HI Mark, so I was able to create skull masks as you suggested. Now I'm trying to run sienax on the *_brain and *_brain_skull images I've manually created. I opened up the sienax script, commented out the first line of "extract brain": bet ${I} ${I}_brain -s -m $betoptions As I said, I created two images one called T1_brain.nii,gz and T1_brain_skull.nii.gz, but somehow the script doesn't seem to find them. So when I launch the edited sienax script (which of course I launch with " > sineax T1.nii.gz") I get the following error: ***ERROR: (nifti_image_read): failed to find header file for image 'T1_brain' Any suggestion? best Martin On 23/09/2011 09:49, Mark Jenkinson wrote: > Yeah - or maybe even less. > I'm not sure what will work best, so have a play and see > how you get on. > > All the best, > Mark > > On 23 Sep 2011, at 17:44, Martin M Monti wrote: > >> Hi Mark, >> >> thank you. Just to be clear, by "subtracting a proportion" you mean something like subtracting a 70% (or so) version of the betted brain? As in: >> >> fslmaths t1_brain.nii.gz -mul 0.7 t1_brain_70 >> fslmaths t1.nii.gz -sub t1_brain_70.nii.gz t1_4skull_estimation >> >> thank you >> >> martin >> >> >> On 9/23/2011 5:05 AM, Mark Jenkinson wrote: >>> Dear Martin, >>> >>> What you are suggesting all sounds sensible. >>> The one thing that might prove tricky is the skull estimation. >>> You need to avoid there being an "edge" of intensity change >>> right at the brain edge, or otherwise it won't find the skull and >>> will be normalising to the brain size, which is not what you >>> want for determining atrophy. >>> >>> So try just subtracting a proportion of the brain from the >>> original image, just to dark this boundary but leave the skull/scalp >>> boundary as a stronger one. Try that and run BET on it and see >>> if you are getting a decent result for the skull/scalp points. Note >>> that they are never perfect but as long as over half are on the >>> correct surface then things should work OK. The best way of >>> telling whether it is working well is to look at the registration outputs >>> and check that the skull/scalp is well aligned. If not, then it will >>> still require some fixing. >>> >>> I hope this helps. >>> All the best, >>> Mark >>> >>> >>> >>> On 22 Sep 2011, at 22:28, Martin M Monti wrote: >>> >>>> Hi, I am working with sienax to get some volumetric info on a group of patients, but the brains are so pathological that automatic bet and registration are really thrown off. Indeed, for many of these patients I had to manually go in and delete bits of skull/eyeballs/neck that I just can't seem to remove with bet. >>>> >>>> Now, I do have (manually adjusted) brain extracted images for each of these patients, so I am trying to see if I can use them to work-aroud the sienax script. This would require 2 things: >>>> >>>> 1) generate a skull image (which unfortunately I do not have..). Is there a way I could generate them from the bet-ted brain (e.g. if I subtracted the bet-ted brain from the original image, would that be usable for the purposes of sienax as a *_skull.nii.gz image)? >>>> 2) Once I have _brain and _skull images I should be able to comment out the bet command in the sienax script and run it from there? >>>> >>>> Does it sound possible? Is there a better/different way to work with these "unbettable" brains? >>>> >>>> cheers >>>> >>>> Martin >>>> >>>> >>>> >>>> -- >>>> Martin M Monti, PhD >>>> Assistant Professor >>>> 7461E Franz Hall >>>> UCLA Department of Psychology >>>> BOX 951563, >>>> Los Angeles, CA 90095-1563 >>>> 310-825-8546 >>>> http://montilab.psych.ucla.edu >>>> http://faculty.psych.ucla.edu/directory/faculty.php?id=187&area=3<http://faculty.psych.ucla.edu/directory/faculty.php?id=187&area=3%20> >>>> >>>> “Well! I’ve often seen a cat without a grin,” thought Alice, >>>> “but a grin without a cat! It’s the most curious thing I ever >>>> saw in my life!” [Lewis Carroll, Alice in Wonderland] >>>> >> -- >> Martin M Monti, PhD >> Assistant Professor >> 7461E Franz Hall >> UCLA Department of Psychology >> BOX 951563, >> Los Angeles, CA 90095-1563 >> 310-825-8546 >> http://montilab.psych.ucla.edu >> http://faculty.psych.ucla.edu/directory/faculty.php?id=187&area=3<http://faculty.psych.ucla.edu/directory/faculty.php?id=187&area=3%20> >> >> “Well! I’ve often seen a cat without a grin,” thought Alice, >> “but a grin without a cat! It’s the most curious thing I ever >> saw in my life!” [Lewis Carroll, Alice in Wonderland] >> -- Martin M Monti, PhD Assistant Professor 7461E Franz Hall UCLA Department of Psychology BOX 951563, Los Angeles, CA 90095-1563 310-82*5-8546* http://faculty.psych.ucla.edu/directory/faculty.php?id=187&area=3 “Well! I’ve often seen a cat without a grin,” thought Alice, “but a grin without a cat! It’s the most curious thing I ever saw in my life!” [Lewis Carroll, Alice in Wonderland]