Dear HCP experts, I would like to analyze some HCP diffusion data. I am using the preprocessed HCP data from the 900 subjects release.
I would like to do dtifit and run bedpostx and then tractography (I know dtifit is unrelated to the latter bt I'm mentioning it because I would like to be consistent in my analysis). Two questions: a) I found this dtifit command in the HCP mail list archives: dtifit -k data.nii.gz -r bvecs -b bvals -m nodif_brain_mask.nii.gz -o >>> > $OUTDIR/$SUBJECT/dti --gradnonlin=grad_dev.nii.gz > But also I found this code for voxel-wise correction of dMRI gradients: > > https://www.humanconnectome.org/storage/app/media/documentation/data_release/Q1_Release_Appendix_II.pdf > *When I run the dtifit command above do I use the new_bvals and new_bvecs?* Hence do I run: > dtifit -k data.nii.gz -r new_bvecs -b new_bvals -m nodif_brain_mask.nii.gz > -o >>> $OUTDIR/$SUBJECT/dti --gradnonlin=grad_dev.nii.gz > or does the "--gradnonlin=grad_dev.nii.gz" in the command does the same job as the code I found in the Q1_Release_Appendix_II.pdf? b) *When I run bedpostx_gpu do I need to use the new_bvals* in a script like this: bedpostx_gpu T1w/Diffusion -n 3 -b 3000 -model 3 -g —rician Thank you. Best, *Athanasia Metoki* Psychology Doctoral Student - Brain and Cognitive Sciences Program Cognitive Neuroscience Laboratory Temple University Department of Psychology 1701 N 13th St. Philadelphia, PA 19122 Email: [email protected] _______________________________________________________________________________ The contents of this email message and any attachments are intended solely for the addressee(s) and may contain confidential and/or privileged information and may be legally protected from disclosure. If you are not the intended recipient of this message or their agent, or if this message has been addressed to you in error, please immediately alert the sender by reply email and then delete this message and any attachments. If you are not the intended recipient, you are hereby notified that any use, dissemination, copying, or storage of this message or its attachments is strictly prohibited. _______________________________________________ HCP-Users mailing list [email protected] http://lists.humanconnectome.org/mailman/listinfo/hcp-users
