[Freesurfer] System requirements.

Hello All, I have a P4 1.5 GHZ, 1GB ram, 65GB hard disk running redhat fedora core release 5. I am planning to install the latest version of freesurfer on it. It will be a dedicated system for a small study with the only task of processing the data on freesurfer. Will this work? I understand that

[Freesurfer] aseg label

Hello, I am trying to identify structures around a hippocampus using the labsl in aparc+aseg.img and FreeSurferColorLUT.txt. I see some structures labeled with 238, 232, 248 and I can't find these numbers on FreeSurferColorLUT.txt. Is there different table for aparc+aseg.mgz than one for

Re: [Freesurfer] aseg label

When you load it as a segmentation in tkmedit, what name do those voxels get? You cann also try loadining the aparc+aseg as the -aux volume in tkmedit. The value indicated in the tkmedit control window will be the index into the color table. On Wed, 11 Apr 2007 [EMAIL PROTECTED] wrote:

Re: [Freesurfer] func2tal

Do you want to register them or reslice them? What common space? We use mni305. What version of freesurfer are you using? Usually, you would register (not reslice) your bold to your freesurfer anatomical. As part of the freesurfer recon, the anat is registered (not resliced) to mni305, and

Re: [Freesurfer] cortical thickness problem

It sounds like you need to change the tksurfer color scale to give it more dynamic range. On Wed, 11 Apr 2007, burak ozkalayci wrote: Dear surfers, I ran the recon-all -s bert -autorecon1 recon-all -s bert -autorecon2 recon-all -s bert -autorecon3 commands and all of them finished without

Re: [Freesurfer] cortical thickness problem

Hi Burak, it's all red because the red/green inflection point is at 0. You need to change it for the thickness to show up well (set it the midpoint at 2 or so). And no, the thickness is a property of the surface(s), so you can't make voxel maps of it Bruce On Wed, 11 Apr 2007, burak

Re: [Freesurfer] cortical thickness problem

Burak, The file bert/stats/?h.aparc.stats contains thickness data for parcellated regions. You can get the raw thickness data with: mris_convert -c lh.thickness lh.white lh.thickness.asc where lh.thickness.asc will contain: vertex x y z thickness in mm noting that the x,y,z pertains to

[Freesurfer] Manuals and Scuba

Dear FreeSurfer Team I'm a new user of freesurfer and I would like to ask you few questions. 1.Where can I find more information regarding SCUBA? 2.I read very carefully through the freesurfer website, (all the work flow and tutorials) however, I was wondering weather every time I do any kind

Re: [Freesurfer] Manuals and Scuba

1.Where can I find more information regarding SCUBA? https://surfer.nmr.mgh.harvard.edu/fswiki/Scuba 3. What is the newest version of the FreeSurfer Manual and where can I find it The freesurfer wiki at that address is our current live documentation. -- Kevin Teich

[Freesurfer] Volumes for labels

Hi, I was just wandering exactly how the grey matter volume for a given label is calculated in mris_anatomical_stats. Multiplying the average thickness by the area estimate I get in the output file does not give me exactly the same estimate of grey matter volume as what mris_anatomical_stats