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I would just use the preprocessed HCP data and not try to redo any of it.


Matt.

 

From: <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of yunus soleymani <soleymani.yunus@yahoo.com>
Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Date: Monday, December 4, 2023 at 8:12 AM
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] skull stripping error

 

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Alright, we were not aware of this point. Thank you very much for informing us. However, we would like to know your suggestion regarding rsfMRI data. Is it advisable to work on unprocessed data using the currently available software, or should we download and use preprocessed packages of HCP fMRI data? We would greatly appreciate it if you could answer this question. It would be very helpful for us.

best,

Yunus

 

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Yunus Soleymani


Ph.D. Candidate of Neuroimaging 
Tehran University of Medical Sciences
 
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On Monday, December 4, 2023 at 05:29:41 PM GMT+3:30, Glasser, Matt <glasserm@wustl.edu> wrote:

 

 

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FreeSurfer 7.X is not working well with HCP data right now, so your results will be substantially less accurate (this is being actively worked on by the HCP group and FreeSurfer group).  Also, FreeSurfer needs to be called as a part of the HCP Pipelines, not run by itself for optimal performance in HCP data.

 

Matt.

 

From: <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of yunus soleymani <soleymani.yunus@yahoo.com>
Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Date: Monday, December 4, 2023 at 7:53 AM
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] skull stripping error

 

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Yes, you are right. However, the original HCP runs were based on Freesurfer version 5.3, which is an older version. Recent studies have reported significant differences in Freesurfer outputs across versions, especially in the case of cortical thicknesses. The advice is always to use the latest version. We plan to perform the volumetrics using version 7.4.1 of Freesurfer. Then, we will use both our results and the original HCP runs in our modeling, and maybe compare them.

 bests,

Yunus

 

 
  

 

 

On Monday, December 4, 2023 at 05:00:40 PM GMT+3:30, Glasser, Matt <glasserm@wustl.edu> wrote:

 

 

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Why are you rerunning FreeSurfer on HCP data?  You are unlikely to match the quality of the original FreeSurfer runs.


Matt.

 

From: <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of yunus soleymani <soleymani.yunus@yahoo.com>
Reply-To: Freesurfer Support List <freesurfer@nmr.mgh.harvard.edu>
Date: Monday, December 4, 2023 at 4:59 AM
To: Freesurfer Support List <freesurfer@nmr.mgh.harvard.edu>
Subject: [Freesurfer] skull stripping error

 

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Hello Freesurfers,

 

I recently analyzed about 600 subjects from HCP database using the Freesurfer recon-all algorithm. However, I noticed that in almost one third of the subjects, the software did not perform the skull stripping correctly when I checked the results in Freeview. To address this issue, I repeated the skull stripping step for each subject using the code "recon-all -skullstrip -wsthresh 35 -clean-bm -s <subject name>". The skull stripping went well, and then I repeated the analysis using the code "recon-all -autorecon-pial -subjid <subject name>".

 

When I compared the pre and post-correction stats folder, I noticed that some volumetric values had changed, especially in the specific areas related to the initial skull stripping error. However, my concern is that when I loaded the .pial and .aseg files into Freeview, there was no change compared to before the correction visually. Is this okay, or should I take additional steps? I would appreciate your help.

 

Thank you,

Yunus

Bellow is an example. NumberS 1 and 2 are brain masks before and after correction. Numbers 2 and 3 are superimposed .aseg files before and after correction.

 

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