- could the file be damaged?

[miladseyfi]

Hi dear developers I got following error :

File: /home/milad/Desktop/test/result/fmriprep/sub-08/log/20210304-221324_8b77a574-cdeb-4299-befe-57d549bc0e9a/crash-20210304-221402-milad-res_tmpl-29740927-47ae-498b-ab8a-66a9457776d8.txt Working Directory: /home/milad/Desktop/test/work/fmriprep_wf/single_subject_08_wf/anat_preproc_wf/brain_extraction_wf/res_tmpl Inputs: clip: True in_file: /home/milad/.cache/templateflow/tpl-OASIS30ANTs/tpl-OASIS30ANTs_res-01_T1w.nii.gz order: 3 smooth: True zooms: (4.0, 4.0, 4.0) Traceback (most recent call last): File "/home/milad/anaconda3/lib/python3.7/site-packages/nipype/pipeline/plugins/multiproc.py", line 67, in run_node result["result"] = node.run(updatehash=updatehash) File "/home/milad/anaconda3/lib/python3.7/site-packages/nipype/pipeline/engine/nodes.py", line 516, in run result = self._run_interface(execute=True) File "/home/milad/anaconda3/lib/python3.7/site-packages/nipype/pipeline/engine/nodes.py", line 635, in _run_interface return self._run_command(execute) File "/home/milad/anaconda3/lib/python3.7/site-packages/nipype/pipeline/engine/nodes.py", line 741, in _run_command result = self._interface.run(cwd=outdir) File "/home/milad/anaconda3/lib/python3.7/site-packages/nipype/interfaces/base/core.py", line 434, in run runtime = self._run_interface(runtime) File "/home/milad/anaconda3/lib/python3.7/site-packages/niworkflows/interfaces/images.py", line 75, in _run_interface smooth=self.inputs.smooth, File "/home/milad/anaconda3/lib/python3.7/site-packages/niworkflows/utils/images.py", line 200, in resample_by_spacing data = gaussian_filter(in_file.get_fdata(), smooth) File "/home/milad/anaconda3/lib/python3.7/site-packages/nibabel/dataobj_images.py", line 356, in get_fdata data = np.asanyarray(self._dataobj, dtype=dtype) File "/home/milad/anaconda3/lib/python3.7/site-packages/numpy/core/_asarray.py", line 138, in asanyarray return array(a, dtype, copy=False, order=order, subok=True) File "/home/milad/anaconda3/lib/python3.7/site-packages/nibabel/arrayproxy.py", line 393, in array arr = self._get_scaled(dtype=dtype, slicer=()) File "/home/milad/anaconda3/lib/python3.7/site-packages/nibabel/arrayproxy.py", line 360, in _get_scaled scaled = apply_read_scaling(self._get_unscaled(slicer=slicer), scl_slope, scl_inter) File "/home/milad/anaconda3/lib/python3.7/site-packages/nibabel/arrayproxy.py", line 339, in _get_unscaled mmap=self._mmap) File "/home/milad/anaconda3/lib/python3.7/site-packages/nibabel/volumeutils.py", line 534, in array_from_file getattr(infile, 'name', 'object'))) OSError: Expected 64364544 bytes, got 2249417 bytes from object

• could the file be damaged?

---

version : 20.2.1

command : fmriprep //home/milad/Desktop/test/flanker/ /home/milad/Desktop/test/result/ participant --fs-license-file /home/milad/free_home/license.txt -w /home/milad/Desktop/test/work/

Any help will be appreciated

[effigies]

I would try deleting /home/milad/.cache/templateflow/tpl-OASIS30ANTs/tpl-OASIS30ANTs_res-01_T1w.nii.gz and letting fMRIPrep re-download it.

[miladseyfi]

thanks for quick reply I did as you said but the processing stopped again with new error :

error tab in HTML file :

mri_cc -aseg aseg.auto_noCCseg.mgz -o aseg.auto.mgz -lta /home/milad/Desktop/test/result/freesurfer/sub-08/mri/transforms/cc_up.lta sub-08

will read input aseg from aseg.auto_noCCseg.mgz writing aseg with cc labels to aseg.auto.mgz will write lta as /home/milad/Desktop/test/result/freesurfer/sub-08/mri/transforms/cc_up.lta reading aseg from /home/milad/Desktop/test/result/freesurfer/sub-08/mri/aseg.auto_noCCseg.mgz reading norm from /home/milad/Desktop/test/result/freesurfer/sub-08/mri/norm.mgz 45862 voxels in left wm, 53689 in right wm, xrange [168, 195] searching rotation angles z=[-20 -6], y=[-4 10]

