I don't know what 3dDeconvolve does, but if you used it to try to do anything spatial (spatial sharpening, PSF, etc), then the files produced by wb_command -cifti-convert would be entirely inappropriate. The only meaningful operations that can be done on -cifti-convert "volume-ish" files are temporal processing, because the spatial aspects are completely jumbled.
That said, yes, if you made a volume-ish file by -cifti-convert and put that through an afni tool, the cifti-template can be the input file you used in -cifti-convert to make the volume-ish input in the first place. If the cifti files you are using are standard 91k grayordinates, you could use the appropriate file from the Pipelines/global/templates folder if that was somehow more convenient. Since we do not expect tools to preserve anything about the volume-ish files except the dimensions, we can't use the volume-ish file to also store the information required to put the "voxels" back into the right vertices, which is why a cifti file is required as the template, to define what "voxel" actually represents each vertex, etc. You will likely need the -reset-scalars option, as I expect the statistics output is a different number of frames than the timeseries. Tim On Fri, Jun 21, 2019 at 12:24 PM Pipoly, Marco A <marco-pip...@uiowa.edu> wrote: > Hello All, > > > I am relatively new to working with HCP tfMRI connectome data and am > running into a bit of confusion about the following: I have statistical map > outputs (in stats.nii.gz format) from, CIFTI data converted to NIFTI data > that I put into AFNI 3dDeconvolve. I am interested in converting this > output (stats.nii.gz) back into CIFTI in order to regain respect to the > surface and structure information (that does not appear to remain when you > wb_command CIFTI->NIFTI). > > > It appears this will do the trick?: > > [-from-nifti] - convert a NIFTI (1 or 2) file made with this command back > into CIFTI > <nifti-in> - the input nifti file > <cifti-template> - a cifti file with the dimension(s) and mapping(s) > that should be used > <cifti-out> - output - the output cifti file > > If so, what exactly does it mean by "cifti-template?" Would this be the > original dtseries file I used to procure the AFNI 3dDeconvolve outputs or > is there a generic template brain(s) for the various CIFTI data types? > > > Best, > > > Marco A. Pipoly, B.S. > NSF Graduate Research Fellow > Graduate Student, PhD in Neuroscience > University of Iowa > marco-pip...@uiowa.edu > > > > > > > _______________________________________________ > HCP-Users mailing list > HCP-Users@humanconnectome.org > http://lists.humanconnectome.org/mailman/listinfo/hcp-users > _______________________________________________ HCP-Users mailing list HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users
