[HCP-Users] FW: Probtrackx surface analysis

[Glasser, Matthew]

From: Stamatios Sotiropoulos <stamatios.sotiropou...@ndcn.ox.ac.uk> Date: Friday, July 11, 2014 at 6:35 AM To: Linden Parkes <linden.par...@monash.edu> Cc: Matt Glasser <glass...@wusm.wustl.edu>, "s...@fmrib.ox.ac.uk" <s...@fmrib.ox.ac.uk> Subject: Re: [HCP-Users] Probtrackx surface analysis I think  wb_command -gifti-label-to-roi  will do. Cheers Stam On 11 Jul 2014, at 11:18, Linden Parkes <linden.par...@monash.edu> wrote: Cool. I'll try this asap. How do you split label.gii into func.gii files? Cheers, Linden On 11 July 2014 20:16, Stamatios Sotiropoulos <stamatios.sotiropou...@ndcn.ox.ac.uk> wrote: OK, Saad’s recommendation earlier this morning should work then.  Cheers Stam   On 11 Jul 2014, at 10:41, Linden Parkes <linden.par...@monash.edu> wrote: Hi Stam, Certainly. I want to perform segmentation of subcortical areas based on tractography to cortical surfaces. To this end I created volumetric binary masks of the subcortical areas of interest (e.g. left caudate) and I wanted to use the aparc cortical parcellation as targets. I could create a bunch of volume rois of these cortical areas based on freesurfer look up tables (exactly the same as what I did for the subcortical rois just mentioned) but I read that it is better to use surface files than volumes. But I haven't had any success feeding in .gii files as targets to probtrackx. So perhaps I am better just using volumes? Cheers Linden On 11/07/2014 7:32 pm, "Stamatios Sotiropoulos" <stamatios.sotiropou...@ndcn.ox.ac.uk> wrote: Hi Linden Can you please tell us briefly what you want to do? Is it extracting a particular gifti label (from HCP label files) and use that in tractography? You may or may not be able to do that currently. Thanks Stam On 11 Jul 2014, at 01:41, Linden Parkes <linden.par...@monash.edu> wrote: Hi,  Does anyone have any input on this? Cheers, Linden On 9 July 2014 12:45, Glasser, Matthew <glass...@wusm.wustl.edu> wrote: Hi Saad and Stam, I’m guessing label2surf does work with GIFTI surface and label files, so can you help Linden? Thanks, Matt. From: Linden Parkes <linden.par...@monash.edu> Date: Tuesday, July 8, 2014 at 7:46 PM To: Matt Glasser <glass...@wusm.wustl.edu> Subject: Re: [HCP-Users] Probtrackx surface analysis Yes but these do not work with the label2surf command. atleast not using the syntax that the FDT user guide puts forward. Cheers, Linden On 9 July 2014 10:27, Glasser, Matthew <glass...@wusm.wustl.edu> wrote: Have a look back at the e-mail I sent earlier where I list the label file.  We don’t use FreeSurfer proprietary formats, so these are GIFTI label files. Peace, Matt. From: Linden Parkes <linden.par...@monash.edu> Date: Tuesday, July 8, 2014 at 7:21 PM To: Matt Glasser <glass...@wusm.wustl.edu> Subject: Re: [HCP-Users] Probtrackx surface analysis Okay, I'll uncheck the matrix options. Under "using freesurfer surfaces" there are only two steps: registration & label files. Not needing to do registration as you say, makes sense. But the 'label files' step assumes the presence on a series of .label files which are used with the label2surf command which I can't find within the HCP datasets Cheers, Linden On 9 July 2014 09:41, Glasser, Matthew <glass...@wusm.wustl.edu> wrote: You wouldn’t need matrix2 (or any of the other matrices), just the normal output seeds to targets would be fine.   You don’t need to do any registration, as I said below, that’s already taken care of for you by the HCP Pipelines.   If you are using the FDT GUI, I don’t know how to use that (I’ve only used the command line) so you might need to ask on the FSL list about how to use the FDT GUI (though I’d recommend using the command line).   Peace, Matt. From: Linden Parkes <linden.par...@monash.edu> Date: Tuesday, July 8, 2014 at 6:34 PM To: Timothy Coalson <tsc...@mst.edu> Cc: Matt Glasser <glass...@wusm.wustl.edu>, "hcp-users@humanconnectome.org" <hcp-users@humanconnectome.org> Subject: Re: [HCP-Users] Probtrackx surface analysis Hey - Thanks for the crash course on CIFTI. That cleared a few things up for me, but I'm still not sure how to perform the tractography. Cheers, Linden On 9 July 2014 07:14, Timothy Coalson <tsc...@mst.edu> wrote: The extension for CIFTI files is .[type].nii, where type is dconn, dtseries, dscalar, dlabel, pconn, or another such specifier.  It ends in .nii because CIFTI uses the NIFTI-2 format, which specifies that the extension must be .nii, but includes a specialized XML header extension instead of using the NIFTI header for spacing info, etc.  Also, we usually gzip our volume files (CIFTI must not be gzipped when used, as we need on-disk random access due to large file sizes), so volume files we distribute will generally end in .nii.gz. The standard extensions are listed in the specification, see Appendix A in http://www.nitrc.org/forum/attachment.php?attachid=342&group_id=454&forum_id=1955 for the list, but refer to the main specification in http://www.nitrc.org/forum/forum.php?thread_id=4380&forum_id=1955 for how "unknown" works (it still must end in .nii). Tim On Mon, Jul 7, 2014 at 11:17 PM, Linden Parkes <linden.par...