|
HCP data is NIFTI/GIFTI/CIFTI, so the particular files you have there are NIFTI volumes. The GIFTI surface aparc data are in
${StudyFolder}/${Subject}/MNINonLinear/fsaverage_LR32k/100307.${Hemisphere}.aparc.32k_fs_LR.label.gii
To use them with probtrackx2, you’ll need to follow the instructions here (unfortunately probtrackx2 currently doesn’t support standard GIFTI surfaces and label files):
To know what matrix you should use, I’d need to know a little bit more about the question you are asking. matrix2 with nodif_brain_mask as the tract space mask will produce an enormous file.
Peace,
Matt.
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.
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
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.
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
|
