Hi - you need to add commands into the script to copy those files into the SIENAX working directory.
Cheers.
On 12 Oct 2011, at 06:47, Martin M Monti wrote:
> 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]
>
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