[Freesurfer] Use Hippocampal segmentation sub-nuclei on other brain softwares

External Email - Use Caution Dear All, I have been stuck on this issue for quite some time. What I am trying to do is running a segmentation on both amygdala and hippocampus, and then to look at the different activation of the segmented sub-fields of both structures during a s

[Freesurfer] mkcontrast2 typo in 7.1.1

External Email - Use Caution On line 106: if($FS_MKCON_USE_BIN == 0 && UseOctave == 0) then there should be a "$" before the "UseOctave" to make the line read: if($FS_MKCON_USE_BIN == 0 && $UseOctave == 0) then Apologies if this has been already corrected, I didn't come across

[Freesurfer] perl version needed for FS5.3

External Email - Use Caution Hi all, we have problems in launching the recon-all command of FS5.3 (needed for a reconstruction of old results): during the nu_correct command various perl commands are called with a fix #!/usr/bin/perl -w The primary error is some "Can't used

[Freesurfer] addon question perl version needed for FS5.3

External Email - Use Caution Hi all, sorry for a short additional question on the same perl topic: I found that the critical syntax of an "if(defined(@...)" has been omitted in FS6.0. Where there other changes to the perl scripts in the subfolder "mni" or could they be exch

[Freesurfer] mri_segstats to report empty and non-empty segmentation

External Email - Use Caution Hello Experts, I am using mri_segstats with the --ctab flag to extract dti and suvr values from a white matter hyperintensities parcellation. Running mri_segstats on the image and parcellation with --ctab only reports on non-empty segmentations. I want

Re: [Freesurfer] Use Hippocampal segmentation sub-nuclei on other brain softwares

External Email - Use Caution Hi Gregorio, you need to transform the *mgz output images accordingy to NIFTIs images. Here is some exemplary shell code for the left hemisphere - operating in a subject's mri folder, using the FS6.0 type of aggregation (if you used FS7.1, you might

[Freesurfer] Some func. error during recon-all process

External Email - Use Caution Hi Yoonho, I'm not an expert but since your inquiry doesn't yet have a reply I thought I'd try to answer it as much as I can. 1. -whitesurf process is preceded over smooth2 and inflated2 in recon-all file, really it is not. why? It seems the second sm

Re: [Freesurfer] Some func. error during recon-all process

External Email - Use Caution To list, Sorry this was meant to be a reply to some previous email but it went out with a wrong subject and wrong formattings. Best, Horsng > On Apr 13, 2021, at 7:48 AM, Horsng Junn wrote: > > Hi Yoonho, > > I'm not an expert but since your inqui

Re: [Freesurfer] question about mapping fsaverage surface atlas to subject's native volume space

Did you use mri_surf2surf to map the data from fsaverage to a surface in the subject space first? From: freesurfer-boun...@nmr.mgh.harvard.edu On Behalf Of Ren, Xueying Sent: Monday, April 12, 2021 9:21 PM To: Freesurfer support list Subject: [Freesurfer] question about mapping fsaverage surfa