Hello Freesurfer Support Team,
I have encountered an issue running recon-all -lgi that I believe is due to a zcat issue on mac OSx where a .Z is added to the end of the file name the resulting error looks like this...
reading filled volume...
zcat: can't stat: /Users/dandrews/data/test/12011/surf/tmp-mris_compute_lgi-lh.pial/lh.pial.filled.mgz (/Users/dandrews/data/test/12011/surf/tmp-mris_compute_lgi-lh.pial/lh.pial.filled.mgz.Z): No such file or directory
Upon reading through some message boards it appears replacing zcat with gzcat can solve this issue, however I am unsure where this troublesome zcat command is (it does not appear in the mriscomputelgi script).
Any suggestions or work throughs would be appreciated.
Best, Derek
________________________________
Derek Sayre Andrews, MSc PhD Candidate
The Sackler Institute for Translational Neurodevelopment
Department of Forensic and Neurodevelopmental Sciences
Institute of Psychiatry, Psychology & Neuroscience, King's College London
Telephone: +44 (0)20 7848 5701 Email: Derek.Andrews@kcl.ac.uk
you can find out where it is with which zcat
On 11/03/2015 07:42 AM, Andrews, Derek wrote:
Hello Freesurfer Support Team,
I have encountered an issue running recon-all –lgi that I believe is due to a zcat issue on mac OSx where a .Z is added to the end of the file name the resulting error looks like this…
reading filled volume...
zcat: can't stat: /Users/dandrews/data/test/12011/surf/tmp-mris_compute_lgi-lh.pial/lh.pial.filled.mgz (/Users/dandrews/data/test/12011/surf/tmp-mris_compute_lgi-lh.pial/lh.pial.filled.mgz.Z): No such file or directory
Upon reading through some message boards it appears replacing zcat with gzcat can solve this issue, however I am unsure where this troublesome zcat command is (it does not appear in the mriscomputelgi script).
Any suggestions or work throughs would be appreciated.
Best, Derek
*Derek Sayre Andrews, MSc* PhD Candidate
The Sackler Institute for Translational Neurodevelopment
Department of Forensic and Neurodevelopmental Sciences
Institute of Psychiatry, Psychology & Neuroscience, King's College London
Telephone: +44 (0)20 7848 5701 Email: Derek.Andrews@kcl.ac.uk
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Dear Douglas,
Thank you for response. To clarify, I need to find out where in the lGI scripts zcat is being called so that I can change the code to use something like gunzip.
Best, Derek
________________________________________ Derek Sayre Andrews, MSc PhD Candidate
The Sackler Institute for Translational Neurodevelopment Department of Forensic and Neurodevelopmental Sciences Institute of Psychiatry, Psychology & Neuroscience, King's College London
Telephone: +44 (0)20 7848 5701 Email: Derek.Andrews@kcl.ac.uk
On 03/11/2015 17:41, "Douglas N Greve" greve@nmr.mgh.harvard.edu wrote:
you can find out where it is with which zcat
On 11/03/2015 07:42 AM, Andrews, Derek wrote:
Hello Freesurfer Support Team,
I have encountered an issue running recon-all lgi that I believe is due to a zcat issue on mac OSx where a .Z is added to the end of the file name the resulting error looks like thisŠ
reading filled volume...
zcat: can't stat:
/Users/dandrews/data/test/12011/surf/tmp-mris_compute_lgi-lh.pial/lh.pial .filled.mgz
(/Users/dandrews/data/test/12011/surf/tmp-mris_compute_lgi-lh.pial/lh.pia l.filled.mgz.Z): No such file or directory
Upon reading through some message boards it appears replacing zcat with gzcat can solve this issue, however I am unsure where this troublesome zcat command is (it does not appear in the mriscomputelgi script).
Any suggestions or work throughs would be appreciated.
Best, Derek
*Derek Sayre Andrews, MSc* PhD Candidate
The Sackler Institute for Translational Neurodevelopment
Department of Forensic and Neurodevelopmental Sciences
Institute of Psychiatry, Psychology & Neuroscience, King's College London
Telephone: +44 (0)20 7848 5701 Email: Derek.Andrews@kcl.ac.uk
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
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The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Dear FreeSurfer support team,
It appears that ‘zcat’ appears in line 126 of the load.mgh script, I have changed this to gzcat which appears to have solved the issue.
Again, thank you for your support. It is very appreciated!
