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
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>>>>>>> University of Nottingham may be monitored as permitted by UK
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>>>>>>>
>>>>>>>
>>>>>>>
>>>>>> _______________________________________________
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>>>>>> the e-mail
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>>>>>> 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
>>>> gr...@nmr.mgh.harvard.edu <mailto: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/
>>>>
>>>> _______________________________________________
>>>> 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
>> 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/
>>
>> _______________________________________________
>> 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
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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