That seems reasonable, however I would use the matlab CIFTI tools to wrap the 
CIFTI to GIFTI conversion and loading into matlab all in one step:

https://wiki.humanconnectome.org/display/PublicData/HCP+Users+FAQ#HCPUsersFAQ-2.HowdoyougetCIFTIfilesintoMATLAB?

Matt.

From: 
<hcp-users-boun...@humanconnectome.org<mailto:hcp-users-boun...@humanconnectome.org>>
 on behalf of Mohammadhesam Ahmadian 
<ahmadian.mhe...@gmail.com<mailto:ahmadian.mhe...@gmail.com>>
Date: Saturday, August 11, 2018 at 5:09 AM
To: "hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>" 
<hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>>
Subject: [HCP-Users] HCP_MMP1.0 parcellation of the Resting State fMRI 
FIX-Denoised (Compact) data using workbench.exe

Dear all,


We have already downloaded the data of Resting State fMRI FIX-Denoised 
(Compact) of 100 unrelated subjects. We wanted to do some analysis on these 
data (rfMRI_REST1_LR_Atlas_hp2000_clean.dtseries.nii), so we used the following 
command (for the first session of the first subject):

wb_command.exe -cifti-parcellate 
rfMRI_REST1_LR_Atlas_MSMAll_hp2000_clean.dtseries.nii 
Q1-Q6_RelatedValidation210.CorticalAreas_dil_Final_Final_Areas_Group_Colors.32k_fs_LR.dlabel.nii
 COLUMN glasser_100307_s1_parcellation.ptseries.nii

And then we used the following command on the result of the previous command:


-cifti-convert -to-gifti-ext


Which gave a '.gii' output and then read it with the gifti command in Matlab 
and it gave a 360 by 1200 matrix which is dimensionally right, but we were 
wondering if what we have done is correct and has given the correct result.


Thanks in advance,


Hesam

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