[Freesurfer] Hippocampus ROI

External Email - Use Caution Dear FreeSurfer experts, I am trying to create a hippocampus ROI in FSL (MNI 152_2mm brain space) from the FreeSurfer 7.0 hippocampal/amygdala segmentation. How do I create this ROI? Best, Jessica ___ Free

Re: [Freesurfer] FreeSurfer error when running Hippocampal Subfields

Hi Joana, I agree with Eugenio that if this is failing from within python, then python is probably messing with your environment. Based on that error log, it’s tough to say whether this is a freesurfer problem or matlab. The fact that it runs fine on linux seems to suggest it’s a macOS-specific

Re: [Freesurfer] Freeview Update using MAC

Hi Erika, Can you untar the file you downloaded instead of the "HighSierra" version. There was a small typo in the UpdateFreeview instructions that mentioned high-sierra. The freeview you downloaded should work fine for 10.12 Best, Andrew From: freesurfer-boun...@nmr.mgh.harvard.edu on behal

Re: [Freesurfer] memory allocation error

Hi Fabio, How much memory are you allowing for this process? You might want to just try increasing the limit on the slurm job to see if that works. Best Andrew From: freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Bernardoni, Fabio Date: Tuesday, May 11, 2021 at 4:22 AM To: freesurfer m

Re: [Freesurfer] Cerebellum Segementation

External Email - Use Caution Thanks a lot for your help! Get Outlook for iOS

Re: [Freesurfer] Cerebellum Segementation

All of our binaries read any of our supported formats, so that should be fine as like as the direction cosines are correct Cheers Bruce From: freesurfer-boun...@nmr.mgh.harvard.edu On Behalf Of A.R. Sekar Sent: Wednesday, May 19, 2021 7:12 AM To: Freesurfer support list Subject: Re: [Freesurf

[Freesurfer] fspalm output

External Email - Use Caution Dear experts, I used the function fspalm to run permutations with the following options: fspalm --glmdir /my_glmdir/ --cft 1.3 --name palm --iters 1 --cwp .05 --onetail Checking the palmcofig.txt file that is generated as output, I realized that e

[Freesurfer] SUIT cerebellum parcellations

External Email - Use Caution Dear FS Experts, Just wondering if it's possible to use the SUIT labels in the LUT to obtain cerebellar quantification measures and also to make masks for tractography specific to each area? Thanks in advance Erik __

Re: [Freesurfer] Cerebellum Segementation

External Email - Use Caution Hello, Just a follow up question: can I run the isolate function on 1. Co-registered nii files? Or do they have to be mgz files? Thanks! Akila From: freesurfer-boun...@nmr.mgh.harvard.edu on behalf of A.R. Sekar Date: Tuesday, 18 May 2021 at 17

[Freesurfer] Problem with talairach check in Freesurfer 7

External Email - Use Caution I try to describe in more detail my problems with talairach check/correction in Freesurfer 7. In earlier versions, I used tkregister2 to check and correct talairach registration and it worked perfectly. The green line (orig surface of the subject) was v

[Freesurfer] C.Thickness: Statistical analyses with three groups

External Email - Use Caution Dear Freesurfer experts, My goal is to compare the cortical thickness between three groups. For that purpose, I performed whole brain analysis with a F-contrast to evaluate a group effect. Since the F-test was significant, I performed pairwise comparis