What is your advice for me now? Should I abandon the approach or is there anyway to dig deeper into it and solve the error?

 

No, we have not talked

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So yes running it from scratch would work. But I was trying to implement fmriprep approach in which they have chosen the optimal approaches for skull-stripping or intensity normalization via other applications like ANTs or FSL and they imported those to be used in Freesurfer instead of internally calculated skull-strip brain mask (brainmask.mgz).  The last step of autorecon-1 is where the skull stripping needs to be off and that’s where it fails, cause its waiting for that brainmask.mgz and cant find it. Has there been any collaboration between freesurfer and fmriprep people on this matter?

 

Thanks

Shervin

 

From: "Douglas N. Greve" <dgreve@mgh.harvard.edu>
Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Date: Friday, April 16, 2021 at 11:08 AM
To: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] Autorecon1 failure

 

If you run it from scratch (recon-all -s subject -all), does it work? If you are going to pick and chose which options to apply, then there is a high risk of missing steps

On 4/14/2021 2:23 PM, Abdollahi, Shervin (NIH/NINDS) [C] wrote:

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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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