Apply other Atlas

[zhaopluseins]

Dear developer,

Thank you very much for providing such a great tool.

I would like to know how I can apply other Atlas to extract QSM values for ROIs . Should I modify the shell file in the function, or is it possible to extract them after the calculation is completed using other software?

Thank you for your time and assistance.

[vzachari]

Greetings,

There are a couple of ways to use additional ROIs with Ironsmith:

1. ATLAS/ROIs are in MNI space

    #Your mask in MNI space needs to be in $Subj/QSM/FreeSurf_QSM_Masks/MNI152_QSM
    singularity run -e --bind $OutFolder/$Subj/QSM/FreeSurf_QSM_Masks/MNI152_QSM \
    	$Path/Functions/QSM_Container.simg \
    	3dNwarpApply -source YOUR_MASK_IN_MNI_GOES_HERE.nii.gz \
    	  -master ${Subj}_freesurfer_brain_AL_Mag_MNI152+tlrc \
    	  -ainterp NN -iwarp -nwarp "anat.un.aff.qw_WARP.nii anat.un.aff.Xat.1D" \
    	  -prefix NAME_FOR_YOUR_MASK_IN_NATIVE_SPACE_GOES_HERE.nii.gz
   

2. ATLAS/ROIs are in native space

Align your ATLAS/ROIs with ${Subj}_freesurfer_brain_AL_Mag.nii.gz and resample the output to the QSM resolution/grid, then extract QSM values from your custom aligned/resampled ROIs.