Re: [Freesurfer] Tracula the inverse of TBSS results

their freesurfer aseg's and see if any of the white matter was classified as a hypointensity there? a.y On Wed, 3 Apr 2013, Sean Hatton wrote: This is Tracula 5.2 with FLIRT and the vectors are correctly aligned (V1 over FA). From the literature and what is seen in my TBSS is reduced FA in the minor

Re: [Freesurfer] Tracula the inverse of TBSS results

part of a tract shows a decrease and other parts don't. Have you looked at the FA as a function of position along the tract from tracula (the other stats file that it gives you)? On Thu, 4 Apr 2013, Sean Hatton wrote: Yes, TBSS has reductions in FA in the patients' ATR cf controls (TFCE

Re: [Freesurfer] Tracula the inverse of TBSS results

I reinitialised the tracts and they all make sense now :) Hope to see you all at ISMRM. Sean Hatton Brain and Mind Research Institute University of Sydney. On 5/04/13 7:21 AM, Anastasia Yendiki ayend...@nmr.mgh.harvard.edu wrote: It's the pathstats.byvoxel.txt file. On Thu, 4 Apr 2013

[Freesurfer] Alternate seed points in Tracula

in diffusion space. Is this feasible? I would get connection strength but how would I get FA, AD, RD etc? Should I correct for ICV? Or am I barking up the wrong tree? Sean Hatton Brain and Mind Research Institute University of Sydney

Re: [Freesurfer] tracula FS 5.2

FYI: In the -prep and -path sections I can run a 77 direction DWI on 33 training subjects with 8Gb RAM, Ubuntu 12.04 but it spills over into the swap memory. The -bedp section is not a memory hog at all. Cheers, Sean On 3/05/13 4:51 PM, Jürgen Hänggi j.haen...@psychologie.uzh.ch wrote:

[Freesurfer] Cortical labels for WM seeding

else? Kind regards, Sean Hatton Brain Mind Research Institute University of Sydney, Australia. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail

Re: [Freesurfer] Cortical labels for WM seeding

voxels? You could you a slightly dilated version of the aparc+aseg as a mask. You can use bbregister to map it to the subject's DWI space. a.y On Mon, 9 Sep 2013, Sean Hatton wrote: Hello FS Gurus, I would like to export FS labels as seed regions for deterministic tractography in TrackVis

[Freesurfer] DOSS and FDR in QDec

Hi FreeSurfers, These should be a simple questions but they have been bugging me. 1. I have two diagnostic groups that I want to compare controlling for gender and age. I am entering them in Qdec with diagnosis and gender as discrete factors and age as continuous (n=89). If I use DODS I get

[Freesurfer] FreeSurfer 5.2 TRACULA and FSL 5

. fslver=(`cat $FSLDIR/etc/fslversion | sed 's/\./ /g'`) Is this syntax correct? Is TRACULA compatible with FSL 5+? Sean Hatton Brain and Mind Research Institute University of Sydney ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https

[Freesurfer] Tracula the inverse of TBSS results

tract stats? Thank you in advance, Sean Hatton Brain and Mind Research Institute University of Sydney ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e