1) No, a simple fread cannot correctly read any of our usual data file formats (the -to-gifti-ext conversion is not a "usual" data format, see #4) - they have headers on them, some of them are gzip compressed, and gifti is not a binary format anyway (it is XML, which in unusual circumstances can make use of a secondary binary file). There is matlab code available specifically for the task of correctly reading in cifti and gifti data:
https://wiki.humanconnectome.org/display/PublicData/HCP+Users+FAQ#HCPUsersFAQ-2.HowdoyougetCIFTIfilesintoMATLAB ? The gifti toolbox it mentions is the recommended way to read gifti files into matlab. Behind the scenes, ciftiopen and ciftisave use -cifti-convert, and then the gifti toolbox, to prevent any guessing and data scrambling on your part. 2) No, -cifti-restrict-dense-map will not expand the file to add the medial wall indices with zeroes. What are you wanting to do with it that you need these extra zeroes in the matrix? This can be done with -cifti-create-dense-from-template, but first you'll need to make a template 32k cifti file (only needs 1 map, not an entire square) with -cifti-create-dense-scalar or similar. 3) No, .surf.gii files cannot be used as ROIs, they are surface geometry (coordinate) files. You can use the standard grayordinate space ROIs (in the pipelines repository, global/templates/91282_Greyordinates/*.shape.gii) or just make some all-1s metric files (.func.gii) with -metric-math, the result of -cifti-restrict-dense-map will be 29k with either (as long as you don't cross your hemispheres). 4) -cifti-convert does not create metric files (metric files are single surface, all vertices). It abuses whichever output format is chosen in order to stuff the entire cifti matrix into it, to allow for tricks for exchanging cifti data with other tools that don't have cifti support. Tim On Tue, Mar 14, 2017 at 11:31 AM, Estrid Jakobsen <[email protected]> wrote: > Hi Tim, > > Thanks for your reply. I see my mistake was in assuming the output from > cifti-separate would be 32k x 32k and loading it in to matlab as such, > using *fread(fid,[32492 32492], 'float32')*. Since the file is actually > 32k x 91k it's no wonder the vertices aren't correct. > > Is it possible to get to the 32k x 32k matrices using > -cifti-restrict-dense-map (instead of 29k x 29k) and if so, can you advise > how? Can I simply use a surf.gii file as -left-roi and -right-roi? > > Presumably I can follow this with -cifti-convert -to-gifti-ext to convert > from dconn to metric and then load the matrix into matlab using fread as > before? > > Thanks again! > > Estrid > > On Mon, Mar 13, 2017 at 7:51 PM, Timothy Coalson <[email protected]> wrote: > >> That command should do what you intended, though it will give you two 32k >> x 91k files, not 32k x 32k. Another possibility for doing this (which can >> also get you to the single-hemisphere 29k x 29k cifti file by running it >> twice) is -cifti-restrict-dense-map, which is also far less painful to load >> the results into wb_view, as it remains a dconn file (data loaded on >> demand, not in advance, knows not to show it as 91k maps in a combobox). >> >> I ran the exact command you quoted on the same file downloaded from >> ConnectomeDB, using workbench v1.1.1 linux64 (debian/ubuntu) as previously >> released on our website, and the resulting files I got look nothing like >> your capture (I am trying it again with v1.2.3 now, but it takes a while to >> run things on files this large - very little has changed in this command, >> so I expect the same result). Did you do anything after the >> -cifti-separate that you didn't mention? Which map(s) in the output file >> did you check? What version of workbench and OS did you run it on, and how >> much memory did the machine have? >> >> Tim >> >> >> On Mon, Mar 13, 2017 at 10:13 AM, Estrid Jakobsen <[email protected]> >> wrote: >> >>> Hi folks, >>> >>> I have a question regarding extracting the left and right hemispheres >>> from .dconn cifti files. I've tried using wb_command -cifti-separate on the >>> 820-subject group average dense connectome (see command below), but when I >>> then visualize a connectivity vector from the resulting 32k x 32k matrix, >>> the vertices appear to be scrambled (see attached image). I'm guessing this >>> might have something to do with the command not being intended for >>> separating symmetrical matrices and perhaps only extracting correctly along >>> one dimension...? >>> >>> Is there a way to extract the left and right 32k matrices from the dense >>> connectome, or would I have to go back and create them myself from the PCA >>> Eigenmaps? >>> >>> Thanks in advance! >>> >>> Estrid >>> >>> wb_command -cifti-separate >>> HCP_S900_820_rfMRI_MSMAll_groupPCA_d4500ROW_zcorr.dconn.nii >>> ROW -metric CORTEX_RIGHT HCP_S900_820_rfMRI_MSMAll_grou >>> pPCA_d4500ROW_zcorr_RIGHT.func.gii -metric CORTEX_LEFT >>> HCP_S900_820_rfMRI_MSMAll_groupPCA_d4500ROW_zcorr_LEFT.func.gii >>> >>> >>> **************** >>> Estrid Jakobsen >>> >>> Postdoctoral Fellow >>> Cognitive Neurosciences >>> Montreal Neurological Institute and Hospital, McGill University >>> >>> Max Planck Research Group Neuroanatomy and Connectivity >>> Max Planck Institute for Human Cognitive and Brain Sciences, Leipzig >>> >>> _______________________________________________ >>> HCP-Users mailing list >>> [email protected] >>> http://lists.humanconnectome.org/mailman/listinfo/hcp-users >>> >> >> > > > -- > **************** > Estrid Jakobsen > > Postdoctoral Fellow > Cognitive Neurosciences > Montreal Neurological Institute and Hospital, McGill University > > Max Planck Research Group Neuroanatomy and Connectivity > Max Planck Institute for Human Cognitive and Brain Sciences, Leipzig > _______________________________________________ HCP-Users mailing list [email protected] http://lists.humanconnectome.org/mailman/listinfo/hcp-users
