On Mar 8, 2018, at 7:00 PM, Moises Hernandez <[log in to unmask]> wrote:Hi Ricardo,Did you take a look at the bedpostx output?I would check that the dyads1.nii.gz file (orientations) is correct,and that mean_fsumsamples (fraction of anisotropic compartments) makes sense.You could also draw a mask by hand, with few seeds in the white matter, and check that the tool reconstructs the tracts as expected.It seems that the only ROI that is reached by the streamlines is the 4th one.So, there must be something in the data that prevent streamlines to reach the other ROIs.On 8 March 2018 at 18:32, Ricardo Valle <[log in to unmask]> wrote:Hi Moises,Thank you very much for replying so quickly! Very nice picture on your website by the way!The probtrackx version you linked to solved the —invxfm error. I have rerun probtrackx as follows:probtrackx2_gpu -s ${HOME}/Documents/diffusion/data.bedpostX/merged -m ${HOME}/Documents/diffusion/ data.bedpostX/nodif_brain_mask -x ${HOME}/Documents/diffusion/ network/masks/seed_list.txt --dir=${HOME}/Documents/ diffusion/network --forcedir --network --xfm=${HOME}/Documents/ diffusion/reg/str2diff.mat --seedref=${HOME}/Documents/ diffusion/anat/T1w.nii.gz --invxfm=${HOME}/Documents/ diffusion/reg/diff2str.mat --opd -P 5 -S 1000 I am attaching the resulting fdt_network_matrix to my email. The matrix is still all 0s except for the last column. I tried to attach a screenshot of fdt_paths.nii.gz and the masks, but they are too large. Both seem fine to me. What do you think might be the issue?Best regards,RuyOn Mar 8, 2018, at 6:29 PM, Ricardo Valle <[log in to unmask]> wrote:Hi Moises,<Screen Shot 2018-03-08 at 6.19.41 PM.png>Thank you very much for replying so quickly! Very nice picture on your website by the way!The probtrackx version you linked to solved the —invxfm error. I have rerun probtrackx as follows:probtrackx2_gpu -s ${HOME}/Documents/diffusion/data.bedpostX/merged -m ${HOME}/Documents/diffusion/ data.bedpostX/nodif_brain_mask -x ${HOME}/Documents/diffusion/ network/masks/seed_list.txt --dir=${HOME}/Documents/ diffusion/network --forcedir --network --xfm=${HOME}/Documents/ diffusion/reg/str2diff.mat --seedref=${HOME}/Documents/ diffusion/anat/T1w.nii.gz --invxfm=${HOME}/Documents/ diffusion/reg/diff2str.mat --opd -P 5 -S 1000 I am attaching the resulting fdt_network_matrix as well as a picture with the resulting fdt_paths.nii.gz and masks overlayed on the T1 image. The matrix is still all 0s except for the last column. What do you think might be the issue?Best regards,Ruy<fdt_network_matrix>On Mar 8, 2018, at 5:29 PM, Moises Hernandez <[log in to unmask]> wrote:Hi Ricardo,would you mind to download the last version of the tool and try again?I have just updated it:This version should solve the —invxfm error related.About the 0 values, please let me know if it continues happening.Several things can be causing it, but most likely:- ROIs not well defined- Seeds space to Diffusion space transformations are not goodOne thing you can try for checking this is to run the tool with just few samples per seed (-P 5),few steps per streamline (-S 5), and generates the path distribution map (--opd).Then, you can open the nifti file (containing that map) and see from where the streamlines are propagated,i.e. check if seed points are correct.Moies.On 8 March 2018 at 16:34, Ricardo Valle <[log in to unmask]> wrote:Dear FSL community,
I have been trying to generate a connectivity matrix from a volumetric Freesurfer parcellation. The command I’ve been running is:
probtrackx2_gpu -s ${HOME}/Documents/diffusion/data.bedpostX/merged -m ${HOME}/Documents/diffusion/da ta.bedpostX/nodif_brain_mask -x ${HOME}/Documents/diffusion/ne twork/masks/seed_list.txt --dir=${HOME}/Documents/diffus ion/network/ --forcedir --network --seedref=${HOME}/Documents/an at/T1w.nii.gz --xfm=${HOME}/Documents/diffus ion/reg/str2diff.mat
I have run this several times with different seeds listed in seed_list.txt and consistently get an fdt_network_matrix with either all 0s or values in the order of 10^5 or 10^6 in the last column, 0s in the last row, and 0s everywhere else.
I’ve also tried passing —invxfm=${HOME}/Documents/reg/diff2str.mat to probtrackx. This causes the script to crash with a CUDA error that says it’s getting an invalid resource handle.
Do you know why these two things may be happening?
Thank you,
All the best,
Ruy