Hi Marie,
I've attached the log file.
Thanks very much,
Sarina Iwabuchi
Hi Sarina,
Can you please send me the full log of the LGI (e.g. recon-all.log) for this subject?
Thanks,
Marie
On Jul 28, 2014, at 7:23 AM, "Sarina Iwabuchi" <Sarina.Iwabuchi at nottingham.ac.uk<mailto:Sarina.Iwabuchi at nottingham.ac.uk>> wrote:
Hi all,
I have been trying to run localGI and have been coming across errors. It creates the filled.mgz file and opens matlab (running 2012a) but crashes straight after with the below errors:
reading filled volume...
set: Variable name must begin with a letter. gunzip: Command not found. ERROR: problem reading fname set: Variable name must begin with a letter. rm: Command not found. SWITCH expression must be a scalar or string constant.
Error in load_mgh (line 158) switch type
Error in MRIread (line 87) [mri.vol, M, mr_parms, volsz] = load_mgh(fspec,[],[],headeronly);
Error in make_outer_surface (line 24) vol=MRIread(filled_volume);
Has anyone come across this? I do have gunzip on my system.
Thanks very much,
Sarina Iwabuchi Division of Psychiatry and Applied Psychology Room B07 Institute of Mental Health Triumph Road University of Nottingham Nottingham NG7 2TU
Sarina Iwabuchi Division of Psychiatry and Applied Psychology Room B07 Institute of Mental Health Triumph Road University of Nottingham Nottingham NG7 2TU
This message and any attachment are intended solely for the addressee and may contain confidential information. If you have received this message in error, please send it back to me, and immediately delete it. Please do not use, copy or disclose the information contained in this message or in any attachment. Any views or opinions expressed by the author of this email do not necessarily reflect the views of the University of Nottingham.
This message has been checked for viruses but the contents of an attachment
may still contain software viruses which could damage your computer system, you are advised to perform your own checks. Email communications with the University of Nottingham may be monitored as permitted by UK legislation.
On 29 Jul 2014, at 11:29, Sarina Iwabuchi wrote:
Hi Marie,
I've attached the log file.
Thanks very much,
Sarina Iwabuchi
This message and any attachment are intended solely for the addressee and may contain confidential information. If you have received this message in error, please send it back to me, and immediately delete it. Please do not use, copy or disclose the information contained in this message or in any attachment. Any views or opinions expressed by the author of this email do not necessarily reflect the views of the University of Nottingham.
This message has been checked for viruses but the contents of an attachment may still contain software viruses which could damage your computer system, you are advised to perform your own checks. Email communications with the University of Nottingham may be monitored as permitted by UK legislation.
Hi Sarina,
Can you please send me the full log of the LGI (e.g. recon-all.log) for this subject?
Thanks,
Marie
On Jul 28, 2014, at 7:23 AM, "Sarina Iwabuchi" <Sarina.Iwabuchi at nottingham.ac.uk<mailto:Sarina.Iwabuchi at nottingham.ac.uk>> wrote:
Hi all,
I have been trying to run localGI and have been coming across errors. It creates the filled.mgz file and opens matlab (running 2012a) but crashes straight after with the below errors:
reading filled volume...
set: Variable name must begin with a letter. gunzip: Command not found. ERROR: problem reading fname set: Variable name must begin with a letter. rm: Command not found. SWITCH expression must be a scalar or string constant.
Error in load_mgh (line 158) switch type
Error in MRIread (line 87) [mri.vol, M, mr_parms, volsz] = load_mgh(fspec,[],[],headeronly);
Error in make_outer_surface (line 24) vol=MRIread(filled_volume);
Has anyone come across this? I do have gunzip on my system.
Thanks very much,
Sarina Iwabuchi Division of Psychiatry and Applied Psychology Room B07 Institute of Mental Health Triumph Road University of Nottingham Nottingham NG7 2TU
Sarina Iwabuchi Division of Psychiatry and Applied Psychology Room B07 Institute of Mental Health Triumph Road University of Nottingham Nottingham NG7 2TU
<recon-all.log>
Sarina Iwabuchi Division of Psychiatry and Applied Psychology Room B07 Institute of Mental Health Triumph Road University of Nottingham Nottingham NG7 2TU
This message and any attachment are intended solely for the addressee and may contain confidential information. If you have received this message in error, please send it back to me, and immediately delete it. Please do not use, copy or disclose the information contained in this message or in any attachment. Any views or opinions expressed by the author of this email do not necessarily reflect the views of the University of Nottingham.
This message has been checked for viruses but the contents of an attachment
may still contain software viruses which could damage your computer system, you are advised to perform your own checks. Email communications with the University of Nottingham may be monitored as permitted by UK legislation.
Hi Sarina,
Thanks for the log, I see better the problem. However I unfortunately don't know the answer. The lGI calls MRIread and load_mgh, and the error seems to related to load_mgh.m itself.
Bruce / Doug / Nick, any guess what can yield such a "switch expression must be a scalar or string constant" error in load_mgh? (full log attached in Sarina's previous email)
Thanks a lot,
Marie
On Jul 29, 2014, at 3:29 AM, Sarina Iwabuchi <Sarina.Iwabuchi@nottingham.ac.ukmailto:Sarina.Iwabuchi@nottingham.ac.uk> wrote:
Hi Marie,
I've attached the log file.
Thanks very much,
Sarina Iwabuchi
This message and any attachment are intended solely for the addressee and may contain confidential information. If you have received this message in error, please send it back to me, and immediately delete it. Please do not use, copy or disclose the information contained in this message or in any attachment. Any views or opinions expressed by the author of this email do not necessarily reflect the views of the University of Nottingham.
