Dear Robert,
The answer to your first question is here:
https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=fsl;10b2ef5c.1203
For the second question, you can use fslstats to extract the volume of ROIs
and use sienax to get a scaling measure, equivalent to TIC (you can apply
the scaling to the standard brain's TIC). We do not provide further statistical
tools for these analyses though, as it is standard statistics on small sets of
numbers (not massive voxel-based stats) and so we recommend you use
a standard stats package (e.g. SPSS) for the analysis of the volumetric data.
All the best,
Mark
On 7 Jun 2012, at 06:03, Robert S.C. Amaral wrote:
> Hi all,
>
> I have a couple of questions about FSLview.
>
> First, I am creating rois using FSLview (3.1.2) via FSL (4.1.4) on pc (64bit) running off of ubuntu (32bit). I have my original image in .nii format converted from dicom however when I attempt to save my mask it will not let me save into .nii, just .hdr. there seems to be no way around this.
>
> Strangely, if I open my terminal and run fsl from there and consequently run fslview (still locally) it allows me to save in .nii.gz. does anyone have any guesses as to what is occurring or how I can save rois straight to .nii?
>
> Second, I later plan to do volumetric analysis of these rois, can FSL do this, if not, can anyone recommend any specific programs? Specifically, I will need to obtain volumes for each of my ROIs (i.e., how many voxels within each ROI) and I will also need to obtain a measure of total intracranial capacity (TIC).
>
> Thank you for any help,
> Robert
>
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