[Freesurfer] (no subject)

Could someone please tell me how to unsubscribe from this list? I couldn't find it on the website. Thanks On Jul 2, 2015 4:56 AM, "Milde, Christopher" < christopher.mi...@zi-mannheim.de> wrote: > Dear Freesurfers, > > I have problems converting .nii.gz files into .mgh files needed e.g. for > perf

[Freesurfer] lobe mapping

Hi all, I'm interested in getting a lobar segmentation of the cortex and I've already ran recon-all on my subjects. I'm now confused by the outputs and was wondering if someone could tell me which output file contains segmentation that can be merged to get a 4 lobe parcellation similar to: htt

Re: [Freesurfer] lobe mapping

: > Try running mri_annotation2label with the --lobesStrict option > doug > > > On 11/19/2013 11:15 AM, Mojdeh Zamyadi wrote: >> Hi all, >> >> I'm interested in getting a lobar segmentation of the cortex and I've >> already ran recon-all on my subjects. I'm n

[Freesurfer] converting cortical labels into volumetric ROIs

Hi all, I want to convert the cortical labels I get in freeSurfer to volumetric ROIs in the subject space and I've followed the steps mentioned in: http://brainybehavior.com/neuroimaging/2010/05/converting-cortical-labels-from-freesurfer-to-volumetric-masks/ except since I'm interested in lobe m

Re: [Freesurfer] converting cortical labels into volumetric ROIs

ing you with so many questions! -M On 11/21/2013 01:42 PM, Douglas N Greve wrote: > use mri_aparc2aseg instead of label2vol. This is how aparc+aseg.mgz is > created. Look in the recon-all.log file for the command line used. > > doug > > > On 11/21/2013 10:44 AM, Mojdeh Zamyad

Re: [Freesurfer] converting cortical labels into volumetric ROIs

s, -Mojdeh On 11/21/2013 04:32 PM, Mojdeh Zamyadi wrote: > Thanks! so this is the command I've used: > mri_aparc2aseg --annot freeSurfer_lobes --s P2 --o > freeSurfer_Results/P2/labels/freeSurfer_lobes.nii.gz > > a couple of question I have now: > > 1. what lables (numbe

[Freesurfer] major lobes

Hi all, Since I haven't heard back about my question so far, I'm posting it again! Sorry about this but I really need your help! As mentioned in my previous posts, I'm interested in having the GM volumetric lobar masks (frontal, parietal, temporal, occipital, and insular) with the final goal o

Re: [Freesurfer] major lobes

> color table, run mri_annotation2label with --ctab, then merge the two > ctabs you get (lh and rh). You don't need to rerun mri_aparc2aseg > doug > > > > On 11/29/13 3:09 PM, Mojdeh Zamyadi wrote: >> Hi all, >> >> Since I haven't heard back about m

Re: [Freesurfer] major lobes

Thanks a lot! it worked :) -M On 12/04/2013 11:52 AM, Douglas N Greve wrote: > > mri_annotation2label --subject P2 --hemi lh --ctab new_ColorTable.txt > --lobesStrict freeSurfer_Results/P2/label/lh.freeSurfer_lobes.annot ___ Freesurfer mailing list Fr

[Freesurfer] cortical thickness and ICA of resting state fMRI

group clusters found using ICA analysis of resting state fMRI. Thanks, Mojdeh Zamyadi, MSc Clinical Research Project Assistant The Hospital for Sick Children 555 University Avenue Toronto ON M5G 1X8 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu

[Freesurfer] Fwd: issues with the Talairach transformation

it seems my initial message is not going through because I had some files attached! is there a way I can attach files here? thanks, -Mojdeh Original Message Subject:issues with the Talairach transformation Date: Thu, 19 Jul 2012 15:20:24 -0400 From: Mojdeh Zamyadi

[Freesurfer] Talairach registration

to attach example coronal, sagittal and horizontal slices of one of my subjects but apparently it was too big for the mailing list. Pleas let me know if there is a way to attach images here. I greatly appreciate your advice. Thanks, Mojdeh Zamyadi, MSc Clinical Research Project Assistant The Hospi

Re: [Freesurfer] Talairach registration

ngs like hippocampal > volume. Are you using version 5.1? If so, that's the problem. Nick has > a fix for this that he can direct you about, or you can wait for 5.2 > and rerun the Talairach registration then. > > cheers > Bruce > > > On Fri, 20 Jul 2012, Mojde

Re: [Freesurfer] Talairach registration

u are experienced. Mostly > just see if the ?h.white and pial surface are visually accurate, and > if not see if some small intervention might fix them. > > cheers > Bruce > > > > On Fri, 20 Jul 2012, Mojdeh Zamyadi wrote: > >> Hi Bruce, >> >> Than

[Freesurfer] space of T1.mgz

bjects are in the same space so that the segmentation I do is accurate for all. Thanks for your help, Mojdeh Zamyadi, MSc Clinical Research Project Assistant The Hospital for Sick Children 555 University Avenue Toronto ON M5G 1X8 ___ Freesurfer ma

Re: [Freesurfer] space of T1.mgz

8/2012 12:18 PM, Douglas N Greve wrote: > Hi Mojdeh, try looking at this doc > http://surfer.nmr.mgh.harvard.edu/fswiki/FsAnat-to-NativeAnat > doug > > On 12/18/2012 11:09 AM, Mojdeh Zamyadi wrote: >> Hi all, >> >> I want to segment the hippocampus into head/body/tai

Re: [Freesurfer] space of T1.mgz

n 12/18/2012 12:58 PM, Bruce Fischl wrote: > Hi Mojdeh > > they are not in atlas space and the volumes are for that subject, so > you shouldn't have to do anything if I understand you correctly > > cheers > Bruce > > On Tue, 18 Dec 2012, Mojdeh Zamyadi wrote: &g

[Freesurfer] extracting hippocampus volume using asegstats2table

Hi all, I have a question about the volume of the hippocampus. I want to know why when I convert the left and right hippocampus from mgz to nii (after extracting the labels from aseg.mgz) the number of voxels in the masks don't match the number I get from the aseg