Re: [HCP-Users] error while writing cifti with Matlab

[Glasser, Matthew]

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 <mha...@wustl.edu> Date: Wednesday, December 10, 2014 at 3:38 PM To: Julien Dubois <jdub...@caltech.edu>, "hcp-users@humanconnectome.org" <hcp-users@humanconnectome.org> 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: mha...@wustl.edu From: Julien Dubois <jdub...@caltech.edu> Date: Wednesday, December 10, 2014 3:30 PM To: "hcp-users@humanconnectome.org" <hcp-users@humanconnectome.org> 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 = ""> >> 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 HCP-Users@humanconnectome.org 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 HCP-Users@humanconnectome.org 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 HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users