@monash.edu> wrote: Ah okay, what is the file extension for CIFTI? I can only see .nii and .gii files. I tried following those instructions but came unstuck at the “FreeSurfer Registration” step because I could not find the struct.nii.gz file in the HCP datasets. I’d like to perform striatal segmentation with tractography. Specifically, using subcortical regions such as the accumbens, caudate and putamen. To this end, I figured that using the aparc cortical regions as “Classification targets”  and choosing Matrix2 was most appropriate. One method I thought of trying was just to get binary volume masks for all the cortical regions in aparc and submitting them. But from my reading of the FSL mailing list, it appears that using surfaces as opposed to volumes is preferable. However, as mentioned above, I came unstuck following the FSL user guide. Hope this makes sense Cheers, Linden —————————————————————— Linden Parkes PhD Candidate Monash Clinical & Imaging Neuroscience (MCIN) School of Psychological Sciences Monash Biomedical Imaging Monash University A: 770 Blackburn Rd, Clayton, 3168, Vic, Australia T: +61 3 9902 9435  |  0402 516 574 E: linden.par...@monash.edu W: www.med.monash.edu.au/psych/mcin/ B7AE8BF0-4F0C-4F0B-9BDE-B582B9331FA1 From: Glasser, Matthew glass...@wusm.wustl.edu Reply: Glasser, Matthew glass...@wusm.wustl.edu Date: 8 July 2014 at 2:05:55 pm To: Linden Parkes linden.par...@monash.edu Cc: hcp-users@humanconnectome.orghcp-users@humanconnectome.org Subject:  Re: [HCP-Users] Probtrackx surface analysis HCP data is NIFTI/GIFTI/CIFTI, so the particular files you have there are NIFTI volumes.  The GIFTI surface aparc data are in  ${StudyFolder}/${Subject}/MNINonLinear/fsaverage_LR32k/100307.${Hemisphere}.aparc.32k_fs_LR.label.gii To use them with probtrackx2, you’ll need to follow the instructions here (unfortunately probtrackx2 currently doesn’t support standard GIFTI surfaces and label files): http://fsl.fmrib.ox.ac.uk/fsl/fslwiki/FDT/UserGuide#Using_surfaces To know what matrix you should use, I’d need to know a little bit more about the question you are asking.  matrix2 with nodif_brain_mask as the tract space mask will produce an enormous file. Peace, Matt. From: Linden Parkes <linden.par...@monash.edu> Date: Monday, July 7, 2014 at 5:21 PM To: Matt Glasser <glass...@wusm.wustl.edu> Cc: "hcp-users@humanconnectome.org" <hcp-users@humanconnectome.org> Subject: Re: [HCP-Users] Probtrackx surface analysis Oh, I thought the HCP data was distributed in cifti and gifti? As a first pass I wanted to use all surfaces in aparc as classification targets for a few subcortical volumes rois and am a bit unsure on how to do that. I'd like to pull out matrix2 for this (seems most appropriate). Can I submit the nodif_brain_mask as the "tract space mask" for this? Cheers Linden On 08/07/2014 2:08 am, "Glasser, Matthew" <glass...@wusm.wustl.edu> wrote: You would use the white matter surfaces in ${StudyFolder}/${Subject}/T1w/fsaverage_LR32k.  The distributed diffusion data are already in T1w space, so you don’t need to provide transformation matrices.  The surface reference image can be any of the files in ${StudyFolder}/${Subject}/T1w or ${StudyFolder}/${Subject}/T1w/Diffusion.   Neither of the files you mention are CIFTI files.  What cortical regions are you wanting to track from? Peace, Matt. From: Linden Parkes <linden.par...@monash.edu> Date: Monday, July 7, 2014 at 3:49 AM To: "hcp-users@humanconnectome.org" <hcp-users@humanconnectome.org> Subject: [HCP-Users] Probtrackx surface analysis Hi HCP users, I’m trying to run probtrackX on some HCP data, can someone provide some guidance on how to run this using surfaces? I’m following the FSL user guide but they often refer to files which are absent from the HCP data as far I can tell. (e.g., "and also that you have a file called struct.nii.gz that you have used as an input to FreeSurfer recon_all program." Basically, I’d like to define subcortical seeds and track to cortical surfaces. For the subcortical seed regions I can easily create binary masks to use as seeds using fslmaths based on intensity values from the freesurfer LUTs. I could do the same with the cortical regions but I have read that tracking to cortical regions is best done with surfaces instead of volumes. So, when selecting “classification targets” can I simply add in a cifti file? (e.g., 100307/T1w/aparc+aseg.nii.gz OR 100307/T1w/aparc.a2009s+aseg.nii.gz)** and then tell probtrackX to output the matrices I want? **I assume using the files in the T1w dir is best because these are in the same space as the diffusion data and therefore don’t require transformation. On a different note, if I select a surface file as a seed instead, it asks for a “surface reference image” for Freesurfer. Which file is best used for this purpose? Cheers, Linden —————————————————————— Linden Parkes PhD Candidate Monash Clinical & Imaging Neuroscience (MCIN) School of Psychological Sciences Monash Biomedical Imaging Monash University A: 770 Blackburn Rd, Clayton, 3168, Vic, Australia T: +61 3 9902 9435  |  0402 516 574 E: linden.par...@monash.edu W: www.med.monash.edu.au/psych/mcin/ B7AE8BF0-4F0C-4F0B-9BDE-B582B9331FA1 _______________________________________________ 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. 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. 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