Oh, I thought the HCP data was distributed in cifti and gifti? As a first pass I wanted to use all surfaces in aparc as classification targets for a few subcortical volumes rois and am a bit unsure on how to do that. I'd like to pull out matrix2 for this (seems most appropriate). Can I submit the nodif_brain_mask as the "tract space mask" for this?
Cheers Linden On 08/07/2014 2:08 am, "Glasser, Matthew" <[email protected]> wrote: > You would use the white matter surfaces in > ${StudyFolder}/${Subject}/T1w/fsaverage_LR32k. The distributed diffusion > data are already in T1w space, so you don’t need to provide transformation > matrices. The surface reference image can be any of the files in > ${StudyFolder}/${Subject}/T1w > or ${StudyFolder}/${Subject}/T1w/Diffusion. > > Neither of the files you mention are CIFTI files. What cortical > regions are you wanting to track from? > > Peace, > > Matt. > > From: Linden Parkes <[email protected]> > Date: Monday, July 7, 2014 at 3:49 AM > To: "[email protected]" <[email protected]> > Subject: [HCP-Users] Probtrackx surface analysis > > Hi HCP users, > > I’m trying to run probtrackX on some HCP data, can someone provide some > guidance on how to run this using surfaces? I’m following the FSL user > guide but they often refer to files which are absent from the HCP data as > far I can tell. (e.g., "and also that you have a file called > struct.nii.gz that you have used as an input to FreeSurfer > <http://fsl.fmrib.ox.ac.uk/fsl/fslwiki/FreeSurfer> recon_all program." > > Basically, I’d like to define subcortical seeds and track to cortical > surfaces. > > For the subcortical seed regions I can easily create binary masks to use > as seeds using fslmaths based on intensity values from the freesurfer LUTs. > I could do the same with the cortical regions but I have read that tracking > to cortical regions is best done with surfaces instead of volumes. > > So, when selecting “classification targets” can I simply add in a cifti > file? (e.g., 100307/T1w/aparc+aseg.nii.gz OR > 100307/T1w/aparc.a2009s+aseg.nii.gz)** and then tell probtrackX to output > the matrices I want? > > **I assume using the files in the T1w dir is best because these are in > the same space as the diffusion data and therefore don’t require > transformation. > > On a different note, if I select a surface file as a seed instead, it > asks for a “surface reference image” for Freesurfer. Which file is best > used for this purpose? > > Cheers, > Linden > > —————————————————————— > > *Linden Parkes* > > *PhD Candidate* > *Monash Clinical & Imaging Neuroscience (MCIN)* > *School of Psychological Sciences* > *Monash Biomedical Imaging* > *Monash University* > > *A: 770 Blackburn Rd, Clayton, 3168, **Vic, Australia* > *T: +61 3 9902 9435 <%2B61%203%209902%209435> | 0402 516 574* > *E: [email protected] <[email protected]>* > *W: www.med.monash.edu.au/psych/mcin/ > <http://www.med.monash.edu.au/psych/mcin/>* > > B7AE8BF0-4F0C-4F0B-9BDE-B582B9331FA1 > > _______________________________________________ > HCP-Users mailing list > [email protected] > http://lists.humanconnectome.org/mailman/listinfo/hcp-users > > > ------------------------------ > > The materials in this message are private and may contain Protected > Healthcare Information or other information of a sensitive nature. If you > are not the intended recipient, be advised that any unauthorized use, > disclosure, copying or the taking of any action in reliance on the contents > of this information is strictly prohibited. If you have received this email > in error, please immediately notify the sender via telephone or return mail. > _______________________________________________ HCP-Users mailing list [email protected] http://lists.humanconnectome.org/mailman/listinfo/hcp-users