This message has been checked for viruses but the contents of an attachment may still contain software viruses which could damage your computer system, you are advised to perform your own checks. Email communications with the University of Nottingham may be monitored as permitted by UK legislation.
Hi Sarina,
Can you please send me the full log of the LGI (e.g. recon-all.log) for this subject?
Thanks,
Marie
On Jul 28, 2014, at 7:23 AM, "Sarina Iwabuchi" <Sarina.Iwabuchi at nottingham.ac.ukhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer<mailto:Sarina.Iwabuchi at nottingham.ac.ukhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>> wrote:
Hi all,
I have been trying to run localGI and have been coming across errors. It creates the filled.mgz file and opens matlab (running 2012a) but crashes straight after with the below errors:
reading filled volume...
set: Variable name must begin with a letter. gunzip: Command not found. ERROR: problem reading fname set: Variable name must begin with a letter. rm: Command not found. SWITCH expression must be a scalar or string constant.
Error in load_mgh (line 158) switch type
Error in MRIread (line 87) [mri.vol, M, mr_parms, volsz] = load_mgh(fspec,[],[],headeronly);
Error in make_outer_surface (line 24) vol=MRIread(filled_volume);
Has anyone come across this? I do have gunzip on my system.
Thanks very much,
Sarina Iwabuchi Division of Psychiatry and Applied Psychology Room B07 Institute of Mental Health Triumph Road University of Nottingham Nottingham NG7 2TU
Sarina Iwabuchi Division of Psychiatry and Applied Psychology Room B07 Institute of Mental Health Triumph Road University of Nottingham Nottingham NG7 2TU
<recon-all.log>
Hmmm, I'm not sure what is going on either. The problem seems to be that the file is not getting unzipped (and so does not have anything to do with the switch statement per se).
Sarina, try going into matlab and running
a = MRIread('/Volumes/HD-PNTU3/MISSEDDATA/extn003/surf/tmp-mris_compute_lgi-lh.pial/lh.pial.filled.mgz');
and let me know if that works or whether it generates the same error
doug
On 07/29/2014 01:22 PM, Marie Schaer wrote:
Hi Sarina,
Thanks for the log, I see better the problem. However I unfortunately don't know the answer. The lGI calls MRIread and load_mgh, and the error seems to related to load_mgh.m itself.
Bruce / Doug / Nick, any guess what can yield such a "switch expression must be a scalar or string constant" error in load_mgh? (full log attached in Sarina's previous email)
Thanks a lot,
Marie
On Jul 29, 2014, at 3:29 AM, Sarina Iwabuchi <Sarina.Iwabuchi@nottingham.ac.uk mailto:Sarina.Iwabuchi@nottingham.ac.uk> wrote:
Hi Marie, I've attached the log file. Thanks very much, Sarina Iwabuchi
This message and any attachment are intended solely for the addressee and may contain confidential information. If you have received this message in error, please send it back to me, and immediately delete it. Please do not use, copy or disclose the information contained in this message or in any attachment. Any views or opinions expressed by the author of this email do not necessarily reflect the views of the University of Nottingham.
This message has been checked for viruses but the contents of an attachment may still contain software viruses which could damage your computer system, you are advised to perform your own checks. Email communications with the University of Nottingham may be monitored as permitted by UK legislation.
Hi Sarina,
Can you please send me the full log of the LGI (e.g. recon-all.log) for this subject?
Thanks,
Marie
On Jul 28, 2014, at 7:23 AM, "Sarina Iwabuchi" <Sarina.Iwabuchi at nottingham.ac.uk https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer<mailto:Sarina.Iwabuchi at nottingham.ac.uk https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>> wrote:
Hi all,
I have been trying to run localGI and have been coming across errors. It creates the filled.mgz file and opens matlab (running 2012a) but crashes straight after with the below errors:
/ reading filled volume...
/set: Variable name must begin with a letter. gunzip: Command not found. ERROR: problem reading fname set: Variable name must begin with a letter. rm: Command not found. SWITCH expression must be a scalar or string constant.
Error in load_mgh (line 158) switch type
Error in MRIread (line 87) [mri.vol, M, mr_parms, volsz] = load_mgh(fspec,[],[],headeronly);
Error in make_outer_surface (line 24) vol=MRIread(filled_volume);
Has anyone come across this? I do have gunzip on my system.
Thanks very much,
Sarina Iwabuchi Division of Psychiatry and Applied Psychology Room B07 Institute of Mental Health Triumph Road University of Nottingham Nottingham NG7 2TU
Sarina Iwabuchi Division of Psychiatry and Applied Psychology Room B07 Institute of Mental Health Triumph Road University of Nottingham Nottingham NG7 2TU
<recon-all.log>
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hi Doug,
I get the following error:
Undefined function 'MRIread' for input arguments of type 'char'.
Sarina
On 29 Jul 2014, at 18:34, Douglas N Greve wrote:
a = MRIread('/Volumes/HD-PNTU3/MISSEDDATA/extn003/surf/tmp-mris_compute_lgi-lh.pial/lh.pial.filled.mgz');
Sarina Iwabuchi Division of Psychiatry and Applied Psychology Room B07 Institute of Mental Health Triumph Road University of Nottingham Nottingham NG7 2TU
This message and any attachment are intended solely for the addressee and may contain confidential information. If you have received this message in error, please send it back to me, and immediately delete it. Please do not use, copy or disclose the information contained in this message or in any attachment. Any views or opinions expressed by the author of this email do not necessarily reflect the views of the University of Nottingham.
