Extra ROI Variable in HO Atlas

[mnarayan]

According to the documentation, you should have 110 rois for this parcellation. However the actual dataset has an extra variable, I suspect variable 83 which does not seem to correspond to any legitimate cortical or subcortical region. The nifti atlas provided in the documentation suggests that 83 corresponds to two seemingly arbitrary voxels.

Also note that the documentation for many of the atlases do not provide ROI label files.

Harvard-Oxford (HO): The HO atlas distributed with FSL is split into cortical and subcortical probabilistic atlases. A 25% threshold was applied to each of these atlases and they were subsequently bisected into left and right hemispheres at the midline (x=0). ROIs representing left/right WM, left/right GM, left/right CSF and brainstem were removed from the subcortical atlas. The subcortical and cortical ROIs were combined and then fractionated into functional resolution using nearest-neighbor interpolation. [Atlas][Labels]

[mnarayan]

Here ho_masks is the nifti file containing the roi masks.

>> unique(ho_masks.img)'

ans =

  Columns 1 through 22

      0     10     11     12     13     17     18     26     49     50     51     52     53     54     58    101    102    201    202    301    302    401

  Columns 23 through 44

    402    501    502    601    602    701    702    801    802    901    902   1001   1002   1101   1102   1201   1202   1301   1302   1401   1402   1501

  Columns 45 through 66

   1502   1601   1602   1701   1702   1801   1802   1901   1902   2001   2002   2101   2102   2201   2202   2301   2302   2401   2402   2501   2502   2601

  Columns 67 through 88

   2602   2701   2702   2801   2802   2901   2902   3001   3002   3101   3102   3201   3202   3301   3302   3401   3402   3455   3501   3502   3601   3602

  Columns 89 through 110

   3701   3702   3801   3802   3901   3902   4001   4002   4101   4102   4201   4202   4301   4302   4401   4402   4501   4502   4601   4602   4701   4702

  Columns 111 through 112

   4801   4802

>> find(ho_masks.img==3455)'                                                             

ans =

       82980       87985

[meestabig]

Has this been resolved? I am stuck on the same issue and there's no reply nor approval to post in the Abide Preprocessed google forum.

[mnarayan]

I simply get rid of the offending ROI number 83 in downstream analyses.

[meestabig]

Thanks a lot!