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. 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 > _______________________________________________ HCP-Users mailing list [email protected] http://lists.humanconnectome.org/mailman/listinfo/hcp-users
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