[Freesurfer] Cerebellar Vermis

We are interested in using the Cerebellar vermis for an analysis with our PET data. Is the cerebellar vermis segmented during the FreeSurfer pipeline analysis? If it is, which file is it located in or how can I export a nifti file containing this segmentation? Thanks, Cyrus Sarosh

Re: [Freesurfer] (no subject)

The XQuartz upgrade from v2.7.5 to v2.7.6 broke some of the FreeSurfer GUIs. Please reinstall XQuartz v2.7.5. It can be downloaded from this page (http://xquartz.macosforge.org/trac/wiki/Releases). On 07/14/2014 04:41 AM, Hugh Pemberton wrote: Hi everyone, I'm getting the follow error and it's

Re: [Freesurfer] Cerebellar Vermis

Hi there: As of now, FreeSurfer does not parcellate the cerebellar vermis. It gives you 4 measurements of the cerebellum (Left total, left WM, Right total and right WM). There is a toolbox called SUIT that works within SPM 8 that can accomplish this for you. See details at the website below:

[Freesurfer] Making Substancia Nigra label

Dear Freesurfer experts, I have a set of T2w Dicoms from Parkinson's patients and Control subjects. I want to extract and visualize the Substancia Nigra regions of each of these brains. Can you please suggest a way to do this (command line instructions would be great)? Thanks in advance.

[Freesurfer] Updated process v. files excel sheet?

Hi all, I like the excel presentation of the recon-all process/files table for Freesurfer 3.0.5 found here: https://surfer.nmr.mgh.harvard.edu/fswiki/ReconAllFilesVsSteps Is there an updated document for a more recent version? (I am using 5.3.0) Also, are 5.2 and 5.3 similar enough to

[Freesurfer] bad freesurfer segmentation

Hi Bruce, Thanks for your reply. Yes I realize now that this is causing me the troubles. But since fsl is able to do a good segmentation, I think Freesurfer should also be able to do this? I am now using MRI_segment, in which I want to set new limits for the white matter, but it doesn't seem to

Re: [Freesurfer] bad freesurfer segmentation

Hi Doety our segmentation assumes we can resolve cortex as it used an adaptive filtering that estimates the orientation of the gray/white boundary in spatial neighborhoods. It may be more sensitive to low resolution than FSL. Not sure if anyone has a script for importing FSL segmentations into

Re: [Freesurfer] Temporal lobe reconstruction problem

Hi Bruce, I was wondering whether you have seen my email below? Thanks so much Cheers, James On Sat, Jul 12, 2014 at 9:18 AM, james pardon james.pardo...@gmail.com wrote: Hi Bruce, I have sent the link for a problem subject via a private message. Please note since MS causes hypointense

Re: [Freesurfer] mri_cor2label revisited

Are you trying to view it in the volume or the surface? When I run freeview viewing the surface and load the label using the Load Label button (not File-LoadLabel), it works for me. Can you try the tksurfer command below? It runs for me. You can ignore the warning about 0 nonzero vertices

Re: [Freesurfer] Fw: Re: Problem with uploading Cluster Simulation data

You have to load a surface and then load the overlay on top of that. See the freeview tutorial doug ps. Please post to the list! On 07/15/2014 09:03 AM, car...@van-vlodrop.de wrote: I have opened freeview with the commands 'freesurfer' and 'freeview'. I thought that I could upload the data

Re: [Freesurfer] Is there any saving a brain from this type of error?

Hi Jon maybe, depending on the quality of the image. Did the intensity normalization fail? Looks like it might have eaten into the gray matter. Compare the brain.mgz and the orig.mgz. If cortex is intensity-normalized to look like wm try using the -gentle flag, otherwise try setting some of

[Freesurfer] sulcal depth

Hi Freesurfer experts, I did thickness group analysis in pts and healthy subject groups in qdec (age corrected( and got thicker cortex in left insula and thinner precentral gyrus bilaterally that survived FDR 0.01 Surface area and curvature analysis found no difference. However, sulcal depth

[Freesurfer] recon-all exits after mri_nu_correct

Hi All, I'm trying to reconstruct surfaces using recon-all. Though many of the subjects have succeeded, a few are failing at the mri_nu_correct stage. The error file (posted below) provides little detail as to why the error is occurring. Even if it is not fixable, it would be nice to know what