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,