Hi,
Good - this is the correct file.
If you look at the image it contains all structures, each with a
unique label number as specified in:
http://www.fmrib.ox.ac.uk/fsl/first/cma_subcortical_label.html
In order to calculate the volume of one structure (e.g. left-caudate =
11)
you do:
fslstats result_all_th4_first.nii.gz -l 10.5 -u 11.5 -V
All the best,
Mark
On 23 Jun 2009, at 05:42, Nickolas Papanikolaou wrote:
> Dear Mark,
>
> I get only a file like outputname_all_th4_first.nii.gz. Now if I run
> the following:
>
> fslstats result_all_th4_first.nii.gz -V
>
> I get a single number which I presume corresponds to the total
> volume of the segmented structures. I would like to have each
> individual volume calculated. Is that possible?
> Thanks for your support.
>
> All the best
> Nick
>
> On Jun 22, 2009, at 10:09 PM, Mark Jenkinson wrote:
>
>> Hi,
>>
>> Do you have any files like *_firstseg.nii.gz or *_origsegs.nii.gz ?
>> These should be the images that you will calculate the volume
>> from. Note that they do not start with the structure names as
>> they contain all the structures in them.
>>
>> If you do not have these files please look at the *.e* files in
>> the log directory and see if there are any error messages.
>>
>> All the best,
>> Mark
>>
>>
>> On 22 Jun 2009, at 19:49, Nick Papanikolaou wrote:
>>
>>> Dear Mark,
>>>
>>> Thanks for your fast response. I tried the run_first_all and all I
>>> get is some .vtk and .bvars
>>> files. Any idea how can I proceed to calculate the volumes?
>>>
>>> Nick
>>>
>
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