Re: [Freesurfer] FreeSurfer LocalGI error

[Manoj Kumar]

Thank you very much, Dear Andrew! for your expert advise. I really
appreciated.
Its worked.

Best Regards
Manoj

On Tue, Jan 16, 2018 at 10:39 PM, Hoopes, Andrew 
wrote:

> Hi Manoj,
>
> This probably has to do with SIP being enabled, which blocks libraries
> stored in /usr. I would suggest disabling SIP and rerunning to see if
> that fixes things:
> http://osxdaily.com/2015/10/05/disable-rootless-system-
> integrity-protection-mac-os-x/
>
> best,
> Andrew
>
>
> On Jan 16, 2018, at 2:59 AM, Manoj Kumar  wrote:
>
> Hello Dear FreeSurfer Experts,
>
> I am trying to run "recon-all -s subject  -localGI" command on my Mac bash
> terminal. I am getting following error.
>
> I am using using Freesurfer V 6.0 and running on MacOS High Sierra
> (version 10.13)
>
> I also run the istallation update :"sudo -E fs_update" as per suggestion
> on the release note but still getting same error.
>
> Any help to resolve this issue would be greatly appreciated.
> Thank you so much for all your help and support.
>
> Best regards
> Manoj
>
> ***
> Manojs-iMac:cases manojkumar$ export SUBJECTS_DIR=/Users/
> manojkumar/fs_dmd_process/cases/HRUDAY/bert/surf
> Manojs-iMac:cases manojkumar$ cd $SUBJECTS_DIR
> Manojs-iMac:surf manojkumar$ mris_compute_lgi --i lh.pial
> =
> rm -Rf /Users/manojkumar/fs_dmd_process/cases/HRUDAY/bert/
> surf/tmp-mris_compute_lgi-lh.pial
> =
> =
> mkdir -p /Users/manojkumar/fs_dmd_process/cases/HRUDAY/bert/
> surf/tmp-mris_compute_lgi-lh.pial
> =
> =
> mris_fill -c -r 1 lh.pial /Users/manojkumar/fs_dmd_
> process/cases/HRUDAY/bert/surf/tmp-mris_compute_lgi-lh.
> pial/lh.pial.filled.mgz
> =
> dyld: lazy symbol binding failed: Symbol not found: ___emutls_get_address
>   Referenced from: /Applications/freesurfer/bin/.
> ./lib/gcc/lib/libgomp.1.dylib
>   Expected in: /usr/lib/libSystem.B.dylib
>
> dyld: Symbol not found: ___emutls_get_address
>   Referenced from: /Applications/freesurfer/bin/.
> ./lib/gcc/lib/libgomp.1.dylib
>   Expected in: /usr/lib/libSystem.B.dylib
>
> Abort
> ERROR: mris_fill -c -r 1 lh.pial /Users/manojkumar/fs_dmd_
> process/cases/HRUDAY/bert/surf/tmp-mris_compute_lgi-lh.pial/lh.pial.filled.mgz
> failed!
> Manojs-iMac:surf manojkumar$
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>
>
>
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Re: [Freesurfer] FreeSurfer LocalGI error

[Hoopes, Andrew]

Hi Manoj,

This probably has to do with SIP being enabled, which blocks libraries stored 
in /usr. I would suggest disabling SIP and rerunning to see if that fixes 
things:
http://osxdaily.com/2015/10/05/disable-rootless-system-integrity-protection-mac-os-x/

best,
Andrew


On Jan 16, 2018, at 2:59 AM, Manoj Kumar 
mailto:verman...@gmail.com>> wrote:

Hello Dear FreeSurfer Experts,

I am trying to run "recon-all -s subject  -localGI" command on my Mac bash 
terminal. I am getting following error.

I am using using Freesurfer V 6.0 and running on MacOS High Sierra (version 
10.13)

I also run the istallation update :"sudo -E fs_update" as per suggestion on the 
release note but still getting same error.

Any help to resolve this issue would be greatly appreciated.
Thank you so much for all your help and support.

Best regards
Manoj

***
Manojs-iMac:cases manojkumar$ export 
SUBJECTS_DIR=/Users/manojkumar/fs_dmd_process/cases/HRUDAY/bert/surf
Manojs-iMac:cases manojkumar$ cd $SUBJECTS_DIR
Manojs-iMac:surf manojkumar$ mris_compute_lgi --i lh.pial
=
rm -Rf 
/Users/manojkumar/fs_dmd_process/cases/HRUDAY/bert/surf/tmp-mris_compute_lgi-lh.pial
=
=
mkdir -p 
/Users/manojkumar/fs_dmd_process/cases/HRUDAY/bert/surf/tmp-mris_compute_lgi-lh.pial
=
=
mris_fill -c -r 1 lh.pial 
/Users/manojkumar/fs_dmd_process/cases/HRUDAY/bert/surf/tmp-mris_compute_lgi-lh.pial/lh.pial.filled.mgz
=
dyld: lazy symbol binding failed: Symbol not found: ___emutls_get_address
  Referenced from: /Applications/freesurfer/bin/../lib/gcc/lib/libgomp.1.dylib
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ___emutls_get_address
  Referenced from: /Applications/freesurfer/bin/../lib/gcc/lib/libgomp.1.dylib
  Expected in: /usr/lib/libSystem.B.dylib

Abort
ERROR: mris_fill -c -r 1 lh.pial 
/Users/manojkumar/fs_dmd_process/cases/HRUDAY/bert/surf/tmp-mris_compute_lgi-lh.pial/lh.pial.filled.mgz
 failed!
Manojs-iMac:surf manojkumar$
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[Freesurfer] FreeSurfer LocalGI error

[Manoj Kumar]

Hello Dear FreeSurfer Experts,


I am trying to run "recon-all -s subject  -localGI" command on my Mac bash
terminal. I am getting following error.


