Re: [Freesurfer] Remapping Volume

what was your vol2surf command line? Make sure that it is using nearest neighbor interpolation On Tue, 11 Oct 2016, Crawford, Anna wrote: > Hi, > > I am trying to remap a volume. I am using aparc+aseg.mgz volume. I loaded it > into Matlab using load_mgh. In Matlab I remap the volume to different

[Freesurfer] Use Atlas (Binary ROIs) made in 3DSlicer in as parcellation atlas in Freesurfer

Hi All, We made an average subject for a non-human species and made ROI in nifiti format in Slicer, it's basically an atlas were each region corresponds to a different number. My question is if there is any way to import this into Freesurfer and be able to use this as any other parcellation atlas

Re: [Freesurfer] mri_average vs mri_concat

Hi Doug Any thoughts on this? Trisanna -- Ph.D. Candidate McGill University Integrated Program in Neuroscience Psychology On Thu, Oct 6, 2016 at 10:37 PM, Trisanna Sprung-Much < trisanna.sprung-m...@mail.mcgill.ca> wrote: > Hi Doug > > So the pixel values are 0 and 1 *in the original .mnc*. I

[Freesurfer] MRI_segstats for adc.nii from dt recon - increasing decimal digits

Hi! I ran mri_segstats as instructed in the wiki to extract ADC values from adc.nii. And as you can see below in my output, I think the decimal digits are truncated and missing the following decimal values. Is there an option or other way to get around this problem and extract ADC values from

Re: [Freesurfer] question about Unpaired T-test group analysis

Hi there, Is there anyone can answer my questions? Thank you. 2016-10-11 11:41 GMT-04:00 kinson li : > *Hello, * > > *Question 1: I would like to conduct an Unpaired T-test group analysis, I > have two group of people, Group A8 age is 8 and Group A9 age is 9, and I to > test the* change in thic

Re: [Freesurfer] Volume to Surface

When I do this for PET data for example and use the bbregister-generated.dat file, will that be with --srcreg bbregister-generated.dat ? If so, will I still use --regheader ? Thank you, Anna From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun.

[Freesurfer] Using caudate as a seed

Hi, Is there any way in FSFAST to use caudate as a seed for connectivity analysis? I was checking to see if it had a seg id for which I could run fc-seed-config, but it only had ids for caudate intensity abnormalities. Thank you! Best, Talia ___ Freesur

[Freesurfer] Segmentation editing

Dear experts   after editing aseg the Segmentations wiki says one: " could recreate the final surfaces with the command: recon-all -autorecon2-noaseg -subjid " Is there any need to run this specific command? The surfaces look just fine. Only left pallidum wasn't outlined correctly and needed m

Re: [Freesurfer] FreeSurfer 6 beta and mac osx el capitan

Hi, I downloaded the archive with Firefox instead of Safari and problem is solved. Strangely, the archive downloaded with Safari was not full. Damien > On 10 Oct 2016, at 16:56, Damien MARIE wrote: > > Hi, > > I would like to install the FreeSurfer 6 beta on my macbook pro (OS X El > capit