[Freesurfer] SNR Tracula

Hi, Tracula outputs the SNR for each volume in a txt file. I was wondering if anyone can point me to some literature on how the SNR is being calculated? Cheers, Scott Quadrelli ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.

Re: [Freesurfer] Drawing a circle around a vertex on a surface

The only code I am aware of for doing this is in mne-python. hth d On 11/8/15 5:36 PM, Reza Rajimehr wrote: > Hi, > > I want to draw a circle around a vertex on the smoothwm or pial surface, > with a particular radius (e.g. 10 mm), fill the circular region and save it > as a label file, then repe

Re: [Freesurfer] Curvilinear interaction with age

Thanks so much for your help! -- Daniel Yang, Ph.D. Yale Child Study Center E-mail: daniel.yj.y...@yale.edu On 11/6/15, 9:23 PM, "freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Martin Reuter" wrote: >Hi Daniel, > >you can always specify your own design matrix X in mri_glmfit. So just

[Freesurfer] Drawing a circle around a vertex on a surface

Hi, I want to draw a circle around a vertex on the smoothwm or pial surface, with a particular radius (e.g. 10 mm), fill the circular region and save it as a label file, then repeat this for all the vertices on the surface. I need this for doing a searchlight analysis. Does anyone have a script/co

[Freesurfer] Tracula - configuration file error

Dear all, I am facing an error at the configuration file for trac-all. I am trying to run a single subject, for who there is a folder with all DWI DICOMs and a folder with the recon-all processing (Freesurfer 5.3). However, I am facing the following error, although no run list is specified.

Re: [Freesurfer] cannot start freesurfer from terminal

Hi Bruce, Normally it then starts listening a few lines like FREESURFER_HOME, FSFAST_HOME, FS_OUTPUT_FORMAT etc. Similar to Zeke's terminal here: https://surfer.nmr.mgh.harvard.edu/fswiki/MacOsInstall#SetupandConfiguration Afterwards I was able to use FS commands like for instance mri_label2vol

Re: [Freesurfer] cannot start freesurfer from terminal

Hi Andre what are you expecting to happen? The sourcing just sets a bunch of environment variables and paths - it doesn't start anything cheers Bruce On Sun, 8 Nov 2015, André Schmidt wrote: Dear FS experts, Surprisingly, I am no longer able to start freesurfer from the terminal: Andres-

[Freesurfer] cannot start freesurfer from terminal

Dear FS experts, Surprisingly, I am no longer able to start freesurfer from the terminal: Andres-MacBook-Pro:~ andre$ export FREESURFER_HOME=/Applications/freesurfer Andres-MacBook-Pro:~ andre$ source $FREESURFER_HOME/SetUpFreeSurfer.sh Do you know what I am doing wrong? Thank you Andre ___

Re: [Freesurfer] node coordinates

Hi Bruce Thanks for your help. This is what I have done: - I used recon-all to define 84 brain regions. - I ran tractography with these 84 regions as seeds. - Then I used network-based statistics to compared the obtained connectivity matrices (84 x 84) between two groups. To visualize the output

Re: [Freesurfer] node coordinates

Hi Andre are you going to do a group analysis afterwards, or so you just want the node coords? The fsaverage subject is already in MNI coords so you can transform to it I believe (Doug can confirm). cheers Bruce On Sun, 8 Nov 2015, André Schmidt wrote: Hi Bruce, Thanks for your reply. B

Re: [Freesurfer] Two recons with different vertex coordinates

Hi Reza the surface labels are sets of vertex indices (and voxel coords). Neither of these applies to a surface constructed from a different session. You need to use mri_label2label to transform the surface from one timepoint to another. You can either use the surface registration, which is a

Re: [Freesurfer] node coordinates

Hi Bruce, Thanks for your reply. But where can I find the node coords? So far I only have names for the nodes. I guess the second step would then be to transform them from Talairach to MNI. Thanks again. Andre Von: freesurfer-boun...@nmr.mgh.harvard.edu

[Freesurfer] Two recons with different vertex coordinates

Hi, We have run recon-all twice on a single subject, both times without any error. Using a functional localizer, we have made a surface-based label for an ROI (FFA) in the ventral temporal cortex of the inflated surface from the first recon. When we visualize the same label on the inflated surface