23:03:39.405333:Conversion required 5.796813 seconds (0.702813 for core code).
INFO: stdout 2019-02-12T23:03:39.405333:Conversion required 5.796813 seconds (0.702813 for core code).
190212-23:03:39,448 nipype.workflow INFO:
[Node] Finished “convert”.
INFO: [Node] Finished “convert”.
190212-23:03:40,471 nipype.workflow INFO:
[Node] Setting-up “embedder” in “/tmp/embedmeta2k8pykfj/embedder”.
INFO: [Node] Setting-up “embedder” in “/tmp/embedmeta2k8pykfj/embedder”.
190212-23:03:40,542 nipype.workflow INFO:
[Node] Running “embedder” (“nipype.interfaces.utility.wrappers.Function”)
INFO: [Node] Running “embedder” (“nipype.interfaces.utility.wrappers.Function”)
190212-23:03:40,549 nipype.workflow INFO:
[Node] Finished “embedder”.
INFO: [Node] Finished “embedder”.
INFO: Post-treating /base/Nifti/sub-001/ses-01/func/sub-001_ses-01_task-exp_bold.json file
INFO: Converting /base/Nifti/sub-001/ses-01/func/sub-001_ses-01_task-rest_run-1_bold (480 DICOMs) -> /base/Nifti/sub-001/ses-01/func . Converter: dcm2niix . Output types: (‘nii.gz’,)
190212-23:03:40,566 nipype.workflow INFO:
[Node] Setting-up “convert” in “/tmp/dcm2niix7vml9cft/convert”.
INFO: [Node] Setting-up “convert” in “/tmp/dcm2niix7vml9cft/convert”.
190212-23:03:40,756 nipype.workflow INFO:
[Node] Running “convert” (“nipype.interfaces.dcm2nii.Dcm2niix”), a CommandLine Interface with command:
dcm2niix -b y -z y -x n -t n -m n -f func -o . -s n -v n /tmp/dcm2niix7vml9cft/convert
INFO: [Node] Running “convert” (“nipype.interfaces.dcm2nii.Dcm2niix”), a CommandLine Interface with command:
dcm2niix -b y -z y -x n -t n -m n -f func -o . -s n -v n /tmp/dcm2niix7vml9cft/convert
190212-23:03:41,307 nipype.interface INFO:
stdout 2019-02-12T23:03:41.307827:Chris Rorden’s dcm2niiX version v1.0.20180622 GCC6.3.0 (64-bit Linux)
INFO: stdout 2019-02-12T23:03:41.307827:Chris Rorden’s dcm2niiX version v1.0.20180622 GCC6.3.0 (64-bit Linux)
190212-23:03:41,308 nipype.interface INFO:
stdout 2019-02-12T23:03:41.307827:Found 480 DICOM file(s)
INFO: stdout 2019-02-12T23:03:41.307827:Found 480 DICOM file(s)
190212-23:03:41,308 nipype.interface INFO:
stdout 2019-02-12T23:03:41.307827:slices stacked despite varying acquisition numbers (if this is not desired please recompile)
INFO: stdout 2019-02-12T23:03:41.307827:slices stacked despite varying acquisition numbers (if this is not desired please recompile)
190212-23:03:41,308 nipype.interface INFO:
stdout 2019-02-12T23:03:41.307827:Convert 480 DICOM as ./func (84x72x60x480)
INFO: stdout 2019-02-12T23:03:41.307827:Convert 480 DICOM as ./func (84x72x60x480)
190212-23:03:46,350 nipype.interface INFO:
stdout 2019-02-12T23:03:46.350402:compress: “/usr/bin/pigz” -n -f -6 “./func.nii”
INFO: stdout 2019-02-12T23:03:46.350402:compress: “/usr/bin/pigz” -n -f -6 “./func.nii”
190212-23:03:46,350 nipype.interface INFO:
stdout 2019-02-12T23:03:46.350402:Conversion required 5.584305 seconds (0.687461 for core code).
INFO: stdout 2019-02-12T23:03:46.350402:Conversion required 5.584305 seconds (0.687461 for core code).
190212-23:03:46,393 nipype.workflow INFO:
[Node] Finished “convert”.
INFO: [Node] Finished “convert”.
190212-23:03:47,427 nipype.workflow INFO:
[Node] Setting-up “embedder” in “/tmp/embedmetaq4dbbpsm/embedder”.
