Hi, Steve thank you for your feedback.
I had used qsiprep-docker, installed this week, and this one calls a previous version of the container. However, when I use this version 0.16.0RC3, without qsiprep-docker, I have some problems again.
1-the log error full
IMPORTANT:nipype.workflow:
Running qsirecon version 0.16.0RC3:
* BIDS dataset path: /data.
* Participant list: [‘PSL00076’].
* Run identifier: 20220629-235927_b1d12a7c-5441-4027-934b-20150f7bcc2b.
220629-23:59:28,484 nipype.workflow INFO:
found [’/out/qsiprep/sub-PSL00076/dwi/sub-PSL00076_space-T1w_desc-preproc_dwi.nii.gz’] in /out/qsiprep
INFO:nipype.workflow:found [’/out/qsiprep/sub-PSL00076/dwi/sub-PSL00076_space-T1w_desc-preproc_dwi.nii.gz’] in /out/qsiprep
220629-23:59:28,489 nipype.workflow INFO:
Missing T1w QSIPrep outputs found: /out/qsiprep/sub-PSL00076/anat/sub-PSL00076_desc-brain_mask.nii.gz /out/qsiprep/sub-PSL00076/anat/sub-PSL00076_desc-preproc_T1w.nii.gz
INFO:nipype.workflow:Missing T1w QSIPrep outputs found: /out/qsiprep/sub-PSL00076/anat/sub-PSL00076_desc-brain_mask.nii.gz /out/qsiprep/sub-PSL00076/anat/sub-PSL00076_desc-preproc_T1w.nii.gz
220629-23:59:28,492 nipype.workflow INFO:
Missing T1w QSIPrep outputs found: /out/qsiprep/sub-PSL00076/anat/sub-PSL00076_from-T1w_to-MNI152NLin2009cAsym_mode-image_xfm.h5 /out/qsiprep/sub-PSL00076/anat/sub-PSL00076_from-MNI152NLin2009cAsym_to-T1w_mode-image_xfm.h5
INFO:nipype.workflow:Missing T1w QSIPrep outputs found: /out/qsiprep/sub-PSL00076/anat/sub-PSL00076_from-T1w_to-MNI152NLin2009cAsym_mode-image_xfm.h5 /out/qsiprep/sub-PSL00076/anat/sub-PSL00076_from-MNI152NLin2009cAsym_to-T1w_mode-image_xfm.h5
220629-23:59:28,492 nipype.workflow INFO:
No FreeSurfer inputs available for PSL00076
INFO:nipype.workflow:No FreeSurfer inputs available for PSL00076
220629-23:59:28,492 nipype.workflow INFO:
Anatomical (T1w) available for recon: {‘has_qsiprep_5tt_fast’: False, ‘has_qsiprep_5tt_hsvs’: False, ‘has_freesurfer_5tt_hsvs’: False, ‘has_freesurfer’: False, ‘has_qsiprep_t1w’: False, ‘has_qsiprep_t1w_transforms’: False}
INFO:nipype.workflow:Anatomical (T1w) available for recon: {‘has_qsiprep_5tt_fast’: False, ‘has_qsiprep_5tt_hsvs’: False, ‘has_freesurfer_5tt_hsvs’: False, ‘has_freesurfer’: False, ‘has_qsiprep_t1w’: False, ‘has_qsiprep_t1w_transforms’: False}
Process Process-12:
Traceback (most recent call last):
File “/usr/local/miniconda/lib/python3.8/multiprocessing/process.py”, line 315, in _bootstrap
self.run()
File “/usr/local/miniconda/lib/python3.8/multiprocessing/process.py”, line 108, in run
self._target(*self._args, **self._kwargs)
File “/usr/local/miniconda/lib/python3.8/site-packages/qsiprep/cli/run.py”, line 1169, in build_recon_workflow
retval[‘workflow’] = init_qsirecon_wf(
File “/usr/local/miniconda/lib/python3.8/site-packages/qsiprep/workflows/recon/base.py”, line 89, in init_qsirecon_wf
single_subject_wf = init_single_subject_wf(
File “/usr/local/miniconda/lib/python3.8/site-packages/qsiprep/workflows/recon/base.py”, line 244, in init_single_subject_wf
workflow.connect([(anat_ingress_wf, dwi_recon_wfs[dwi_file], to_connect)])
File “/usr/local/miniconda/lib/python3.8/site-packages/nipype/pipeline/engine/workflows.py”, line 239, in connect
raise Exception("\n".join([“Some connections were not found”] + infostr))
Exception: Some connections were not found
Module anat_ingress_wf has no output called outputnode.orig_to_t1_mode_forward_transform
Module anat_ingress_wf has no output called outputnode.t1_2_mni_forward_transform
Module anat_ingress_wf has no output called outputnode.t1_2_mni_reverse_transform
Module anat_ingress_wf has no output called outputnode.t1_aparc
Module anat_ingress_wf has no output called outputnode.t1_aseg
Module anat_ingress_wf has no output called outputnode.t1_brain_mask
Module anat_ingress_wf has no output called outputnode.t1_csf_probseg
Module anat_ingress_wf has no output called outputnode.t1_gm_probseg
