I tried this and here I get the error: Done loading samples. does not exist
Using the command: probtrackx2 -x L.STS.fsl.gii --onewaycondition --omatrix3 --lrtarget3=../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 Any idea what this means? -M On Fri, Jul 10, 2015 at 3:34 PM, Moises Hernandez Fernandez < [email protected]> wrote: > 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
