External Email - Use Caution
Hello FreeSurfer Developers,
We are attempting to run the command recon-all on pediatric MRI images (1-13 yrs), as described on your website: cmd=”recon-all -i $Dir/*.nii.gz -s sub02_test -all”
The command worked well for some of our subjects. For others, however, hard failures occurred and recon-all did not finish or we received the following error (please find the recon-all.log attached): “recon-all -s sub02_reconall exited with ERRORS at….”
Would you have any recommendations on how to trouble-shoot these issues? We have attached the recon-all.log documents in case it's of any use.
1) FreeSurfer version: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c 2) Platform: Linux 4) recon-all.log: see attached.
We would very much appreciate your help!
Kind regards, Nina Wilpert
Nina-Maria Wilpert | medical student T +49 (0) 30 450559858 | M +49 (0) 15783851445 E nina-maria.wilpert@charite.demailto:nina-maria.wilpert@charite.de Department of Neuropediatrics Charité, Universitätsmedizin Berlin Institute of Anatomy University of Leipzig Genetics and Development of the Cerebral Cortex Hôpital Necker-Enfants malades & IMAGINE, Paris
Hi Nina, The recon all pipeline uses an adult atlas. We have had collaborators successfully using it with subjects all the way down to age 4.5yrs, but under that it would not be recommended. Have you looked at the infant pipeline? Best, Lilla ________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Wilpert, Nina- Maria nina-maria.wilpert@charite.de Sent: Tuesday, August 4, 2020 10:51 AM To: freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu Cc: Schülke-Gerstenfeld, Markus markus.schuelke@charite.de Subject: [Freesurfer] mri: recon-all error
External Email - Use Caution
Hello FreeSurfer Developers,
We are attempting to run the command recon-all on pediatric MRI images (1-13 yrs), as described on your website:
cmd=”recon-all -i $Dir/*.nii.gz -s sub02_test -all”
The command worked well for some of our subjects. For others, however, hard failures occurred and recon-all did not finish or we received the following error (please find the recon-all.log attached):
“recon-all -s sub02_reconall exited with ERRORS at….”
Would you have any recommendations on how to trouble-shoot these issues? We have attached the recon-all.log documents in case it's of any use.
1) FreeSurfer version: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c
2) Platform: Linux
4) recon-all.log: see attached.
We would very much appreciate your help!
Kind regards,
Nina Wilpert
Nina-Maria Wilpert | medical student T +49 (0) 30 450559858 | M +49 (0) 15783851445 E nina-maria.wilpert@charite.demailto:nina-maria.wilpert@charite.de
Department of Neuropediatrics
Charité, Universitätsmedizin Berlin
Institute of Anatomy
University of Leipzig
Genetics and Development of the Cerebral Cortex
Hôpital Necker-Enfants malades & IMAGINE, Paris
External Email - Use Caution
Hello Lilla,
Many thanks for you kind and helpful respond! We have just applied for the code for the infant pipeline and would be happy to utilize it.
Kind regards, Nina Wilpert
Nina-Maria Wilpert | medical student T +49 (0) 30 450559858 | M +49 (0) 15783851445 E nina-maria.wilpert@charite.de Department of Neuropediatrics Charité, Universitätsmedizin Berlin Institute of Anatomy University of Leipzig Genetics and Development of the Cerebral Cortex Hôpital Necker-Enfants malades & IMAGINE, Paris
Von: freesurfer-bounces@nmr.mgh.harvard.edu im Auftrag von "Zollei, Lilla,Ph.D." LZOLLEI@MGH.HARVARD.EDU Antworten an: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Datum: Dienstag, 4. August 2020 um 22:56 An: "freesurfer@nmr.mgh.harvard.edu" freesurfer@nmr.mgh.harvard.edu Cc: "Schülke-Gerstenfeld, Markus" markus.schuelke@charite.de Betreff: [ext] Re: [Freesurfer] recon-all error
Hi Nina, The recon all pipeline uses an adult atlas. We have had collaborators successfully using it with subjects all the way down to age 4.5yrs, but under that it would not be recommended. Have you looked at the infant pipeline? Best, Lilla ________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Wilpert, Nina- Maria nina-maria.wilpert@charite.de Sent: Tuesday, August 4, 2020 10:51 AM To: freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu Cc: Schülke-Gerstenfeld, Markus markus.schuelke@charite.de Subject: [Freesurfer] mri: recon-all error
External Email - Use Caution
Hello FreeSurfer Developers,
We are attempting to run the command recon-all on pediatric MRI images (1-13 yrs), as described on your website:
cmd=”recon-all -i $Dir/*.nii.gz -s sub02_test -all”
The command worked well for some of our subjects. For others, however, hard failures occurred and recon-all did not finish or we received the following error (please find the recon-all.log attached):
“recon-all -s sub02_reconall exited with ERRORS at….”
Would you have any recommendations on how to trouble-shoot these issues? We have attached the recon-all.log documents in case it's of any use.
1) FreeSurfer version: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c
2) Platform: Linux
4) recon-all.log: see attached.
We would very much appreciate your help!
Kind regards,
Nina Wilpert
Nina-Maria Wilpert | medical student T +49 (0) 30 450559858 | M +49 (0) 15783851445 E nina-maria.wilpert@charite.demailto:nina-maria.wilpert@charite.de
Department of Neuropediatrics
Charité, Universitätsmedizin Berlin
Institute of Anatomy
University of Leipzig
Genetics and Development of the Cerebral Cortex
Hôpital Necker-Enfants malades & IMAGINE, Paris
freesurfer@nmr.mgh.harvard.edu
-
Wilpert, Nina- Maria -
Zollei, Lilla,Ph.D.