I am using using Freesurfer V 6.0 and running on MacOS High Sierra (version
10.13)


I also run the istallation update :"sudo -E fs_update" as per suggestion on
the release note but still getting same error.


Any help to resolve this issue would be greatly appreciated.

Thank you so much for all your help and support.


Best regards

Manoj


***

Manojs-iMac:cases manojkumar$ export
SUBJECTS_DIR=/Users/manojkumar/fs_dmd_process/cases/HRUDAY/bert/surf

Manojs-iMac:cases manojkumar$ cd $SUBJECTS_DIR

Manojs-iMac:surf manojkumar$ mris_compute_lgi --i lh.pial

=

rm -Rf
/Users/manojkumar/fs_dmd_process/cases/HRUDAY/bert/surf/tmp-mris_compute_lgi-lh.pial

=

=

mkdir -p
/Users/manojkumar/fs_dmd_process/cases/HRUDAY/bert/surf/tmp-mris_compute_lgi-lh.pial

=

=

mris_fill -c -r 1 lh.pial
/Users/manojkumar/fs_dmd_process/cases/HRUDAY/bert/surf/tmp-mris_compute_lgi-lh.pial/lh.pial.filled.mgz

=

dyld: lazy symbol binding failed: Symbol not found: ___emutls_get_address

  Referenced from:
/Applications/freesurfer/bin/../lib/gcc/lib/libgomp.1.dylib

  Expected in: /usr/lib/libSystem.B.dylib


dyld: Symbol not found: ___emutls_get_address

  Referenced from:
/Applications/freesurfer/bin/../lib/gcc/lib/libgomp.1.dylib

  Expected in: /usr/lib/libSystem.B.dylib


Abort

ERROR: mris_fill -c -r 1 lh.pial
/Users/manojkumar/fs_dmd_process/cases/HRUDAY/bert/surf/tmp-mris_compute_lgi-lh.pial/lh.pial.filled.mgz
failed!

Manojs-iMac:surf manojkumar$
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addressed. If you believe this e-mail was sent to you in error and the e-mail
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but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

Re: [Freesurfer] LocalGI error {Disarmed}

[Douglas N Greve]

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 =
>
>   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
>>>
>>>
>>> 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
>>
>>
>> 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 o

Re: [Freesurfer] LocalGI error {Disarmed}

[Sarina Iwabuchi]

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
>> 
>> 
>> 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
> 
> 
> 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 
 https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
 
 
>>> 
>>> -- 
>>> Douglas N. Greve, Ph.D.
>>> MGH-NMR Center
>>> gr...@nmr.mgh.harvard.edu 

Re: [Freesurfer] LocalGI error {Disarmed}

[Douglas N Greve]

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 
 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 
>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>>
>>>
>>
>> -- 
>> Douglas N. Greve, Ph.D.
>> MGH-NMR Center
>> gr...@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/
>>
>> ___

Re: [Freesurfer] LocalGI error {Disarmed}

[Sarina Iwabuchi]

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
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>>> ___
>>> Freesurfer mailing list
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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.
>> 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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>> 
>> 
> 
> -- 
> Douglas N. Greve, Ph.D.
> MGH-NMR Center
> gr...@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
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> 
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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

Re: [Freesurfer] LocalGI error {Disarmed}

[Douglas N Greve]

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
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>> 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.
>
>
>
>
>
> ___
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> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>

-- 
Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@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
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Re: [Freesurfer] LocalGI error {Disarmed}

[Sarina Iwabuchi]

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
> 
> 
> 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.





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Re: [Freesurfer] LocalGI error {Disarmed}

[Bruce Fischl]

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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but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

Re: [Freesurfer] LocalGI error {Disarmed}

[Sarina Iwabuchi]

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.









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contains patient information, please contact the Partners Compliance HelpLine at
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but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

Re: [Freesurfer] LocalGI error {Disarmed}

[Douglas N Greve]

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 
>  >
>  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" > nottingham.ac.uk  
>> >  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
>>
>> 
>
>
>
> ___
> 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
gr...@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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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.

Re: [Freesurfer] LocalGI error {Disarmed}

[Marie Schaer]

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 
mailto:sarina.iwabu...@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" 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



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contains patient information, please contact the Partners Compliance HelpLine at
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but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

Re: [Freesurfer] LocalGI error

[Sarina Iwabuchi]

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"  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
> 
> 

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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Re: [Freesurfer] LocalGI error {Disarmed}

[Sarina Iwabuchi]

  


Hi Marie,I've attached the log file.Thanks very much,Sarina Iwabuchi

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recon-all.log
Description: Binary data
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" > 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 IwabuchiDivision of Psychiatry and Applied PsychologyRoom B07 Institute of Mental HealthTriumph RoadUniversity of NottinghamNottingham NG7 2TU

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Re: [Freesurfer] LocalGI error

[Marie Schaer]

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" 
mailto:sarina.iwabu...@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



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Nottingham may be monitored as permitted by UK legislation.

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[Freesurfer] LocalGI error

[Sarina Iwabuchi]

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


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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