Re: [Freesurfer] Infant MRI segmentation

Hi Berdakh, We do not have any publicly available processing stream that would work for this age range. I do have some preliminary tools though, so if you are interested send me an email with a bit more details about your dataset and I can tell you whether I could help. Lilla On Tue, 27 Jan

Re: [Freesurfer] retinotopy in subject volumetric space

This is a bug in 5.3. I've put a new version for you here. Let me know if that works ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_surf2vol On 01/27/2015 01:26 PM, Benjamin Zimmerman wrote: > Hello, > > When I try your recommended code, I am able to get the data back into >

Re: [Freesurfer] MNI to RAS?

Depends on what you mean by easy:). Check out this web page http://surfer.nmr.mgh.harvard.edu/fswiki/CoordinateSystems On 01/27/2015 03:27 PM, Chu, Catherine,M.D. wrote: > > Hi, > > Is there an easy way to convert MNI coordinates to Freesurfer RAS > coordinate space? > > Thanks! > > Cat > > >

Re: [Freesurfer] pial extends to cerebellum even after edits

Hi Team, Can anyone please share if they have been successful in editing extending pial to the cerebellum and which method has been successful in reference to the email below. Thanks, Sneha From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mg

Re: [Freesurfer] pial extends to cerebellum even after edits

Hi Sneha can you send us some snapshots? Or upload the entire subject and we will take a look. You can always erase cerebellum from brain.finalsurfs and rerun recon3 cheers Bruce On Wed, 28 Jan 2015, Sneha Pandya wrote: > Hi Team, > > Can anyone please share if they have been successful in

Re: [Freesurfer] Extraction of T2 map statistics-per-segment

Dear Doug — Your suggestion worked perfectly. I’ve loaded the segmentation data (aparc+aseg.mgz) and the registered T2 maps into MATLAB and was able to detect a few outliers that biased the standard-deviation of the statistics. I’ll apply the same approach to collect statistics for the rest of

[Freesurfer] Volumes differ in geometry

Dear experts, Recently I run freesurfer longitudinal analysis (freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0), during the creation of the BASE, I get the following error "Volumes differ in geometry row=1 col=4 diff=4.745766(4.74577)". We did not change the protocol during the study period. I ch

Re: [Freesurfer] Volumes differ in geometry

Hi Yawu Can you upload those two volumes so we can take a look? Cheers Bruce > On Jan 28, 2015, at 4:33 PM, Liu Y wrote: > > Dear experts, > Recently I run freesurfer longitudinal analysis > (freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0), during the creation of > the BASE, I get the fo

Re: [Freesurfer] Extraction of T2 map statistics-per-segment

mri_segstats also has a --mask option. It will exclude anything not in the mask. There are a few mask options like setting thresholds, etc doug On 1/28/15 4:17 PM, Ben Eliezer, Noam wrote: Dear Doug — Your suggestion worked perfectly. I’ve loaded the segmentation data (aparc+aseg.mgz) and t

[Freesurfer] Resolving issue" undefined symbol: ncerr"

Hi all, While running freesurfer I encountered this problem "Mris_make_surfaces: symbol lookup error: Mris_make_surfaces: undefined symbol :ncerr (Standard_in)2 : error : comparison in expression" Can you pls help me fix these issue ? ___ Freesurfer m

Re: [Freesurfer] Volumes differ in geometry

Hi Bruce,I have uploaded the baseline K_EL03_1.nii.gz and followup K_EL03_2.nii.gz via FTP File Exchange. Thanks, Yawu On Thu, Jan 29, 2015 at 3:28 AM, Bruce Fischl wrote: > Hi Yawu > > Can you upload those two volumes so we can take a look? > Cheers > Bruce > > > > On Jan 28, 2015, at 4:33 PM