Dear experts,
I’m running into a slice timing issue when using the singularity version of fmriprep version 21.0.2.
We’re using a multiband sequence with a multiband acceleration factor of 6 and 60 slices without online motion correction on a Siemens Prisma fit.
I get an error stating that saying “slice_timing.1D has 60 values but have 61 slices” (see error text of th html report below). I therefore checked the slice timing command, which I believe recognized the sequence as a multiband sequence (I’m no expert here though, so please see the content of the command.txt file below).
Further, I checked the respective nifti file and the dim3 output of the fslinfo command indicates 60 slices. I also checked the json file which seems to have 60 slice timings (see below).
I’m grateful for any input on this issue!
Best,
Martin
HTML report:
File: /home/PerPain/AVC/BIDS/derivatives/sub-017/log/20220823-105700_2e6ecbd5-0832-4c2c-8a3c-9e5b4a9754aa/crash-20220823-105955-martin.loeffler-slice_timing_correction-b1ee02c9-128e-4fdf-aaa7-87df886c411b.txt
Working Directory: /home/PerPain/AVC/FMRIPREP/fmriprep_wf/single_subject_017_wf/func_preproc_task_aversive_run_01_wf/bold_stc_wf/slice_timing_correction
Inputs:
args:
environ: {}
ignore:
in_file:
interp:
num_threads: 1
out_file:
outputtype: NIFTI_GZ
rlt:
rltplus:
slice_encoding_direction: k
slice_timing: [0.0, 0.825, 0.47, 0.1175, 0.9425, 0.59, 0.235, 1.06, 0.7075, 0.3525, 0.0, 0.825, 0.47, 0.1175, 0.9425, 0.59, 0.235, 1.06, 0.7075, 0.3525, 0.0, 0.825, 0.47, 0.1175, 0.9425, 0.59, 0.235, 1.06, 0.7075, 0.3525, 0.0, 0.825, 0.47, 0.1175, 0.9425, 0.59, 0.235, 1.06, 0.7075, 0.3525, 0.0, 0.825, 0.47, 0.1175, 0.9425, 0.59, 0.235, 1.06, 0.7075, 0.3525, 0.0, 0.825, 0.47, 0.1175, 0.9425, 0.59, 0.235, 1.06, 0.7075, 0.3525]
tpattern:
tr: 1.2s
tslice:
tzero: 0.53
Traceback (most recent call last):
File "/opt/conda/lib/python3.8/site-packages/nipype/pipeline/plugins/multiproc.py", line 67, in run_node
result["result"] = node.run(updatehash=updatehash)
File "/opt/conda/lib/python3.8/site-packages/nipype/pipeline/engine/nodes.py", line 516, in run
result = self._run_interface(execute=True)
File "/opt/conda/lib/python3.8/site-packages/nipype/pipeline/engine/nodes.py", line 635, in _run_interface
return self._run_command(execute)
File "/opt/conda/lib/python3.8/site-packages/nipype/pipeline/engine/nodes.py", line 741, in _run_command
result = self._interface.run(cwd=outdir)
File "/opt/conda/lib/python3.8/site-packages/nipype/interfaces/base/core.py", line 428, in run
runtime = self._run_interface(runtime)
File "/opt/conda/lib/python3.8/site-packages/nipype/interfaces/afni/base.py", line 124, in _run_interface
return super(AFNICommandBase, self)._run_interface(
File "/opt/conda/lib/python3.8/site-packages/nipype/interfaces/base/core.py", line 822, in _run_interface
self.raise_exception(runtime)
File "/opt/conda/lib/python3.8/site-packages/nipype/interfaces/base/core.py", line 749, in raise_exception
raise RuntimeError(
RuntimeError: Command:
3dTshift -ignore 0 -prefix sub-017_task-aversive_run-01_bold_tshift.nii.gz -tpattern @slice_timing.1D -TR 1.2s -tzero 0.53 /home/PerPain/AVC/FMRIPREP/fmriprep_wf/single_subject_017_wf/func_preproc_task_aversive_run_01_wf/bold_stc_wf/slice_timing_correction/sub-017_task-aversive_run-01_bold.nii.gz
Standard output:
Standard error:
++ 3dTshift: AFNI version=AFNI_22.1.02 (Apr 6 2022) [64-bit]
e[7m*+ WARNING:e[0m If you are performing spatial transformations on an oblique dset,
such as /home/PerPain/AVC/FMRIPREP/fmriprep_wf/single_subject_017_wf/func_preproc_task_aversive_run_01_wf/bold_stc_wf/slice_timing_correction/sub-017_task-aversive_run-01_bold.nii.gz,
or viewing/combining it with volumes of differing obliquity,
you should consider running:
3dWarp -deoblique
on this and other oblique datasets in the same session.
See 3dWarp -help for details.
