Run an ROI analysis with a custom atlas

[tayebeh ebrahimi]

Dear ExploreASL experts,

I would like to quantitatively measure the CBF of some patients by running an ROI analysis with Harvard Oxford Atlas (HO_CONN) and then create a colormap of CBF values. 

According to the ExploreASL_QC_WalkThrough, I must pick a data type as the entrance for x.S.InputDataStr. But I do not realize which data I must pick. I mean, shall I pick CBF.nii obtained after running ExploreASL function which is located in the ASL folder?

or shall I pick qCBF_sub-001_ASL_1.nii located in population folder?

Your help will be appreciated. 

Best Regards,

Tayyebe.

[Jan Petr]

Hi Tayyebe,

To obtain the quantitative values in the HO atlas, you simply need to go to the analysis folder for your study in 'Population/Stats' there should be automatically created tables with CBF values per region. Check for the file name to select the correct file with HO, CBF, mean or median, PVC0.

For the individual color maps, you can indeed either pick the CBF.nii in the ASL folder (that's the native space), or the qCBF in the population folder (the same map in the standard space). This should give you the CBF colormap, or do you want colormap where each HO region is assigned one color?

best,

Jan