INFO: [Node] Setting-up “embedder” in “/tmp/embedmetaq4dbbpsm/embedder”.
190212-23:03:47,496 nipype.workflow INFO:
[Node] Running “embedder” (“nipype.interfaces.utility.wrappers.Function”)
INFO: [Node] Running “embedder” (“nipype.interfaces.utility.wrappers.Function”)
190212-23:03:47,504 nipype.workflow INFO:
[Node] Finished “embedder”.
INFO: [Node] Finished “embedder”.
INFO: Post-treating /base/Nifti/sub-001/ses-01/func/sub-001_ses-01_task-rest_run-1_bold.json file
INFO: Converting /base/Nifti/sub-001/ses-01/fmap/sub-001_ses-01_magnitude (100 DICOMs) -> /base/Nifti/sub-001/ses-01/fmap . Converter: dcm2niix . Output types: (‘nii.gz’,)
190212-23:03:47,509 nipype.workflow INFO:
[Node] Setting-up “convert” in “/tmp/dcm2niixphmybaqi/convert”.
INFO: [Node] Setting-up “convert” in “/tmp/dcm2niixphmybaqi/convert”.
190212-23:03:47,551 nipype.workflow INFO:
[Node] Running “convert” (“nipype.interfaces.dcm2nii.Dcm2niix”), a CommandLine Interface with command:
dcm2niix -b y -z y -x n -t n -m n -f fmap -o . -s n -v n /tmp/dcm2niixphmybaqi/convert
INFO: [Node] Running “convert” (“nipype.interfaces.dcm2nii.Dcm2niix”), a CommandLine Interface with command:
dcm2niix -b y -z y -x n -t n -m n -f fmap -o . -s n -v n /tmp/dcm2niixphmybaqi/convert
190212-23:03:47,623 nipype.interface INFO:
stdout 2019-02-12T23:03:47.623814:Chris Rorden’s dcm2niiX version v1.0.20180622 GCC6.3.0 (64-bit Linux)
INFO: stdout 2019-02-12T23:03:47.623814:Chris Rorden’s dcm2niiX version v1.0.20180622 GCC6.3.0 (64-bit Linux)
190212-23:03:47,624 nipype.interface INFO:
stdout 2019-02-12T23:03:47.623814:Found 100 DICOM file(s)
INFO: stdout 2019-02-12T23:03:47.623814:Found 100 DICOM file(s)
190212-23:03:47,624 nipype.interface INFO:
stdout 2019-02-12T23:03:47.623814:slices not stacked: echo varies (TE 4.89, 7.35; echo 1, 2). Use ‘merge 2D slices’ option to force stacking
INFO: stdout 2019-02-12T23:03:47.623814:slices not stacked: echo varies (TE 4.89, 7.35; echo 1, 2). Use ‘merge 2D slices’ option to force stacking
190212-23:03:47,624 nipype.interface INFO:
stdout 2019-02-12T23:03:47.623814:Convert 50 DICOM as ./fmap_e1 (64x64x50x1)
INFO: stdout 2019-02-12T23:03:47.623814:Convert 50 DICOM as ./fmap_e1 (64x64x50x1)
190212-23:03:47,642 nipype.interface INFO:
stdout 2019-02-12T23:03:47.642738:compress: “/usr/bin/pigz” -n -f -6 “./fmap_e1.nii”
INFO: stdout 2019-02-12T23:03:47.642738:compress: “/usr/bin/pigz” -n -f -6 “./fmap_e1.nii”
190212-23:03:47,642 nipype.interface INFO:
stdout 2019-02-12T23:03:47.642738:slices not stacked: echo varies (TE 7.35, 4.89; echo 2, 1). Use ‘merge 2D slices’ option to force stacking
INFO: stdout 2019-02-12T23:03:47.642738:slices not stacked: echo varies (TE 7.35, 4.89; echo 2, 1). Use ‘merge 2D slices’ option to force stacking
190212-23:03:47,643 nipype.interface INFO:
stdout 2019-02-12T23:03:47.642738:Convert 50 DICOM as ./fmap_e2 (64x64x50x1)
INFO: stdout 2019-02-12T23:03:47.642738:Convert 50 DICOM as ./fmap_e2 (64x64x50x1)
190212-23:03:47,657 nipype.interface INFO:
stdout 2019-02-12T23:03:47.657945:compress: “/usr/bin/pigz” -n -f -6 “./fmap_e2.nii”
INFO: stdout 2019-02-12T23:03:47.657945:compress: “/usr/bin/pigz” -n -f -6 “./fmap_e2.nii”
190212-23:03:47,658 nipype.interface INFO:
stdout 2019-02-12T23:03:47.657945:Conversion required 0.096665 seconds (0.057536 for core code).
