wb_command GIFTI output incompatible with MATLAB gifti package

[Madeline Peterson]

Hi, 

I am looking for guidance on an issue reading GIFTI files into MATLAB using the gifti package (https://github.com/ThomasYeoLab/CBIG/blob/08a7c025edc634660872ab136b4212d68106152f/external_packages/matlab/default_packages/cifti-matlab/%40gifti/gifti.m). The error is " [GIFTI] Invalid object construction.". 

GIFTI conversion

The GIFTI files were created by taking HCP dtseries cifti files and converting them to fsaverage6 space through the process described in the HCP Users FAQ #9. The specific command used was: wb_command -metric-resample ${DATA_DIR}/${sub}/sub-${sub}_tstat1_RH.shape.gii ${FSLR_DIR}/fs_LR-deformed_to-fsaverage.R.sphere.32k_fs_LR.surf.gii ${FSAVERAGE_DIR}/fsaverage6_std_sphere.R.41k_fsavg_R.surf.gii ADAP_BARY_AREA ${DATA_DIR}/${sub}/sub-${sub}_tstat1_R_fsaverage6.func.gii -area-metrics ${FSLR_DIR}/fs_LR.R.midthickness_va_avg.32k_fs_LR.shape.gii ${FSAVERAGE_DIR}/fsaverage6.R.midthickness_va_avg.41k_fsavg_R.shape.gii

The files were then binarized with the following command: wb_command -metric-math '(x > 0)' ${DATA_DIR}/${sub}/sub-${sub}_FS6_lang_bin_rh.shape.gii -var x ${DATA_DIR}/${sub}/sub-${sub}_tstat1_R_fsaverage6.func.gii

MATLAB error

Before reading in the file into MATLAB, I was able to successfully view the file in wb_view and it appeared as expected. In MATLAB, I received the error: " [GIFTI] Invalid object construction." The path to the file was correct, and the read/write permissions were set appropriately. In another effort, I attempted to save the GIFTI files as BASE64 Binary using -gifti-convert but this resulted in the same error. 

Interestingly, a similar (but unresolved) issue was also noted on NITRC: https://www.nitrc.org/forum/forum.php?set=custom&forum_id=254&style=nested&max_rows=75

Example file

To replicate the error, I have uploaded an example file to Github: https://github.com/peter3200/trial_repo/blob/master/sub-100206_tstat1_L_fsaverage6.func.gii

Any suggestions or insights would be highly appreciated! Thank you for your time and help!

Sincerely,

Maddy 

[Glasser, Matt]

Maybe try it with the latest standalone GIFTI package?  Or keep the data in CIFTI and load it in with the cifti-matlab toolbox that does not depend on GIFTI (https://github.com/Washington-University/HCPpipelines/tree/master/global/matlab/cifti-matlab).  This sounds like it is most likely a bug in the GIFTI matlab toolbox. 

 

Matt.

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[Rosen, Burke]

GIfTI 2.0 (https://www.gllmflndn.com/software/matlab/gifti/ ) can read your example file. 

-Burke

To view this discussion on the web visit https://groups.google.com/a/humanconnectome.org/d/msgid/hcp-users/5DEC1328-A24D-437A-8E22-83DE20A6FA93%40wustl.edu.

[Madeline Peterson]

Thank you both for your suggestions! Using GIfTI version 2.0 did the trick. 

Thanks again, 

Maddy