Issue with XCP_D on HPC and TemplateFlow

jsein · October 3, 2022, 9:24pm

I created a Github issue on this topic:

error in finding template space of the input

opened 09:22PM - 03 Oct 22 UTC

bug

## Summary Hi, thank you for providing and supporting this nice tool. I am an h…eavy user of FMRIPREP and new user of XCP_D. My first try with XCP_D didn't go through, it crashes almost immediately with two kind of errors, depending which output spaces were asked to FMRIPREP: - if `MNI152NLin2009cAsym` only was requested in fmriprep, the error is the following: ``` Process Process-2: 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/xcp_d/cli/run.py", line 617, in build_workflow retval['workflow'] = init_xcpd_wf( File "/usr/local/miniconda/lib/python3.8/site-packages/xcp_d/workflow/base.py", line 148, in init_xcpd_wf single_subj_wf = init_subject_wf( File "/usr/local/miniconda/lib/python3.8/site-packages/xcp_d/workflow/base.py", line 329, in init_subject_wf anatomical_wf = init_anatomical_wf( File "/usr/local/miniconda/lib/python3.8/site-packages/xcp_d/workflow/anatomical.py", line 364, in init_anatomical_wf h5_file = fnmatch.filter( IndexError: list index out of range ``` - if ```MNI152NLin2009cAsym MNI152NLin6Asym T1w```were requested to FMRIPREP, the error in XCP_D is the following: ``` Downloading https://templateflow.s3.amazonaws.com/tpl-MNI152NLin2009cAsym/tpl-MNI152NLin2009cAsym_res-02_desc-brain_mask.nii.gz 0%| | 0.00/28.0 [00:00<?, ?B/s] 29.0B [00:00, 324B/s] Process Process-2: 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/xcp_d/cli/run.py", line 617, in build_workflow retval['workflow'] = init_xcpd_wf( File "/usr/local/miniconda/lib/python3.8/site-packages/xcp_d/workflow/base.py", line 148, in init_xcpd_wf single_subj_wf = init_subject_wf( File "/usr/local/miniconda/lib/python3.8/site-packages/xcp_d/workflow/base.py", line 395, in init_subject_wf bold_postproc_wf = init_boldpostprocess_wf( File "/usr/local/miniconda/lib/python3.8/site-packages/xcp_d/workflow/bold.py", line 341, in init_boldpostprocess_wf bold2MNI_trans, bold2T1w_trans = get_transformfilex( File "/usr/local/miniconda/lib/python3.8/site-packages/xcp_d/utils/utils.py", line 87, in get_transformfilex t1w_to_mni = glob.glob(mnisf + 'from-T1w_to-' + template + UnboundLocalError: local variable 'template' referenced before assignment ``` ## Additional details - xcp_d version 0.1.3+0.g9fec4d8.dirty with Singularity on a HPC. - fmriprep version : 21.0.2 with Singularity on a HPC. ### What actually happened? Immediate crash ## Reproducing the bug Here is my XCP_D command: ``` singularity run -B /scratch/jsein/BIDS:/work,$HOME/.templateflow:$HOME/.cache/templateflow \ /scratch/jsein/my_images/xcp_d-0.1.3.simg \ /work/$study/derivatives/fmriprep /work/$study/derivatives/xcpd \ participant --participant-label $sub \ -w /work/temp_data_${study}\ --mem_gb 50 --omp-nthreads 10 --nthreads 12 --smoothing 4 \ --nuissance-regressors acompcor --despike --lower-bpf 0.01 --upper-bpf 0.08 ``` And a typical fmriprep command: ``` singularity run -B /scratch/jsein/BIDS:/work,$HOME/.templateflow:/opt/templateflow --cleanenv /scratch/jsein/my_images/fmriprep-21.0.2.simg \ --fs-license-file /work/freesurfer/license.txt /work/$study /work/$study/derivatives/fmriprep_nosbref \ participant --participant-label $sub \ -w /work/temp_data_${study}\ --mem-mb 50000 --omp-nthreads 10 --nthreads 12 \ --fd-spike-threshold 0.5 --dvars-spike-threshold 2.0 --bold2t1w-dof 9 --cifti-output 91k \ --output-spaces MNI152NLin2009cAsym MNI152NLin6Asym T1w --ignore slicetiming --fs-subjects-dir /work/$study/derivatives/fmriprep/sourcedata/freesurfer ``` Thank you for your support!