INFO: stdout 2019-02-12T23:03:47.657945:Conversion required 0.096665 seconds (0.057536 for core code).
190212-23:03:47,678 nipype.workflow INFO:
[Node] Finished “convert”.
INFO: [Node] Finished “convert”.
WARNING: For now not embedding BIDS and info generated .nii.gz itself since sequence produced multiple files
INFO: Converting /base/Nifti/sub-001/ses-01/fmap/sub-001_ses-01_phasediff (50 DICOMs) -> /base/Nifti/sub-001/ses-01/fmap . Converter: dcm2niix . Output types: (‘nii.gz’,)
190212-23:03:47,693 nipype.workflow INFO:
[Node] Setting-up “convert” in “/tmp/dcm2niix9yp7yhh1/convert”.
INFO: [Node] Setting-up “convert” in “/tmp/dcm2niix9yp7yhh1/convert”.
190212-23:03:47,715 nipype.workflow INFO:
[Node] Running “convert” (“nipype.interfaces.dcm2nii.Dcm2niix”), a CommandLine Interface with command:
dcm2niix -b y -z y -x n -t n -m n -f fmap -o . -s n -v n /tmp/dcm2niix9yp7yhh1/convert
INFO: [Node] Running “convert” (“nipype.interfaces.dcm2nii.Dcm2niix”), a CommandLine Interface with command:
dcm2niix -b y -z y -x n -t n -m n -f fmap -o . -s n -v n /tmp/dcm2niix9yp7yhh1/convert
190212-23:03:47,758 nipype.interface INFO:
stdout 2019-02-12T23:03:47.758376:Chris Rorden’s dcm2niiX version v1.0.20180622 GCC6.3.0 (64-bit Linux)
INFO: stdout 2019-02-12T23:03:47.758376:Chris Rorden’s dcm2niiX version v1.0.20180622 GCC6.3.0 (64-bit Linux)
190212-23:03:47,758 nipype.interface INFO:
stdout 2019-02-12T23:03:47.758376:Found 50 DICOM file(s)
INFO: stdout 2019-02-12T23:03:47.758376:Found 50 DICOM file(s)
190212-23:03:47,758 nipype.interface INFO:
stdout 2019-02-12T23:03:47.758376:Convert 50 DICOM as ./fmap_e2_ph (64x64x50x1)
INFO: stdout 2019-02-12T23:03:47.758376:Convert 50 DICOM as ./fmap_e2_ph (64x64x50x1)
190212-23:03:47,769 nipype.interface INFO:
stdout 2019-02-12T23:03:47.769150:compress: “/usr/bin/pigz” -n -f -6 “./fmap_e2_ph.nii”
INFO: stdout 2019-02-12T23:03:47.769150:compress: “/usr/bin/pigz” -n -f -6 “./fmap_e2_ph.nii”
190212-23:03:47,769 nipype.interface INFO:
stdout 2019-02-12T23:03:47.769150:Conversion required 0.044770 seconds (0.029837 for core code).
INFO: stdout 2019-02-12T23:03:47.769150:Conversion required 0.044770 seconds (0.029837 for core code).
190212-23:03:47,788 nipype.workflow INFO:
[Node] Finished “convert”.
INFO: [Node] Finished “convert”.
190212-23:03:47,800 nipype.workflow INFO:
[Node] Setting-up “embedder” in “/tmp/embedmeta2hh4m1pd/embedder”.
INFO: [Node] Setting-up “embedder” in “/tmp/embedmeta2hh4m1pd/embedder”.
190212-23:03:47,810 nipype.workflow INFO:
[Node] Running “embedder” (“nipype.interfaces.utility.wrappers.Function”)
INFO: [Node] Running “embedder” (“nipype.interfaces.utility.wrappers.Function”)
190212-23:03:47,814 nipype.workflow INFO:
[Node] Finished “embedder”.
INFO: [Node] Finished “embedder”.
INFO: Post-treating /base/Nifti/sub-001/ses-01/fmap/sub-001_ses-01_phasediff.json file
INFO: Converting /base/Nifti/sub-001/ses-01/dwi/sub-001_ses-01_run-1_dwi (4680 DICOMs) -> /base/Nifti/sub-001/ses-01/dwi . Converter: dcm2niix . Output types: (‘nii.gz’,)
190212-23:03:47,975 nipype.workflow INFO:
[Node] Setting-up “convert” in “/tmp/dcm2niix5il0o9uz/convert”.
INFO: [Node] Setting-up “convert” in “/tmp/dcm2niix5il0o9uz/convert”.
190212-23:03:49,826 nipype.workflow INFO:
