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Hi Douglas, Sure, here is the copy of recon-all.log

 

From: "Douglas N. Greve" <dgreve@MGH.HARVARD.EDU>
Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Date: Wednesday, April 14, 2021 at 10:32 AM
To: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] Autorecon1 failure

 

Sorry, can you resend the recon-all.log file?

On 4/7/2021 8:45 AM, Abdollahi, Shervin (NIH/NINDS) [C] wrote:

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From: "Abdollahi, Shervin (NIH/NINDS) [C]" <shervin.abdollahi@nih.gov>
Date: Thursday, March 18, 2021 at 12:42 PM
To: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu>
Subject: Autorecon1 failure

 

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

 

 



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