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Hi all, any comments related to these errors we get with trac-all -prep in FS 7.2?
Thanks. Jim
From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu On Behalf Of Alexopoulos, Dimitrios Sent: Friday, February 25, 2022 2:05 PM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] error with trac-all -prep in FS7.2 tracula
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External Email - Use Caution Hi all,
We are reprocessing some of our data with FS 7.2 to evaluate the new updates to Tracula, however, we are getting errors from the trac-all -prep -c configfile step. The last 20 lines of output are shown below. Anyone have any comments on how to correct this? ------------------------------------- trac-preproc exited with ERRORS at Fri Feb 11 18:18:29 CST 2022lines:
1DIAGNOSTIC, 24, -4.743908838687e-01, 5.860622007851e-05, 4.2190e+01, 1.4997e+00, 1DIAGNOSTIC, 25, -4.743823138430e-01, 4.831431802083e-05, 4.3721e+01, 1.5312e+00, 1DIAGNOSTIC, 26, -4.744830990496e-01, 3.946018283887e-05, 4.5293e+01, 1.5718e+00, 1DIAGNOSTIC, 27, -4.744857576549e-01, 3.343839305766e-05, 4.6879e+01, 1.5857e+00, 1DIAGNOSTIC, 28, -4.744568952592e-01, 2.896457797682e-05, 4.8446e+01, 1.5669e+00, 1DIAGNOSTIC, 29, -4.744930355970e-01, 2.351784987169e-05, 5.0045e+01, 1.5996e+00, 1DIAGNOSTIC, 30, -4.744428763349e-01, 1.764564796251e-05, 5.1621e+01, 1.5762e+00, 1DIAGNOSTIC, 31, -4.744390742695e-01, 1.211632175497e-05, 5.3234e+01, 1.6130e+00, 1DIAGNOSTIC, 32, -4.744465209349e-01, 6.742111363235e-06, 5.4833e+01, 1.5989e+00, 1DIAGNOSTIC, 33, -4.743750058790e-01, 8.816157837238e-07, 5.6420e+01, 1.5867e+00, Elapsed time (stage 2): 58.59
Total elapsed time: 71.08 ConvertTransformFile 3 /data/shimony/shimony2/neonatal/wunder_9_10yo/freesurfer7.2/neo289e/dmri/xfms/diff2syn0GenericAffine.mat /data/shimony/shimony2/neonatal/wunder_9_10yo/freesurfer7.2/neo289e/dmri/xfms/diff2syn0GenericAffine.txt --hm --ras ConvertTransformFile: Command not found.
Linux hopper 5.3.0-40-generic #32~18.04.1-Ubuntu SMP Mon Feb 3 14:05:59 UTC 2020 x86_64 x86_64 x86_64 GNU/Linux
That piece of code is part of the ANTS library. When I look at the code this is what I see (or don't see for that matter)
# Register FA nonlinearly to FA template with SyN set cmd = $ANTSPATH/antsRegistrationSyNQuick.sh <-- This ANTs code has $ANTSPATH set cmd = ($cmd -d 3) set cmd = ($cmd -m $dwidir/dtifit_FA.nii.gz) set cmd = ($cmd -f $intertrg) set cmd = ($cmd -o $xfmdir/diff2syn) echo $cmd |& tee -a $LF |& tee -a $CF if ($RunIt) then $cmd |& tee -a $LF if ($status) goto error_exit endif
# Convert affine transform to .lta set cmd = ConvertTransformFile <-- This ANTs code DOES NOT have $ANTSPATH
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