[Freesurfer] Calling segmentThalamicNuclei.sh Issue

External Email - Use Caution Hello FreeSurfers, I have a student who is trying to run the segmentThalamicNuclei module on some T1 images, using the segmentThalamicNuclei.sh script. All of the subjects have been run through the main recon-all pipeline and each participant has th

Re: [Freesurfer] Issue with mri_vol2surf nearest interpolation

External Email - Use Caution Can you send the full terminal output? On 8/4/2023 1:20 PM, Sun, Wendy wrote: External Email - Use Caution Good afternoon, We are encountering an issue with getting non-integer values (input file has all integers) when using the “nearest” i

Re: [Freesurfer] Errors Running tkmedit

External Email - Use Caution we are not supporting tkmedit anymore (and have not for a long time). Have you tried using freeview (or tkmeditfv which is a frontend for freeview that takes tkmedit-like options). FV is not available in 5.3, but you can still use it on 5.3 data. On

Re: [Freesurfer] How to compute the merged volume of both hemispheres per each ROI

External Email - Use Caution You'll have to do it by hand or maybe in matlab; you can use fast_ldtable.m to load in the tables in matlab On 8/5/2023 4:54 AM, inbal paran wrote: External Email - Use Caution Hello FreeSurfer Developers, I need to compute the volume of sp

Re: [Freesurfer] Question about group analysis

External Email - Use Caution It is worse -- we do not support qdec anymore On 8/5/2023 6:04 AM, inbal paran wrote: External Email - Use Caution Hello FreeSurfer Developers, I have a question regarding group analysis: When I followed the instructions on how to build my

Re: [Freesurfer] mri_segstats --sbTIVin

External Email - Use Caution Hmm, it does not look like that option was ever added (ie, that wiki page is incorrect). On 8/6/2023 8:13 AM, Woo-Suk Tae wrote: External Email - Use Caution Dear Freesurfer developer. According to the explanation in the *MailScanner has de

[Freesurfer] Use freeview to visualize white and pial surface

External Email - Use Caution I have a question about freeview. Recently, when I loaded lh.pial and lh.white at the same time, the freeview was suddenly aborted and reported the following error. ../mesa-22.0.3/src/mesa/vbo/vbo_attrib_tmp.h:234:_save_Vertex3fv: Assertion `used

Re: [Freesurfer] Use freeview to visualize white and pial surface

External Email - Use Caution What is your freeview command line/ From: freesurfer-boun...@nmr.mgh.harvard.edu On Behalf Of DS Sent: Monday, August 7, 2023 2:51 PM To: freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] Use freeview to visualize white and pial surface

Re: [Freesurfer] Use freeview to visualize white and pial surface

External Email - Use Caution Hi expert, Thanks for your reply. I used the following command line. freeview -f \ lh.white:edgecolor=blue \ lh.pial:edgecolor=red I also tried to load these images by clicking the icons on the interface of Freeview. But, both approaches do not work.

Re: [Freesurfer] Use freeview to visualize white and pial surface

External Email - Use Caution Maybe you are at the edge of how much ram you have in that machine? How much free memory do you have? From: freesurfer-boun...@nmr.mgh.harvard.edu On Behalf Of DS Sent: Monday, August 7, 2023 3:48 PM To: Freesurfer support list Subject: Re: [Freesu

Re: [Freesurfer] Use freeview to visualize white and pial surface

External Email - Use Caution Hi expert, I do not think it's related to RAM. When I try to load some images larger than the image that it fails to load, it also works. So, I guess it might be related to other issues. PS. the current free RAM is 6GB. Best, Cain At 2023-08

Re: [Freesurfer] Use freeview to visualize white and pial surface

External Email - Use Caution Hmm, can you try running mris_info lh.white mris_info lh.pial and see if those work? What if you just bring up the pial and not the white? Maybe you can put those files in a dropbox and one of us (Ruopeng?) can take a look? From: freesurfer-boun..

Re: [Freesurfer] Use freeview to visualize white and pial surface

External Email - Use Caution Hi expert, Thanks for your tips. Here is the output after typing "mris_info lh.white" SURFACE INFO type: MRIS_TRIANGULAR_SURFACE=MRIS_ICO_SURFACE num vertices: 15 num faces : 319994 num strips : 0

Re: [Freesurfer] Calling segmentThalamicNuclei.sh Issue

External Email - Use Caution That error is usually from using the wrong shell being used to run a script..  Could you send along the command being used or maybe a screenshot of how it is being run from the terminal ? - R. On Aug 7, 2023, at 07:11, Rowan Lawrence