Hi FSL Experts,
I have encountered Topup error report on ubuntu saying 'Sorry, the application applytop has stopped unexpectedly', while performing perfusion analysis using BASIL. The same message appears during both the command-line and the gui versions of BASIL. The analysis still goes on and produce the results as mentioned in the primer example box (http://www.neuroimagingprimers.org/examples/introduction-to-perfusion-quantification-using-asl/). Does this mean no distortion correction was applied during the analysis? Should I ignore this or fix this?
The output from the run looks like this:
/home/amnah/Downloads/oxford_asl/oxford_asl -i "/home/amnah/Desktop/ASL_Oxford_Primers_GUI/Example_2/singlePLDpcASL/asltc.nii.gz" --ibf=rpt --iaf=tc --tis 3.60 --bolus 1.80 --casl --slicedt 0.04520 -c "/home/amnah/Desktop/ASL_Oxford_Primers_GUI/Example_2/singlePLDpcASL/aslcalib.nii.gz" --tr 4.80 --cgain 1.00 --cmethod voxel --cblip="/home/amnah/Desktop/ASL_Oxford_Primers_GUI/Example_2/singlePLDpcASL/aslcalib_PA.nii.gz" --echospacing=0.06000 --pedir=y --wp --t1b 1.65 --alpha 0.85 --fixbolus --spatial --mc --artoff -o "oxasl"
OXFORD_ASL - running
Version: v3.9.21 Mon Nov 19 14:31:46 2018
Saving results in natve (ASL aquisition) space to oxasl/native_space
Pre-processing
Motion Correction
Number of voxels is:98304
Number of repeats in data is:30
Outputting ASL data mean at each TI
Done.
Number of inversion times: 1
Number of timepoints in data: 30
Number of repeats in data: 30
3.60 3.60 3.60 3.60 3.60 3.60 3.60 3.60 3.60 3.60 3.60 3.60 3.60 3.60 3.60 3.60 3.60 3.60 3.60 3.60 3.60 3.60 3.60 3.60 3.60 3.60 3.60 3.60 3.60 3.60
Creating mask
Distortion correction: running topup
For TOPUP using total read-out time of ( 64 - 1) x 0.06000 s = 3.78000 s
Part of FSL (ID: 6.0.0)
topup
Usage:
topup --imain=<some 4D image> --datain=<text file> --config=<text file with parameters> --out=my_topup_results
Compulsory arguments (You MUST set one or more of):
--imain name of 4D file with images
--datain name of text file with PE directions/times
Optional arguments (You may optionally specify one or more of):
--out base-name of output files (spline coefficients (Hz) and movement parameters)
--fout name of image file with field (Hz)
--iout name of 4D image file with unwarped images
--logout Name of log-file
--warpres (approximate) resolution (in mm) of warp basis for the different sub-sampling levels, default 10
--subsamp sub-sampling scheme, default 1
--fwhm FWHM (in mm) of gaussian smoothing kernel, default 8
--config Name of config file specifying command line arguments
--miter Max # of non-linear iterations, default 5
--lambda Weight of regularisation, default depending on --ssqlambda and --regmod switches. See user documetation.
--ssqlambda If set (=1), lambda is weighted by current ssq, default 1
--regmod Model for regularisation of warp-field [membrane_energy bending_energy], default bending_energy
--estmov Estimate movements if set, default 1 (true)
--minmet Minimisation method 0=Levenberg-Marquardt, 1=Scaled Conjugate Gradient, default 0 (LM)
--splineorder Order of spline, 2->Qadratic spline, 3->Cubic spline. Default=3
--numprec Precision for representing Hessian, double or float. Default double
--interp Image interpolation model, linear or spline. Default spline
--scale If set (=1), the images are individually scaled to a common mean, default 0 (false)
--regrid If set (=1), the calculations are done in a different grid, default 1 (true)
-h,--help display help info
-v,--verbose Print diagonostic information while running
-h,--help display help info
Topup: msg=topup_clp::topup_clp: Mismatch between /tmp/fsl_wW0Wyf_ox_asl/calib_blipped and /tmp/fsl_wW0Wyf_ox_asl/topup_params.txt
Distortion Correction using TOPUP
terminate called after throwing an instance of 'TOPUP::TopupFileIOException'
what(): TopupFileIO:: msg=TopupFileReader::TopupFileReader: Unable to read file /tmp/fsl_wW0Wyf_ox_asl/topupresult
/home/amnah/Downloads/oxford_asl/oxford_asl: line 1687: 2453 Aborted (core dumped) applytopup --imain=$tempdir/calib,$tempdir/cblip --inindex=1,2 --datain=$tempdir/topup_params.txt --topup=${topupresult} --out=$tempdir/calib --method=jac
terminate called after throwing an instance of 'TOPUP::TopupFileIOException'
what(): TopupFileIO:: msg=TopupFileReader::TopupFileReader: Unable to read file /tmp/fsl_wW0Wyf_ox_asl/topupresult
/home/amnah/Downloads/oxford_asl/oxford_asl: line 1687: 2459 Aborted (core dumped) applytopup --imain=$tempdir/asldata --datain=$tempdir/topup_params.txt --inindex=1 --topup=${topupresult} --out=$tempdir/asldata --method=jac
Number of voxels is:98304
Number of repeats in data is:30
Outputting ASL data mean at each TI
Done.
