Dear FS members
I am having trouble with using the "recon-all" function on one particular subject. "recon-all" does not complete and finishes with errors, it seems it does not complete both hemispheres. I am no expert in FS so I don't really understand why this is happening and I am unable to understand the log (attached). Could someone help interpret the log so that I may be able to process this subject?
Many thanks
Karen
Karen Bunday, PhD Research Associate Sobell Department of Motor Neuroscience and Movement Disorders Institute of Neurology, University College London 33 Queen Square London WC1N 3BG
That is a strange error. Can you run the following command to try to replicate:
cd /Applications/freesurfer/subjects/subjKZ/surf
mris_calc -o lh.area.mid lh.area.mid div 2
also, make sure that you have not run out of space on that disk
On 02/06/2017 09:56 AM, Bunday, Karen wrote:
Dear FS members
I am having trouble with using the “recon-all” function on one particular subject. “recon-all” does not complete and finishes with errors, it seems it does not complete both hemispheres. I am no expert in FS so I don’t really understand why this is happening and I am unable to understand the log (attached). Could someone help interpret the log so that I may be able to process this subject?
Many thanks
Karen
Karen Bunday, PhD
Research Associate
Sobell Department of Motor Neuroscience and Movement Disorders
Institute of Neurology, University College London
33 Queen Square
London
WC1N 3BG
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hi
Thank you for your email.
I checked the disk space and there is over 300 GB left.
I ran the code as you suggested, this is the output:
"WARNING: # of slices=-92 in header - assuming 124... Read_signal (/Applications/Freesurfer/subjects/subjKZ/surf/I.001): could not open file
No such file or directory
mris_calc: could not establish read access to 'lh.area.mid'
No such file or directory"
It's odd as I did manage to run this subject before, but needed to re-run with a different .nii and now it will not complete.
BW Karen
Karen Bunday, PhD Research Associate Sobell Department of Motor Neuroscience and Movement Disorders Institute of Neurology, University College London
-----Original Message----- From: freesurfer-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] On Behalf Of Douglas N Greve Sent: 06 February 2017 18:05 To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Recon-all - finished with errors
That is a strange error. Can you run the following command to try to replicate:
cd /Applications/freesurfer/subjects/subjKZ/surf
mris_calc -o lh.area.mid lh.area.mid div 2
also, make sure that you have not run out of space on that disk
On 02/06/2017 09:56 AM, Bunday, Karen wrote:
Dear FS members
I am having trouble with using the "recon-all" function on one particular subject. "recon-all" does not complete and finishes with errors, it seems it does not complete both hemispheres. I am no expert in FS so I don't really understand why this is happening and I am unable to understand the log (attached). Could someone help interpret the log so that I may be able to process this subject?
Many thanks
Karen
Karen Bunday, PhD
Research Associate
Sobell Department of Motor Neuroscience and Movement Disorders
Institute of Neurology, University College London
33 Queen Square
London
WC1N 3BG
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.
Is that the entire terminal output?
On 2/7/17 6:46 AM, Bunday, Karen wrote:
Hi
Thank you for your email.
I checked the disk space and there is over 300 GB left.
I ran the code as you suggested, this is the output:
"WARNING: # of slices=-92 in header - assuming 124... Read_signal (/Applications/Freesurfer/subjects/subjKZ/surf/I.001): could not open file
No such file or directory
mris_calc: could not establish read access to 'lh.area.mid'
No such file or directory"
It's odd as I did manage to run this subject before, but needed to re-run with a different .nii and now it will not complete.
BW Karen
Karen Bunday, PhD Research Associate Sobell Department of Motor Neuroscience and Movement Disorders Institute of Neurology, University College London
-----Original Message----- From: freesurfer-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] On Behalf Of Douglas N Greve Sent: 06 February 2017 18:05 To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Recon-all - finished with errors
That is a strange error. Can you run the following command to try to replicate:
cd /Applications/freesurfer/subjects/subjKZ/surf
mris_calc -o lh.area.mid lh.area.mid div 2
also, make sure that you have not run out of space on that disk
On 02/06/2017 09:56 AM, Bunday, Karen wrote:
Dear FS members
I am having trouble with using the "recon-all" function on one particular subject. "recon-all" does not complete and finishes with errors, it seems it does not complete both hemispheres. I am no expert in FS so I don't really understand why this is happening and I am unable to understand the log (attached). Could someone help interpret the log so that I may be able to process this subject?
