Re: [Freesurfer] Segmentation of hippocampal subfields / version 6.0 release date

Hi Josh, the module is already in the development version of FS, and will be released along with FS6 hopefully very soon. Cheers, /Eugenio Juan Eugenio Iglesias Postdoctoral researcher BCBL www.jeiglesias.com www.bcbl.eu Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer --

Re: [Freesurfer] Taking a measure of cluster width and length on flat surface

Hi Bruce Thanks for the information on the flat patch, thats great that the relationships are preserved! With that in mind do you know if freesurfer has any inbuilt functions to take the kind of measurements that I was describing? Or will my MATLAB based proposal be the best option do you thin

Re: [Freesurfer] Data interest of the CorticalParcellation_Yeo2011

Hi Annie, mri_surf2surf is complaining that it cannot write out the annotation. Just to clarify, is your subject called test_run_allindex? In other words, is the variable s equal to test_run_allindex? Does the directory "/home/annie/test_run_allindex/label/" exist? If not, then you first need to

Re: [Freesurfer] Taking a measure of cluster width and length on flat surface

Hi Sarah I don't think we have anything for ellipsoid fitting, although Oliver Hinds did some in his paper on V1. Should be straightforward enough in matlab. The data are in 2D mm coords cheers Bruce On Tue, 12 May 2015, Sarah Finnegan wrote: Hi Bruce  Thanks for the information on the fl

[Freesurfer] Tracula reinit

Hi, The various tracts have different default numbers of control points, with a higher number for more curved paths. In a previous mail Dr. Yendiki recommended changing the number of control points if several attempts rerunning reinit don't produce a satisfactory result. Is it always better to hav

Re: [Freesurfer] Data interest of the CorticalParcellation_Yeo2011

Hi Annie, I assume this means 5202 is your subject ID? Maybe you should check if /home/annie/test_run_allindex/5202/label/lh.Yeo2011_7Networks_N1000.annot exist? If so, you can run mris_anatomical_stats to generate statistics for the parcellation. Cheers, Thomas On Tue, May 12, 2015 at 6:29 PM,

Re: [Freesurfer] Freeview

Can you please provide me with the contents of your $FREESURFER_HOME/build-stamp.txt file? -Zeke On 05/11/2015 07:33 PM, Isabelle Deschamps wrote: > Dear Freesurfer Users, > > I am trying to update the freeview file. However, I cannot find the > folder $FREESURFER_HOME/Freeview.app/Contents/Mac

Re: [Freesurfer] Segmentation of hippocampal subfields / version 6.0 release date

Josh, You can get an FS version that is close to v6 here: ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/dev Any testing on top of the hippocampal fields functionality would be greatly appreciated! Nick > On May 12, 2015, at 5:42 AM, Eugenio Iglesias wrote: > > Hi Josh, > the module i

Re: [Freesurfer] Interaction contrast setup

I'm trying to see if two behavioral variables interact (they are factors 1 and 2) while controlling for the demographics also included in the fsgd file. I would also like to run an interaction with age and factor1. Here are the first few lines of my fsgd file. Thanks GroupDescriptorFile 1 Title S

Re: [Freesurfer] tracking edits

Thanks alot! Deirdre On Fri, May 8, 2015 at 3:23 PM, Nick Schmansky, MGH < ni...@nmr.mgh.harvard.edu> wrote: > Deirdre, > > the -show-edits flag in recon-all will print edits. > > N. > > On Thu, 2015-05-07 at 12:29 -0400, Deirdre O Shea wrote: > > Dear Freesurfer experts, > > > > > > I wondered h

[Freesurfer] Whitening in FSFAST

Hi Doug, I wanted to ask what kind of noise model FSFAST employs for whitening. Is it the one described in Worsley, neuroimage 2002? Is there a place on the wiki or elsewhere where I could find a description? Thanks, Caspar ___ Freesurfer mailing list Fr