[Freesurfer] morphometric stats and global measure of volume

I want to know which atlas is used by Freesurfer to calculate morphometric stats and global measure of volume. Specifically for the sub-cortical regions. Thank you. Best, Naveed ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail

Re: [Freesurfer] Is there any way to measure the volume of substantia nigra and red nucleus via FS?

HI Nellie not really. We have some prototype tools for this, but nothing we are able to distribute at this time (except for the relatively coarse brainstem targets that are in V6) cheers Bruce On Wed, 2 Nov 2016, nellie wrote: Hi, FreeSurfer experts, I would like to know is there any comma

Re: [Freesurfer] morphometric stats and global measure of volume

Hi Naveed the atlas is composed of 40 subjects distributed in age and pathology (AD), following the CMA conventions that we cite in our Neuron paper. cheers Bruce On Wed, 2 Nov 2016, Muhammad Naveed Iqbal Qureshi wrote: I want to know which atlas is used by Freesurfer to calculate morpho

[Freesurfer] Fw: recon-all steps question

Re: [Freesurfer] mapping ROI to surface space

Hello Freesurfer Developers, I have gotten ahold of the dev version of mri_label2label. Currently I have a .w file that I need to “fill in the holes” on. Could you please specify the steps I will need to take to make my .w file an acceptable input for mri_label2label, and any recommendations you

[Freesurfer] mri_binarize --gm option unknown

Hello everyone, I am trying to run a mri_binarize command on FS v 5.2, Linux 64bit, but when I use the option -gm (also for -subcort-gm). I am getting an error that says the -gm option is not recognized. Here is the command line and the following error (from the mri folder of a subject): mri_bi

Re: [Freesurfer] ROI NumVert

Hi, When i try running make_folding_atlas I get xhemireg Trout2016 Wed Nov 2 13:11:23 EDT 2016 #@# xhemireg --s Trout2016 pbsubmit: Command not found. Launched 9 xhemireg processes #%# Waiting for 9 xhemireg processes Wed Nov 2 13:11:33 EDT 2016 #%# Waiting for 9 xhemireg processes Wed Nov 2

Re: [Freesurfer] ROI NumVert

oh, sorry, it does assume that you have pbsubmit, I had forgotten that. You can actually follow the instructions for building your own atlas at the bottom of the xhemi web page http://surfer.nmr.mgh.harvard.edu/fswiki/Xhemi This does the same thing as make_folding_atlas. It takes a long time if

Re: [Freesurfer] mri_binarize --gm option unknown

try this version https://gate.nmr.mgh.harvard.edu/safelinks/greve/mri_binarize On 11/02/2016 12:37 PM, HOSSU Gabriela wrote: > > Hello everyone, > > I am trying to run a mri_binarize command on FS v 5.2, Linux 64bit, > but when I use the option —gm (also for –subcort-gm). > > I am getting an err

[Freesurfer] Error on rawavg

Hi all, As I’m doing manual edits, one of my subjects stops running due to the following error: ERROR: could not read subj1/mri/rawavg.mgz as type 3 Any ideas how to correct this? Please let me know. Noah ___ Freesurfer mailing list Freesurfer@nmr.m

Re: [Freesurfer] Error on rawavg

Hi Noah We need the full command you ran, the screen output and the recon-all.log Cheers Bruce > On Nov 3, 2016, at 12:13 AM, Noah Markowitz wrote: > > Hi all, > > As I’m doing manual edits, one of my subjects stops running due to the > following error: > > ERROR: could not read subj1/mri/ra