This message has been checked for viruses but the contents of an attachment
may still contain software viruses which could damage your computer system, you are advised to perform your own checks. Email communications with the University of Nottingham may be monitored as permitted by UK legislation.
Hi Sarina,
you need to have $FREESURFER_HOME/matlab in your matlab path. Try:
addpath(sprintf('%s/matlab', getenv('FREESURFER_HOME')))
cheers Bruce
On Wed, 30 Jul 2014, Sarina Iwabuchi wrote:
Hi Doug, I get the following error:
Undefined function 'MRIread' for input arguments of type 'char'.
Sarina
On 29 Jul 2014, at 18:34, Douglas N Greve wrote:
a =MRIread('/Volumes/HD-PNTU3/MISSEDDATA/extn003/surf/tmp-mris_compute_lgi-lh. pial/lh.pial.filled.mgz');
Sarina IwabuchiDivision of Psychiatry and Applied Psychology Room B07 Institute of Mental Health Triumph Road University of Nottingham Nottingham NG7 2TU
This message and any attachment are intended solely for the addressee and may contain confidential information. If you have received this message in error, please send it back to me, and immediately delete it. Please do not use, copy or disclose the information contained in this message or in any attachment. Any views or opinions expressed by the author of this email do not necessarily reflect the views of the University of Nottingham.
This message has been checked for viruses but the contents of an attachment may still contain software viruses which could damage your computer system, you are advised to perform your own checks. Email communications with the University of Nottingham may be monitored as permitted by UK legislation.
Hi Bruce,
It still shows the same error:
set: Variable name must begin with a letter. gunzip: Command not found. ERROR: problem reading fname set: Variable name must begin with a letter. rm: Command not found. SWITCH expression must be a scalar or string constant.
Error in load_mgh (line 158) switch type
Error in MRIread (line 87) [mri.vol, M, mr_parms, volsz] = load_mgh(fspec,[],[],headeronly);
Sarina
On 30 Jul 2014, at 14:23, Bruce Fischl wrote:
Hi Sarina,
you need to have $FREESURFER_HOME/matlab in your matlab path. Try:
addpath(sprintf('%s/matlab', getenv('FREESURFER_HOME')))
cheers Bruce
On Wed, 30 Jul 2014, Sarina Iwabuchi wrote:
Hi Doug, I get the following error:
Undefined function 'MRIread' for input arguments of type 'char'.
Sarina
On 29 Jul 2014, at 18:34, Douglas N Greve wrote:
a =MRIread('/Volumes/HD-PNTU3/MISSEDDATA/extn003/surf/tmp-mris_compute_lgi-lh. pial/lh.pial.filled.mgz');
Sarina IwabuchiDivision of Psychiatry and Applied Psychology Room B07 Institute of Mental Health Triumph Road University of Nottingham Nottingham NG7 2TU
This message and any attachment are intended solely for the addressee and may contain confidential information. If you have received this message in error, please send it back to me, and immediately delete it. Please do not use, copy or disclose the information contained in this message or in any attachment. Any views or opinions expressed by the author of this email do not necessarily reflect the views of the University of Nottingham.
This message has been checked for viruses but the contents of an attachment may still contain software viruses which could damage your computer system, you are advised to perform your own checks. Email communications with the University of Nottingham may be monitored as permitted by UK legislation.
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Sarina Iwabuchi Division of Psychiatry and Applied Psychology Room B07 Institute of Mental Health Triumph Road University of Nottingham Nottingham NG7 2TU
This message and any attachment are intended solely for the addressee and may contain confidential information. If you have received this message in error, please send it back to me, and immediately delete it. Please do not use, copy or disclose the information contained in this message or in any attachment. Any views or opinions expressed by the author of this email do not necessarily reflect the views of the University of Nottingham.
This message has been checked for viruses but the contents of an attachment may still contain software viruses which could damage your computer system, you are advised to perform your own checks. Email communications with the University of Nottingham may be monitored as permitted by UK legislation.
Is gunzip in your path? When you open a shell and type which gunzip
what is printed out?
On 07/30/2014 10:45 AM, Sarina Iwabuchi wrote:
Hi Bruce,
It still shows the same error:
set: Variable name must begin with a letter. gunzip: Command not found. ERROR: problem reading fname set: Variable name must begin with a letter. rm: Command not found. SWITCH expression must be a scalar or string constant.
Error in load_mgh (line 158) switch type
Error in MRIread (line 87) [mri.vol, M, mr_parms, volsz] = load_mgh(fspec,[],[],headeronly);
Sarina
On 30 Jul 2014, at 14:23, Bruce Fischl wrote:
Hi Sarina,
you need to have $FREESURFER_HOME/matlab in your matlab path. Try:
addpath(sprintf('%s/matlab', getenv('FREESURFER_HOME')))
cheers Bruce
On Wed, 30 Jul 2014, Sarina Iwabuchi wrote:
Hi Doug, I get the following error:
Undefined function 'MRIread' for input arguments of type 'char'.
Sarina
On 29 Jul 2014, at 18:34, Douglas N Greve wrote:
a =MRIread('/Volumes/HD-PNTU3/MISSEDDATA/extn003/surf/tmp-mris_compute_lgi-lh. pial/lh.pial.filled.mgz');
Sarina IwabuchiDivision of Psychiatry and Applied Psychology Room B07 Institute of Mental Health Triumph Road University of Nottingham Nottingham NG7 2TU
This message and any attachment are intended solely for the addressee and may contain confidential information. If you have received this message in error, please send it back to me, and immediately delete it. Please do not use, copy or disclose the information contained in this message or in any attachment. Any views or opinions expressed by the author of this email do not necessarily reflect the views of the University of Nottingham.
