fmriprep trying to create folder that ends with a dot in its name in Windows?

[sangillee]

Hi! I am running fmriPrep version 20.0.5
and I just began using it for a test run on a BIDS validated dataset.
However, right after the automatically generated boilerplate message, I get several of the following errors (attached at the end).
I checked my work directory and the folder is there, it just doesn't have the dot at the end of the name. i.e., there is a folder for
/scratch/fmriprep_wf/single_subject_01_wf/func_preproc_task_faceplace_run_1_wf/bold_std_trans_wf/_std_target_MNI152NLin2009cAsym
but fmriprep is trying to search for a one with a dot at the end, which cannot be created in windows.
Any help please?

200321-03:36:03,119 nipype.workflow ERROR:
Node select_tpl.a0 failed to run on host df005cc66f24.
200321-03:36:03,127 nipype.workflow ERROR:
Saving crash info to /out/fmriprep/sub-01/log/20200321-033522_2ca6d4d0-5af9-41b4-ab04-daec6f3f9c76/crash-20200321-033603-root-select_tpl.a0-1735d110-e35e-4f4e-b31b-b2e4f8379f09.txt
Traceback (most recent call last):
File "/usr/local/miniconda/lib/python3.7/site-packages/nipype/pipeline/plugins/multiproc.py", line 344, in _send_procs_to_workers
self.procs[jobid].run(updatehash=updatehash)
File "/usr/local/miniconda/lib/python3.7/site-packages/nipype/pipeline/engine/nodes.py", line 507, in run
os.makedirs(outdir, exist_ok=True)
File "/usr/local/miniconda/lib/python3.7/os.py", line 211, in makedirs
makedirs(head, exist_ok=exist_ok)
File "/usr/local/miniconda/lib/python3.7/os.py", line 221, in makedirs
mkdir(name, mode)
FileNotFoundError: [Errno 2] No such file or directory: '/scratch/fmriprep_wf/single_subject_01_wf/func_preproc_task_faceplace_run_1_wf/bold_std_trans_wf/_std_target_MNI152NLin2009cAsym.'

When creating this crashfile, the results file corresponding
to the node could not be found.
200321-03:36:03,252 nipype.workflow ERROR:
Node split_target.a0 failed to run on host df005cc66f24.
200321-03:36:03,254 nipype.workflow ERROR:
Saving crash info to /out/fmriprep/sub-01/log/20200321-033522_2ca6d4d0-5af9-41b4-ab04-daec6f3f9c76/crash-20200321-033603-root-split_target.a0-599129f2-8891-48ce-97c2-deb3a7001f48.txt
Traceback (most recent call last):
File "/usr/local/miniconda/lib/python3.7/site-packages/nipype/pipeline/plugins/multiproc.py", line 344, in _send_procs_to_workers
self.procs[jobid].run(updatehash=updatehash)
File "/usr/local/miniconda/lib/python3.7/site-packages/nipype/pipeline/engine/nodes.py", line 507, in run
os.makedirs(outdir, exist_ok=True)
File "/usr/local/miniconda/lib/python3.7/os.py", line 221, in makedirs
mkdir(name, mode)
FileNotFoundError: [Errno 2] No such file or directory: '/scratch/fmriprep_wf/single_subject_01_wf/func_preproc_task_faceplace_run_1_wf/bold_std_trans_wf/_std_target_MNI152NLin2009cAsym./split_target'

[mgxd]

This looks similar to #1944, what is the command you're using? Windows may require you to be more explicit with your output spaces.

[sangillee]

I see. Yes, indeed I was using the default output space. I'll try explicit specification and see if that resolves the issue.

[sangillee]

So, specifying the output space explicitly helped get over that particular error. This is the command I used:
fmriprep-docker M:/FacePlace/BIDS M:/FacePlace/derivatives participant -w M:/ZZ_bench/workdir --fs-no-reconall --fs-license-file C:/FreeSurfer/license.txt --output-spaces MNI152NLin2009cAsym:res-2 --nthreads 16 --omp-nthreads 16 --skip_bids_validation --participant-label 02

But this time, I got a different error (maybe a related error) a bit farther down the road:

Node: fmriprep_wf.single_subject_02_wf.func_preproc_task_faceplace_run_1_wf.bold_reg_wf.fsl_bbr_wf.flt_bbr_init
Working directory: /scratch/fmriprep_wf/single_subject_02_wf/func_preproc_task_faceplace_run_1_wf/bold_reg_wf/fsl_bbr_wf/flt_bbr_init

Node inputs:

angle_rep =
apply_isoxfm =
apply_xfm =
args =
bbrslope =
bbrtype =
bgvalue =
bins =
coarse_search =
compress_report = auto
cost =
cost_func =
datatype =
display_init =
dof = 6
echospacing =
environ = {'FSLOUTPUTTYPE': 'NIFTI_GZ'}
fieldmap =
fieldmapmask =
fine_search =
force_scaling =
in_file =
in_matrix_file =
in_weight =
interp =
min_sampling =
no_clamp =
no_resample =
no_resample_blur =
no_search =
out_file =
out_log =
out_matrix_file =
out_report = report.svg
output_type = NIFTI_GZ
padding_size =
pedir =
ref_weight =
reference =
rigid2D =
save_log =
schedule =
searchr_x =
searchr_y =
searchr_z =
sinc_width =
sinc_window =
uses_qform = True
verbose =
wm_seg =
wmcoords =
wmnorms =