[Node] Running “convert” (“nipype.interfaces.dcm2nii.Dcm2niix”), a CommandLine Interface with command:
dcm2niix -b y -z y -x n -t n -m n -f dwi -o . -s n -v n /tmp/dcm2niix5il0o9uz/convert
INFO: [Node] Running “convert” (“nipype.interfaces.dcm2nii.Dcm2niix”), a CommandLine Interface with command:
dcm2niix -b y -z y -x n -t n -m n -f dwi -o . -s n -v n /tmp/dcm2niix5il0o9uz/convert
190212-23:03:52,844 nipype.interface INFO:
stdout 2019-02-12T23:03:52.844433:Chris Rorden’s dcm2niiX version v1.0.20180622 GCC6.3.0 (64-bit Linux)
INFO: stdout 2019-02-12T23:03:52.844433:Chris Rorden’s dcm2niiX version v1.0.20180622 GCC6.3.0 (64-bit Linux)
190212-23:03:52,844 nipype.interface INFO:
stdout 2019-02-12T23:03:52.844433:Found 4680 DICOM file(s)
INFO: stdout 2019-02-12T23:03:52.844433:Found 4680 DICOM file(s)
190212-23:03:52,845 nipype.interface INFO:
stdout 2019-02-12T23:03:52.844433:slices stacked despite varying acquisition numbers (if this is not desired please recompile)
INFO: stdout 2019-02-12T23:03:52.844433:slices stacked despite varying acquisition numbers (if this is not desired please recompile)
190212-23:03:52,845 nipype.interface INFO:
stdout 2019-02-12T23:03:52.844433:Warning: Saving 65 DTI gradients. Validate vectors (image slice orientation not reported, e.g. 2001,100B).
INFO: stdout 2019-02-12T23:03:52.844433:Warning: Saving 65 DTI gradients. Validate vectors (image slice orientation not reported, e.g. 2001,100B).
190212-23:03:52,845 nipype.interface INFO:
stdout 2019-02-12T23:03:52.844433:Convert 4680 DICOM as ./dwi (128x128x72x65)
INFO: stdout 2019-02-12T23:03:52.844433:Convert 4680 DICOM as ./dwi (128x128x72x65)
190212-23:03:55,202 nipype.interface INFO:
stdout 2019-02-12T23:03:55.202795:compress: “/usr/bin/pigz” -n -f -6 “./dwi.nii”
INFO: stdout 2019-02-12T23:03:55.202795:compress: “/usr/bin/pigz” -n -f -6 “./dwi.nii”
190212-23:03:55,202 nipype.interface INFO:
stdout 2019-02-12T23:03:55.202795:Conversion required 5.358445 seconds (2.609329 for core code).
INFO: stdout 2019-02-12T23:03:55.202795:Conversion required 5.358445 seconds (2.609329 for core code).
190212-23:03:55,484 nipype.workflow INFO:
[Node] Finished “convert”.
INFO: [Node] Finished “convert”.
190212-23:03:55,785 nipype.workflow INFO:
[Node] Setting-up “embedder” in “/tmp/embedmeta75hmjz7q/embedder”.
INFO: [Node] Setting-up “embedder” in “/tmp/embedmeta75hmjz7q/embedder”.
190212-23:03:56,368 nipype.workflow INFO:
[Node] Running “embedder” (“nipype.interfaces.utility.wrappers.Function”)
INFO: [Node] Running “embedder” (“nipype.interfaces.utility.wrappers.Function”)
190212-23:03:56,406 nipype.workflow INFO:
[Node] Finished “embedder”.
INFO: [Node] Finished “embedder”.
INFO: Post-treating /base/Nifti/sub-001/ses-01/dwi/sub-001_ses-01_run-1_dwi.json file
INFO: Converting /base/Nifti/sub-001/ses-01/dwi/sub-001_ses-01_run-2_dwi (72 DICOMs) -> /base/Nifti/sub-001/ses-01/dwi . Converter: dcm2niix . Output types: (‘nii.gz’,)
190212-23:03:56,411 nipype.workflow INFO:
[Node] Setting-up “convert” in “/tmp/dcm2niixmsc8j9o_/convert”.
INFO: [Node] Setting-up “convert” in “/tmp/dcm2niixmsc8j9o_/convert”.
190212-23:03:56,441 nipype.workflow INFO:
[Node] Running “convert” (“nipype.interfaces.dcm2nii.Dcm2niix”), a CommandLine Interface with command:
