Hi, Both the gifti toolbox and ciftiopen run into memory problems when loading such large files, even with 128GB of RAM available, which is why I have previously used fread to load "external binary gifti" files created with -cifti-convert (which seems to work correctly). I will try using -cifti-restrict-dense-map to create the 29k matrices and then manually insert the medial wall mask in matlab. I want to visualize maps using SurfStat, so the extra zeros are necessary.
Thanks again, Estrid On Tue, Mar 14, 2017 at 11:23 PM, Timothy Coalson <[email protected]> wrote: > 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 >> > > -- **************** 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