This message has been checked for viruses but the contents of an attachment may still contain software viruses which could damage your computer system, you are advised to perform your own checks. Email communications with the University of Nottingham may be monitored as permitted by UK legislation.
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Sarina Iwabuchi Division of Psychiatry and Applied Psychology Room B07 Institute of Mental Health Triumph Road University of Nottingham Nottingham NG7 2TU
This message and any attachment are intended solely for the addressee and may contain confidential information. If you have received this message in error, please send it back to me, and immediately delete it. Please do not use, copy or disclose the information contained in this message or in any attachment. Any views or opinions expressed by the author of this email do not necessarily reflect the views of the University of Nottingham.
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I get:
/usr/bin/gunzip
On 30 Jul 2014, at 15:58, Douglas N Greve wrote:
Is gunzip in your path? When you open a shell and type which gunzip
what is printed out?
On 07/30/2014 10:45 AM, Sarina Iwabuchi wrote:
Hi Bruce,
It still shows the same error:
set: Variable name must begin with a letter. gunzip: Command not found. ERROR: problem reading fname set: Variable name must begin with a letter. rm: Command not found. SWITCH expression must be a scalar or string constant.
Error in load_mgh (line 158) switch type
Error in MRIread (line 87) [mri.vol, M, mr_parms, volsz] = load_mgh(fspec,[],[],headeronly);
Sarina
On 30 Jul 2014, at 14:23, Bruce Fischl wrote:
Hi Sarina,
you need to have $FREESURFER_HOME/matlab in your matlab path. Try:
addpath(sprintf('%s/matlab', getenv('FREESURFER_HOME')))
cheers Bruce
On Wed, 30 Jul 2014, Sarina Iwabuchi wrote:
Hi Doug, I get the following error:
Undefined function 'MRIread' for input arguments of type 'char'.
Sarina
On 29 Jul 2014, at 18:34, Douglas N Greve wrote:
a =MRIread('/Volumes/HD-PNTU3/MISSEDDATA/extn003/surf/tmp-mris_compute_lgi-lh. pial/lh.pial.filled.mgz');
Sarina IwabuchiDivision of Psychiatry and Applied Psychology Room B07 Institute of Mental Health Triumph Road University of Nottingham Nottingham NG7 2TU
This message and any attachment are intended solely for the addressee and may contain confidential information. If you have received this message in error, please send it back to me, and immediately delete it. Please do not use, copy or disclose the information contained in this message or in any attachment. Any views or opinions expressed by the author of this email do not necessarily reflect the views of the University of Nottingham.
This message has been checked for viruses but the contents of an attachment may still contain software viruses which could damage your computer system, you are advised to perform your own checks. Email communications with the University of Nottingham may be monitored as permitted by UK legislation.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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Sarina Iwabuchi Division of Psychiatry and Applied Psychology Room B07 Institute of Mental Health Triumph Road University of Nottingham Nottingham NG7 2TU
This message and any attachment are intended solely for the addressee and may contain confidential information. If you have received this message in error, please send it back to me, and immediately delete it. Please do not use, copy or disclose the information contained in this message or in any attachment. Any views or opinions expressed by the author of this email do not necessarily reflect the views of the University of Nottingham.
This message has been checked for viruses but the contents of an attachment may still contain software viruses which could damage your computer system, you are advised to perform your own checks. Email communications with the University of Nottingham may be monitored as permitted by UK legislation.
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
Sarina Iwabuchi Division of Psychiatry and Applied Psychology Room B07 Institute of Mental Health Triumph Road University of Nottingham Nottingham NG7 2TU
This message and any attachment are intended solely for the addressee and may contain confidential information. If you have received this message in error, please send it back to me, and immediately delete it. Please do not use, copy or disclose the information contained in this message or in any attachment. Any views or opinions expressed by the author of this email do not necessarily reflect the views of the University of Nottingham.
This message has been checked for viruses but the contents of an attachment
may still contain software viruses which could damage your computer system, you are advised to perform your own checks. Email communications with the University of Nottingham may be monitored as permitted by UK legislation.
And in matlab, what do you get if you type
unix('which gunzip')
On 07/30/2014 11:08 AM, Sarina Iwabuchi wrote:
I get:
/usr/bin/gunzip
On 30 Jul 2014, at 15:58, Douglas N Greve wrote:
Is gunzip in your path? When you open a shell and type which gunzip
what is printed out?
On 07/30/2014 10:45 AM, Sarina Iwabuchi wrote:
Hi Bruce,
It still shows the same error:
set: Variable name must begin with a letter. gunzip: Command not found. ERROR: problem reading fname set: Variable name must begin with a letter. rm: Command not found. SWITCH expression must be a scalar or string constant.
Error in load_mgh (line 158) switch type
Error in MRIread (line 87) [mri.vol, M, mr_parms, volsz] = load_mgh(fspec,[],[],headeronly);
Sarina
On 30 Jul 2014, at 14:23, Bruce Fischl wrote:
Hi Sarina,
you need to have $FREESURFER_HOME/matlab in your matlab path. Try:
addpath(sprintf('%s/matlab', getenv('FREESURFER_HOME')))
cheers Bruce
On Wed, 30 Jul 2014, Sarina Iwabuchi wrote:
Hi Doug, I get the following error:
Undefined function 'MRIread' for input arguments of type 'char'.
