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 ######################################################################## To unsubscribe from the FSL list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=FSL&A=1