dcm2niix -b y -z y -x n -t n -m n -f dwi -o . -s n -v n /tmp/dcm2niixmsc8j9o_/convert
INFO: [Node] Running “convert” (“nipype.interfaces.dcm2nii.Dcm2niix”), a CommandLine Interface with command:
dcm2niix -b y -z y -x n -t n -m n -f dwi -o . -s n -v n /tmp/dcm2niixmsc8j9o_/convert
190212-23:03:56,504 nipype.interface INFO:
stdout 2019-02-12T23:03:56.504069:Chris Rorden’s dcm2niiX version v1.0.20180622 GCC6.3.0 (64-bit Linux)
INFO: stdout 2019-02-12T23:03:56.504069:Chris Rorden’s dcm2niiX version v1.0.20180622 GCC6.3.0 (64-bit Linux)
190212-23:03:56,504 nipype.interface INFO:
stdout 2019-02-12T23:03:56.504069:Found 72 DICOM file(s)
INFO: stdout 2019-02-12T23:03:56.504069:Found 72 DICOM file(s)
190212-23:03:56,504 nipype.interface INFO:
stdout 2019-02-12T23:03:56.504069:Warning: This diffusion series does not have a B0 (reference) volume
INFO: stdout 2019-02-12T23:03:56.504069:Warning: This diffusion series does not have a B0 (reference) volume
190212-23:03:56,504 nipype.interface INFO:
stdout 2019-02-12T23:03:56.504069:Note: this appears to be a b=0+trace DWI; ADC/trace removal has been disabled.
INFO: stdout 2019-02-12T23:03:56.504069:Note: this appears to be a b=0+trace DWI; ADC/trace removal has been disabled.
190212-23:03:56,504 nipype.interface INFO:
stdout 2019-02-12T23:03:56.504069:Warning: Volume 0 appears to be an ADC map (non-zero b-value with zero vector length)
INFO: stdout 2019-02-12T23:03:56.504069:Warning: Volume 0 appears to be an ADC map (non-zero b-value with zero vector length)
190212-23:03:56,504 nipype.interface INFO:
stdout 2019-02-12T23:03:56.504069:Warning: Saving 1 DTI gradients. Validate vectors (image slice orientation not reported, e.g. 2001,100B).
INFO: stdout 2019-02-12T23:03:56.504069:Warning: Saving 1 DTI gradients. Validate vectors (image slice orientation not reported, e.g. 2001,100B).
190212-23:03:56,504 nipype.interface INFO:
stdout 2019-02-12T23:03:56.504069:Convert 72 DICOM as ./dwi (128x128x72x1)
INFO: stdout 2019-02-12T23:03:56.504069:Convert 72 DICOM as ./dwi (128x128x72x1)
190212-23:03:56,521 nipype.interface INFO:
stdout 2019-02-12T23:03:56.521709:compress: “/usr/bin/pigz” -n -f -6 “./dwi.nii”
INFO: stdout 2019-02-12T23:03:56.521709:compress: “/usr/bin/pigz” -n -f -6 “./dwi.nii”
190212-23:03:56,521 nipype.interface INFO:
stdout 2019-02-12T23:03:56.521709:Conversion required 0.070095 seconds (0.046532 for core code).
INFO: stdout 2019-02-12T23:03:56.521709:Conversion required 0.070095 seconds (0.046532 for core code).
190212-23:03:56,541 nipype.workflow INFO:
[Node] Finished “convert”.
INFO: [Node] Finished “convert”.
190212-23:03:56,553 nipype.workflow INFO:
[Node] Setting-up “embedder” in “/tmp/embedmetaphx1fn9m/embedder”.
INFO: [Node] Setting-up “embedder” in “/tmp/embedmetaphx1fn9m/embedder”.
190212-23:03:56,565 nipype.workflow INFO:
[Node] Running “embedder” (“nipype.interfaces.utility.wrappers.Function”)
INFO: [Node] Running “embedder” (“nipype.interfaces.utility.wrappers.Function”)
190212-23:03:56,570 nipype.workflow INFO:
[Node] Finished “embedder”.
INFO: [Node] Finished “embedder”.
INFO: Post-treating /base/Nifti/sub-001/ses-01/dwi/sub-001_ses-01_run-2_dwi.json file
INFO: Populating template files under /base/Nifti/
INFO: PROCESSING DONE: {‘subject’: ‘001’, ‘outdir’: ‘/base/Nifti/’, ‘session’: ‘01’}

