Hi,
If you have a look at the contents you'll see problems in three of the
basic first.e* files - the ones for structures 1, 9 and 17. These are
the left and right accumbens and the brainstem. The messages for
the accumbens indicate that FIRST found a very small structure and
could not find any interior voxels. Is your resolution poor in these
images? The error for the brainstem showed that it crashed, which
can happen if you FOV is too small (doesn't go low enough to cover
the whole brainstem).
If you are not particularly interested in any of these structures, then
I suggest you re-run FIRST without these structures, which should work.
You can do this just by adding:
-s
L_Amyg
,L_Caud
,L_Hipp
,L_Late
,L_Pall,L_Puta,L_Thal,R_Amyg,R_Caud,R_Hipp,R_Late,R_Pall,R_Puta,R_Thal
to your run_first_all command.
If you are interested in the accumbens or brainstem then we will
need to investigate your images further.
All the best,
Mark
On 29 Jan 2010, at 15:06, Adil Javed wrote:
> Than you so much for your help.
> Here are the *.e* files from the First logs directory. I actually
> don't even see the *_origsegs.nii.gz file. Just the original T1
> image, *.bvars,*.vtk, *com, *std_sub.mat, *std_sub.nii.gz, and logs
> directory. That's it.
> again, many thanks.
> aj
>
>
> --- On Fri, 1/29/10, Mark Jenkinson <[log in to unmask]> wrote:
>
>> From: Mark Jenkinson <[log in to unmask]>
>> Subject: Re: [FSL] problem with FIRST
>> To: [log in to unmask]
>> Date: Friday, January 29, 2010, 2:09 AM
>> Hi,
>>
>> The recommended way of getting the volume is to use
>> fslstats on the
>> *_firstseg.nii.gz volume, as described in:
>> http://www.fmrib.ox.ac.uk/fsl/first/index.html
>>
>> If you do not get this output image then that is a serious
>> problem
>> and needs to be fixed before trying anything else.
>>
>> Can you please look at the *.e* files in your log directory
>> and
>> send us the contents (giving the name of the file it comes
>> from)
>> so that we can try and diagnose your problem?
>>
>> One thing we have found before is that for images with a
>> limited
>> FOV, the brainstem and/or cerebellum segmentation can
>> cause
>> problems. If this is the case you should be able to
>> see it in the
>> individual segmentation outputs (the *_origsegs.nii.gz
>> file).
>> Have you checked this file? Do the segmentations all
>> look correct?
>> And have you checked that the registrations have all
>> worked?
>>
>> Let us know the answers to the above questions.
>> All the best,
>> Mark
>>
>>
>> On 29 Jan 2010, at 07:24, Adil Javed wrote:
>>
>>> Hi,
>>> I am running the script run_first_all on my T1
>> images. This script does not always generates the
>> all_fast_firstseg.nii.gz file, which I need to do the
>> volumetric analysis of subcortical structures. It does
>> generate all the other .vtk, bvars, and .com files.
>>> Ant ideas why this happens?
>>>
>>> Also, can I use the .vtk file to get the volume info?
>>> for example: first_utils --meshToVol -m mesh.vtk -i
>> t1_image.nii.gz -l fill_value -o output_name
>>>
>>> and then get the volume by:
>>> fslstats output_name -l 16.5 -u 17.5 -V ?
>>>
>>> I tried volume analysis using both .vtk and
>> all_fast_firstseg.nii.gz files on one of the subjects, but
>> these two methods five different results. not sure why this
>> ocurs?
>>>
>>> Any ideas?
>>>
>>> Tx so much for your help,
>>>
>>> aj
>>>
> <log.zip>
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