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 <[email protected]> wrote: > Can you repost your commands with absolute paths (at least as far as > ${StudyFolder})? > > Peace, > > Matt. > > From: Maarten Vaessen <[email protected]> > Date: Friday, July 24, 2015 at 1:43 AM > To: Matt Glasser <[email protected]> > Cc: "[email protected]" <[email protected]> > 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 < > [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. >> > > > ------------------------------ > > 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
