[Freesurfer] From SUMA Dset file to Freesurfer file( overlay an gii file on fsaverage brain)

Dear Freesurfer experts, If you are not skilled in SUMA, you can directly skip to part 2. I have a trouble when I converted a SUMA dset file to Freesurfer file which can be overlayed on Freesurfer's fsaveraage brain. Part 1: converting SUAM dset file to Freesurfer gii file I followed the in

Re: [Freesurfer] Using a2009s.annot as seed masks for tractography

Hi Anastasia, Sorry for not being clearer. According to your email, I labelled all my regions of interest as follows: "mri_binarize --match ID --i aparc.a2009s+aseg.mgz --o labelID.nii.gz" Let's take the left putmane as an example: cmdline mri_binarize --match 12 --i aparc+aseg.mgz --o left_pu

[Freesurfer] NUCLEAR MEDICINE/SPECT APPLICATIONS

Dear Freesurfer Users: I'm new to freesurfer and to your website and very much appreciate your time invested in addressing my question! I'm a physician interested in using freesurfer in a combined structural and functional MRI and single photon emission computed tomography (SPECT) study using

Re: [Freesurfer] Multiple and equidistant circular ROIs on the surface

Thanks Bruce and Doug, this works. Currently, I am trying to do a similar thing, but delimiting the parcellation in one concrete region instead the whole cortex.To do that i tried: 1) Convert the label (concrete brain region) into an annot file [ mris_label2annot ]. 2) Use mris_divide_parcellatio

Re: [Freesurfer] Multiple and equidistant circular ROIs on the surface

Hi Victor we need the full command line and screen output in order to help you. cheers Bruce On Wed, 18 Mar 2015, Victor Montal Blancafort wrote: Thanks Bruce and Doug, this works. Currently, I am trying to do a similar thing, but delimiting the parcellation in one concrete region instead t

Re: [Freesurfer] Multiple and equidistant circular ROIs on the surface

Thank you for your fast reply, Bruce. (1) *** mris_label2annot: [ejones:test] (nmr-stable53-env) mris_label2annot --s fsaverage/ --h lh --ctab ColorTest.txt --a test --l mask_region_ROIS.label Reading ctab ColorTest.txt Number of ctab entries 2 $Id: mris_label2annot.c,v 1.17 2011/03/02 00:04:3

[Freesurfer] automatically saving images from tksurfer

Hi folks, Is there anyway to get freesurfer to pop up a surface with an overlay from the command line and get it to just save the image to .tiff and die. Im trying to make a movie from 300 frames of surface with overlay. I can do the popping up the image with overlay from command line of course,

Re: [Freesurfer] automatically saving images from tksurfer

Hi Greg yes, you can do this with the --screenshot flag in freeview. Check out the help. Or you can write a tcl script in tksurfer cheers Bruce On Wed, 18 Mar 2015, Gregory Kirk wrote: > Hi folks, > > Is there anyway to get freesurfer to pop up a surface with an overlay from > the command lin

Re: [Freesurfer] Drawing ROIs using coordinates in another space?

Thanks, Doug! I'm still unsure though- how would I create the label file for the BV coordinates though, given that Freesurfer and BV are in different spaces? (BV coordinates are in Talairach space). Would I need to convert Talairach to MNI? And how would I be able to go about drawing a spherical

[Freesurfer] fslswapdim.fsl: Command not found

Hello Freesurfer experts, I am trying to learn dti using data downloaded from the martinis and everything was running fine till I got this message: Wed Mar 18 16:54:54 CDT 2015 --s Diff001 --mov /Users/Sampada/Desktop/dtimartinos/diffusion_tutorial/Diff001/dtrecon/tmp.bbregister.49197/template.ni

Re: [Freesurfer] fslswapdim.fsl: Command not found

Hello Sampada, Can you please tell me the contents of the "build-stamp.txt" file in your FREESURFER_HOME directory? -Zeke On 03/18/2015 06:06 PM, Dr Sampada Sinha wrote: > Hello Freesurfer experts, > > I am trying to learn dti using data downloaded from the martinis and > everything was running

Re: [Freesurfer] fslswapdim.fsl: Command not found

I hope you are looking for this: Last login: Tue Mar 17 15:48:52 on ttys009 rmbp:~ Sampada$ export FREESURFER_HOME=/Applications/freesurfer rmbp:~ Sampada$ source $FREESURFER_HOME/SetUpFreeSurfer.sh freesurfer-Darwin-snowleopard-i686-stable-pub-v5.3.0 Setting up environment for F

Re: [Freesurfer] fslswapdim.fsl: Command not found

Hello Sampada, It appears you are running the 32bit version of freesurfer on your 64bit Mac machine. Which is fine, but you would probably get better performance if you installed the 64bit bit version of freesurfer onto your machine. In regard to the error you are experiencing, you have 2 opti

Re: [Freesurfer] fslswapdim.fsl: Command not found

Hello Zeke, Thanks for you valuable reply! I will go with option first of reinstalling freesurfer for 64bit version. I have a quick question though: my fsl binaries already have fslswapdim in it. If I go with an option second (just in case), do I still need to download fsl binaries? Thanks and re