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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:
1. T1w reference: realigning and then averaging T1w images 2. Brain Extraction and INU (bias field) correction (antsBrainExtraction.sh) 3. Brian tissue segmentation (@fsl_fast) 4. Spatial normalization to standard space (antsRegistration) 5. 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.
1. Freesurfer version: 7.1.1 (freesurfer-darwin-macOS-7.1.1-20200811-8b40551) 2. Platform: macOS Catalina, Version 10.15.7 3. 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 4. Recon-all.log: see attached