Wow, thank you all for the extremely quick support! much appreciated. The solution to load a .dtseries.nii and replace the data with a (all grayordinates) x 1 vector worked well.
Tim, thank you for the suggestion to use cifti-average-roi-correlation, Ill look into it. - Julien On Wed, Dec 10, 2014 at 1:47 PM, Timothy Coalson <[email protected]> wrote: > -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