Sarina
On 29 Jul 2014, at 18:34, Douglas N Greve wrote:
a =MRIread('/Volumes/HD-PNTU3/MISSEDDATA/extn003/surf/tmp-mris_compute_lgi-lh. pial/lh.pial.filled.mgz');
Sarina IwabuchiDivision of Psychiatry and Applied Psychology Room B07 Institute of Mental Health Triumph Road University of Nottingham Nottingham NG7 2TU
This message and any attachment are intended solely for the addressee and may contain confidential information. If you have received this message in error, please send it back to me, and immediately delete it. Please do not use, copy or disclose the information contained in this message or in any attachment. Any views or opinions expressed by the author of this email do not necessarily reflect the views of the University of Nottingham.
This message has been checked for viruses but the contents of an attachment may still contain software viruses which could damage your computer system, you are advised to perform your own checks. Email communications with the University of Nottingham may be monitored as permitted by UK legislation.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto: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.
Sarina Iwabuchi Division of Psychiatry and Applied Psychology Room B07 Institute of Mental Health Triumph Road University of Nottingham Nottingham NG7 2TU
This message and any attachment are intended solely for the addressee and may contain confidential information. If you have received this message in error, please send it back to me, and immediately delete it. Please do not use, copy or disclose the information contained in this message or in any attachment. Any views or opinions expressed by the author of this email do not necessarily reflect the views of the University of Nottingham.
This message has been checked for viruses but the contents of an attachment may still contain software viruses which could damage your computer system, you are advised to perform your own checks. Email communications with the University of Nottingham may be monitored as permitted by UK legislation.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto: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 mailto: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
Sarina Iwabuchi Division of Psychiatry and Applied Psychology Room B07 Institute of Mental Health Triumph Road University of Nottingham Nottingham NG7 2TU
This message and any attachment are intended solely for the addressee and may contain confidential information. If you have received this message in error, please send it back to me, and immediately delete it. Please do not use, copy or disclose the information contained in this message or in any attachment. Any views or opinions expressed by the author of this email do not necessarily reflect the views of the University of Nottingham.
This message has been checked for viruses but the contents of an attachment may still contain software viruses which could damage your computer system, you are advised to perform your own checks. Email communications with the University of Nottingham may be monitored as permitted by UK legislation.
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set: Variable name must begin with a letter. gunzip: Command not found.
ans =
1
On 30 Jul 2014, at 16:27, Douglas N Greve wrote:
And in matlab, what do you get if you type
unix('which gunzip')
On 07/30/2014 11:08 AM, Sarina Iwabuchi wrote:
I get:
/usr/bin/gunzip
On 30 Jul 2014, at 15:58, Douglas N Greve wrote:
Is gunzip in your path? When you open a shell and type which gunzip
what is printed out?
On 07/30/2014 10:45 AM, Sarina Iwabuchi wrote:
Hi Bruce,
It still shows the same error:
set: Variable name must begin with a letter. gunzip: Command not found. ERROR: problem reading fname set: Variable name must begin with a letter. rm: Command not found. SWITCH expression must be a scalar or string constant.
Error in load_mgh (line 158) switch type
Error in MRIread (line 87) [mri.vol, M, mr_parms, volsz] = load_mgh(fspec,[],[],headeronly);
Sarina
On 30 Jul 2014, at 14:23, Bruce Fischl wrote:
Hi Sarina,
you need to have $FREESURFER_HOME/matlab in your matlab path. Try:
addpath(sprintf('%s/matlab', getenv('FREESURFER_HOME')))
cheers Bruce
On Wed, 30 Jul 2014, Sarina Iwabuchi wrote:
Hi Doug, I get the following error:
Undefined function 'MRIread' for input arguments of type 'char'.
Sarina
On 29 Jul 2014, at 18:34, Douglas N Greve wrote:
a =MRIread('/Volumes/HD-PNTU3/MISSEDDATA/extn003/surf/tmp-mris_compute_lgi-lh. pial/lh.pial.filled.mgz');
Sarina IwabuchiDivision of Psychiatry and Applied Psychology Room B07 Institute of Mental Health Triumph Road University of Nottingham Nottingham NG7 2TU
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Sarina Iwabuchi Division of Psychiatry and Applied Psychology Room B07 Institute of Mental Health Triumph Road University of Nottingham Nottingham NG7 2TU
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-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
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Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Sarina Iwabuchi Division of Psychiatry and Applied Psychology Room B07 Institute of Mental Health Triumph Road University of Nottingham Nottingham NG7 2TU
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-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
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Sarina Iwabuchi Division of Psychiatry and Applied Psychology Room B07 Institute of Mental Health Triumph Road University of Nottingham Nottingham NG7 2TU
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OK, so there is something going wrong with your unix environment inside of matlab (this is not a freesurfer problem per se). Is there someone around that you can ask about it? Can someone else try this last command to see if it works? There might be something wrong with the resource file of the shell you are using. Sorry, I don't know quite what else to suggest. doug
On 07/30/2014 11:32 AM, Sarina Iwabuchi wrote:
set: Variable name must begin with a letter. gunzip: Command not found.
ans =
1On 30 Jul 2014, at 16:27, Douglas N Greve wrote:
And in matlab, what do you get if you type
unix('which gunzip')
On 07/30/2014 11:08 AM, Sarina Iwabuchi wrote:
I get:
/usr/bin/gunzip
On 30 Jul 2014, at 15:58, Douglas N Greve wrote:
Is gunzip in your path? When you open a shell and type which gunzip
what is printed out?
On 07/30/2014 10:45 AM, Sarina Iwabuchi wrote:
Hi Bruce,
It still shows the same error:
set: Variable name must begin with a letter. gunzip: Command not found. ERROR: problem reading fname set: Variable name must begin with a letter. rm: Command not found. SWITCH expression must be a scalar or string constant.
