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 <[email protected]> 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 <[email protected]> > Date: Sunday, July 19, 2015 at 12:03 PM > To: Matt Glasser <[email protected]> > Cc: "[email protected]" <[email protected]> > 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 <[email protected] > > 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 <[email protected]> >> Date: Sunday, July 19, 2015 at 3:41 AM >> To: Matt Glasser <[email protected]> >> 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 < >> [email protected]> 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: <[email protected]> on behalf of Maarten >>> Vaessen <[email protected]> >>> Date: Wednesday, July 15, 2015 at 4:44 AM >>> To: "[email protected]" <[email protected]> >>> 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 >>> <[email protected]<mailto:[email protected] <[email protected]>>> >>> 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 >>> [email protected]<mailto:[email protected] >>> <[email protected]>>http://lists.humanconnectome.org/mailman/listinfo/hcp-users >>> >>> >>> _______________________________________________ >>> HCP-Users mailing >>> [email protected]http://lists.humanconnectome.org/mailman/listinfo/hcp-users >>> >>> _______________________________________________ >>> 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. 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