Traceback (most recent call last):
File "/usr/local/miniconda/lib/python3.7/site-packages/nipype/pipeline/plugins/multiproc.py", line 67, in run_node
result["result"] = node.run(updatehash=updatehash)
File "/usr/local/miniconda/lib/python3.7/site-packages/nipype/pipeline/engine/nodes.py", line 516, in run
result = self._run_interface(execute=True)
File "/usr/local/miniconda/lib/python3.7/site-packages/nipype/pipeline/engine/nodes.py", line 635, in _run_interface
return self._run_command(execute)
File "/usr/local/miniconda/lib/python3.7/site-packages/nipype/pipeline/engine/nodes.py", line 741, in _run_command
result = self._interface.run(cwd=outdir)
File "/usr/local/miniconda/lib/python3.7/site-packages/nipype/interfaces/base/core.py", line 398, in run
runtime = self._post_run_hook(runtime)
File "/usr/local/miniconda/lib/python3.7/site-packages/niworkflows/interfaces/registration.py", line 176, in _post_run_hook
self._moving_image = self.aggregate_outputs(runtime=runtime).out_file
File "/usr/local/miniconda/lib/python3.7/site-packages/nipype/interfaces/fsl/preprocess.py", line 731, in aggregate_outputs
runtime=runtime, needed_outputs=needed_outputs
File "/usr/local/miniconda/lib/python3.7/site-packages/nipype/interfaces/base/core.py", line 476, in aggregate_outputs
predicted_outputs = self._list_outputs() # Predictions from _list_outputs
File "/usr/local/miniconda/lib/python3.7/site-packages/nipype/interfaces/mixins/reporting.py", line 56, in _list_outputs
outputs = super(ReportCapableInterface, self)._list_outputs()
File "/usr/local/miniconda/lib/python3.7/site-packages/nipype/interfaces/base/core.py", line 927, in _list_outputs
outputs[out_name] = os.path.abspath(fname)
File "/usr/local/miniconda/lib/python3.7/posixpath.py", line 376, in abspath
cwd = os.getcwd()
FileNotFoundError: [Errno 2] No such file or directory

[hippocampeli]

Hi!
I'm getting a similar error message using fmriprep via docker on win10 when explicitly specifying output spaces

I'm running the following command (fmriprep 21.0.2):
docker run -ti --rm -v path/to/nifti:/data -v path/to/derivatives:/out -v path/to/workdir:/work -v path/to/fslicense:/licensePath nipreps/fmriprep:21.0.2 /data /out/fmriprep participant --participant-label 01 -w /work --output-space T1w --stop-on-first-crash --fs-license-file /licensePath/freesurfer.txt

Previously i successfully computed standard outputs (i.e. standard MNI152NLin2009cAsym) where i did not specify any output spaces. The same error persists when using the latest version of fmriprep.
The dataset is bids compatible.

This is the error log:
230220-10:32:51,994 nipype.workflow ERROR:
Saving crash info to /out/fmriprep/sub-01/log/20230220-102810_39d36581-9bc2-4a40-8b6f-9a1ca4ae6719/crash-20230220-103251-root-split_target.a0-f7845e58-629a-47eb-8c8a-ce0e7775b7c5.txt
Traceback (most recent call last):
File “/opt/conda/lib/python3.8/site-packages/nipype/pipeline/plugins/multiproc.py”, line 344, in _send_procs_to_workers
self.procs[jobid].run(updatehash=updatehash)
File “/opt/conda/lib/python3.8/site-packages/nipype/pipeline/engine/nodes.py”, line 507, in run
os.makedirs(outdir, exist_ok=True)
File “/opt/conda/lib/python3.8/os.py”, line 223, in makedirs
mkdir(name, mode)
FileNotFoundError: [Errno 2] No such file or directory: ‘/work/fmriprep_wf/single_subject_01_wf/func_preproc_task_encoding_run_04_wf/bold_std_trans_wf/_std_target_MNI152NLin2009cAsym./split_target’

The folder being tried to access "_std_target_MNI152NLin2009cAsym." does not exist, only a version without the "." at the end. This directory in turn is empty so no files were stored here / can be accessed.
Any tips or help would be much appreciated.
Thx

[effigies]

@hippocampeli What about using --output-spaces? I'm surprised --output-space doesn't produce an error...

[hippocampeli]

@hippocampeli What about using --output-spaces? I'm surprised --output-space doesn't produce an error...

hey, thanks for your reply. it didn't throw an error.. "fmriprep started successfully.. ". However, using --output-spaces doesn't change anything - same result.

[effigies]

Okay. The easiest thing to do will just be to add --output-spaces MNI152NLin2009cAsym:res-2 (or res-native). I can't figure out at the moment where nipype is constructing these driectory names, so it's hard to tell how easy of a fix this will be. But it will almost certainly need to be in nipype, not fMRIPrep.