PeerHerholz · February 13, 2019, 8:58am

Ahoi hoi @hcp4715,

you already did a great job!

Going through your heuristic.py a small, but important problem is noticeable: you missed an .append wrt the resting scans. In more detail, you set info[func_rest] = [s.series_id] which works correctly, converting and creating one resting file, that is the first one it finds within the DICOMs. However, as you have multiple resting scans, you need to create a list that stores and subsequently converts all matching files. You actually did that for the dwis: info[dwi].append(s.series_id). So the only thing you would need to change would be the corresponding line for the resting scans from: info[func_rest] = [s.series_id] to info[func_rest].append(s.series_id). After that, everything should work as expected.

Please don’t hesitate to post again if this fix didn’t solve your issue, my explanation was not clear or if you have further questions.

Cheers, Peer

P.S.: It goes without saying and I know you’re aware of it, but just for the sake of completeness: make sure to use one version of the BIDS validator after you’ve created your dataset to make sure everything is there and fits!

hcp4715 · February 13, 2019, 11:06pm

Hi, Peer,
It’s almost one year since your workshop at Marburg, shame that I am still struggle about the basics. The good thing is that I didn’t give up ;-).

Your are right, I didn’t check the ‘append’ and ‘=’ carefully. Now all the data were converted!
But validator still report one error on DTI data and 2 warnings.

The error says that

The number of volumes in this scan does not match the number of volumes in the corresponding .bvec and .bval files

I guess it is related to this issue here, but it has been solved in 2017:

Below is the error log I downloaded:

File Path: The number of volumes in this scan does not match the number of volumes in the corresponding .bvec and .bval files.

Type: Error
File: sub-001_ses-01_run-2_dwi.nii.gz
Location: Nifti/sub-001/ses-01/dwi/sub-001_ses-01_run-2_dwi.nii.gz
Reason: The number of volumes in this scan does not match the number of volumes in the corresponding .bvec and .bval files.

======================================================

File Path: Not all subjects/sessions/runs have the same scanning parameters.

Type: Warning
File: sub-001_ses-01_run-2_dwi.nii.gz
Location: Nifti/sub-001/ses-01/dwi/sub-001_ses-01_run-2_dwi.nii.gz
Reason: The most common set of dimensions is: 128,128,72,65 (voxels), This file has the dimensions: 128,128,72 (voxels). The most common resolution is: 2.00mm x 2.00mm x 2.00mm x 9.10s, This file has the resolution: 2.00mm x 2.00mm x 2.00mm.

======================================================

File Path: Tabular file contains custom columns not described in a data dictionary

Type: Warning
File: participants.tsv
Location: Nifti/participants.tsv
Reason: Tabular file contains custom columns not described in a data dictionary
Evidence: Columns: age, sex, group not defined, please define in: /participants.json

Type: Warning
File: sub-001_ses-01_task-exp_events.tsv
Location: Nifti/sub-001/ses-01/func/sub-001_ses-01_task-exp_events.tsv
Reason: Tabular file contains custom columns not described in a data dictionary
Evidence: Columns: TODO – fill in rows and add more tab-separated columns if desired not defined, please define in: /task-exp_events.json, /events.json,/sub-001/sub-001_task-exp_events.json,/sub-001/sub-001_events.json,/sub-001/ses-01/sub-001_ses-01_task-exp_events.json,/sub-001/ses-01/sub-001_ses-01_events.json,/sub-001/ses-01/func/sub-001_ses-01_task-exp_events.json,/sub-001/ses-01/func/sub-001_ses-01_events.json

