Re: [HCP-Users] Probtrackx surface analysis

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 inst

Re: [HCP-Users] MNI or Anatomical coordinate space?

I’m not sure how the qform and sform names are set in NIFTI, but it is possible FSL, FreeSurfer, or Connectome Workbench sets them differently.  The sforms and voxel grids should all be the same. Peace, Matt. From: Sang-Yun Oh Date: Monday, July 7, 2014 at 10:53 PM To: "hc

[HCP-Users] MNI or Anatomical coordinate space?

Hello, It seems that sform_code and qform_code maybe inaccurate, and I am trying to be completely certain of coordinate space information in the headers. (I am new to neuroscience field) For example, 100307/MNINonLinear/brainmask_fs.nii.gz qform_name MNI_152 sform_name MNI_152 100307/MN

Re: [HCP-Users] Probtrackx surface analysis

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 n

Re: [HCP-Users] merge traj files

To finally answer this, no, -wbsparse-merge-dense does not have any sparse summation logic, it is meant only for the dense (brain models) dimension, for concatenation. We don't currently have a command to do such a summation, trajectory support is somewhat a work in progress. I don't know why run

[HCP-Users] Intermittent orbitofrontal artifact in a limited number of HCP fMRI scans

To all users of HCP data: Intermittent orbitofrontal artifact affecting a limited number of rfMRI and tfMRI scans HCP has identified an artifact caused by intermittent technical problems with the 32 channel head coil in a limited number of fMRI scan session (26 rfMRI scans in 19 subjects; 7 tfMRI

Re: [HCP-Users] Probtrackx surface analysis

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 ${S

[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 str