Hello, I was curious if anyone had used the pre-threshold masking option in fsl's feat to mask by a specific ROI? When I load the output from an analysis of this type it looks no different from an unmasked analysis, regardless of which file I load (zstat, thresh_zstat, etc). Any help would be greatly appreciated! Kim
That one still looks unmasked as well. I know the mask has to be in the same space (MNI or functional depending on what level you're doing the masking at) so since I'm doing it at the 3rd level, I tried a functional ROI that I had drawn from a previous 3rd level analysis and it is still not working. Am I maybe missing something else about the type of mask you can use?
Yep...it is a nii.gz file and when I load it in showsrs2 on matlab the mask is all 1 and everything else is 0. I've also tried it with an .hdr file and that didn't work either.
so i just tried it with a mask i made via fsl .. and everything labeled "thresh_zstat" (or rendered_thresh_zstat) is masked by my input roi (but only the thresh_zstat ... no tstat,etc)
check in your cope1.feat/logs folder for "feat4_post" ... that is the log file that shows if the masking was done.
any line that looks like this shows the masking step: /usr/local/packages/fsl/bin/fslmaths thresh_zstat2 -mas /mnt/users/petty/selye/data2/MemSupp.01/Analysis/fsl/3rdLevel/look.gfeat/10mm_pMask.nii.gz thresh_zstat2
Sweet! It didn't look like it had run in earlier attempts...perhaps the ROIs weren't in the right space after all or something. So, I redrew the ROI of choice and now I think it might finally be working! Thanks so much for your help!!!
Pre-threshold masking in fsl
Posted - Mar 12 2009 : 12:57:47 PM
