PhysIO toolbox aCompCor denoising in subject space

[gracehsu]

Dear Tapas developers,

Thanks for developing this toolbox which is very handy. :) Currently, I have preprocessed rsfMRI data by SPM12 (i.e., coregister (func >> anat), realignment and slice timing). However, we didn't do normalisation coz we want to keep it in subject space. Does PhysIO toolbox allows non-MNI space?

I used *ar.nii for fMRI Time Series Files(s), and *c2 & *c3 for Noise ROI Image File(s). And I chose "Yes" for Force Coregister. Then I got some errors as below. Is there anyway to run aCompCor step in subject space? Thank you in advance.

SPM12: spm_reslice (v7141) 17:31:54 - 23/05/2022

Completed : 17:31:55 - 23/05/2022 23-May-2022 17:31:55 - Done ‘Coregister: Estimate & Reslice’ 23-May-2022 17:31:55 - Done 23-May-2022 17:31:56 - Failed ‘TAPAS PhysIO Toolbox’ Reference to non-existent field ‘cm’. In file “/usr/local/spm12/toolbox/PhysIO/code/model/tapas_physio_create_noise_rois_regressors.m” (???), function “tapas_physio_create_noise_rois_regressors” at line 186. In file “/usr/local/spm12/toolbox/PhysIO/code/tapas_physio_main_create_regressors.m” (???), function “tapas_physio_main_create_regressors” at line 360. In file “/usr/local/spm12/toolbox/code/tapas_physio_cfg_matlabbatch.m” (???), function “run_physio” at line 1661.

[benoitberanger]

Hello @gracehsu,

Does PhysIO toolbox allows non-MNI space?

TAPAS/PhysIO does not depend on the space it-self (native vs normalized). The noiseROI part checks the geometry = orientation(header) + gridsize(resolution). They need to be identical : or you let tapas_physio_create_noise_rois_regressors perform the coregister & reslice, or you provided masks already with the same geometry.

Reference to non-existent field ‘cm’.

This error looks like this one : #187 #117 Could you try the same solution : physio.verbose.level = 1; ?

Best, Benoît

[gracehsu]

Thank you so much Benoît! I tried verbose.level = 1, and it worked!