call when you are done
On Jul 11, 2010, at 8:38 AM, Rolf Heckemann wrote:
> Since you are sending this to the FSL list, even though you are
> addressing us as "SPM users", I will assume you are looking for a
> suggestion based on FSL.
>
> If you have a label image (i.e. an image volume that defines ROIs by
> assigning nominal values to the voxels that belong to them) it is
> straightforward to calculate the ROI volumes with fslstats. Example:
> if you have three ROIs labelled 1, 2 and 3 on a background of zeros,
> you can use the histogram feature:
>
> fslstats labelimage -h 4
>
> This lists the volume of each label in voxels, including background. Use
>
> fslstats labelimage -h 4 | nl -v 0
>
> to have the ROIs numbered in the output.
>
> To get the volume of an individual ROI in mm^3, use the volume option
> with thresholding. For ROI 2, use
>
> fslstats labelimage -l 1 -u 3 -V
>
> Without thresholding, -V will work for images defining a single ROI,
> independent of the values of the voxels within the ROI. That means you
> can use it for MR images where an ROI has been masked.
>
> Hope that helps.
>
> Rolf
>
>
> On 11 July 2010 12:04, Alexander Lebedev <[log in to unmask]> wrote:
>> Dear SPM users,
>>
>> Sorry for disturbing. Could you please advice me the best way (software)
>> to create and calculate ROI volumes?
>>
>> My task is to calculate volumes of
>> several CSF spaces.
>>
>> My tactics:
>>
>> 1. Segmentation in SPM (getting data for CSF);
>> 2. Starting MRICroN and combining my original (T1) data with segmented
>> image (in order to perform adequate navigation);
>> 3. Easily creating a VOI and...
>> getting stuck with it... because I have no idea what should I do
>> next (as far as I understood, all tools in MRICroN are for group
>> analysis)...
>>
>> Please, help me if it is possible...
>> Thank you beforehand!
>> --
>> Sincerely Yours,
>> Alexander Lebedev,
>>
>> I.P. Pavlov State Medical University,
>> 197022, Lev Tolstoy str. 6/8,
>> Saint Petersburg, Russian Federation.
>>
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