Many thanks
Karen
Karen Bunday, PhD
Research Associate
Sobell Department of Motor Neuroscience and Movement Disorders
Institute of Neurology, University College London
33 Queen Square
London
WC1N 3BG
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
Yes, that's it. It just back to the command line after that.
What do you think the problem is?
BW Karen
Karen Bunday, PhD Research Associate Sobell Department of Motor Neuroscience and Movement Disorders Institute of Neurology, University College London
-----Original Message----- From: freesurfer-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] On Behalf Of Douglas Greve Sent: 07 February 2017 23:08 To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Recon-all - finished with errors
Is that the entire terminal output?
On 2/7/17 6:46 AM, Bunday, Karen wrote:
Hi
Thank you for your email.
I checked the disk space and there is over 300 GB left.
I ran the code as you suggested, this is the output:
"WARNING: # of slices=-92 in header - assuming 124... Read_signal (/Applications/Freesurfer/subjects/subjKZ/surf/I.001): could not open file
No such file or directory
mris_calc: could not establish read access to 'lh.area.mid'
No such file or directory"
It's odd as I did manage to run this subject before, but needed to re-run with a different .nii and now it will not complete.
BW Karen
Karen Bunday, PhD Research Associate Sobell Department of Motor Neuroscience and Movement Disorders Institute of Neurology, University College London
-----Original Message----- From: freesurfer-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] On Behalf Of Douglas N Greve Sent: 06 February 2017 18:05 To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Recon-all - finished with errors
That is a strange error. Can you run the following command to try to replicate:
cd /Applications/freesurfer/subjects/subjKZ/surf
mris_calc -o lh.area.mid lh.area.mid div 2
also, make sure that you have not run out of space on that disk
On 02/06/2017 09:56 AM, Bunday, Karen wrote:
Dear FS members
I am having trouble with using the "recon-all" function on one particular subject. "recon-all" does not complete and finishes with errors, it seems it does not complete both hemispheres. I am no expert in FS so I don't really understand why this is happening and I am unable to understand the log (attached). Could someone help interpret the log so that I may be able to process this subject?
Many thanks
Karen
Karen Bunday, PhD
Research Associate
Sobell Department of Motor Neuroscience and Movement Disorders
Institute of Neurology, University College London
33 Queen Square
London
WC1N 3BG
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 mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
that is bizarre. Can you upload
lh.area.mid to our file drop (see end of email)
On 02/08/2017 05:21 AM, Bunday, Karen wrote:
Yes, that's it. It just back to the command line after that.
What do you think the problem is?
BW Karen
Karen Bunday, PhD Research Associate Sobell Department of Motor Neuroscience and Movement Disorders Institute of Neurology, University College London
-----Original Message----- From: freesurfer-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] On Behalf Of Douglas Greve Sent: 07 February 2017 23:08 To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Recon-all - finished with errors
Is that the entire terminal output?
On 2/7/17 6:46 AM, Bunday, Karen wrote:
Hi
Thank you for your email.
I checked the disk space and there is over 300 GB left.
I ran the code as you suggested, this is the output:
"WARNING: # of slices=-92 in header - assuming 124... Read_signal (/Applications/Freesurfer/subjects/subjKZ/surf/I.001): could not open file
No such file or directory
mris_calc: could not establish read access to 'lh.area.mid'
No such file or directory"
It's odd as I did manage to run this subject before, but needed to re-run with a different .nii and now it will not complete.
BW Karen
Karen Bunday, PhD Research Associate Sobell Department of Motor Neuroscience and Movement Disorders Institute of Neurology, University College London
-----Original Message----- From: freesurfer-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] On Behalf Of Douglas N Greve Sent: 06 February 2017 18:05 To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Recon-all - finished with errors
That is a strange error. Can you run the following command to try to replicate:
cd /Applications/freesurfer/subjects/subjKZ/surf
mris_calc -o lh.area.mid lh.area.mid div 2
also, make sure that you have not run out of space on that disk
On 02/06/2017 09:56 AM, Bunday, Karen wrote:
Dear FS members
I am having trouble with using the "recon-all" function on one particular subject. "recon-all" does not complete and finishes with errors, it seems it does not complete both hemispheres. I am no expert in FS so I don't really understand why this is happening and I am unable to understand the log (attached). Could someone help interpret the log so that I may be able to process this subject?
Many thanks
Karen
Karen Bunday, PhD
Research Associate
Sobell Department of Motor Neuroscience and Movement Disorders
Institute of Neurology, University College London
33 Queen Square
London
WC1N 3BG
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 mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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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Bunday, Karen -
Douglas Greve -
Douglas N Greve