ASL oxford help

Emma Tinney — Tue, 27 Sep 2022 13:20:11 GMT

Hi all,

I am getting an error for ALS_oxford. It seems like it cant find the appropriate files. Below is my command that I used and then the output. It continues to run throughout and outputs the images correctly but I'm not sure why I am getting these errors.
"oxford_asl -i ASL.nii -o oxasl_voxel --spatial --iaf=tc --ibf=tis --tis 0.2,0.7,1.2,1.7,2.2 --rpts=12,12,12,20,30 --casl --bolus 1.5 -c aslcalib --tr 6.00 --te=19 --slicedt=0.0511 --sliceband=6 --fixbolus --cmethod=voxel --fmap=my_AP_PA_fieldmap_rads.nii --fmapmag=my_fieldmap_mag.nii --fmapmagbrain=my_fieldmap_mag_brain.nii --echospacing=0.000569995 --pedir=y --mc -m eroded_mask.nii"
Input file is: /tmp/fsl_5j8ht7_ox_asl/pwi
Creating output directory
Registration FINAL stage (BBR)
Image Exception : #63 :: No image files match: /tmp/fsl_PGSxuJ_asl_reg/low2high_final_fast_wmseg
terminate called after throwing an instance of 'std::runtime_error'
what(): No image files match: /tmp/fsl_PGSxuJ_asl_reg/low2high_final_fast_wmseg
/shared/centos7/fsl/6.0.3-cuda9.1/bin/epi_reg: line 329: 39958 Aborted $FSLDIR/b
in/fslmaths ${vout}_fast_wmseg -edge -bin -mas ${vout}_fast_wmseg ${vout}_fast_wmedge
cp: cannot stat '/tmp/fsl_5j8ht7_ox_asl/asl2struct.mat': No such file or directory
Registering fieldmap to structural
Image Exception : #63 :: No image files match: /tmp/fsl_5j8ht7_ox_asl/struc_bet
Image Exception : #22 :: Failed to read volume /tmp/fsl_5j8ht7_ox_asl/struc_bet

Display of ASL toolbox

Krystal Yau — Thu, 19 May 2022 8:46:13 GMT

Dear expert,

Would you please kindly advise on how to resize the window display to make it readable? Some words are off the range.

Thanks for your attention!

Sincerely,
Krystal

Welcome to Open-Discussion

Christian Haselgrove — Mon, 17 Aug 2009 21:12:56 GMT

Welcome to Open-Discussion

NITRC ASL data processing tool box Forum: open-discussion

ASL oxford help

Display of ASL toolbox

Welcome to Open-Discussion