Setting up BASIL
Instructing BASIL to use automated spatial smoothing
Calling BASIL on data - conventional perusion image
Creating output directory: /tmp/fsl_wW0Wyf_ox_asl/init/basil
here
STEP 1: VB - Tissue
----------------------
Welcome to FABBER v3.9.2-97-g3b6aec1
----------------------
Last commit: Wed Sep 12 10:12:07 2018
Logfile started: /tmp/fsl_wW0Wyf_ox_asl/init/basil/step1/logfile
0%1%2%3%4%5%6%7%8%9%10%11%12%13%14%15%16%17%18%19%20%21%22%23%24%25%26%27%28%29%30%31%32%33%34%35%36%37%38%39%40%41%42%43%44%45%46%47%48%49%50%51%52%53%54%55%56%57%58%59%60%61%62%63%64%65%66%67%68%69%70%71%72%73%74%75%76%77%78%79%80%81%82%83%84%85%86%87%88%89%90%91%92%93%94%95%96%97%98%99%100%
Final logfile: /tmp/fsl_wW0Wyf_ox_asl/init/basil/step1/logfile
STEP 2: Spatial VB Tissue - init with STEP 1
----------------------
Welcome to FABBER v3.9.2-97-g3b6aec1
----------------------
Last commit: Wed Sep 12 10:12:07 2018
Logfile started: /tmp/fsl_wW0Wyf_ox_asl/init/basil/step2/logfile
0%5%10%15%20%25%30%35%40%45%50%55%60%65%70%75%80%85%90%95%100%
Final logfile: /tmp/fsl_wW0Wyf_ox_asl/init/basil/step2/logfile
End.
Fabber variance calculator
Working in /tmp/fsl_wW0Wyf_ox_asl/init/basil/step2
Calculating variance for: ftiss
FABBER: MVNtool
FabberRunDataNewimage::Loading mask data from '/tmp/fsl_wW0Wyf_ox_asl/mask'
FabberRunDataNewimage::Dimensions: x=64, y=64, z=24, vols=1
FabberRunDataNewimage::Voxel size: x=3.4375mm, y=3.4375mm, z=4.95mm, TR=1 sec
FabberRunDataNewimage::Intents: 0, 0, 0, 0
FabberRunDataNewimage::Setting coordinates from extent
FabberRunDataNewimage::Loading data from '/tmp/fsl_wW0Wyf_ox_asl/init/basil/step2/finalMVN'
FabberRunDataNewimage::Dimensions: x=64, y=64, z=24, vols=10
FabberRunDataNewimage::Voxel size: x=3.4375mm, y=3.4375mm, z=4.95mm, TR=1 sec
FabberRunDataNewimage::Intents: 1005, 0, 0, 0
FabberRunDataNewimage::Applying mask to data...
FabberRunData::GetVoxelData: input=/tmp/fsl_wW0Wyf_ox_asl/init/basil/step2/finalMVN mean value=1.13134e+06
FabberRunDataNewimage::Saving to nifti: /tmp/fsl_wW0Wyf_ox_asl/init/basil/step2/var_ftiss
Calculating variance for: delttiss
FABBER: MVNtool
FabberRunDataNewimage::Loading mask data from '/tmp/fsl_wW0Wyf_ox_asl/mask'
FabberRunDataNewimage::Dimensions: x=64, y=64, z=24, vols=1
FabberRunDataNewimage::Voxel size: x=3.4375mm, y=3.4375mm, z=4.95mm, TR=1 sec
FabberRunDataNewimage::Intents: 0, 0, 0, 0
FabberRunDataNewimage::Setting coordinates from extent
FabberRunDataNewimage::Loading data from '/tmp/fsl_wW0Wyf_ox_asl/init/basil/step2/finalMVN'
FabberRunDataNewimage::Dimensions: x=64, y=64, z=24, vols=10
FabberRunDataNewimage::Voxel size: x=3.4375mm, y=3.4375mm, z=4.95mm, TR=1 sec
FabberRunDataNewimage::Intents: 1005, 0, 0, 0
FabberRunDataNewimage::Applying mask to data...
