Re: [Freesurfer] Changing roi label display color in tkmedit

Hi Lena, Have you tried loading your labels as a segmentation volume? As long as each of your labels has a different voxel value, you can load that label volume as a segmentation, and then make a corresponding color look up table making each label whatever color you want (as long as you can fi

[Freesurfer] Job Announcement - Research Assistant in Brain Imaging

Job Announcement: Research Assitant in Brain Imaging Boston, MA, USA Full time research assistant positions are available in structural and functional imaging of several clinical conditions including degenerative brain changes in individuals with neurological diseases, traumatic brain injury,

[Freesurfer] Research Assistant Position

Two Research Assistant Positions in Neuroimaging of Traumatic Brain Injury and Post Traumatic Stress Disorder: Boston, MA, 02130, USA Employer: VA Boston Healthcare System Tags: Neuroimaging Neuropsychology/neuropsychological assessment/cognitive neuroscience Traumatic Brain Injury Post Traumatic

[Freesurfer] Postdoctoral Position

Postdoctoral Position in Neuroimaging of Traumatic Brain Injury and Post Traumatic Stress Disorder: Boston, MA, 02130, USA Employer: VA Boston Healthcare System Tags: Neuroimaging Neuropsychology/neuropsychological assessment/cognitive neuroscience Traumatic Brain Injury Post Traumatic Stress Diso

[Freesurfer] multimodel wm hypointensity labeling?

Hello, Are there any freesurfer tools that allow labeling of wm hypointensities using imput from both T1 and T2 or lowb images? Also, I was wondering if there was further documentation for the use of the mri_relabel_hypointensities command? I got the impression this script dealt somehow with c

[Freesurfer] bbregister: seg fault

Hi, I have successfully run 126 subjects through bbregister and mri_vol2vol in order to translate the wmparc volume into TBSS space. However, there are 2 subjects that exited prematurely from bbregister. I think it may have to do with my naming system? 126 of the subjects have the subjid CVRA

[Freesurfer] bbregister

Hello, I used bbregister to create a register.dat file aligning a subject's T2(lowb) dti image to their FreeSurfer orig volume. I am now wondering with what command can I apply this register.dat file to the other diffusion measures such as FA to bring them into alignment with the orig, as they

[Freesurfer] contrast matrix question

Hello, I apologize if this is a very simple question, but how would you set up a contrast matrix to look at the interaction of 2 variables on a measure? For example, my fsgd file contains: class=1 variables=2 Input Subjid class var1 var2 When I tried using a contrast of 0_1_1 the significance

[Freesurfer] manually continue surfcluster on unfinished sim?

Hi, I am processing several multiple comparison jobs on launchpad: 'mri_glmfit-sim --glmdir lh.physio2_chol_final.cvram.115.thickness.07092009.doss.30.glmdir --sim mc-z 5000 1.3 mc-z.pos.1.3 --sim-sign pos --bg 6' and I believe that the job is almost finished running the simulation (it has be

[Freesurfer] recon-all qcache

Hello, I was hoping to get some more information about the qcache option. Would running all my subjects with qcache save me any time if I plan on using mri_glmfit instead of qdec? The GLMs I am running have to be sent through mris_preproc and mri_surf2surf each time since some inputs are #'d

[Freesurfer] v 1.20 asegstats2table bug

Hello, I am having a bit of trouble using asegstats2table. I have tried using different versions of this command and if only I could combine the two, it would work perfectly. I am trying to compile wmparc stats for about 160 subjects. Unlike the new aparcstats2table, asegstats2table seems to

Re: [Freesurfer] scatterplots in tkmedit

has been masked to only leave a skeleton of white matter tracts. The order of the FSGD file corresponds to the order of each subject's registered FA skeleton map in the 4D volume. On Wed, 25 Feb 2009, Douglas N Greve wrote: Is is already registered to a subject? Victoria Williams

[Freesurfer] scatterplots in tkmedit

Hello, I ran a GLM using a 4d skeletonized Fractional Anisotropy volume as my input into mri_glmfit with one variable. As this analysis is not surface based, I must open the results (sig.mgh) using tkmedit as an overlay. My goal is to open a scatterplot similar to that in tksurfer which sho

[Freesurfer] tksurfer: Load GDF command line?

Hi All, I was wondering if there was a flag or command in tksurfer that would allow me to load a group descriptor file (y.fsgd) using the command line. I looked through the tutorial and couldn't seem to find anything. I only found resources for loading a timecourse. This isn't the same thin

[Freesurfer] 6 direction mgh gradient sequence

Hello, Can anyone point me to where I could find a mgh gradient file for dti processing with 6 directions? I am trying to rerun some old data through dt_recon and the gradient_mgh_dti sequence packs start at 13. Any suggestions? Thanks, Tori ___

Re: [Freesurfer] unpacking from CD backup

Hi Jake, I'm pretty sure you can just use the unpacksdcmdir command just as if you were unpacking from a server. Here is the command line I use: unpacksdcmdir -src -targ -fsfast -cfg Hope that helps, Tori On Fri, 17 Oct 2008 [EMAIL PROTECTED] wrote: Hi, Could someone please explai