Type: Warning
File: sub-001_ses-01_task-fam_events.tsv
Location: Nifti/sub-001/ses-01/func/sub-001_ses-01_task-fam_events.tsv
Reason: Tabular file contains custom columns not described in a data dictionary
Evidence: Columns: TODO – fill in rows and add more tab-separated columns if desired not defined, please define in: /task-fam_events.json, /events.json,/sub-001/sub-001_task-fam_events.json,/sub-001/sub-001_events.json,/sub-001/ses-01/sub-001_ses-01_task-fam_events.json,/sub-001/ses-01/sub-001_ses-01_events.json,/sub-001/ses-01/func/sub-001_ses-01_task-fam_events.json,/sub-001/ses-01/func/sub-001_ses-01_events.json

Type: Warning
File: sub-001_ses-01_task-rest_run-1_events.tsv
Location: Nifti/sub-001/ses-01/func/sub-001_ses-01_task-rest_run-1_events.tsv
Reason: Tabular file contains custom columns not described in a data dictionary
Evidence: Columns: TODO – fill in rows and add more tab-separated columns if desired not defined, please define in: /sub-001/ses-01/func/sub-001_ses-01_events.json, /sub-001/ses-01/func/sub-001_ses-01_task-rest_events.json,/sub-001/ses-01/sub-001_ses-01_events.json,/sub-001/ses-01/sub-001_ses-01_task-rest_events.json,/sub-001/sub-001_events.json,/sub-001/sub-001_task-rest_events.json,/events.json,/task-rest_events.json,/sub-001/ses-01/func/sub-001_ses-01_task-rest_run-1_events.json

Type: Warning
File: sub-001_ses-01_task-rest_run-2_events.tsv
Location: Nifti/sub-001/ses-01/func/sub-001_ses-01_task-rest_run-2_events.tsv
Reason: Tabular file contains custom columns not described in a data dictionary
Evidence: Columns: TODO – fill in rows and add more tab-separated columns if desired not defined, please define in: /sub-001/ses-01/func/sub-001_ses-01_events.json, /sub-001/ses-01/func/sub-001_ses-01_task-rest_events.json,/sub-001/ses-01/sub-001_ses-01_events.json,/sub-001/ses-01/sub-001_ses-01_task-rest_events.json,/sub-001/sub-001_events.json,/sub-001/sub-001_task-rest_events.json,/events.json,/task-rest_events.json,/sub-001/ses-01/func/sub-001_ses-01_task-rest_run-2_events.json

Type: Warning
File: sub-001_ses-01_scans.tsv
Location: Nifti/sub-001/ses-01/sub-001_ses-01_scans.tsv
Reason: Tabular file contains custom columns not described in a data dictionary
Evidence: Columns: operator, randstr not defined, please define in: /scans.json, /sub-001/sub-001_scans.json,/sub-001/ses-01/sub-001_ses-01_scans.json

======================================================

update:
I found that the dicominfo seems not quit right, but not sure.
so here is part information from the dicominfo.tsv:

dcm_dir_name	unspecified2	unspecified3	dim1	dim2	dim3	dim4	TR	TE
localizer_Series0001	-	-	512	512	3	1	0.0086	4
resting1_mb4_TR_1000_Series0002	-	-	72	84	60	480	1	29
fmri_Tag1_mb4_TR_1000_fam_Series0003	-	-	72	84	60	217	1	29
fmri_Tag1_mb4_TR_1000_Series0004	-	-	72	84	60	496	1	29
resting2_mb4_TR_1000_Series0005	-	-	72	84	60	480	1	29
t1_mpr_ns_sag_p2_iso08_Series0006	-	-	320	320	224	1	1.9	2.54
t2_tse_tra_448_p2_3mm_Series0007	-	-	448	448	45	1	6.1	79
gre_field_mapping_Series0008	-	-	64	64	100	1	1.03	7.35
gre_field_mapping_Series0009	-	-	64	64	50	1	1.03	7.35
ep2d_diff_mddw_64_p2_b=1000_Series0010	-	-	128	128	4680	1	9.1	85
ep2d_diff_mddw_64_p2_b=1000_TRACEW_Series0011	-	-	128	128	72	1	9.1	85

Here is how my folder looks like, the dim4 of T1w, T2, gre_field, and DTI are all 1, but the number of dicom are not 1.

