Thanks Tim, yes, bad choice of words on my part by referring to the analysis on the "fake nifti" as volume based.
On Mon, May 11, 2015 at 3:43 PM, Timothy Coalson <[email protected]> wrote: > Doing things with the nifti output of -cifti-convert is not what we mean > by "volume-based analysis". What we mean by volume-based analysis is > relying on volume-based registration to align the cortex, and combining > same-index voxels across subjects in an attempt to get statistics or other > results for a particular piece of cortex. This approach is undesirable, as > volume-based registration does not correctly align cortex with normal > variability of folding patterns, so the same post-registration voxel in > different subjects can refer to different parts of cortex (or something > entirely outside of cortex). It also is not well suited to aligning cortex > based on features other than anatomical shape. > > When you use -cifti-convert, you are still using grayordinates, the > programs running on that data just don't know it. All -cifti-convert does > is stuff the data matrix from the cifti file into the nifti-1 format so > that tools meant for volume files can read it, no resampling or mapping or > other conversion is done, so the values related to cortex still represent > data on the surface, not in voxels. Thus, nothing you can do on the > converted files is actually volume-based analysis, hence why it has been > called "fake nifti". The downside to this is that you can't use > neighborhood/spatial information while using a fake-nifti file, so you > can't do smoothing, gradient, resampling, etc. The advantage is, since the > cortex has been registered with surface-based registration, you can combine > the same-index vertex (represented in a fake-nifti file by a "fake voxel", > if you will) across subjects and get a valid result, as each vertex > represents the same cortical location across subjects, and is never > something outside of cortex. > > We generally only use one grayordinate space in the HCP released data, so > any HCP cifti file that has a grayordinates mapping should be usable as the > template, including the one you mentioned. > > Tim > > > On Mon, May 11, 2015 at 12:12 PM, Carolina Ramirez < > [email protected]> wrote: > >> Hi, >> >> I'm doing volume based analysis (with non-spatial relationships) of task >> fMRIby converting the volumes in >> MNINonlinear/Results/taskname/taskname_Atlas.dtseries.nii CIFTIs to NIFTI >> using wb_command -cifti-convert. >> >> First, since we want to do group level analysis, I'm wondering if it's >> correct or not to use the standard Conte69 >> '91282_Greyordinates.dscalar.nii' CIFTI as a template in the conversion >> back from CIFTI to NIFTI, given the comments in this thread: >> https://www.mail-archive.com/hcp-users%40humanconnectome.org/msg00601.html >> >> Second, I understand that the purpose of creating the CIFTI format and >> the higher level pipelines is to be able to do all the processing and >> analysis in grayordinate space. Also, in a more recent thread you mention >> that some people have had success with this "fake nifti" approach. >> It's probably out of the scope of the HCP project, but still, can I ask >> you if at some point you did some comparison between the results of a >> 'cifti to nifti' volume based analysis with the grayordinates space >> analysis? >> In theory both approaches should yield somewhat equivalent results, but >> the Pipelines are optimized for grayordinates, so it would be reasonable to >> expect that the HCP task analysis Pipelines will give better(more >> complete?) results in general, right? >> >> Thanks, >> >> Carolina. >> >> >> _______________________________________________ >> HCP-Users mailing list >> [email protected] >> http://lists.humanconnectome.org/mailman/listinfo/hcp-users >> > > -- Carolina _______________________________________________ HCP-Users mailing list [email protected] http://lists.humanconnectome.org/mailman/listinfo/hcp-users
