mrconvert: [ERROR] unknown format for image "null"
Opened this issue · 2 comments
soichih commented
I am seeing the following error messager on 1.4 branch.
+ set -e
++ jq -r .diff config.json
+ DIFF=../5fb339585079852dfbdaf4e5/output/dwi.nii.gz
++ jq -r .bval config.json
+ BVAL=../5fb339585079852dfbdaf4e5/output/dwi.bvals
++ jq -r .bvec config.json
+ BVEC=../5fb339585079852dfbdaf4e5/output/dwi.bvecs
++ jq -r .anat config.json
+ ANAT=null
++ jq -r .ens_lmax config.json
+ ENS_LMAX=null
++ jq -r .imaxs config.json
+ IMAXS=16
++ jq -r .curvs config.json
+ CURVS=35
++ jq -r .num_fibers config.json
+ NUM_FIBERS=1500000
++ jq -r .min_length config.json
+ MIN_LENGTH=25
++ jq -r .max_length config.json
+ MAX_LENGTH=220
++ jq -r .tensor_fit config.json
+ TENSOR_FIT=null
++ jq -r .norm config.json
+ NORM=null
++ jq -r .do_prb2 config.json
+ DO_PRB2=true
++ jq -r .do_prb1 config.json
+ DO_PRB1=null
++ jq -r .do_detr config.json
+ DO_DETR=null
++ jq -r .do_dtdt config.json
+ DO_DTDT=null
++ jq -r .do_dtpb config.json
+ DO_DTPB=null
++ jq -r .do_fact config.json
+ DO_FACT=null
++ jq -r .fact_dirs config.json
+ FACT_DIRS=null
++ jq -r .fact_fibs config.json
+ FACT_FIBS=null
++ jq -r .premask config.json
+ PREMASK=null
+ rm -rf ./tmp
+ mkdir ./tmp
+ difm=dwi
+ mask=mask
+ anat=t1
+ echo 'Converting raw data into MRTrix3 format...'
+ mrconvert -fslgrad ../5fb339585079852dfbdaf4e5/output/dwi.bvecs ../5fb339585079852dfbdaf4e5/output/dwi.bvals ../5fb339585079852dfbdaf4e5/output/dwi.nii.gz dwi.mif --export_grad_mrtrix dwi.b -force -nthreads 8 -quiet
+ bet ../5fb339585079852dfbdaf4e5/output/dwi.nii.gz bet -R -m -f 0.3
+ mrconvert bet_mask.nii.gz mask.mif -force -nthreads 8 -quiet
+ mrconvert null t1.mif -force -nthreads 8 -quiet
mrconvert: [ERROR] unknown format for image "null"
mrconvert: [ERROR] error opening image "null"
real 0m16.051s
user 0m12.297s
sys 0m1.789s
soichih commented
The config.json fed to this was
"min_length": 25,
"max_length": 220,
"imaxs": 16,
"curvs": 35,
"num_fibers": 1500000,
"do_prb2": true,
"diff": "../5fb339585079852dfbdaf4e5/output/dwi.nii.gz",
"bvec": "../5fb339585079852dfbdaf4e5/output/dwi.bvecs",
"bval": "../5fb339585079852dfbdaf4e5/output/dwi.bvals",
"t1": "../5fb338ca5079859dd6daf4ca/5fae16596b11522ce4dfab76/t1.nii.gz",
soichih commented
I've updated "t1" to "anat" in the app registration. Now the App is running all the way to the end, but it looks like it's just skipping all tracking.
time="2020-11-19T17:55:52-05:00" level=warning msg="\"/run/user/1589653\" directory set by $XDG_RUNTIME_DIR does not exist. Either create the directory or unset $XDG_RUNTIME_DIR.: stat /run/user/1589653: no such file or directory: Trying to pull image in the event that it is a public image."
