On 3 Jul 2018, at 08:45, Shirin Davies <[log in to unmask]> wrote:
Hi thank you for your email.
I used fslview to make the mask and then fslmaths to binarize it.
The mask is in nifti and so are my 4D images.
my problem is that my mask is in a different space (the standard space) and my 4D fMRI data in another. This seems to be the reason I can not use the mask in pre-thresholding masking in post stat step of FEAT.
Is there a command that would change the orientation of the mask?
Many thanks,
Shirin
On Mon, Jul 2, 2018 at 3:41 PM, Matthew Webster <[log in to unmask]> wrote:
Hello,Are you using FSLview or FSLeyes to draw the mask - if you are using FSLview we would strongly recommend switching to FSLeyes as it has many improved features. You can use ( e.g. )
fslmaths <inputFile> <outputFile>
To quickly convert an analyze file to NIFTI, however this will not preserve the original orientation data from the original source image (on which the mask was drawn ) - you can use fslcpgeom to copy this.
Kind RegardsMatthew
--------------------------------
Dr Matthew Webster
FMRIB Centre
John Radcliffe Hospital
University of Oxford
On 5 Jun 2018, at 17:49, Morganne Manuel <[log in to unmask]> wrote:
I am new to FSL so I don’t know if this message will have enough detail.
I am trying to make a lesion mask by manuall tracing the lesions. After I make the mask when I save the file it saves as an img and hdr file. How do I get it to save as a nii file?
Morganne
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Shirin Davies, MSci, MSc MedPhysMRI Scientist,BRAIN Unit,Cardiff University Brain Research and Imaging Center &Cardiff and Vale University Health Board
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