Hi all,
I am trying to generate a 3x3 connectivity matrix among 3 surface ROIs of the brain.
For this i am running tractography (probtrackx2_gpu) on the bedpostX preprocessed data for a single subject data of the HCP 1200 release.
The total number of seeds in this case is 97476 and probtrackx2_gpu is not able to allocate enough memory (~38GB seed x seed matrix1) and crashes.
However probtrackx2 runs smoothly as in my knowledge, since it allocates a sparse matrix for the same setup. Is there a similar workaround for probtrackx2_gpu ?
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The command i am using :
probtrackx2_gpu -s /users/govinda_s/subjects/100307/T1w/Diffusion.bedpostX/merged -m /users/govinda_s/subjects/100307/T1w/Diffusion.bedpostX/nodif_brain_mask.nii.gz -x /users/govinda_s/seeds1.txt --seedref=/users/govinda_s/subjects/T1w_acpc_dc_restore_1.25.nii.gz -l -V 2 --forcedir -P 100 --network --omatrix1 --dir=/users/govinda_s/subjects/IMAGE1
My seeds.txt file is :
/users/govinda_s/subjects/ROI_ASC/ROI1.asc
/users/govinda_s/subjects/ROI_ASC/ROI2.asc
/users/govinda_s/subjects/ROI_ASC/ROI3.asc
Where each file is generated using the command :
wb_command -cifti-label-to-roi ~/subjects/Q1-Q6_RelatedValidation210.CorticalAreas_dil_Final_Final_Areas_Group_Colors.32k_fs_LR.dlabel.nii scalar.dscalar.nii -key <ROI_ID>
I converted each of them to ASCII using surf2surf.
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Please point out if am wrong anywhere and suggest corrections if any.
Thanks in Advance !
Joyneel
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