Best, Derek
________________________________________ Derek Sayre Andrews, MSc PhD Candidate
The Sackler Institute for Translational Neurodevelopment Department of Forensic and Neurodevelopmental Sciences Institute of Psychiatry, Psychology & Neuroscience, King's College London
Telephone: +44 (0)20 7848 5701 Email: Derek.Andrews@kcl.ac.uk
On 04/11/2015 11:33, "Andrews, Derek" derek.andrews@kcl.ac.uk wrote:
Dear Douglas,
Thank you for response. To clarify, I need to find out where in the lGI scripts zcat is being called so that I can change the code to use something like gunzip.
Best, Derek
Derek Sayre Andrews, MSc PhD Candidate
The Sackler Institute for Translational Neurodevelopment Department of Forensic and Neurodevelopmental Sciences Institute of Psychiatry, Psychology & Neuroscience, King's College London
Telephone: +44 (0)20 7848 5701 Email: Derek.Andrews@kcl.ac.uk
On 03/11/2015 17:41, "Douglas N Greve" greve@nmr.mgh.harvard.edu wrote:
you can find out where it is with which zcat
On 11/03/2015 07:42 AM, Andrews, Derek wrote:
Hello Freesurfer Support Team,
I have encountered an issue running recon-all lgi that I believe is due to a zcat issue on mac OSx where a .Z is added to the end of the file name the resulting error looks like thisŠ
reading filled volume...
zcat: can't stat:
/Users/dandrews/data/test/12011/surf/tmp-mris_compute_lgi-lh.pial/lh.pia l .filled.mgz
(/Users/dandrews/data/test/12011/surf/tmp-mris_compute_lgi-lh.pial/lh.pi a l.filled.mgz.Z): No such file or directory
Upon reading through some message boards it appears replacing zcat with gzcat can solve this issue, however I am unsure where this troublesome zcat command is (it does not appear in the mriscomputelgi script).
Any suggestions or work throughs would be appreciated.
Best, Derek
*Derek Sayre Andrews, MSc* PhD Candidate
The Sackler Institute for Translational Neurodevelopment
Department of Forensic and Neurodevelopmental Sciences
Institute of Psychiatry, Psychology & Neuroscience, King's College London
Telephone: +44 (0)20 7848 5701 Email: Derek.Andrews@kcl.ac.uk
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
load_mgh.m and load_nifti.m in $FREESURFER_HOME/matlab
On 11/04/2015 06:33 AM, Andrews, Derek wrote:
Dear Douglas,
Thank you for response. To clarify, I need to find out where in the lGI scripts zcat is being called so that I can change the code to use something like gunzip.
Best, Derek
Derek Sayre Andrews, MSc PhD Candidate
The Sackler Institute for Translational Neurodevelopment Department of Forensic and Neurodevelopmental Sciences Institute of Psychiatry, Psychology & Neuroscience, King's College London
Telephone: +44 (0)20 7848 5701 Email: Derek.Andrews@kcl.ac.uk
On 03/11/2015 17:41, "Douglas N Greve" greve@nmr.mgh.harvard.edu wrote:
you can find out where it is with which zcat
On 11/03/2015 07:42 AM, Andrews, Derek wrote:
Hello Freesurfer Support Team,
I have encountered an issue running recon-all lgi that I believe is due to a zcat issue on mac OSx where a .Z is added to the end of the file name the resulting error looks like thisŠ
reading filled volume...
zcat: can't stat:
/Users/dandrews/data/test/12011/surf/tmp-mris_compute_lgi-lh.pial/lh.pial .filled.mgz
(/Users/dandrews/data/test/12011/surf/tmp-mris_compute_lgi-lh.pial/lh.pia l.filled.mgz.Z): No such file or directory
Upon reading through some message boards it appears replacing zcat with gzcat can solve this issue, however I am unsure where this troublesome zcat command is (it does not appear in the mriscomputelgi script).
Any suggestions or work throughs would be appreciated.
Best, Derek
*Derek Sayre Andrews, MSc* PhD Candidate
The Sackler Institute for Translational Neurodevelopment
Department of Forensic and Neurodevelopmental Sciences
Institute of Psychiatry, Psychology & Neuroscience, King's College London
Telephone: +44 (0)20 7848 5701 Email: Derek.Andrews@kcl.ac.uk
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
freesurfer@nmr.mgh.harvard.edu
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Andrews, Derek -
Douglas N Greve