Hi Maarten
There are a few flags in probtrackx2 that I can see need changing:
1) --seedref=102816/MNINonLinear/T1w_restore.nii.gz. You need to give a volume that is compatible with the input masks, which are all in 2x2x2 MNI space. Try something like --seedref=$FSLDIR/data/standard/MNI152_T1_2mm_brain_mask
2) Specify —meshspace=caret, just too make sure that this is specified (it is the default in some versions).
3) Make sure that your seed is in the same space (and resolution) as your “bm_*” masks.
If this still does not work, let us know of your FSL version and we can look into it further.
Cheers
Stam
On 8 Aug 2015, at 10:29, Maarten Vaessen <[log in to unmask]> wrote:
> Hello experts,
>
> This is a cross-post from the HCP user list, as the issue could not be resolved there.
> I am trying to get a seed to whole brain fiber connectivity matrix with probtrackx2 using the --matrix3 option with a mix of volume and surface seeds and targets from the HCP database.
> The probtrackx2 command runs without errors, but the output matrix is extremely sparse and makes no sense. There might be an issue with the transformation of the seeds to dti space, as the coords_for_fdt_matrix3 and tract_space_coords_for_fdt_matrix3 files show some strange values:
>
> 309 -57 38 0 8341
> 308 -57 38 0 8342
> 307 -56 38 0 8343
> 306 -55 37 0 8344
> 306 -55 36 0 8345
>
> Below are posted all the commands to generate and process the data.
>
> Thanks for your help,
>
> -Maarten
>
>
>
>
>
> wb_command -gifti-label-to-roi 102816/MNINonLinear/fsaverage_LR32k/102816.L.aparc.a2009s.32k_fs_LR.label.gii L.STS.func.gii -name S_temporal_sup
> surf2surf -i 102816/MNINonLinear/fsaverage_LR32k/102816.L.white.32k_fs_LR.surf.gii -o L.STS.fsl_MNI_new.asc --outputtype=ASCII --values=L.STS.func.gii
>
> surf2surf -i 102816/MNINonLinear/fsaverage_LR32k/102816.L.white.32k_fs_LR.surf.gii -o brainmap_HCP/a_white.L.asc --outputtype=ASCII --values=102816/MNINonLinear/fsaverage_LR32k/102816.L.atlasroi.32k_fs_LR.shape.gii
> surf2surf -i 102816/MNINonLinear/fsaverage_LR32k/102816.R.white.32k_fs_LR.surf.gii -o brainmap_HCP/a_white.R.asc --outputtype=ASCII --values=102816/MNINonLinear/fsaverage_LR32k/102816.R.atlasroi.32k_fs_LR.shape.gii
> mri_extract_label 102816/MNINonLinear/ROIs/Atlas_ROIs.2.nii.gz 8 102816/T1w/Diffusion/brainmap_HCP/bm_CEREBELLUM_LEFT.nii.gz
> mri_extract_label 102816/MNINonLinear/ROIs/Atlas_ROIs.2.nii.gz 47 102816/T1w/Diffusion/brainmap_HCP/bm_CEREBELLUM_RIGHT.nii.gz
> mri_extract_label 102816/MNINonLinear/ROIs/Atlas_ROIs.2.nii.gz 16 102816/T1w/Diffusion/brainmap_HCP/bm_BRAIN_STEM.nii.gz
