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 <[email protected]> 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 <[email protected]> > Date: Wednesday, July 22, 2015 at 8:50 AM > > To: Matt Glasser <[email protected]> > Cc: "[email protected]" <[email protected]> > 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 <[email protected]> > 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 < >> [email protected]> wrote: >> >>> No I meant the dot convert. >>> >>> Matt. >>> >>> From: Maarten Vaessen <[email protected]> >>> Date: Monday, July 20, 2015 at 3:29 AM >>> To: Matt Glasser <[email protected]> >>> Cc: "[email protected]" <[email protected]> >>> 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 < >>> [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. If you >>>>>> are not the intended recipient, be advised that any unauthorized use, >>>>>> disclosure, copying or the taking of any action in reliance on the >>>>>> contents >>>>>> of this information is strictly prohibited. If you have received this >>>>>> email >>>>>> in error, please immediately notify the sender via telephone or return >>>>>> mail. >>>>>> >>>>> >>>>> >>>>> ------------------------------ >>>>> >>>>> The materials in this message are private and may contain Protected >>>>> Healthcare Information or other information of a sensitive nature. If you >>>>> are not the intended recipient, be advised that any unauthorized use, >>>>> disclosure, copying or the taking of any action in reliance on the >>>>> contents >>>>> of this information is strictly prohibited. If you have received this >>>>> email >>>>> in error, please immediately notify the sender via telephone or return >>>>> mail. >>>>> >>>> >>>> >>>> ------------------------------ >>>> >>>> The materials in this message are private and may contain Protected >>>> Healthcare Information or other information of a sensitive nature. If you >>>> are not the intended recipient, be advised that any unauthorized use, >>>> disclosure, copying or the taking of any action in reliance on the contents >>>> of this information is strictly prohibited. If you have received this email >>>> in error, please immediately notify the sender via telephone or return >>>> mail. >>>> >>> >>> >>> ------------------------------ >>> >>> The materials in this message are private and may contain Protected >>> Healthcare Information or other information of a sensitive nature. If you >>> are not the intended recipient, be advised that any unauthorized use, >>> disclosure, copying or the taking of any action in reliance on the contents >>> of this information is strictly prohibited. If you have received this email >>> in error, please immediately notify the sender via telephone or return mail. >>> >> >> > > ------------------------------ > > The materials in this message are private and may contain Protected > Healthcare Information or other information of a sensitive nature. If you > are not the intended recipient, be advised that any unauthorized use, > disclosure, copying or the taking of any action in reliance on the contents > of this information is strictly prohibited. If you have received this email > in error, please immediately notify the sender via telephone or return mail. > _______________________________________________ HCP-Users mailing list [email protected] http://lists.humanconnectome.org/mailman/listinfo/hcp-users
