I see the problem now, the mask creation has failed. This is only an issue with 5.0.6 as it now expects the structural image and the 're-form' image to have been BETed by the user before processing (in the past this was done internally, but that didn't allow for optimised brain extraction to be performed in difficult cases). My apologies, I should have already updated the tutorial to reflect this - I have now done so and hopefully the new instructions will work for you.
Michael
On 20 Jan 2014, at 23:56, SUBSCRIBE FSL Anonymous <[log in to unmask]> wrote:
> Michael,
>
> Tutorial data:
>
> When I review the mask.nii.gz file (in the native_space directory) there is no mask. There is only a binary image with mainly 1's and very few voxels with a value of 0 (also, there is no struct_space directory generated). I have listed the steps that I used for the tutorial data below.
>
> Steps for data_pcasl
>
> 1. asl_file --data=data_pcasl/asl_raw_data --ntis=5 --ibf=rpt --iaf=tc --diff --mean=pcasl_diffdata
>
> 2. oxford_asl -i pcasl_diffdata -c data_pcasl/calibration_head --tis 1.6,1.8,2.0,2.2,2.4 -o ex2_2 --bolus 1.4 --bat 0.7 --t1 1.3 --t1b 1.66 --artoff --fixbolus --spatial --casl -s data_pcasl/struc --regfrom data_pcasl/asl_raw_data
>
> I end up with the same results with my raw data as well (however, I need to make sure I can accurately process the tutorial data before I move on to my raw data).
>
> Would you recommend I try to reference my own M0.nii.gz binarized mask using the -m function? If not, would you have any additional suggestions?
>
> Thank you for your help!
>
> Cheers,
>
> Nate
>
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