Error in load_mgh (line 158) switch type
Error in MRIread (line 87) [mri.vol, M, mr_parms, volsz] = load_mgh(fspec,[],[],headeronly);
Sarina
On 30 Jul 2014, at 14:23, Bruce Fischl wrote:
Hi Sarina,
you need to have $FREESURFER_HOME/matlab in your matlab path. Try:
addpath(sprintf('%s/matlab', getenv('FREESURFER_HOME')))
cheers Bruce
On Wed, 30 Jul 2014, Sarina Iwabuchi wrote:
> Hi Doug, > I get the following error: > > Undefined function 'MRIread' for input arguments of type 'char'. > > Sarina > > On 29 Jul 2014, at 18:34, Douglas N Greve wrote: > > a = > MRIread('/Volumes/HD-PNTU3/MISSEDDATA/extn003/surf/tmp-mris_compute_lgi-lh. > pial/lh.pial.filled.mgz'); > > > Sarina IwabuchiDivision of Psychiatry and Applied Psychology > Room B07 Institute of Mental Health > Triumph Road > University of Nottingham > Nottingham NG7 2TU > > > This message and any attachment are intended solely for the > addressee and > may contain confidential information. If you have received this > message in > error, please send it back to me, and immediately delete it. > Please do not > use, copy or disclose the information contained in this message or > in any > attachment. Any views or opinions expressed by the author of this > email do > not necessarily reflect the views of the University of Nottingham. > > This message has been checked for viruses but the contents of an > attachment > may still contain software viruses which could damage your > computer system, > you are advised to perform your own checks. Email communications > with the > University of Nottingham may be monitored as permitted by UK > legislation. > > > _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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Sarina Iwabuchi Division of Psychiatry and Applied Psychology Room B07 Institute of Mental Health Triumph Road University of Nottingham Nottingham NG7 2TU
This message and any attachment are intended solely for the addressee and may contain confidential information. If you have received this message in error, please send it back to me, and immediately delete it. Please do not use, copy or disclose the information contained in this message or in any attachment. Any views or opinions expressed by the author of this email do not necessarily reflect the views of the University of Nottingham.
This message has been checked for viruses but the contents of an attachment may still contain software viruses which could damage your computer system, you are advised to perform your own checks. Email communications with the University of Nottingham may be monitored as permitted by UK legislation.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto: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 mailto: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
Sarina Iwabuchi Division of Psychiatry and Applied Psychology Room B07 Institute of Mental Health Triumph Road University of Nottingham Nottingham NG7 2TU
This message and any attachment are intended solely for the addressee and may contain confidential information. If you have received this message in error, please send it back to me, and immediately delete it. Please do not use, copy or disclose the information contained in this message or in any attachment. Any views or opinions expressed by the author of this email do not necessarily reflect the views of the University of Nottingham.
This message has been checked for viruses but the contents of an attachment may still contain software viruses which could damage your computer system, you are advised to perform your own checks. Email communications with the University of Nottingham may be monitored as permitted by UK legislation.
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
Sarina Iwabuchi Division of Psychiatry and Applied Psychology Room B07 Institute of Mental Health Triumph Road University of Nottingham Nottingham NG7 2TU
This message and any attachment are intended solely for the addressee and may contain confidential information. If you have received this message in error, please send it back to me, and immediately delete it. Please do not use, copy or disclose the information contained in this message or in any attachment. Any views or opinions expressed by the author of this email do not necessarily reflect the views of the University of Nottingham.
This message has been checked for viruses but the contents of an attachment may still contain software viruses which could damage your computer system, you are advised to perform your own checks. Email communications with the University of Nottingham may be monitored as permitted by UK legislation.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hi Doug,
I have been getting an error message when preprocessing data on 2 subjects in stable 4 (using the same command worked fine, however, with several others).
The command I ran was: preproc-sess -smout fmcsm6 -fwhm 6 -s Con7_self -df sesspar
The error message I get is pasted below.
Any suggestions about how to fix this would be much appreciated!
Thanks,
Ben
/autofs/space/tyra_001/users/gcoombs/self/subjects/Con7_self/bold 3dvolreg -verbose -dfile 003/fmc.mcdat -base 003/tmp.mc-afni2.6069/tempvol.nii.gz -prefix 003/tmp.mc-afni2.6069/outvol.nii.gz 003/tmp.mc-afni2.6069/invol.nii.gz ++ 3dvolreg: AFNI version=AFNI_2011_12_21_1014 (Aug 29 2012) [64-bit] ++ Authored by: RW Cox *+ WARNING: If you are performing spatial transformations on an oblique dset, such as 003/tmp.mc-afni2.6069/tempvol.nii.gz, or viewing/combining it with volumes of differing obliquity, you should consider running: 3dWarp -deoblique on this and other oblique datasets in the same session. See 3dWarp -help for details. ++ Oblique dataset:003/tmp.mc-afni2.6069/tempvol.nii.gz is 12.500000 degrees from plumb. ++ Reading in base dataset 003/tmp.mc-afni2.6069/tempvol.nii.gz ++ Oblique dataset:003/tmp.mc-afni2.6069/invol.nii.gz is 17.700005 degrees from plumb. ++ centers of base and input datasets are 26.86 mm apart ** Input 003/tmp.mc-afni2.6069/invol.nii.gz and base 003/tmp.mc-afni2.6069/tempvol.nii.gz don't have same dimensions! Input: nx=64 ny=64 nz=33 Base: nx=256 ny=256 nz=128 ** Input 003/tmp.mc-afni2.6069/invol.nii.gz and base 003/tmp.mc-afni2.6069/tempvol.nii.gz don't have same grid spacing! Input: dx= 2.969 dy= 2.969 dz= 3.000 Base: dx= 1.000 dy=-1.000 dz= 1.330 ** Input 003/tmp.mc-afni2.6069/invol.nii.gz and base 003/tmp.mc-afni2.6069/tempvol.nii.gz don't have same orientation! Input: R-L A-P I-S Base: A-P S-I R-L ** FATAL ERROR: perhaps you could make your datasets match? ERROR: 3dvolreg Invalid null command. ERROR: mc-sess failed
Benjamin Brent, M.D., M.S. Massachusetts Mental Health Center 75 Fenwood Road, Room 618 Boston, MA 02115 617-754-1262
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Is the size of the volume (row, cols, or slices) changing between the runs?
