Dear FSL experts,
Thanks so much for your great contribution to FSL!
Now I am self-learning FSL software. I am struggling with three questions for some days and I cannot find them out. Could anybody help me solve them when available? I would very appreciate it.
The first one: how can I calculate the percentage of the abnormal voxels for a certain metric map of the whole brain if I want to compare MS(multiple sclerosis) patients with normal controls? Do I need to use another software to derive the percentage? If not, how can I get the percentage with FSL?
The second one: I have already finished all the TBSS steps and get the spatial distribution of the significant WM tract(MS vs NC), but I don't know how to label the significant WM tracts accurately/how to identify the name of the abnormal regions/tracts/clusters. I tried to use JHU-ICBM atlas, but I don't know how to use the atlas correctly.
The third one: I want to focus on NAWM(normal-appearing WM), but for MS patients, there are so many lesions. So how can I remove lesions? Could I use FSL remove lesions to get NAWM? Similarly, I also want to do ROI analysis for normal-appearing corpus callosum, then how can I remove the T2 lesions in corpus collasum so that I can avoid the influence of lesions?
Thanks so much.
Best.
baixiong
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