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]