On 07/30/2014 04:18 PM, bbrent@bidmc.harvard.edu wrote:
Hi Doug,
I have been getting an error message when preprocessing data on 2 subjects in stable 4 (using the same command worked fine, however, with several others).
The command I ran was: preproc-sess -smout fmcsm6 -fwhm 6 -s Con7_self -df sesspar
The error message I get is pasted below.
Any suggestions about how to fix this would be much appreciated!
Thanks,
Ben
/autofs/space/tyra_001/users/gcoombs/self/subjects/Con7_self/bold 3dvolreg -verbose -dfile 003/fmc.mcdat -base 003/tmp.mc-afni2.6069/tempvol.nii.gz -prefix 003/tmp.mc-afni2.6069/outvol.nii.gz 003/tmp.mc-afni2.6069/invol.nii.gz ++ 3dvolreg: AFNI version=AFNI_2011_12_21_1014 (Aug 29 2012) [64-bit] ++ Authored by: RW Cox *+ WARNING: If you are performing spatial transformations on an oblique dset, such as 003/tmp.mc-afni2.6069/tempvol.nii.gz, or viewing/combining it with volumes of differing obliquity, you should consider running: 3dWarp -deoblique on this and other oblique datasets in the same session. See 3dWarp -help for details. ++ Oblique dataset:003/tmp.mc-afni2.6069/tempvol.nii.gz is 12.500000 degrees from plumb. ++ Reading in base dataset 003/tmp.mc-afni2.6069/tempvol.nii.gz ++ Oblique dataset:003/tmp.mc-afni2.6069/invol.nii.gz is 17.700005 degrees from plumb. ++ centers of base and input datasets are 26.86 mm apart ** Input 003/tmp.mc-afni2.6069/invol.nii.gz and base 003/tmp.mc-afni2.6069/tempvol.nii.gz don't have same dimensions! Input: nx=64 ny=64 nz=33 Base: nx=256 ny=256 nz=128 ** Input 003/tmp.mc-afni2.6069/invol.nii.gz and base 003/tmp.mc-afni2.6069/tempvol.nii.gz don't have same grid spacing! Input: dx= 2.969 dy= 2.969 dz= 3.000 Base: dx= 1.000 dy=-1.000 dz= 1.330 ** Input 003/tmp.mc-afni2.6069/invol.nii.gz and base 003/tmp.mc-afni2.6069/tempvol.nii.gz don't have same orientation! Input: R-L A-P I-S Base: A-P S-I R-L ** FATAL ERROR: perhaps you could make your datasets match? ERROR: 3dvolreg Invalid null command. ERROR: mc-sess failed
Benjamin Brent, M.D., M.S. Massachusetts Mental Health Center 75 Fenwood Road, Room 618 Boston, MA 02115 617-754-1262
This message is intended for the use of the person(s) to whom it may be addressed. It may contain information that is privileged, confidential, or otherwise protected from disclosure under applicable law. If you are not the intended recipient, any dissemination, distribution, copying, or use of this information is prohibited. If you have received this message in error, please permanently delete it and immediately notify the sender. Thank you.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hi Doug,
For the functional runs, it's the same task during each run, so the volumes shouldn't be changing.
Ben
Benjamin Brent, M.D., M.S. Massachusetts Mental Health Center 75 Fenwood Road, Room 618 Boston, MA 02115 617-754-1262
This message is intended for the use of the person(s) to whom it may be addressed. It may contain information that is privileged, confidential, or otherwise protected from disclosure under applicable law. If you are not the intended recipient, any dissemination, distribution, copying, or use of this information is prohibited. If you have received this message in error, please permanently delete it and immediately notify the sender. Thank you. ________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] On Behalf Of Douglas N Greve [greve@nmr.mgh.harvard.edu] Sent: Wednesday, July 30, 2014 4:53 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Preprocessing Error
Is the size of the volume (row, cols, or slices) changing between the runs?
On 07/30/2014 04:18 PM, bbrent@bidmc.harvard.edu wrote:
Hi Doug,
I have been getting an error message when preprocessing data on 2 subjects in stable 4 (using the same command worked fine, however, with several others).
The command I ran was: preproc-sess -smout fmcsm6 -fwhm 6 -s Con7_self -df sesspar
The error message I get is pasted below.
Any suggestions about how to fix this would be much appreciated!
