open-discussion > ASL oxford help
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Sep 27, 2022 01:09 PM | Emma Tinney
ASL oxford help
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
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