> mri_extract_label 102816/MNINonLinear/ROIs/Atlas_ROIs.2.nii.gz 17 102816/T1w/Diffusion/brainmap_HCP/bm_HIPPOCAMPUS_LEFT.nii.gz
> mri_extract_label 102816/MNINonLinear/ROIs/Atlas_ROIs.2.nii.gz 53 102816/T1w/Diffusion/brainmap_HCP/bm_HIPPOCAMPUS_RIGHT.nii.gz
> mri_extract_label 102816/MNINonLinear/ROIs/Atlas_ROIs.2.nii.gz 18 102816/T1w/Diffusion/brainmap_HCP/bm_AMYGDALA_LEFT.nii.gz
> mri_extract_label 102816/MNINonLinear/ROIs/Atlas_ROIs.2.nii.gz 54 102816/T1w/Diffusion/brainmap_HCP/bm_AMYGDALA_RIGHT.nii.gz
> mri_extract_label 102816/MNINonLinear/ROIs/Atlas_ROIs.2.nii.gz 28 102816/T1w/Diffusion/brainmap_HCP/bm_DIENCEPHALON_VENTRAL_LEFT.nii.gz
> mri_extract_label 102816/MNINonLinear/ROIs/Atlas_ROIs.2.nii.gz 60 102816/T1w/Diffusion/brainmap_HCP/bm_DIENCEPHALON_VENTRAL_RIGHT.nii.gz
> mri_extract_label 102816/MNINonLinear/ROIs/Atlas_ROIs.2.nii.gz 12 102816/T1w/Diffusion/brainmap_HCP/bm_PUTAMEN_LEFT.nii.gz
> mri_extract_label 102816/MNINonLinear/ROIs/Atlas_ROIs.2.nii.gz 51 102816/T1w/Diffusion/brainmap_HCP/bm_PUTAMEN_RIGHT.nii.gz
> mri_extract_label 102816/MNINonLinear/ROIs/Atlas_ROIs.2.nii.gz 13 102816/T1w/Diffusion/brainmap_HCP/bm_PALLIDUM_LEFT.nii.gz
> mri_extract_label 102816/MNINonLinear/ROIs/Atlas_ROIs.2.nii.gz 52 102816/T1w/Diffusion/brainmap_HCP/bm_PALLIDUM_RIGHT.nii.gz
> mri_extract_label 102816/MNINonLinear/ROIs/Atlas_ROIs.2.nii.gz 10 102816/T1w/Diffusion/brainmap_HCP/bm_THALAMUS_LEFT.nii.gz
> mri_extract_label 102816/MNINonLinear/ROIs/Atlas_ROIs.2.nii.gz 49 102816/T1w/Diffusion/brainmap_HCP/bm_THALAMUS_RIGHT.nii.gz
> mri_extract_label 102816/MNINonLinear/ROIs/Atlas_ROIs.2.nii.gz 26 102816/T1w/Diffusion/brainmap_HCP/bm_ACCUMBENS_LEFT.nii.gz
> mri_extract_label 102816/MNINonLinear/ROIs/Atlas_ROIs.2.nii.gz 58 102816/T1w/Diffusion/brainmap_HCP/bm_ACCUMBENS_RIGHT.nii.gz
> mri_extract_label 102816/MNINonLinear/ROIs/Atlas_ROIs.2.nii.gz 11 102816/T1w/Diffusion/brainmap_HCP/bm_CAUDATE_LEFT.nii.gz
> mri_extract_label 102816/MNINonLinear/ROIs/Atlas_ROIs.2.nii.gz 50 102816/T1w/Diffusion/brainmap_HCP/bm_CAUDATE_RIGHT.nii.gz
>
>
> echo 102816/T1w/Diffusion/brainmap_HCP/a_white.L.asc > 102816/T1w/Diffusion/brainmap_HCP/brainmap_filelist.txt
> echo 102816/T1w/Diffusion/brainmap_HCP/a_white.R.asc >> 102816/T1w/Diffusion/brainmap_HCP/brainmap_filelist.txt
> echo 102816/T1w/Diffusion/brainmap_HCP/bm_ACCUMBENS_LEFT.nii.gz >> 102816/T1w/Diffusion/brainmap_HCP/brainmap_filelist.txt
> echo 102816/T1w/Diffusion/brainmap_HCP/bm_ACCUMBENS_RIGHT.nii.gz >> 102816/T1w/Diffusion/brainmap_HCP/brainmap_filelist.txt
> echo 102816/T1w/Diffusion/brainmap_HCP/bm_AMYGDALA_LEFT.nii.gz >> 102816/T1w/Diffusion/brainmap_HCP/brainmap_filelist.txt
