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 <[email protected]> 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 <[email protected]> > 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 <%2B61%203%209902%209435> | 0402 516 574* >> *E: [email protected] <[email protected]>* >> *W: www.med.monash.edu.au/psych/mcin/ >> <http://www.med.monash.edu.au/psych/mcin/>* >> >> >> From: Glasser, Matthew [email protected] >> Reply: Glasser, Matthew [email protected] >> Date: 8 July 2014 at 2:05:55 pm >> To: Linden Parkes [email protected] >> >> Cc: [email protected] [email protected] >> 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 <[email protected]> >> Date: Monday, July 7, 2014 at 5:21 PM >> To: Matt Glasser <[email protected]> >> Cc: "[email protected]" <[email protected]> >> 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" <[email protected]> >> 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 <[email protected]> >>> Date: Monday, July 7, 2014 at 3:49 AM >>> To: "[email protected]" <[email protected]> >>> 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 >>> <http://fsl.fmrib.ox.ac.uk/fsl/fslwiki/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 <%2B61%203%209902%209435> | 0402 516 574* >>> *E: [email protected] <[email protected]>* >>> *W: www.med.monash.edu.au/psych/mcin/ >>> <http://www.med.monash.edu.au/psych/mcin/>* >>> >>> B7AE8BF0-4F0C-4F0B-9BDE-B582B9331FA1 >>> >>> _______________________________________________ >>> 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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