Hi Maarten, you can use Matrix3:
--omatrix3 --target3='seeds' --lrtarget3='wholebrain' Best, Moises. On 10 July 2015 at 11:12, Maarten Vaessen <[email protected]> wrote: > Thanks for the reply. I am using FSL v5.0.8, but have also tried with > 5.0.6. > > Does that mean that there is no way to do seed-to-wholebrain connectivity > based on surfaces right now? Or is it possible to do a similar thing using > one of the other --omatrix options? > > -M > > > On Thu, Jul 9, 2015 at 5:49 PM, Glasser, Matthew <[email protected]> > wrote: > >> That error suggests that that particular flag is not ready for surfaces >> yet and is looking for a NIFTI volume. Do you have the latest version of >> FSL? Perhaps Stam can comment on whether --target2 will be able to handle >> surfaces in the future. >> >> Peace, >> >> Matt. >> >> From: <[email protected]> on behalf of Maarten >> Vaessen <[email protected]> >> Date: Thursday, July 9, 2015 at 9:43 AM >> To: "[email protected]" <[email protected]> >> Subject: [HCP-Users] probtrackx2 surface tracking in matrix2 mode >> >> Hello experts, >> >> I am trying track from a seed surface roi to all WM surface vertices >> using matrix2 mode in probtackx2 using data from the HCP. I have followed >> the guide on how to convert surfaces using the surf2surf command where >> necessary. However I get this error when running probtrackx2 >> >> Done loading samples. >> Image Exception : #22 :: ERROR: Could not open image >> ../fsaverage_LR32k/102816.L.white.32k_fs_LR.surf.gii >> terminate called after throwing an instance of 'RBD_COMMON::BaseException' >> Aborted >> >> I am not sure what is wrong, the file is definitely there. Moreover >> when I take this file as the seed (-x >> ../fsaverage_LR32k/102816.L.white.32k_fs_LR.surf.gii), there is no error >> when loading the seeds: >> >> Running in seedmask mode >> load seeds >> read gifti >> done. >> >> Here is the full command: >> >> probtrackx2 -x L.STS.fsl.gii --onewaycondition --omatrix2 >> --target2=../fsaverage_LR32k/102816.L.white.32k_fs_LR.surf.gii -P 50 >> --forcedir --dir=./test_surf_track_STS_Lwhite -s >> ../Diffusion.bedpostX/merged -m nodif_brain_mask.nii.gz >> --seedref=nodif_brain_mask.nii.gz >> >> >> Thanks for the help! >> >> -Maarten >> >> _______________________________________________ >> 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 > _______________________________________________ HCP-Users mailing list [email protected] http://lists.humanconnectome.org/mailman/listinfo/hcp-users