PeerHerholz · February 15, 2019, 2:42pm

Hi @hcp4715,

sorry for the late reply.
Yeah, keeping on is one of the most crucial parts!

Ok, glad it solved the first issue.
Now to the rest. First of all, could you provide us with further information on your setup and the corresponding sequences? Looks like a Siemens scanner, no?

The validator is right and gives you a hint that the two DTI sequences you have apparently differ in some sort, which is also visible in the dcm_dir_name and the dim3. Could you let us know what’s the difference between both? Maybe a diverging phase encoding direction (as e.g. evident in the tutorial you linked)? However, checking your dicom.tsv that might not be all, which transitions into your second question.
The relationship between number of dcm and nii also depends on your setup and the data acquisition protocol parameters. For example using a Siemens scanner there’s something that is called mosaic format, that is a DICOM format in which a 3D image is stored on a 2D grid instead of a series of 2D slices. For example, if you check your resting scans: they have dim3=60 and dim4=480, meaning that the 60 slices you acquire within each TR are on one 2D grid, aka the mosaic and therefore you have 480 dcm. If that wouldn’t be the case your number of dcm would be n slice X n measured volumes, that is 28800 dcm. Now within the t1w, t2w and dwi you see that dim3 matches your number of dcm, as you sample the measurement volume once and not multiple times, that is one dcm for each slice.
Wrt your dwi scans: if we divide dim3 of the first dwi sequence by dim3 of the second, that is 4680/72, we get 65, which might hint to dim4 of the first dwi sequence being stacked in dim3. I’m by far no DTI person, but that should be the number of volumes, aka your gradient directions. So, instead of having one 3D mosaic for each gradient direction, you have n slices X n gradient directions. As this furthermore stresses an existent difference wrt your second dwi scan, I would suggest you define two separate dwi identifiers, for example indicating the phase encoding direction (for an example check this neurostars post).

I’m sorry for this confusing answer, I’m super bad at explained these things.
Let’s hope other, more expert-mode folks will intervene if I’m completely off…

Cheers, Peer

hcp4715 · February 15, 2019, 3:47pm

Hi, Peer,
Thanks so much for you reply.
Now I understand the dim3 and dim4 stuff.
For my dataset.
(1), Yes, it is collected by Simens 3 T Trio;
(2), The parameter of DTI acquisition (I’ve no idea about it either, just used the old sequence from our lab), as written in method part, is 72 slices, voxel-size: 2mm isotropic, TR:9100 sm, TE:85 ms, number of direction: 64, diffusion weight:2, be-value1:0s/mm2, b-value 2: 1000s/mm2). I asked my colleagues, what I understand so far is that: one DTI scan is the baseline, the other is the real data, and we need to subtract the baseline from the real data when we analyse the data.

As I checked the link (Getting data into BIDS format), as well as this video: https://www.youtube.com/watch?v=O1kZAuR7E00.

I found it is related to our scanning sequence.
I compare the DTI information in the youtube video, the two scans, each has more than 1000 dicom files. but for our scanning, we have one scan with 4860 dicom files and one scan with 72 dicom files. The error was from the later scan.

As the error message was

The number of volumes in this scan does not match the number of volumes in the corresponding .bvec and .bval files.

So, I opened the .bvec and .bval files,
.bvec shows

0
0
0

.bval shows:

1000

satra · February 18, 2019, 5:13pm

in the following section, if you change the heuristic to pay attention to dim3, your conversion should be fine. the last diffusion scan is likely a derivative created by the scanner rather than a diffusion scan. the alternative is that it is just a b0 scan (from the looks of your output). you will have to decide whether that single 3d image is required. this would be true, if your other scan does not contain any b0 images.

on a related note, it seems that dcmstack is not being able to group your data appropriately. i’m flagging @mgxd to see if there is any update.

hcp4715 · February 18, 2019, 5:26pm

Hi, Satra.

Thanks a lot for your response!!
You are right, the last diffusion scan is a derivative created by the scanner (will add a screenshot later). So in this case, what shall I do to preserve all the information? I guess just ignoring the last diffusion scan is not the best choice, please correct me if I am wrong.

satra · February 18, 2019, 5:49pm

one possibility is to use a different key for that one and assign the scan to it. NAME should be replaced with an appropriate extension from bids-derivatives diffusion proposal.

hcp4715 · February 18, 2019, 8:04pm

Hi, Satra,

Thank you so much! Problem solved!