[Freesurfer] 2 surface mri_glmfit as independent variables

External Email - Use Caution Hi FreeSurfer team, I have a question about running mri_glmfit with 2 different surface modalities as the independent variable and a single value per participant as the dependent variable. I'm trying to examine the unique and shared contribution of

Re: [Freesurfer] Freesurfer installation on Ubuntu virtual machine

External Email - Use Caution I should have said at the end for installation under $HOME to set, $ export FREESURFER_HOME=$HOME/freesurfer - R. fsbuildMarch 3, 2020 at 15:39 External Email - Use Caution Hello Ben, For packages to install,

[Freesurfer] LGI help

Hello Freesurfer users/developers, I want to run recon-all localGI on a subject who has been processed with Freesurfer 5.3. Whenever I run recon-all -localGI, I always get an error on “make_roi_paths”. There error can be found at the end of this email. I looked at the 5.3 release notes and

Re: [Freesurfer] Freesurfer installation on Ubuntu virtual machine

External Email - Use Caution Hello Ben, For packages to install, see the following wiki page, https://surfer.nmr.mgh.harvard.edu/fswiki/BuildRequirements Usually to expand the freesurfer *.tar.gz archive under /usr/local, you would need sudo/root privileges, e.g. $ cd

[Freesurfer] Registration of DIR (Double Inversion Recovery) series

External Email - Use Caution Hi all, I want to register DIR (Double Inversion Recovery) series to T1 series using Freesurfer. I used the command line similar to that used for FLAIR registration: bbregister --s subject001 --mov

[Freesurfer] Freesurfer installation on Ubuntu virtual machine

External Email - Use Caution Dear Freesurfer experts, Even though this problem has been raised in the archives, I was not able to find a specific solution to my problem. I installed Freesurfer on a virtual machine which runs Ubuntu 18.04.4 (Host system: Windows 10). But it seems

[Freesurfer] segmentation issue

External Email - Use Caution External Email - Use Caution Dear Freesurfeer experts, After running the recon-all in one of my subjets, part of the temporal lobe was partially excluded. Then, I tried to use the watershed algorithm to be less agressive in the skull

[Freesurfer] petsurfer

External Email - Use Caution Dear Freesurfer experts, I have compared the PVC uptake values of gtm.stats with the values of gtm.nii.gz with the function load_nii in matlab. I noted that values in matlab are reversed, i. e., the first value in gtm.stats matches with the last value

[Freesurfer] (no subject)

External Email - Use Caution Dear Freesurfeer experts, After running the recon-all in one of my subjets, part of the temporal lobe was partially excluded. Then, I tried to use the watershed algorithm to be less agressive in the skull stripping as follows: recon-all -skullstrip

Re: [Freesurfer] Control Points

Hi Doro it's hard to tell from your image, but it looks like at least one of your cps is not in wm but in the gm. This will mess everything up. Make sure that they are in unpartial-volumed wm cheers Bruce On Tue, 3 Mar 2020, Meike Hettwer wrote: >External Email - Use Caution > >

[Freesurfer] Control Points

External Email - Use Caution Dear Freesurfer Team, I am currently performing manual edits using freesurfer v. 6.0.1. (on Debian /Linux 7). While brainmask edits work perfectly, the control points i set (mainly in temporal and frontopolar regions, running recon-all

[Freesurfer] comparison within same subjects for different conditions

External Email - Use Caution Dear Freesurfers, sorry for the additional message but I really need your help. I'm running the retinotopy analysis to study population receptive fields on healthy subjects. Structurals have been reconstructed using "recon-all -qcache". The stimuli I

[Freesurfer] CBF data for mri_glmfit processing

External Email - Use Caution Hello everyone, I am using Freesurfer 6.0 on linux cluster. We are analyzing CBF data (ASL derived) coupled with fMRI task in longitudinal design. The fMRI data was analyzed in FS-FAST (with paired-diff) and now we want to repeat the group analyses