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Hello Freesurfer
Developers,
am trying to use run
freesurfer that is configured inside
smriprep.workflow.anatomical.py under init_anat_preproc_wf
pipeline. this workflow, does the following:
- T1w reference:
realigning and then averaging T1w images
- Brain Extraction and
INU (bias field) correction (antsBrainExtraction.sh)
- Brian tissue
segmentation (@fsl_fast)
- Spatial normalization
to standard space (antsRegistration)
- Surface
reconstruction with Freesurfer
When it gets to step
5, it takes skull-stripped t1, ants_segm, and
bias_corrected image to use in freesurfer recon-all
command. In the surface reconstruction section, it starts
by running the following command:
recon-all
-autorecon1
-i /path-to
/sub-03_ses-20140624_T1w.nii
-T2
/path-to/sub-03_ses-20140624_T2w.nii
-noskullstrip
-hires
-openmp 1
-subjid sub-03
-sd
/Users/abdollahis2/Desktop/fcd_nipype/derivatives/freesurfer
-expert
/Users/abdollahis2/Desktop/fcd_nipype/single_subject_03/anat_preproc_wf/surface_recon_wf/_subject_id_03/autorecon1/expert.opts
And surely soon, it
gives me an error that it can not read mgh file
(brainmask.mgz). looking into freesurfer/sub-03/mri
directory I can see that brainmask.mgz is not created and
I am not sure if this is because the option -noskullstrip
was used? I have attached the recon-all.log file. I would
appreciate any suggestion on how to debug this problem.
-
Freesurfer version: 7.1.1
(freesurfer-darwin-macOS-7.1.1-20200811-8b40551)
-
Platform: macOS Catalina,
Version 10.15.7
-
uname -a: Darwin
ndsd-eeg-cedar 19.6.0 Darwin Kernel Version 19.6.0: Tue
Jan 12 22:13:05 PST 2021;
root:xnu-6153.141.16~1/RELEASE_X86_64 x86_64
-
Recon-all.log: see attached
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