-cifti-convert will happily reset a dconn file to scalars along row (ie, make a dscalar file), that is not the issue.
It sounds like you are trying to go from an input of (some voxels) x (all grayordinates) to an output of (all brainordinates) x (subjects). The ciftisavereset function doesn't read the cifti XML, and thus can't transpose the mappings on it, and it always resets the mapping along the row. If this is the case, you could transpose the dconn you are reading in and replacing the data of, making it (all grayordinates) x (some voxels), or as Matt suggests, using a dtseries or dscalar for that template file instead. Also, while -cifti-average-roi-correlation may not do exactly what you did, it does something similar, and may be worth a look: http://www.humanconnectome.org/software/workbench-command.php?function=-cifti-average-roi-correlation You can also use -cifti-merge to horizontally concatenate cifti files. Tim On Wed, Dec 10, 2014 at 3:40 PM, Glasser, Matthew <[email protected]> wrote: > Let’s hear a confirmation from Tim Coalson that a dconn header would > actually be properly reset, I’m not sure that is true. > > Matt. > > From: <Harms>, Michael <[email protected]> > Date: Wednesday, December 10, 2014 at 3:38 PM > To: Julien Dubois <[email protected]>, "[email protected]" < > [email protected]> > Subject: Re: [HCP-Users] error while writing cifti with Matlab > > > Hi, > I haven't used the 'ciftisavereset' function, but a dscalar.nii should > have grayordinates as the first dimension, so try saving the transpose of > your data (i.e., an [nGrayOrdinates x 1] vector). > > cheers, > -MH > > -- > Michael Harms, Ph.D. > ----------------------------------------------------------- > Conte Center for the Neuroscience of Mental Disorders > Washington University School of Medicine > Department of Psychiatry, Box 8134 > 660 South Euclid Ave. Tel: 314-747-6173 > St. Louis, MO 63110 Email: [email protected] > > From: Julien Dubois <[email protected]> > Date: Wednesday, December 10, 2014 3:30 PM > To: "[email protected]" <[email protected]> > Subject: [HCP-Users] error while writing cifti with Matlab > > Hello list > > I am testing out the cifti format with Matlab, and am running into an > error that I dont seem to be able to figure out. Its likely quite simple, > so here it is. > > I created a cifti file for the correlation between some voxels (defined > by a volume mask) and the rest of the brain, using wb_command > -cifti-correlation and the -roi-override option. I did this for a bunch of > subjects, and now want to look at the average across subjects. I am loading > the result for each subject with ciftiopen.m, which gives me a matrix > nVoxInRoi x nVoxInBrain. I then average along the rows, giving a row vector > with the average correlation of the voxels in the ROI to the rest of the > brain. I concatenate all the row vectors for all subjects, and end up with > a matrix nSub x nVoxInBrain (this is all done in Atlas space). I then > average this matrix across subjects, giving a row vector again, finalRes (1 > x nVoxInBrain). I want to save this vector to a cifti file so I can display > it in connectome workbench. I use ciftisavereset, but get the following > error: > >> cii = ciftiopen('subject1testconn.dconn.nii','/usr/bin/wb_command'); > >> newcii = cii > >> newcii.data = finalRes > >> ciftisavereset(newcii,'finalRes.dscalar.nii','/usr/bin/wb_command') > > While running '/usr/bin/wb_command -cifti-convert -from-gifti-ext > finalRes.dscalar.nii.gii finalRes.dscalar.nii -reset-scalars': > ERROR: dimensions of input gifti array do not match dimensions in the > embedded Cifti XML > /usr/bin/wb_command -cifti-convert -from-gifti-ext > finalRes.dscalar.nii.gii finalRes.dscalar.nii -reset-scalars: Signal 127 > > Im not sure how to get around this error. Im sure it stems from my poor > understanding of the cifti format (which I will try to improve on). Any > hints on how to circumvent this error? > > Thanks! > - Julien > > > _______________________________________________ > 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. > > _______________________________________________ > 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. > > _______________________________________________ > 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
