Re: [Freesurfer] Saving more than one label in a single volume file

sorry, not sure what you mean. do you mean you want to extract, say, two labels (amygdala and hippocampus) into a single volume file? If so, you can run something like mri_binarize --i aseg.mgz --match 17 18 --o amyg-hippo.lh.mask.mgz mri_mask aseg.mgz amyg-hippo.lh.mask.mgz amyg-hippo.lh.mgz wh

[Freesurfer] volumetric to surface using mri_vol2surf: tpl-MNI152NLin2009cAsym

Hi Freesurfers, I was wondering if there is a registration matrix (from volumetric to surface) for MNI152NLIN2009cAsym template. I was not able to find any (relevant) dat files in $FREESURFER_HOME/average/. I have some data in that space and would like to map them on the surface for visualizati

Re: [Freesurfer] Segmentation error with T2w

Hi Jakob, I believe we fixed the bug in FS 7.4 release. Can you give it a try? Best, Yujing From: freesurfer-boun...@nmr.mgh.harvard.edu On Behalf Of Litsch, Jakob Benjamin Sent: Wednesday, December 6, 2023 10:40 AM To: freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] Segmentation error w

[Freesurfer] Freesurfer 7.3.1 MCR 2019b

External Email - Use Caution Dear Freesurfer Experts, I'm building a docker file with freesurfer and matlab run time. May I know if freesurfer 7.3.1 should be compatible with matlab run time 2019b? If so, what else can I make the environment setting correct in order to run local

[Freesurfer] Faces and vertices error !

External Email - Use Caution Hi FreeSurfer community, I am trying to map subject-specific cortical thickness map to standard fsaverage space and I ran the following command where sub1_filled is my individual subject in native: mri_surf2surf --srcsubject sub1_filled --srcsurfreg t

Re: [Freesurfer] Faces and vertices error !

I think you need to specify ‘--src_type curv’ and ‘--trg_type curv’ to read thickness files. It looks like you passed ‘thickness’ to the wrong flag. Use ‘—srcsurfval’ and ‘—trgsurfval’ instead. Here is wiki help page - https://surfer.nmr.mgh.harvard.edu/fswiki/mri_surf2surf Best, Yujing From

Re: [Freesurfer] Automatic prompt reply for freesurfer subsegmentations

>From what I understand, segmentBS.sh copies 'imagedump.mgz' from >$FREESURFER_HOME/average/BrainstemSS/atlas/AtlasDump.mgz. it then tries to >replace it with the image generated by mri_robust_register. All these happen >in Matlab using system(cp), and system(mv). So, I think "mode 0444 >(r--r

[Freesurfer] Longitudinal pipeline with multiple scans at one time point

External Email - Use Caution I have a dataset consisting of individuals scanned at two time points 7 years apart. At the first time point, a single MPRAGE scan was collected for each individual; at the second, the same MPRAGE scan was collected, as well as an additional set of

[Freesurfer] Correlation Line Plot for FS Group Analysis

External Email - Use Caution Hello, I am to generate a plot to visualize the slopes between classes for group analysis. I would like to generate something similar to this freesurfer post: https://secure-web.cisco.com/10NQ6nNamVal7BE9lNMpStHRFgMjBEDJy0P_U59n_G56YhJF2b1UWd5wJjejj

Re: [Freesurfer] Freesurfer 7.3.1 MCR 2019b

External Email - Use Caution   I believe the assumption is the freesurfer 7.3.1 distribution has already been installed (under /usr/local/freesurfer/7.3.1 by the *.deb or *.rpm linux installer file) and that FREESURFER_HOME is set in the environment  (/usr/local/freesurfer/7.3.