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 <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 >>>> listhcp-us...@humanconnectome.org<mailto:HCP-Users@humanconnectome.org >>>> <HCP-Users@humanconnectome.org>>http://lists.humanconnectome.org/mailman/listinfo/hcp-users >>>> >>>> >>>> _______________________________________________ >>>> HCP-Users mailing >>>> listHCP-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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