searching scale 1 Z rot -20.4
searching scale 1 Z rot -20.2
searching scale 1 Z rot -19.9
searching scale 1 Z rot -19.7
searching scale 1 Z rot -19.4
searching scale 1 Z rot -19.2
searching scale 1 Z rot -18.9
searching scale 1 Z rot -18.7
searching scale 1 Z rot -18.4
searching scale 1 Z rot -18.2
searching scale 1 Z rot -17.9
searching scale 1 Z rot -17.7
searching scale 1 Z rot -17.4
searching scale 1 Z rot -17.2
searching scale 1 Z rot -16.9
searching scale 1 Z rot -16.7
searching scale 1 Z rot -16.4
searching scale 1 Z rot -16.2
searching scale 1 Z rot -15.9
searching scale 1 Z rot -15.7
searching scale 1 Z rot -15.4
searching scale 1 Z rot -15.2
searching scale 1 Z rot -14.9
searching scale 1 Z rot -14.7
searching scale 1 Z rot -14.4
searching scale 1 Z rot -14.2
searching scale 1 Z rot -13.9
searching scale 1 Z rot -13.7
searching scale 1 Z rot -13.4
searching scale 1 Z rot -13.2
searching scale 1 Z rot -12.9
searching scale 1 Z rot -12.7
searching scale 1 Z rot -12.4
searching scale 1 Z rot -12.2
searching scale 1 Z rot -11.9
searching scale 1 Z rot -11.7
searching scale 1 Z rot -11.4
searching scale 1 Z rot -11.2
searching scale 1 Z rot -10.9
searching scale 1 Z rot -10.7
searching scale 1 Z rot -10.4
searching scale 1 Z rot -10.2
searching scale 1 Z rot -9.9
searching scale 1 Z rot -9.7
searching scale 1 Z rot -9.4
searching scale 1 Z rot -9.2
searching scale 1 Z rot -8.9
searching scale 1 Z rot -8.7
searching scale 1 Z rot -8.4
searching scale 1 Z rot -8.2
searching scale 1 Z rot -7.9
searching scale 1 Z rot -7.7
searching scale 1 Z rot -7.4
searching scale 1 Z rot -7.2
searching scale 1 Z rot -6.9
searching scale 1 Z rot -6.7
searching scale 1 Z rot -6.4 global minimum found at slice 183.0, rotations (3.23, -13.20) final transformation (x=183.0, yr=3.230, zr=-13.197): 0.97204 0.22830 0.05485 -79.26068; -0.22794 0.97359 -0.01286 77.99773; -0.05634 0.00000 0.99841 2.52578; 0.00000 0.00000 0.00000 1.00000; error: No such file or directory error: mri_cc: no WM voxels found with norm > 40 -- check skull stripping

Command exited with non-zero status 253 @#@FSTIME 2021:03:05:01:19:42 mri_cc N 7 e 49.43 S 0.13 U 50.61 P 102% M 228632 F 6 R 72214 W 0 c 376 w 19 I 1336 O 0 L 3.19 2.79 2.70 @#@FSLOADPOST 2021:03:05:01:20:32 mri_cc N 7 2.85 2.75 2.69 Linux milad-Aspire-A715-71G 5.8.0-44-generic #50~20.04.1-Ubuntu SMP Wed Feb 10 21:07:30 UTC 2021 x86_64 x86_64 x86_64 GNU/Linux

recon-all -s sub-08 exited with ERRORS at ‫جۆمعه ۰۵ مارس ۲۱، ساعات ۰۱:۲۰:۳۲ (+0330)‬

For more details, see the log file /home/milad/Desktop/test/result/freesurfer/sub-08/scripts/recon-all.log To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting

Standard error:

Return code: 1

---

error in the terminal :

210305-01:20:34,768 nipype.workflow ERROR: could not run node: fmriprep_wf.single_subject_08_wf.anat_preproc_wf.surface_recon_wf.autorecon_resume_wf.autorecon2_vol 210305-01:20:34,818 nipype.workflow CRITICAL: fMRIPrep failed: Workflow did not execute cleanly. Check log for details 210305-01:20:35,409 cli ERROR: Preprocessing did not finish successfully. Errors occurred while processing data from participants: 08 (1). Check the HTML reports for details.

[effigies]

error: No such file or directory
error: mri_cc: no WM voxels found with norm > 40 -- check skull stripping

In your FreeSurfer output directory, can you examine mri/T1.mgz and mri/brain.mgz to check the quality of the brain mask?

[miladseyfi]

I checked. The brain.mgz was not created . there were two brain masks(brainmask.mgz & brainmask.auto.mgz ) they were not similar to the brain mask at all !! the mask was only local noisy regions . So what is the solution ? Why the masks should be like this and beain.mgz dose not exist?

[effigies]

Sorry for letting this fall by the wayside. It sounds like skull-stripping went poorly. Would you mind posting some screenshots of your T1w image? If you're able to share the image, we can try to reproduce the issue.