FabberRunData::GetVoxelData: input=/tmp/fsl_wW0Wyf_ox_asl/init/basil/step2/finalMVN mean value=1.13134e+06
FabberRunDataNewimage::Saving to nifti: /tmp/fsl_wW0Wyf_ox_asl/init/basil/step2/var_delttiss
Done.
Creating output directory: /tmp/fsl_wW0Wyf_ox_asl/basil
here
STEP 1: VB - Tissue - init with STEP 0
----------------------
Welcome to FABBER v3.9.2-97-g3b6aec1
----------------------
Last commit: Wed Sep 12 10:12:07 2018
Logfile started: /tmp/fsl_wW0Wyf_ox_asl/basil/step1/logfile
0%1%2%3%4%5%6%7%8%9%10%11%12%13%14%15%16%17%18%19%20%21%22%23%24%25%26%27%28%29%30%31%32%33%34%35%36%37%38%39%40%41%42%43%44%45%46%47%48%49%50%51%52%53%54%55%56%57%58%59%60%61%62%63%64%65%66%67%68%69%70%71%72%73%74%75%76%77%78%79%80%81%82%83%84%85%86%87%88%89%90%91%92%93%94%95%96%97%98%99%100%
Final logfile: /tmp/fsl_wW0Wyf_ox_asl/basil/step1/logfile
STEP 2: Spatial VB Tissue - init with STEP 1
----------------------
Welcome to FABBER v3.9.2-97-g3b6aec1
----------------------
Last commit: Wed Sep 12 10:12:07 2018
Logfile started: /tmp/fsl_wW0Wyf_ox_asl/basil/step2/logfile
0%5%10%15%20%25%30%35%40%45%50%55%60%65%70%75%80%85%90%95%100%
Final logfile: /tmp/fsl_wW0Wyf_ox_asl/basil/step2/logfile
End.
Fabber variance calculator
Working in /tmp/fsl_wW0Wyf_ox_asl/basil/step2
Calculating variance for: ftiss
FABBER: MVNtool
FabberRunDataNewimage::Loading mask data from '/tmp/fsl_wW0Wyf_ox_asl/mask'
FabberRunDataNewimage::Dimensions: x=64, y=64, z=24, vols=1
FabberRunDataNewimage::Voxel size: x=3.4375mm, y=3.4375mm, z=4.95mm, TR=1 sec
FabberRunDataNewimage::Intents: 0, 0, 0, 0
FabberRunDataNewimage::Setting coordinates from extent
FabberRunDataNewimage::Loading data from '/tmp/fsl_wW0Wyf_ox_asl/basil/step2/finalMVN'
FabberRunDataNewimage::Dimensions: x=64, y=64, z=24, vols=10
FabberRunDataNewimage::Voxel size: x=3.4375mm, y=3.4375mm, z=4.95mm, TR=1 sec
FabberRunDataNewimage::Intents: 1005, 0, 0, 0
FabberRunDataNewimage::Applying mask to data...
FabberRunData::GetVoxelData: input=/tmp/fsl_wW0Wyf_ox_asl/basil/step2/finalMVN mean value=0.606532
FabberRunDataNewimage::Saving to nifti: /tmp/fsl_wW0Wyf_ox_asl/basil/step2/var_ftiss
Calculating variance for: delttiss
FABBER: MVNtool
FabberRunDataNewimage::Loading mask data from '/tmp/fsl_wW0Wyf_ox_asl/mask'
FabberRunDataNewimage::Dimensions: x=64, y=64, z=24, vols=1
FabberRunDataNewimage::Voxel size: x=3.4375mm, y=3.4375mm, z=4.95mm, TR=1 sec
FabberRunDataNewimage::Intents: 0, 0, 0, 0
FabberRunDataNewimage::Setting coordinates from extent
FabberRunDataNewimage::Loading data from '/tmp/fsl_wW0Wyf_ox_asl/basil/step2/finalMVN'
FabberRunDataNewimage::Dimensions: x=64, y=64, z=24, vols=10
FabberRunDataNewimage::Voxel size: x=3.4375mm, y=3.4375mm, z=4.95mm, TR=1 sec
FabberRunDataNewimage::Intents: 1005, 0, 0, 0
FabberRunDataNewimage::Applying mask to data...
FabberRunData::GetVoxelData: input=/tmp/fsl_wW0Wyf_ox_asl/basil/step2/finalMVN mean value=0.606532
FabberRunDataNewimage::Saving to nifti: /tmp/fsl_wW0Wyf_ox_asl/basil/step2/var_delttiss
Done.
Number of voxels is:35238
Number of repeats in data is:1
Start extrapolation!
Done.
Output is oxasl/
OXFORD_ASL - done.
Return code: 0
I would really appreciate if someone can clarify this.
Best Regards,
Amnah
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