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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External Email - Use Caution
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
* External Email - Caution *
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
________________________________ The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail.
________________________________ The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail.
Hi Jim - Thanks for pointing this out. I'll make sure to add $ANTSPATH before every ants command. In the meantime, if you include $ANTSPATH in your own Unix path, this should be enough for it to work.
Best, Anastasia.
________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Alexopoulos, Dimitrios dimitriosalexopoulos@wustl.edu Sent: Monday, March 7, 2022 12:45 PM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] error with trac-all -prep in FS7.2 tracula
External Email - Use Caution
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
* External Email - Caution *
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
________________________________
The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail.
________________________________
The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail.
freesurfer@nmr.mgh.harvard.edu
-
Alexopoulos, Dimitrios -
Yendiki, Anastasia