Re: [HCP-Users] Tractography and brainordinates

[Glasser, Matthew]

I’m afraid I’m pretty stumped by this (perhaps cross-posting to the FSL list might help).  All I can say is to reiterate a few things that you’ve probably already checked: All surfaces and volumes need to be in the “seed space” (in your case MNI) except for the arguments to –s and –m. Matrix3 is intended to be used with a whole white matter seed mask so you might try with matrix1 to see if things work better.   Peace, Matt. From: Maarten Vaessen <m.vaes...@gmail.com> Date: Thursday, July 30, 2015 at 3:23 PM To: Matt Glasser <glass...@wusm.wustl.edu> Cc: "hcp-users@humanconnectome.org" <hcp-users@humanconnectome.org> Subject: Re: Tractography and brainordinates Sure, here are the commands for a specific subject. The output is the same when I run it like this. 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 Cheers, -Maarten On Fri, Jul 24, 2015 at 5:03 PM, Glasser, Matthew <glass...@wusm.wustl.edu> wrote: Can you repost your commands with absolute paths (at least as far as ${StudyFolder})? Peace, Matt. From: Maarten Vaessen <m.vaes...@gmail.com> Date: Friday, July 24, 2015 at 1:43 AM To: Matt Glasser <glass...@wusm.wustl.edu> Cc: "hcp-users@humanconnectome.org" <hcp-users@humanconnectome.org> Subject: Tractography and brainordinates Thanks, I tried this. But the real problem seems to be that the matrix does not get filled (e.g. the .dot file is only 8Kb, this is with a low number of samples yes, but it should be much bigger). I am wondering if the problem is not with probtrackx2 and converting a mixed list of surfaces and volumes to dti space: to test this, I did the spatial conversion of the volumes to dti space myself with fnirt and used the native surfaces. And indeed then I get a huge .dot file and the results look fine (plotted in MATLAB). But the I have no correct cifti file to do the conversion as the number of brainordinates is different. Any further suggestions? -M p.s. I changed the subject as this thread got lost in the list somewhere. On Thu, Jul 23, 2015 at 12:25 AM, Glasser, Matthew <glass...@wusm.wustl.edu> wrote: I would try switching row and column and see what happens (the seeds are normally the row and the targets the column). Peace, Matt. From: Maarten Vaessen <m.vaes...@gmail.com> Date: Wednesday, July 22, 2015 at 8:50 AM To: Matt Glasser <glass...@wusm.wustl.edu> Cc: "hcp-users@humanconnectome.org" <hcp-users@humanconnectome.org> Subject: Re: [HCP-Users] tractography Hi, I did some more testing to see what could be the problem. The main weird thing I see is that in the coords_for_fdt_matrix3 file, there are some strange values:  coords_for_fdt_matrix3 : 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   305  -55  36  0  8346   304  -55  35  0  8347   304  -54  34  0  8348   tract_space_coords_for_fdt_matrix3: 263  -44  30  0  0   276  -40  72  0  1   311  -5  42  0  2   266  27  59  0  3   286  -90  23  0  4   313  -52  47  0  5   292  52  5  0  6   If the first 3 values are x-y-z then this is somewhere outside the brain probably. However, when I use the L.STS.fsl_MNI_new.asc and brainmap_filelist.txt  inputs as seeds (-x ) without any matrix options, the outputs (as in fdt_paths.nii.gz) look like expected. So this would indicate that there is no problem in transforming the seeds to dti space and reading them I would think? Any suggestions? -Maarten On Mon, Jul 20, 2015 at 6:29 PM, Maarten Vaessen <m.vaes...@gmail.com> wrote: Ah, of course!  That is: wb_command -probtrackx-dot-convert fdt_matrix3.dot test_dot_to_cifti.dconn.nii -col-surface L.STS.func.gii -row-cifti 91282_Greyordinates.dscalar.nii COLUMN -transpose On Mon, Jul 20, 2015 at 5:54 PM, Glasser, Matthew <glass...@wusm.wustl.edu> wrote: No I meant the dot convert. Matt. From: Maarten Vaessen <m.vaes...@gmail.com> Date: Monday, July 20, 2015 at 3:29 AM To: Matt Glasser <glass...