[Freesurfer] ROI from left to right hemi - cortical thickness

Dear all, I have a ROI on the left hemisphere and I'd like to extract cortical thickness values from the homologous region in the right hemisphere. For this I applied the interhemispheric registration process and got my ROI mapped into the right hemisphere in /subject/xhemi/label. However when I

[Freesurfer] Freeview scripting reference

Hi list, I am looking for a complete reference to scriptable commands for Freeview, comparable to what exists for tksurfer (e.g. http://surfer.nmr.mgh.harvard.edu/fswiki/TkSurferGuide/TkSurferScripting/TkSurferScriptingReference) Does this exist? Thanks! ___ I

[Freesurfer] error longitudinal processing

Hi (Martin), - version 5.1 (Ubuntu 64b) - command: long_mris_slopes --qdec ./qdec/long.qdec.table.n114.dat --meas thickness --hemi lh --do-avg --do-rate --do-pc1 --do-spc --do-stack --do-label --time ISI_years --qcache fsaverage - attached: first 3 lines of qdec table containing the info for subje

Re: [Freesurfer] Freeview scripting reference

Hi Inge, Freeview does not support tcl scripting. It does have lots of command-line options that might fit your need. Run 'freeview -h" will display a complete list of the available options. Best, Ruopeng On 6/29/12 7:16 AM, Inge Kasbohm Amlien wrote: Hi list, I am looking for a complete re

[Freesurfer] surface vertex pairs; voxel coloring for tkmedit

Hi, In regard to the surface files, is it correct to say that the wm and pial vertices correspond to each other (e.g., wm vertex # 12345 corresponds to pial vertex # 12345 as the minimum distance between the two surfaces), and so have the same number of vertices? Also, I would like to "coloriz

Re: [Freesurfer] surface vertex pairs; voxel coloring for tkmedit

Hi John they are guaranteed to have the same # of vertices, so the answer is kind of "yes", but the thickness is not the distance between them, but rather the distance from the closest point (which might or might not be the "same" vertex). You can use mri_surf2vol to sample back into the vol

Re: [Freesurfer] lh.pial question

Hi Mia Why do you care? It's probably optic radiation and won't affect anything Cheers Bruce On Jun 28, 2012, at 2:38 PM, "Borzello, Mia" wrote: > just to make sure. i use tksurfer to edit this right? I attached a > screenshot. There is a small groove sticking up then i need to correct. also

[Freesurfer] Glmfit subtraction between 2 individuals

Hi all, I am trying to visualize the surface map showing the Post Treatment - Pre Treatment cortical thickness in a single subject. The Post and Pre scans are processed like 2 separate subjects. I used the commands: mris_preproc --f /cluster/roffman/users/Stable5_PerRun/Subject_Files/FB12_Pairs/

Re: [Freesurfer] Glmfit subtraction between 2 individuals

Hi Adam, use the "paired" method in the fsgd examples. doug On 06/29/2012 11:58 AM, Adam Nitenson wrote: > Hi all, > > I am trying to visualize the surface map showing the Post Treatment - Pre > Treatment cortical thickness in a single subject. The Post and Pre scans > are processed like 2 separat

Re: [Freesurfer] Glmfit subtraction between 2 individuals

Hi Adam, if you use the longitudinal stream for it (it is designed for that stuff and will increase reliability), you will have the surfaces in the same space and can simply subtract the thickness files (mris_calc) and visualize on any one of them. Best, Martin On Fri, 2012-06-29 at 11:58 -0400

Re: [Freesurfer] error longitudinal processing

Hi Joost, the tp id cannot be the same as the base id: fsid fsid-base ISI_years Group Gender Age ICV 11298 11298 0 patient F 16 1441 11298_2 11298 1.83 patient F 17.92 1396 I am amazed that you were able to process it this way? So either call the first time point 11298_1 or call the base 11298_

Re: [Freesurfer] trac-all: error during trac-paths due to tract missing

Hi Torben - I'm looking at all the invocations of "trac-all -prep" in your log file, and they've both exited with an error (the same bvecs error). > grep prep trac-all.log -prep -c /Users/torben/Desktop/tracon/tracon New invocation of trac-preproc /Applications/MRSoftware/freesurfer/bin/trac-pre

[Freesurfer] Qdec error

I got an error beginning with this. Thanks for any help Error in analyze: command failed: mri_glmfit --y //qdec/LH_insula_thick/y.mgh --fsgd ** Electronic Mail is not secure, may not be read every day, and should not be used for urgent or

[Freesurfer] Qdec Error (more/better info)

Hi everyone, I got the error I just mentioned. Terminal window says "no contrasts specified". I am trying to use "timepoint" (1-4) as a discrete factor to look at thickness across time. I guess I will have to resort to longitudinal processing? Thanks for the help -Anson ***

[Freesurfer] can I run recon-all in parallel

Hi, I am new to freesurfer. It seems recon-all is the most time-consuming command. I tried to run it on a HPC cluster with MPI and got the error "ERROR: it appears that recon-all is already running and re-run" and the job stopped right away. Is the code even parallelized? I had no problem runnin