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
>> 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