Module anat_ingress_wf has no output called outputnode.t1_preproc
Module anat_ingress_wf has no output called outputnode.t1_seg
Module anat_ingress_wf has no output called outputnode.t1_wm_probseg
Module anat_ingress_wf has no output called outputnode.brain
Module anat_ingress_wf has no output called outputnode.aseg
Module anat_ingress_wf has no output called outputnode.fs_5tt_hsvs
Module anat_ingress_wf has no output called outputnode.qsiprep_5tt_hsvs
Module anat_ingress_wf has no output called outputnode.qsiprep_5tt_fast
Module anat_ingress_wf has no output called outputnode.fs_to_qsiprep_transform_itk
Module anat_ingress_wf has no output called outputnode.fs_to_qsiprep_transform_mrtrix
2- this version is 0.16.0RC3
3 I am using docker version
4. I used the following command
docker run --rm -it -v C:\Users\Alumnos\Ra\ReDLat\examples\data1\license.txt:/opt/freesurfer/license.txt:ro -v C:\Users\Alumnos\Ra\ReDLat\examples\data1\bids3:/data:ro -v C:\Users\Alumnos\Ra\ReDLat\examples\data1\out5:/out pennbbl/qsiprep:0.16.0RC3 /data /out participant --dwi-only --skip_bids_validation --output-resolution 2.0 --recon-spec dsi_studio_gqi
5-Preprocesing look fine, exeptep for this warning
WARNING:py.warnings:TemplateFlow: repository not found at /home/qsiprep/.cache/templateflow. Populating a new TemplateFlow stub.
If the path reported above is not the desired location for TemplateFlow, please set the TEMPLATEFLOW_HOME environment variable.
WARNING:py.warnings:TemplateFlow: repository not found at /home/qsiprep/.cache/templateflow. Populating a new TemplateFlow stub.
If the path reported above is not the desired location for TemplateFlow, please set the TEMPLATEFLOW_HOME environment variable.
- This error is not subject specific
Looking at the error, the problem is with the T1w, for than reason I run the same command without --dwi-only
docker run --rm -it -v C:\Users\Alumnos\Ra\ReDLat\examples\data1\license.txt:/opt/freesurfer/license.txt:ro -v C:\Users\Alumnos\Ra\ReDLat\examples\data1\bids3:/data:ro -v C:\Users\Alumnos\Ra\ReDLat\examples\data1\out4:/out pennbbl/qsiprep:0.16.0RC3 /data /out participant --recon-spec dsi_studio_gqi --skip_bids_validation --output-resolution 2.0
This time reconstruction was complete, however only create .txt with the name of the ROIs for every atlas.
IMPORTANT:nipype.workflow:
Running qsirecon version 0.16.0RC3:
* BIDS dataset path: /data.
* Participant list: [‘PSL00076’].
* Run identifier: 20220629-214517_af147cf5-2b93-466a-b06b-8bcf54960791.
220629-21:45:19,923 nipype.workflow INFO:
found [’/out/qsiprep/sub-PSL00076/dwi/sub-PSL00076_space-T1w_desc-preproc_dwi.nii.gz’] in /out/qsiprep
INFO:nipype.workflow:found [’/out/qsiprep/sub-PSL00076/dwi/sub-PSL00076_space-T1w_desc-preproc_dwi.nii.gz’] in /out/qsiprep
220629-21:45:19,934 nipype.workflow INFO:
Found usable QSIPrep-preprocessed T1w image and mask.
INFO:nipype.workflow:Found usable QSIPrep-preprocessed T1w image and mask.
220629-21:45:19,944 nipype.workflow INFO:
Found T1w-to-template transforms
INFO:nipype.workflow:Found T1w-to-template transforms
220629-21:45:19,944 nipype.workflow INFO:
No FreeSurfer inputs available for PSL00076
INFO:nipype.workflow:No FreeSurfer inputs available for PSL00076
220629-21:45:19,945 nipype.workflow INFO:
Anatomical (T1w) available for recon: {‘has_qsiprep_5tt_fast’: False, ‘has_qsiprep_5tt_hsvs’: False, ‘has_freesurfer_5tt_hsvs’: False, ‘has_freesurfer’: False, ‘has_qsiprep_t1w’: True, ‘has_qsiprep_t1w_transforms’: True}
INFO:nipype.workflow:Anatomical (T1w) available for recon: {‘has_qsiprep_5tt_fast’: False, ‘has_qsiprep_5tt_hsvs’: False, ‘has_freesurfer_5tt_hsvs’: False, ‘has_freesurfer’: False, ‘has_qsiprep_t1w’: True, ‘has_qsiprep_t1w_transforms’: True}
220629-21:45:19,959 nipype.workflow INFO:
Transforming ODF ROIs into DWI space for visual report.
INFO:nipype.workflow:Transforming ODF ROIs into DWI space for visual report.
Thanks for the help
Best
Raul