[Freesurfer] Fwd: tralairach error when recon-all

- Hello all, I had two kind of files ( img & hdr). I used fslchfiletype command to create nii.gz files. img and hdr files replaced by nii.gz files. I used mri_convert command to create 001.mgz files and I did. Now, when I'm running recon-all for my data it exits with error: ERROR: talairach_a

Re: [Freesurfer] Hippocampus volume normalization relative to what other volume ?...

The most correlative brain structure with hippocampus (or amygdala) in the normal population is the best normalization referenece. I believe the intracrainal volume is the best reference volume for the volume normalization. Best regards! Woo-Suk, Tae Chucheon, Korea --- Original Mes

Re: [Freesurfer] Vertex numbers from RAS (or, labels + .aparc.annot = interesting points)

Hi Jed, that means that your label was created in the volume. If you load it in tksurfer it will sample it onto the surface and fill in the vertex numbers. Then you can save it and you should be all set. cheers Bruce On Thu, 6 May 2010, Jed Singer wrote: > Hello again! > > I've got a bunch of

Re: [Freesurfer] merge cortical and subcortical labels

I think mri_binarize would do it, or mri_extract_label. cheers Bruce On Thu, 6 May 2010, Stefan Brauns wrote: > Thank you for your immediate response. > > That will probably do it. Would I extract these labels with the command > mri_cor2label or is there an easier way? > > On Thu, May 6, 2010 at

Re: [Freesurfer] Hippocampus volume normalization relative to what other volume ?...

I think most people these days would include ICV as a regressor. cheers, Bruce On Thu, 6 May 2010, Gonzalo Rojas Costa wrote: Hi: If we want to compare the hippocampus volume between different patients, which other volume could I use to normalize it ?... the ICV ?... the volume of each hemis

[Freesurfer] Vertex numbers from RAS (or, labels + .aparc.annot = interesting points)

Hello again! I've got a bunch of brain scans, each having in the neighborhood of 100 points I'm interested in (corresponding to subdural electrode locations). I've also got an .aparc.annot file that has nicely divided up the cortex into (hopefully) meaningful regions. I also have a bunch o

Re: [Freesurfer] merge cortical and subcortical labels

Thank you for your immediate response. That will probably do it. Would I extract these labels with the command mri_cor2label or is there an easier way? On Thu, May 6, 2010 at 5:30 PM, Bruce Fischl wrote: > Hi Stefan, > > can't you just extract the labels you want from the aparc+aseg.mgz? > > che

[Freesurfer] Using qdec

Hello All, We are using qdec for the analysis of relation between thickness, two roi: par Opercularis, par triangularis; two test: fmri broca and edinburgo. When I make a design with thickness, one roi and one test in Qdec appears one question like: Does the correlation between X and Y, accountin

Re: [Freesurfer] merge cortical and subcortical labels

Hi Stefan, can't you just extract the labels you want from the aparc+aseg.mgz? cheers, Bruce On Thu, 6 May 2010, Stefan Brauns wrote: > Dear Freesurfer experts, > > I want to create a medial temporal lobe label. Is it possible to merge > subcortical and cortical labels? Do I therefore need to u

[Freesurfer] merge cortical and subcortical labels

Dear Freesurfer experts, I want to create a medial temporal lobe label. Is it possible to merge subcortical and cortical labels? Do I therefore need to use the --regmethod volume flag of mri_label2label for cortical labels? Many thanks in advance, Stefan __

[Freesurfer] Invitation to connect on LinkedIn

LinkedIn Luke Tseng souhaite se connecter à vous sur LinkedIn : -- Freesurfer, I'd like to add you to my professional network on LinkedIn. - Luke Accepter l'invitation de Luke Tseng http://www.linkedin.com/e/qaAr-Z_86TRZ5lXG-dA9kZQ49qSe59qYFaT

Re: [Freesurfer] Technical Doubts

hi, no, matlab is not used in the default (structural) processing stream. it is only used by the FS-FAST toolset included with freesurfer, which is used for processing fmri data. so you dont need to mention Matlab. n. On Thu, 2010-05-06 at 14:00 -0500, Dr. Luis Guillermo Almeida Montes wrote: >

[Freesurfer] Talairach x MNI 152

Hi, I've been using FS, in which the Talairach transform is applied as a standard space for registration. Instead of the Talairach transformation i would like to use the MNI 152 as it is done in FSL and SPM. Does anybody have some experience with this? What would be the impact on the results of th

Re: [Freesurfer] Group comparison

The data in aparc.stats contain surface area, gray matter volume, and average thickness for whole regions, and are not intended for surface display. If you want to analyze those regional values use 'aparcstats2table' and then import the data into your preferred statistical package for further ana

[Freesurfer] Group comparison

Dear All, I am sorry to post this message again. Since i am not able to find from the tutorial and archives what i need i am posting it. I want to compare cortical thickness values in each region from aparc.stats file between control and patients. I am wondering whether it is possible to compa

[Freesurfer] Hippocampus volume normalization relative to what other volume ?...

Hi: If we want to compare the hippocampus volume between different patients, which other volume could I use to normalize it ?... the ICV ?... the volume of each hemisphere ?... And, if I want to compare the amygdala, for example ?... Sincerely, Gonzalo Rojas Costa Department of Radiology Cl