Re: [HCP-Users] Probtrackx surface analysis

[Glasser, Matthew]

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 <linden.par...@monash.edu> Date: Monday, July 7, 2014 at 3:49 AM To: "hcp-users@humanconnectome.org" <hcp-users@humanconnectome.org> 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 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  |  0402 516 574 E: linden.par...@monash.edu W: www.med.monash.edu.au/psych/mcin/ B7AE8BF0-4F0C-4F0B-9BDE-B582B9331FA1 _______________________________________________ HCP-Users mailing list HCP-Users@humanconnectome.org 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 HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users