++ Oblique dataset:/home/PerPain/AVC/FMRIPREP/fmriprep_wf/single_subject_017_wf/func_preproc_task_aversive_run_01_wf/bold_stc_wf/slice_timing_correction/sub-017_task-aversive_run-01_bold.nii.gz is 12.500000 degrees from plumb.
e[7m** FATAL ERROR:e[0m tpattern file slice_timing.1D has 60 values but have 61 slices
** Program compile date = Apr 6 2022
Return code: 1
The file for the slice timing command **
3dTshift -ignore 0 -prefix sub-017_task-aversive_run-01_bold_tshift.nii.gz -tpattern @slice_timing.1D -TR 1.2s -tzero 0.53 /home/PerPain/AVC/FMRIPREP/fmriprep_wf/single_subject_017_wf/func_preproc_task_aversive_run_01_wf/bold_stc_wf/slice_timing_correction/sub-017_task-aversive_run-01_bold.nii.gz
Here the content of the json file:
{
"Modality": "MR",
"MagneticFieldStrength": 3,
"ImagingFrequency": 123.251,
"Manufacturer": "Siemens",
"ManufacturersModelName": "Prisma_fit",
"InstitutionName": "deleted_to_anonymize_data",
"InstitutionalDepartmentName": "Department",
"InstitutionAddress": "J_5_Mannheim_District_DE_68159",
"DeviceSerialNumber": "167069",
"StationName": "MRC35396",
"BodyPartExamined": "HEAD",
"PatientPosition": "HFS",
"SoftwareVersions": "syngo_MR_E11",
"MRAcquisitionType": "2D",
"SeriesDescription": "cmrr_mbep2d_bold_av_hab",
"ProtocolName": "cmrr_mbep2d_bold_av_hab",
"ScanningSequence": "EP",
"SequenceVariant": "SK_SS",
"ScanOptions": "FS_EXT",
"SequenceName": "epfid2d1_84",
"ImageType": [
"ORIGINAL",
"PRIMARY",
"M",
"MB",
"ND",
"NORM",
"MOSAIC"
],
"SeriesNumber": 17,
"AcquisitionTime": "deleted_to_anonymize_data",
"AcquisitionNumber": 1,
"ImageComments": "Unaliased_MB6_PE3_LB",
"SliceThickness": 2.4,
"SpacingBetweenSlices": 2.4,
"SAR": 0.0404709,
"EchoTime": 0.038,
"RepetitionTime": 1.2,
"FlipAngle": 66,
"PartialFourier": 1,
"BaseResolution": 84,
"ShimSetting": [
-4290,
-11564,
4906,
434,
-19,
200,
10,
4
],
"TxRefAmp": 239.767,
"PhaseResolution": 1,
"ReceiveCoilName": "HeadNeck_64",
"ReceiveCoilActiveElements": "HC1-7",
"PulseSequenceDetails": "%CustomerSeq%_cmrr_mbep2d_bold",
"WipMemBlock": "047ad1ee-3ff9-48f7-b5d8-2601271b87d5||Sequence: R016 ve11c/master r/e634e98; Dec 19 2017 11:00:25 by eja",
"ConsistencyInfo": "N4_VE11C_LATEST_20160120",
"MultibandAccelerationFactor": 6,
"PercentPhaseFOV": 100,
"PercentSampling": 100,
"EchoTrainLength": 84,
"PhaseEncodingSteps": 84,
"AcquisitionMatrixPE": 84,
"ReconMatrixPE": 84,
"BandwidthPerPixelPhaseEncode": 18.896,
"EffectiveEchoSpacing": 0.000630015,
"DerivedVendorReportedEchoSpacing": 0.000630015,
"TotalReadoutTime": 0.0522912,
"PixelBandwidth": 2290,
"DwellTime": 2.6e-06,
"PhaseEncodingDirection": "j",
"SliceTiming": [
0,
0.825,
0.47,
0.1175,
0.9425,
0.59,
0.235,
1.06,
0.7075,
0.3525,
0,
0.825,
0.47,
0.1175,
0.9425,
0.59,
0.235,
1.06,
0.7075,
0.3525,
0,
0.825,
0.47,
0.1175,
0.9425,
0.59,
0.235,
1.06,
0.7075,
0.3525,
0,
0.825,
0.47,
0.1175,
0.9425,
0.59,
0.235,
1.06,
0.7075,
0.3525,
0,
0.825,
0.47,
0.1175,
0.9425,
0.59,
0.235,
1.06,
0.7075,
0.3525,
0,
0.825,
0.47,
0.1175,
0.9425,
0.59,
0.235,
1.06,
0.7075,
0.3525
],
"ImageOrientationPatientDICOM": [
1,
0,
0,
0,
0.976296,
-0.21644
],
"InPlanePhaseEncodingDirectionDICOM": "COL",
"ConversionSoftware": "dcm2niix",
"ConversionSoftwareVersion": "v1.0.20200331",
"Dcm2bidsVersion": "2.1.4",
"TaskName": "aversive"
}