INFO: Using cached SIF image
+ set -e
++ jq -r .diff config.json
+ DIFF=../5fb339585079852dfbdaf4e5/output/dwi.nii.gz
++ jq -r .bval config.json
+ BVAL=../5fb339585079852dfbdaf4e5/output/dwi.bvals
++ jq -r .bvec config.json
+ BVEC=../5fb339585079852dfbdaf4e5/output/dwi.bvecs
++ jq -r .anat config.json
+ ANAT=../5fb338ca5079859dd6daf4ca/5fae16596b11522ce4dfab76/t1.nii.gz
++ jq -r .ens_lmax config.json
+ ENS_LMAX=null
++ jq -r .imaxs config.json
+ IMAXS=4
++ jq -r .curvs config.json
+ CURVS=35
++ jq -r .num_fibers config.json
+ NUM_FIBERS=15000
++ jq -r .min_length config.json
+ MIN_LENGTH=25
++ jq -r .max_length config.json
+ MAX_LENGTH=220
++ jq -r .tensor_fit config.json
+ TENSOR_FIT=null
++ jq -r .norm config.json
+ NORM=null
++ jq -r .do_prb2 config.json
+ DO_PRB2=true
++ jq -r .do_prb1 config.json
+ DO_PRB1=null
++ jq -r .do_detr config.json
+ DO_DETR=null
++ jq -r .do_dtdt config.json
+ DO_DTDT=null
++ jq -r .do_dtpb config.json
+ DO_DTPB=null
++ jq -r .do_fact config.json
+ DO_FACT=null
++ jq -r .fact_dirs config.json
+ FACT_DIRS=null
++ jq -r .fact_fibs config.json
+ FACT_FIBS=null
++ jq -r .premask config.json
+ PREMASK=null
+ rm -rf ./tmp
+ mkdir ./tmp
+ difm=dwi
+ mask=mask
+ anat=t1
+ echo 'Converting raw data into MRTrix3 format...'
+ mrconvert -fslgrad ../5fb339585079852dfbdaf4e5/output/dwi.bvecs ../5fb339585079852dfbdaf4e5/output/dwi.bvals ../5fb339585079852dfbdaf4e5/output/dwi.nii.gz dwi.mif --export_grad_mrtrix dwi.b -force -nthreads 8 -quiet
+ bet ../5fb339585079852dfbdaf4e5/output/dwi.nii.gz bet -R -m -f 0.3
+ mrconvert bet_mask.nii.gz mask.mif -force -nthreads 8 -quiet
+ mrconvert ../5fb338ca5079859dd6daf4ca/5fae16596b11522ce4dfab76/t1.nii.gz t1.mif -force -nthreads 8 -quiet
+ mrmath - mean b0.mif -axis 3 -nthreads 8 -quiet -force
+ dwiextract dwi.mif - -bzero -nthreads 8 -quiet
+ '[' '!' -f b0.mif ']'
++ mrinfo -shell_bvalues dwi.mif
++ wc -w
+ ISHELL=3
+ NSHELL=2
++ mrinfo -shell_sizes dwi.mif
++ awk '{print $1}'
+ NB0s=6
+ EB0=0,
+ '[' 2 -gt 1 ']'
+ MS=1
+ echo 'Multi-shell data: 2 total shells'
+ echo Number of b0s: 6
++ mrinfo -shell_bvalues dwi.mif
+ BVALS='5 1496.94 2995 '
++ mrinfo -shell_sizes dwi.mif
+ COUNTS='6 31 31 '
+ echo -n 'Shell b-values: '
+ echo 5 1496.94 2995
+ echo -n 'Unique Counts: '
+ echo 6 31 31
++ dirstat dwi.b
++ grep lmax
++ awk '{print $8}'
++ sed 's|:||g'
+ MLMAXS='6
6'
+ echo -n 'Maximum Lmax: '
+ echo 6 6
++ echo '6
6'
++ tr ' ' '\n'
++ head -n1
++ sort -nr
+ MAXLMAX=6
+ echo 'Maximum Lmax across shells: 6'
+ '[' -z 4 ']'
++ echo 4
++ wc -w
+ NMAX=1
+ '[' 1 -gt 1 ']'
+ MMAXS=4
+ '[' 4 -gt 6 ']'
+ '[' null == true ']'
+ LMAXS=4
+ '[' 6 -eq 0 ']'
+ RMAX=0
+ iter=1
+ '[' 1 -lt 3 ']'
+ RMAX=0,6
+ iter=2
+ '[' 2 -lt 3 ']'
+ RMAX=0,6,6
+ iter=3
+ '[' 3 -lt 3 ']'
+ echo 'Tractography will be created on lmax(s): 4'
+ TOTAL=0
+ '[' true == true ']'
+ for lmax in '$LMAXS'
+ for curv in '$CURVS'
+ TOTAL=15000
+ '[' null == true ']'
+ '[' null == true ']'
+ '[' null == true ']'
+ '[' null == true ']'
+ '[' null == true ']'
+ echo 'Expecting 15000 streamlines in track.tck.'
+ '[' '!' -z null ']'
++ echo 5 1496.94 2995
++ grep -o null
+ TFE=
real 0m12.362s
user 0m14.372s
sys 0m2.756s