Thanks,
Ben
/autofs/space/tyra_001/users/gcoombs/self/subjects/Con7_self/bold 3dvolreg -verbose -dfile 003/fmc.mcdat -base 003/tmp.mc-afni2.6069/tempvol.nii.gz -prefix 003/tmp.mc-afni2.6069/outvol.nii.gz 003/tmp.mc-afni2.6069/invol.nii.gz ++ 3dvolreg: AFNI version=AFNI_2011_12_21_1014 (Aug 29 2012) [64-bit] ++ Authored by: RW Cox *+ WARNING: If you are performing spatial transformations on an oblique dset, such as 003/tmp.mc-afni2.6069/tempvol.nii.gz, or viewing/combining it with volumes of differing obliquity, you should consider running: 3dWarp -deoblique on this and other oblique datasets in the same session. See 3dWarp -help for details. ++ Oblique dataset:003/tmp.mc-afni2.6069/tempvol.nii.gz is 12.500000 degrees from plumb. ++ Reading in base dataset 003/tmp.mc-afni2.6069/tempvol.nii.gz ++ Oblique dataset:003/tmp.mc-afni2.6069/invol.nii.gz is 17.700005 degrees from plumb. ++ centers of base and input datasets are 26.86 mm apart ** Input 003/tmp.mc-afni2.6069/invol.nii.gz and base 003/tmp.mc-afni2.6069/tempvol.nii.gz don't have same dimensions! Input: nx=64 ny=64 nz=33 Base: nx=256 ny=256 nz=128 ** Input 003/tmp.mc-afni2.6069/invol.nii.gz and base 003/tmp.mc-afni2.6069/tempvol.nii.gz don't have same grid spacing! Input: dx= 2.969 dy= 2.969 dz= 3.000 Base: dx= 1.000 dy=-1.000 dz= 1.330 ** Input 003/tmp.mc-afni2.6069/invol.nii.gz and base 003/tmp.mc-afni2.6069/tempvol.nii.gz don't have same orientation! Input: R-L A-P I-S Base: A-P S-I R-L ** FATAL ERROR: perhaps you could make your datasets match? ERROR: 3dvolreg Invalid null command. ERROR: mc-sess failed
Benjamin Brent, M.D., M.S. Massachusetts Mental Health Center 75 Fenwood Road, Room 618 Boston, MA 02115 617-754-1262
This message is intended for the use of the person(s) to whom it may be addressed. It may contain information that is privileged, confidential, or otherwise protected from disclosure under applicable law. If you are not the intended recipient, any dissemination, distribution, copying, or use of this information is prohibited. If you have received this message in error, please permanently delete it and immediately notify the sender. Thank you.
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.
should not be or do you know for sure because you checked it? doug
On 07/31/2014 10:42 AM, bbrent@bidmc.harvard.edu wrote:
Hi Doug,
For the functional runs, it's the same task during each run, so the volumes shouldn't be changing.
Ben
Benjamin Brent, M.D., M.S. Massachusetts Mental Health Center 75 Fenwood Road, Room 618 Boston, MA 02115 617-754-1262
This message is intended for the use of the person(s) to whom it may be addressed. It may contain information that is privileged, confidential, or otherwise protected from disclosure under applicable law. If you are not the intended recipient, any dissemination, distribution, copying, or use of this information is prohibited. If you have received this message in error, please permanently delete it and immediately notify the sender. Thank you. ________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] On Behalf Of Douglas N Greve [greve@nmr.mgh.harvard.edu] Sent: Wednesday, July 30, 2014 4:53 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Preprocessing Error
Is the size of the volume (row, cols, or slices) changing between the runs?
On 07/30/2014 04:18 PM, bbrent@bidmc.harvard.edu wrote:
Hi Doug,
I have been getting an error message when preprocessing data on 2 subjects in stable 4 (using the same command worked fine, however, with several others).
The command I ran was: preproc-sess -smout fmcsm6 -fwhm 6 -s Con7_self -df sesspar
The error message I get is pasted below.
Any suggestions about how to fix this would be much appreciated!
Thanks,
Ben
/autofs/space/tyra_001/users/gcoombs/self/subjects/Con7_self/bold 3dvolreg -verbose -dfile 003/fmc.mcdat -base 003/tmp.mc-afni2.6069/tempvol.nii.gz -prefix 003/tmp.mc-afni2.6069/outvol.nii.gz 003/tmp.mc-afni2.6069/invol.nii.gz ++ 3dvolreg: AFNI version=AFNI_2011_12_21_1014 (Aug 29 2012) [64-bit] ++ Authored by: RW Cox *+ WARNING: If you are performing spatial transformations on an oblique dset, such as 003/tmp.mc-afni2.6069/tempvol.nii.gz, or viewing/combining it with volumes of differing obliquity, you should consider running: 3dWarp -deoblique on this and other oblique datasets in the same session. See 3dWarp -help for details. ++ Oblique dataset:003/tmp.mc-afni2.6069/tempvol.nii.gz is 12.500000 degrees from plumb. ++ Reading in base dataset 003/tmp.mc-afni2.6069/tempvol.nii.gz ++ Oblique dataset:003/tmp.mc-afni2.6069/invol.nii.gz is 17.700005 degrees from plumb. ++ centers of base and input datasets are 26.86 mm apart ** Input 003/tmp.mc-afni2.6069/invol.nii.gz and base 003/tmp.mc-afni2.6069/tempvol.nii.gz don't have same dimensions! Input: nx=64 ny=64 nz=33 Base: nx=256 ny=256 nz=128 ** Input 003/tmp.mc-afni2.6069/invol.nii.gz and base 003/tmp.mc-afni2.6069/tempvol.nii.gz don't have same grid spacing! Input: dx= 2.969 dy= 2.969 dz= 3.000 Base: dx= 1.000 dy=-1.000 dz= 1.330 ** Input 003/tmp.mc-afni2.6069/invol.nii.gz and base 003/tmp.mc-afni2.6069/tempvol.nii.gz don't have same orientation! Input: R-L A-P I-S Base: A-P S-I R-L ** FATAL ERROR: perhaps you could make your datasets match? ERROR: 3dvolreg Invalid null command. ERROR: mc-sess failed
Benjamin Brent, M.D., M.S. Massachusetts Mental Health Center 75 Fenwood Road, Room 618 Boston, MA 02115 617-754-1262
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