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One option is to feed the structural image into oxford_asl and let it extract the ventricles for you and create the relevant mask. This isn’t always successful - check what results you get - otherwise you need the transformation of the ASL data to the structural image (either created by oxford_asl or using flirt) invert this and then transform the CSF PVE image into the ASL data space and then threshold at a high level >0.95 to get pure CSF. oterhwise you could generate your own manual CSF mask.

Michael


On 22 Jun 2016, at 00:20, shi yao wang <[log in to unmask]> wrote:

Also, how can I make calibration map using current ASL, structure image?

thanks
Lawrence 

On Tue, Jun 21, 2016 at 12:10 PM, shi yao wang <[log in to unmask]> wrote:
Hello Michael, 
Thank you for your reply!
How could I keep similar resolution? I didnot find any options for keep resolution in FAST. 


Thanks
Lawrence

On Tue, Jun 21, 2016 at 6:05 AM, Michael Chappell <[log in to unmask]> wrote:
When you load the CSF segmentation are you doing this as the original high res segmentation from FAST. The GUI only provides the option to give a CSF mask in the same space as the ASL image and that might be where the error comes from.

Michael


On 20 Jun 2016, at 18:26, SUBSCRIBE FSL Anonymous <[log in to unmask]> wrote:

Dear FSL experts,
I am using ASL_GUI to analyze pASL data.

However, it showing flowing error message:

Input file is: /mnt/hgfs/share_fsl/FSL_ASL/VCI_149/native_space/perfusion
Tissue reference is: csf
M0:380.73000000000000000000
ASL_calib - DONE.
Image Exception : #3 :: Attempted to multiply images/ROIs of different sizes
terminate called after throwing an instance of 'RBD_COMMON::BaseException'
/usr/local/fsl/bin/asl_calib: line 701: 23976 Aborted                 (core dumped) fslmaths $temp_calib/calib -mas $mask $temp_calib/calib

I guess it maybe the problem of reference tissue mask in the calibration section.
I use FAST to segmentation GM/WM/CSF, and load seg_2.nii.gz (CSF).

Any suggestions?
Appreciate!!

Lawrence

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Michael Chappell MEng DPhil
Associate Professor, Institute of Biomedical Engineering, University of Oxford.
Director of Training, EPSRC-MRC CDT in Biomedical Imaging
Governing Body Fellow, Wolfson College, Oxford.
Research Fellow, FMRIB Centre