[Freesurfer] Label to ROI volume

Dear FS Experts, I have run recon-all on my subjects. I'm looking to convert the V1 and various BA labels to ROIs in 3D anatomical space (orig.mgz). How would I convert my freesufer label files to ROIs. Thank you! Massieh Moayedi ___ Freesurfer mail

Re: [Freesurfer] Label to ROI volume

Dear Dr. Fischl, Thank you for your respone. What would the --reg and the --temp be in this case? Massieh > Original message -- >From: Bruce Fischl >To: mmoay...@uhnres.utoronto.ca-> >cc: freesurfer@nmr.mgh.harvard.edu-> >Subject: Re: [Freesurfer] Label to ROI

[Freesurfer] Disentangling age effects

Hi, I am studying two groups and have found that age is a confound (or is a covariate with an interaction between the two groups). Simply, when I correlate age between the two groups, there is an interaction (i.e., the slopes are different). My questions are: 1) is it appropriate to proce

[Freesurfer] Anova Statistical Modelling

Hello FreeSurfer Experts, I am trying to run a contrast comparing 3 different classes, and using one covariate as follows (truncated for simplicity's sake!): GroupDescriptorFile 1 Title CTA TMD Patients Low vs Patient High vs Controls Class Control plus blue Class Patient_Low circle green Class

[Freesurfer] Statistical output

Hi everyone, I was hoping you can clarify something for me. I'm comparing two groups using CTA (in freesurfer). When I set up my model, I include age as a covariate of no interest. To do this, I include it as a variable in the fsgd, and in the contrast matrix, I regress out the effects of a

[Freesurfer] ROi analysis within subjects

Hi, We are performing a PRE and POST analysis of our subjects. We have identified ROIs in the PRE scans and would like to display them on the POST scan. However, when we open a label from the PRE scan in the POST scan space, it looks scattered. Is there a method of transforming a label from

[Freesurfer] Error in Recon-All nu_correct

Hi Everyone, We're having a problem in our preprocessing (see below). Any ideas what the problem may be? Many thanks, Massih # #...@# Nu Intensity Correction Thu Nov 19 13:40:47 EST 2009 mri_nu_correct.mni --i orig.mgz --o nu.mgz --n 2 /usr/local/

[Freesurfer] Recon-ALL error

Hi Everyone, Here is a newish error I've encountered- does anyone know how to fix it, or what it means? status file for recon-all: Thu Jan 14 19:48:44 EST 2010 #...@# MotionCor Thu Jan 14 19:48:50 EST 2010 #...@# Nu Intensity Correction Thu Jan 14 19:49:05 EST 2010 #...@# Talairach Thu Jan 14

[Freesurfer] Registering a label from standard space to diffusion space

Hi everyone, I'm trying to use my results from CTA to make a label for diffusion tracking in probtrackx. Is there any way of doing this from the fsaverage (standard space) to the MNI152 (FSL standard) space? I'm hoping to not have to revert the label back to each individual subject, but rath

[Freesurfer] Non-linear correlations

Hi Everyone, I was wondering if there's a method to examine non-linear correlations in FreeSurfer. Specifically, I'd like to use a behavioural correlate and see if there are any correlations in the cortex. The linear correlation wasn't as fruitful as I'd hoped, but there is evidence that a non-

[Freesurfer] Converting an FSL label to Freesurfer space

Hi everyone, I need to convert an FSL label (3D, MNI 152 space, 2mm brain) to FreeSurfer's fsaverage brain inflated surface. Does anyone know how to do this? Thanks, Massih ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.

[Freesurfer] Converting an FSL label to Freesurfer space

Hi, I'm trying to convert the individual FS parcelations to individual space in FSL. I'm not sure how to proceed. I've made a label from the individual subject's parcelation, and have saved it. How would I then convert the label to use it as a mask in the subject's structural space in

[Freesurfer] Freesurfer Average Subject

Dear Dr. Fischl, We have been following the steps you have laid out on the listserv (http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg17601.html) to make an average subject. However, we are not able to proceed with the mris_preproc step. It requires an output file and the hemisphe