2: Check Registrations and Segmentations

Registration errors

In the slicesdir_T1toMNI, open the "index" web page. This shows the outline of the MNI brain traced onto the rigid-body registered T1 file. Look only for gross errors; different brain shapes will mean the outlines rarely line up perfectly.

If there is an error, make sure the manual T1 registration in the T1preprocess subfolder has been done. If the misregistration persists, remove the subject from the analysis (create a new set and re-run).

Segmentation errors

First note that a registration error means the segmentation will fail (because the segmentations are based in part on probabilities in MNI space).

In the "slicesdir_segmentations" folder, open the "index" web page. This shows the outline of structures on  the T1 for each study. Look through for gross errors; it can be easiest to pick one or two slices, and just scroll down through those.

If there is an error, it's probably simplest to remove the subject from the analysis (create a new set and re-run).

Checking individual files

The subject folders in FSL used for segmentation contain the T1, a nifti file with the segmentations, and a folder with logs including errors. The error files have "e" in them, and if there are none then everything ran ok. However, even if there are some errors the segmentations can still be ok. To check, open the T1 file in mricron and overlay the segmentations.

You might want to choose a different colormap. The structures have different values (CMA Standard Labels) which you can see in the bottom-left of the mricron window.

CMA Labels

10 Left-Thalamus-Proper 40
11 Left-Caudate 30
12 Left-Putamen 40
13 Left-Pallidum 40
16 Brain-Stem /4th Ventricle 40
17 Left-Hippocampus 30
18 Left-Amygdala 50
26 Left-Accumbens-area 50
49 Right-Thalamus-Proper 40
50 Right-Caudate 30
51 Right-Putamen 40
52 Right-Pallidum 40
53 Right-Hippocampus 30
54 Right-Amygdala 50
58 Right-Accumbens-area 50