Update / consolidation on this issue:
I believe the issue is with how 3dROIstats is handling surface annotation datasets (or this surface annotation in particular).
I have checked the dataset created from FSread_annot, and everything looks to be in order. The regions are colorized as they should, and each node has a label that corresponds to freesurfer's "annotation value": (B * 256^2) + (G * 256) + (R) (which is why the values are so big).
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freesurfer.net]
While the image looks like a small number of regions relative to 200 per hemi, the LUT varies the colors but 1 at a time, thus giving each of the 200 regions a unique annotation value.
However, the output from 3dROIstats is still confusing. I am only getting 39 columns in the left hemisphere, whereas I should be getting 201. If 3dROIstats was averaging over the regions that are similarly colored in the image in my previous post then I should be getting 57 columns of timeseries.
The expected behavior of 3dROIstats, based on my previous experience, is that if you have a region with a label (eg 5193422 - a surface annotation value corresponding to r: 206 g: 62 b: 79), then 3dROIstats would have a corresponding Mean_5193422 column.
Also, the output labels of 3dROIstats are still confusing (eg Mean_XXXX). Here are the column names I'm getting:
Mean_-32442 Mean_-32186 Mean_-31930 Mean_-30854 Mean_-29577 Mean_-27418 Mean_-27417 Mean_-27162 Mean_-26625 Mean_-26369 Mean_-26113 Mean_-25782 Mean_-25526 Mean_-13269 Mean_-13013 Mean_-1828 Mean_-257 Mean_-2 Mean_-1 Mean_256 Mean_257 Mean_511 Mean_17Networks_LH_VisPeri_ExStrSup_1 Mean_4728 Mean_4984 Mean_10505 Mean_12300 Mean_12935 Mean_12936 Mean_13191 Mean_13505 Mean_15044 Mean_15045 Mean_15300 Mean_16077 Mean_16078 Mean_16333 Mean_30208 Mean_30464
Of note:
- none of those numbers are annotation or node label values.
- Many of the numbers are negative
- There is a weird random string in there (Mean_17Networks_LH_VisPeri_ExStrSup_1)
- I have no idea how 39 regions corresponds to the annotation file
This might have something to do with line 587 in 3dROIstats
AFNI_get_dset_val_label(mask_dset, (double)(i - 32768), sklab);
I'll keep looking, but if anyone has thoughts let me know.
