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
