Re: [Freesurfer] how to calculate total pial surface area?

Great! Thanks! Mihaela On Wed, Jul 13, 2016 at 1:47 PM, Bruce Fischl wrote: > adding the individual ROIs should work and will ignore non-cortical > regions so be more accurate than measuing the surface area of ?h.pial > > cheers > Bruce > > On Wed, 13 Jul > 2016, Mihaela Stefan wrote: > > > Hell

Re: [Freesurfer] how to calculate total pial surface area?

adding the individual ROIs should work and will ignore non-cortical regions so be more accurate than measuing the surface area of ?h.pial cheers Bruce On Wed, 13 Jul 2016, Mihaela Stefan wrote: > Hello Freesurfers, > > We would like to know how to calculate the total pial surface area for eac

[Freesurfer] how to calculate total pial surface area?

Hello Freesurfers, We would like to know how to calculate the total pial surface area for each hemisphere. We extracted the surface area from the 34 ROIs per hemi from lh.aparc.stats but there is no total pial surface area in that file (only white surface area). Does it make sense to just add the

Re: [Freesurfer] Hippocampal subfields total volume differences

Hi Mojmir, ASEG typically gives a larger estimate of the volume, though highly correlated with that from the subfield package. We have found the measurements from the subfield package to be a bit more reliable, though. Cheers, Eugenio Juan Eugenio Iglesias Translational Imaging Group University

[Freesurfer] Hippocampal subfields total volume differences

Hi experts, I'm using Freesurfer 6.0 dev version (Mac) to perform hippocampal subfields segmentation. I only need to measure total hippocampus volume, but measurements from basic `recon-all` were too volatile and I was hoping that using subfields with T2 modality would reduce variance. However, vo

Re: [Freesurfer] When I am run trac-all in Fedora 24 with the developmental version of FreeSurfer, it crashes when running flirt.fsl with this error message

Hi Anastasia Thanks. I am sending my entire trac-all.log Knut Jøgen On 07/12/2016 11:19 PM, Anastasia Yendiki wrote: Hi Knut Jørgen - Can you please send your entire trac-all.log? Thanks! a.y On Mon, 11 Jul 2016, Knut J Bjuland wrote: flirt.fsl -ref /home/knutjbj/subjects/023v4/dmri

[Freesurfer] Post-doctoral position at MRC Cognition and Brain Sciences Unit

MRC Cognition and Brain Sciences Unit - Cambridge Postdoctoral Scientist Salary £27,355 - £30,791 per annum plus benefits Ref OH/260 The MRC Cognition and Brain Sciences Unit (CBSU) is an internationally renowned research institute of cognitive neuroscience. Onsite facilities include dedicated M

Re: [Freesurfer] Regarding: Concatenating hippocampal to generate sig.mgh

Dear Bruce, I am trying to generate the following picture (please see attached) for eod vs lod groups. Can you please tell me how to do this? Thanks and regards, Sampada On Tue, Jul 12, 2016 at 6:44 PM, Bruce Fischl wrote: > Hi Sampada > > why not just take the volume of the hippocampus from t

[Freesurfer] request for newer mri_tessellate (error: max vertices 1000000 exceeded)

Dear Freesurfer team, I am running Falk Luesebrinks hires recon, and am running into the error of "mri_tessellate: max vertices 100 exceeded" when I run the command line "recon-all -maskbfs -segmentation -fill -tessellate -s $SUBJECT" o

Re: [Freesurfer] Hippocampal subfields --> Can't find a *ctf file?

And thanks to Zeke, of course ;-) Juan Eugenio Iglesias Translational Imaging Group University College London http://www.jeiglesias.com http://cmictig.cs.ucl.ac.uk/ On 13 Jul 2016, at 11:19, Iglesias, Eugenio mailto:e.igles...@ucl.ac.uk>> wrote: Dear all, our expert developer Zeke Kaufman fig

Re: [Freesurfer] Hippocampal subfields --> Can't find a *ctf file?

Dear all, our expert developer Zeke Kaufman figured out what the problem was. We have now fixed the Linux version; the MAC version will hopefully be ready as well in a couple of days. I have also fixed other bugs (including the problem that caused the code to get stuck every once in a while). Yo

[Freesurfer] post-doctoral position at MRC Cognition and Brain Sciences Unit, Cambridge

MRC Cognition and Brain Sciences Unit - Cambridge Postdoctoral Scientist Salary £27,355 - £30,791 per annum plus benefits Ref OH/260 The MRC Cognition and Brain Sciences Unit (CBSU) is an internationally renowned research institute of cognitive neuroscience. Onsite facilities include dedicated M

Re: [Freesurfer] TRACULA tract group comparison p-values

That's great, thank you Anastasia! Best wishes, Barbara On 12/07/2016 22:52, Anastasia Yendiki wrote: > Hi Barbara - Unfortunately we are very limited right now in our options > for point set overlay display. I guess there's nothing that would be more > suitable for displaying values that go al