@wusm.wustl.edu> Cc: "hcp-users@humanconnectome.org" <hcp-users@humanconnectome.org> Subject: Re: [HCP-Users] tractography The conversion was done like this: wb_command -gifti-label-to-roi ../../MNINonLinear/fsaverage_LR32k/102816.L.aparc.a2009s.32k_fs_LR.label.gii L.STS.func.gii -name S_temporal_sup surf2surf  -i ../../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 Is this what you were referring to? -Maarten On Sun, Jul 19, 2015 at 10:20 PM, Glasser, Matthew <glass...@wusm.wustl.edu> wrote: The --onewaycondition flag doesn’t seem sensible with matrix3.  Also I don’t know what your command was for doing the conversion.  Here is the probtrackx2 call that didn’t make it onto the list: probtrackx2 -x L.STS.fsl_MNI_new.asc --onewaycondition --omatrix3 --target3=L.STS.fsl_MNI_new.asc --lrtarget3=brainmap_HCP/brainmap_filelist.txt -P 100 --forcedir --dir=./test_surf_track_STS_brainmap_seedspace -s ../Diffusion.bedpostX/merged -m nodif_brain_mask.nii.gz --seedref=../../MNINonLinear/T1w_restore.nii.gz -V 2 --opd --pd --distthresh3=2 --xfm=../../MNINonLinear/xfms/standard2acpc_dc.nii.gz --invxfm=../../MNINonLinear/xfms/acpc_dc2standard.nii.gz Peace, Matt. From: Maarten Vaessen <m.vaes...@gmail.com> Date: Sunday, July 19, 2015 at 12:03 PM To: Matt Glasser <glass...@wusm.wustl.edu> Cc: "hcp-users@humanconnectome.org" <hcp-users@humanconnectome.org> Subject: Re: FW: [HCP-Users] tractography In this case: seed region to whole brain connectivity. The STS seed is mainly for testing purposes (not as many seed points as the whole WM), the final analysis will use all WM voxels as seeds though. In fact,when I run the analysis with WM as the seed the results look equally strange: only connectivity to what appears to be the right inferior posterior cortex. Could this be an issue with the seed-space to dti-space parameters? -M On Sun, Jul 19, 2015 at 5:31 PM, Glasser, Matthew <glass...@wusm.wustl.edu> wrote: What is it that you are trying to achieve?  Usually one uses a seed of all white matter voxels with matrix3. Peace, Matt. From: Maarten Vaessen <m.vaes...@gmail.com> Date: Sunday, July 19, 2015 at 3:41 AM To: Matt Glasser <glass...@wusm.wustl.edu> Subject: Re: [HCP-Users] tractography Hi Matthew, I tried to use the file you suggested, and I can convert the .dot without problem. However, the results don't make any sense, so I think there might be something wrong in my processing pipeline. Would you mind having a quick look at it and see if I do something wrong? Attached is the pipeline and a screenshot from the matrix as loaded in MATLAB. As you can see from the screenshot, there is only very limited number of none zeros. And weirdest of all, they appear at column indices which are probably somewhere in the right hemisphere (seed is in the left). Thanks, -Maarten On Wed, Jul 15, 2015 at 6:20 PM, Glasser, Matthew <glass...@wusm.wustl.edu> wrote: You should be able to use this file:  https://github.com/Washington-University/Pipelines/blob/master/global/templates/91282_Greyordinates/91282_Greyordinates.dscalar.nii Peace, Matt. From: <hcp-users-boun...@humanconnectome.org> on behalf of Maarten Vaessen <m.vaes...@gmail.com> Date: Wednesday, July 15, 2015 at 4:44 AM To: "hcp-users@humanconnectome.org" <hcp-users@humanconnectome.org> Subject: Re: [HCP-Users] tractography Hello, I followed the guide lines below to create a dense connectome with probtrackx. I was just wondering how to proceed with converting the .dot file from probtrackx to cifti using wb_command -probtrackx-dot-convert (for visualisation in wb_view). Specifically, what cifti file can I use as input for the -row-cifti option? So, what files released with the HCP data contain the correct brainmap? Thx -Maarten _______________________________________________________________ Hi You need to create such a file that contains the 90k grayordinates. To ensure consistency we do that in MNI 2mm space: - First create surface files in an FSL friendly format. Use the 32k surfaces, as the vertices are ~2mm apart. Left Surface: surf2surf -i $Subject/MNINonLinear/fsaverage_LR32k/${Subject}.L.white.32k_fs_LR.surf.gii -o white.L.asc --outputtype=ASCII --values=$Subject/MNINonLinear/fsaverage_LR32k//${Subject}.L.atlasroi.32k_fs_LR.shape.gii Right Surface: surf2surf -i $Subject/MNINonLinear/fsaverage_LR32k/${Subject}.R.white.32k_fs_LR.surf.gii -o white.R.asc --outputtype=ASCII --values=$Subject/MNINonLinear/fsaverage_LR32k//${Subject}.R.atlasroi.32k_fs_LR.shape.gii - Then extract the volume subcortical files from e.g. $Subject/MNINonLinear/ROIs/Atlas_Rois.2.nii.gz, let’s say as CIFTI_Structure_{Name}.nii.gz, using e.g. fslmaths or your favourite tool for ROI extraction. You should get 19 of these NIFTI files. (You can obviously use your favourite subcortical parcellation here, but if you want consistency with the CIFTI standard grayordinates, you need to resample the final results, the file above ensures consistency). - Put all the filenames in a text file in the following sequence, to ensure consistency with the rest of the CIFTIs: white.L.asc white.R.asc CIFTI_STRUCTURE_ACCUMBENS_LEFT.nii.gz CIFTI_STRUCTURE_ACCUMBENS_RIGHT.nii.gz CIFTI_STRUCTURE_AMYGDALA_LEFT.nii.gz CIFTI_STRUCTURE_AMYGDALA_RIGHT.nii.gz CIFTI_STRUCTURE_BRAIN_STEM.nii.gz CIFTI_STRUCTURE_CAUDATE_LEFT.nii.gz CIFTI_STRUCTURE_CAUDATE_RIGHT.nii.gz CIFTI_STRUCTURE_CEREBELLUM_LEFT.nii.gz CIFTI_STRUCTURE_CEREBELLUM_RIGHT.nii.gz CIFTI_STRUCTURE_DIENCEPHALON_VENTRAL_LEFT.nii.gz CIFTI_STRUCTURE_DIENCEPHALON_VENTRAL_RIGHT.nii.gz CIFTI_STRUCTURE_HIPPOCAMPUS_LEFT.nii.gz CIFTI_STRUCTURE_HIPPOCAMPUS_RIGHT.nii.gz CIFTI_STRUCTURE_PALLIDUM_LEFT.nii.gz CIFTI_STRUCTURE_PALLIDUM_RIGHT.nii.gz CIFTI_STRUCTURE_PUTAMEN_LEFT.nii.gz CIFTI_STRUCTURE_PUTAMEN_RIGHT.nii.gz CIFTI_STRUCTURE_THALAMUS_LEFT.nii.gz CIFTI_STRUCTURE_THALAMUS_RIGHT.nii.gz - You can then use such a file in FSL probtrackx2 as a seed (for Matrix1) or as a target3 (for Matrix3). Notice that running a single probtrackx2 command with all these seed locations and with many samples per location will require huge processing power and memory. In practice, we run multiple probtrackx2 in parallel, by splitting and parallelising the computation by using the --rseed option in probtrackx2 and using a small number of samples --nsamples per instance. I.e. instead of running one command, which will attempt to propagate 5000 curves per seed, we can run e.g. 100 instances of the above commands, using --nsamples=50 and --rseed=i, i=1..100. Results can then be combined using fdt_matrix_merge (which however also needs quite a lot of memory to produce the final dense connectomes, but at least it is one final process). - Another approach for parallelisation would be to split the seed locations and merge the final matrices. There is no solution that fits all systems, you should try and find the best approach depending on your computing resources. Hope this helps Stam On 19 May 2015, at 01:01, David R. Haynor <hay...@uw.edu<mailto:hay...@uw.edu>> wrote: hi HCP, we are trying to do tractography using FSL and HCP data. i have some questions -- i suspect they have been answered already, but couldn't find those answers: 1. is there a file containing the grayordinate coordinates in the diffusion space for a particular subject, both subcortical voxels and cortical vertices? 2. if i want to use some cortical and subcortical voxels from the list of grayordinates as targets, do i have to run probtrackx2 twice (i.e. once for the cortical surface vertices and once for the subcortical voxels), or can i run it just once? 3. where is the label file for the grayordinate vertices/voxels for a given subject? thanks in advance. -dh _______________________________________________ HCP-Users mailing list HCP-Users@humanconnectome.org<mailto:HCP-Users@humanconnectome.org> http://lists.humanconnectome.org/mailman/listinfo/hcp-users _______________________________________________ HCP-Users mailing list HCP-Users@humanconnectome.orghttp://lists.humanconnectome.org/mailman/listinfo/hcp-users _______________________________________________ HCP-Users mailing list HCP-Users@humanconnectome.org 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. 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