Yes, skullstrip will create that file
On 3/18/2021 12:42 PM, Abdollahi, Shervin (NIH/NINDS) [C] wrote:
External Email - Use Caution
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
_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