> echo 102816/T1w/Diffusion/brainmap_HCP/bm_AMYGDALA_RIGHT.nii.gz >> 102816/T1w/Diffusion/brainmap_HCP/brainmap_filelist.txt
> echo 102816/T1w/Diffusion/brainmap_HCP/bm_BRAIN_STEM.nii.gz >> 102816/T1w/Diffusion/brainmap_HCP/brainmap_filelist.txt
> echo 102816/T1w/Diffusion/brainmap_HCP/bm_CAUDATE_LEFT.nii.gz >> 102816/T1w/Diffusion/brainmap_HCP/brainmap_filelist.txt
> echo 102816/T1w/Diffusion/brainmap_HCP/bm_CAUDATE_RIGHT.nii.gz >> 102816/T1w/Diffusion/brainmap_HCP/brainmap_filelist.txt
> echo 102816/T1w/Diffusion/brainmap_HCP/bm_CEREBELLUM_LEFT.nii.gz >> 102816/T1w/Diffusion/brainmap_HCP/brainmap_filelist.txt
> echo 102816/T1w/Diffusion/brainmap_HCP/bm_CEREBELLUM_RIGHT.nii.gz >> 102816/T1w/Diffusion/brainmap_HCP/brainmap_filelist.txt
> echo 102816/T1w/Diffusion/brainmap_HCP/bm_DIENCEPHALON_VENTRAL_LEFT.nii.gz >> 102816/T1w/Diffusion/brainmap_HCP/brainmap_filelist.txt
> echo 102816/T1w/Diffusion/brainmap_HCP/bm_DIENCEPHALON_VENTRAL_RIGHT.nii.gz >> 102816/T1w/Diffusion/brainmap_HCP/brainmap_filelist.txt
> echo 102816/T1w/Diffusion/brainmap_HCP/bm_HIPPOCAMPUS_LEFT.nii.gz >> 102816/T1w/Diffusion/brainmap_HCP/brainmap_filelist.txt
> echo 102816/T1w/Diffusion/brainmap_HCP/bm_HIPPOCAMPUS_RIGHT.nii.gz >> 102816/T1w/Diffusion/brainmap_HCP/brainmap_filelist.txt
> echo 102816/T1w/Diffusion/brainmap_HCP/bm_PALLIDUM_LEFT.nii.gz >> 102816/T1w/Diffusion/brainmap_HCP/brainmap_filelist.txt
> echo 102816/T1w/Diffusion/brainmap_HCP/bm_PALLIDUM_RIGHT.nii.gz >> 102816/T1w/Diffusion/brainmap_HCP/brainmap_filelist.txt
> echo 102816/T1w/Diffusion/brainmap_HCP/bm_PUTAMEN_LEFT.nii.gz >> 102816/T1w/Diffusion/brainmap_HCP/brainmap_filelist.txt
> echo 102816/T1w/Diffusion/brainmap_HCP/bm_PUTAMEN_RIGHT.nii.gz >> 102816/T1w/Diffusion/brainmap_HCP/brainmap_filelist.txt
> echo 102816/T1w/Diffusion/brainmap_HCP/bm_THALAMUS_LEFT.nii.gz >> 102816/T1w/Diffusion/brainmap_HCP/brainmap_filelist.txt
> echo 102816/T1w/Diffusion/brainmap_HCP/bm_THALAMUS_RIGHT.nii.gz >> 102816/T1w/Diffusion/brainmap_HCP/brainmap_filelist.txt
>
> probtrackx2 -x 102816/T1w/Diffusion/WM_MNI_slice.nii.gz --omatrix3 --target3=102816/T1w/Diffusion/L.STS.fsl_MNI_new.asc --lrtarget3=102816/T1w/Diffusion/brainmap_HCP/brainmap_filelist.txt -P 10 --forcedir --dir=102816/T1w/Diffusion/test_surf_track_STS_brainmap_seedspace -s 102816/T1w/Diffusion.bedpostX/merged -m 102816/T1w/Diffusion/nodif_brain_mask.nii.gz --seedref=102816/MNINonLinear/T1w_restore.nii.gz -V 2 --opd --pd --distthresh3=2 --xfm=102816/MNINonLinear/xfms/standard2acpc_dc.nii.gz --invxfm=102816/MNINonLinear/xfms/acpc_dc2standard.nii.gz
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