As in my previous answer, the best way to get them into matlab is to pick
an option from this FAQ entry:
https://wiki.humanconnectome.org/display/PublicData/HCP+Users+FAQ#HCPUsersFAQ-2.HowdoyougetCIFTIfilesintoMATLAB?
In either case, you will need to install some toolboxes into matlab, and
you will need the gifti toolbox mentioned in order to get the surface
coordinates. Once you have installed these, you can do things like this in
matlab (I may have some things wrong, I don't use matlab very often):
% load the left midthickness surface
surfGifti = gifti('fsaverage_32k/100307.L.midthickness.32k_fs_LR.surf.gii');
firstCoord = surfGifti.vertices(1,:);
Option A from the FAQ:
rfMRICifti =
ft_read_cifti('Results/rfMRI_REST1_LR/rfMRI_REST1_LR_Atlas.dtseries.nii');
% this should have the information of what vertex/voxel each index is, but
I am unsure of its location in the struct
Option B from the FAQ, plus reading the mapping information for left cortex:
rfMRICifti =
ciftiopen('Results/rfMRI_REST1_LR/rfMRI_REST1_LR_Atlas.dtseries.nii',
'wb_command');
% run wb_command to get left cortex section of mapping
system('wb_command -cifti-export-dense-mapping
Results/rfMRI_REST1_LR/rfMRI_REST1_LR_Atlas.dtseries.nii COLUMN -surface
CORTEX_LEFT outmapping.L.txt');
leftmapping = dlmread('outmapping.L.txt') + 1;%text file indices are
0-based, matlab is 1-based
I don't know where to get the left cuneus ROI, perhaps someone else can
help (is it in one of our provided label files?).
By the way, if you would reply to these emails while including the text of
the previous email (most email clients' reply buttons will do this
automatically by default), it would be easier to follow the thread of what
you are wanting to do (including for people who might find your first email
a year from now through a web search, and want to find all of the follow-up
emails that have the more detailed answers).
Tim
On Thu, Feb 19, 2015 at 3:30 PM, Peka Savayan savay...@umn.edu wrote:
Thank you for your answer, Timothy!
I use Matlab.
Can you get the time series for the Left Cuneus, please?
Thank you for your time and efforts.
Best wishes,
Peka
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