Re: [Freesurfer] Matlab error in Freesurfer

2019-03-14 Thread Miguel Ángel Rivas Fernández 
External Email - Use Caution

Could it be a solution to reinstall freesurfer? I tried to install a newer
gcc version and now Matlab gave to me this error



--
ERROR: FreeSurfer environment FREESURFER_HOME is not defined.
  If you are outside the NMR-Martinos Center, please set this
  variable to the location where you installed FreeSurfer.
  If you are inside the NMR-Martinos Center, please source
  the standard environment. If you need to install FreeSurfer,
  go to: http://surfer.nmr.mgh.harvard.edu
--

Attempting to use /Applications/freesurfer directory.
using /Applications/freesurfer/subjects/10018/mri/aseg.mgz aseg volume to
correct midline
setting seed for random number generator to 1234
mris_ca_label: SUBJECTS_DIR not defined in environment
No such file or directory
mris_ca_label -aseg /Applications/freesurfer/subjects/10018/mri/aseg.mgz
-seed 1234 10018 lh
/Applications/freesurfer/subjects/10018/surf/lh.sphere.reg
/Applications/freesurfer/average/lh.curvature.buckner40.filled.desikan_killiany.2010-03-25.gcs
/Applications/freesurfer/subjects/10018/label/lh.aparc.annot: Signal 124

ans =

   252



Best,

El jue., 14 mar. 2019 a las 18:59, Miguel Ángel Rivas Fernández (<
miguelrivasf...@gmail.com>) escribió:

>
> Hello Douglas,
>
> Yes it works
>
> El jue., 14 mar. 2019 a las 18:51, Greve, Douglas N.,Ph.D. (<
> dgr...@mgh.harvard.edu>) escribió:
>
>> It looks like the library is not set up properly. Does freesurfer work
>> outside of matlab?
>>
>> On 3/14/19 1:46 PM, Miguel Ángel Rivas Fernández wrote:
>> >
>> > External Email - Use Caution
>> >
>> >
>> > Dear Freesurfer devs,
>> >
>> >
>> > Have you had occasion to review this error?. Could it be due to the
>> > gcc version?
>> >
>> > Thank you very much for your help.
>> >
>> >
>> > Best regards,
>> >
>> > El mié., 13 mar. 2019 a las 16:09, Miguel Ángel Rivas Fernández
>> > (mailto:miguelrivasf...@gmail.com>>)
>> escribió:
>> >
>> >
>> > Dear Freesurfer experts,
>> >
>> > I am trying to run Freesurfer commands (eg. mri_ca_label) using
>> > Matlab in a Mac computer (macOS High Sierra 10.13.6 version)
>> > and I'm receiving the following error that I suspect are due to
>> > library incompatibilities:
>> >
>> >
>> > 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
>> >
>> > mris_ca_label -aseg
>> > /Applications/freesurfer/subjects/10018/mri/aseg.mgz -seed 1234
>> > 10018 lh
>> > /Applications/freesurfer/subjects/10018/surf/lh.sphere.reg
>> >
>>  
>> /Applications/freesurfer/average/lh.curvature.buckner40.filled.desikan_killiany.2010-03-25.gcs
>> > /Applications/freesurfer/subjects/10018/label/lh.aparc.annot:
>> Aborted
>> >
>> > ans =
>> >
>> >134
>> >
>> >
>> >
>> > I realized that this error has been previously reported
>> > <
>> https://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/2017-November/054961.html
>> >
>> > and, as Andrew said, one of the possible solutions could be to
>> > disable the SIP (System Protection Integrity). I have disabled the
>> > SIP following the instructions indicated here
>> > <
>> http://osxdaily.com/2015/10/05/disable-rootless-system-integrity-protection-mac-os-x/
>> >
>> > but unfortunately Matlab continues giving the same error.
>> >
>> >
>> > How could I solve this problem?. Any help would be appreciated.
>> >
>> >
>> > Thanks in advance.
>> >
>> > Best,
>> >
>> > --
>> > *Miguel Ángel Rivas Fernández*
>> >
>> >
>> >
>> > --
>> > *Miguel Ángel Rivas Fernández*
>> >
>> > ___
>> > Freesurfer mailing list
>> > Freesurfer@nmr.mgh.harvard.edu
>> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>
>>
>> ___
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
>
> --
> *Miguel Ángel Rivas Fernández*
>


-- 
*Miguel Ángel Rivas Fernández*
___
Freesurfer mailing list
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Re: [Freesurfer] Matlab error in Freesurfer

2019-03-14 Thread Miguel Ángel Rivas Fernández 
External Email - Use Caution

Hello Douglas,

Yes it works

El jue., 14 mar. 2019 a las 18:51, Greve, Douglas N.,Ph.D. (<
dgr...@mgh.harvard.edu>) escribió:

> It looks like the library is not set up properly. Does freesurfer work
> outside of matlab?
>
> On 3/14/19 1:46 PM, Miguel Ángel Rivas Fernández wrote:
> >
> > External Email - Use Caution
> >
> >
> > Dear Freesurfer devs,
> >
> >
> > Have you had occasion to review this error?. Could it be due to the
> > gcc version?
> >
> > Thank you very much for your help.
> >
> >
> > Best regards,
> >
> > El mié., 13 mar. 2019 a las 16:09, Miguel Ángel Rivas Fernández
> > (mailto:miguelrivasf...@gmail.com>>)
> escribió:
> >
> >
> > Dear Freesurfer experts,
> >
> > I am trying to run Freesurfer commands (eg. mri_ca_label) using
> > Matlab in a Mac computer (macOS High Sierra 10.13.6 version)
> > and I'm receiving the following error that I suspect are due to
> > library incompatibilities:
> >
> >
> > 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
> >
> > mris_ca_label -aseg
> > /Applications/freesurfer/subjects/10018/mri/aseg.mgz -seed 1234
> > 10018 lh
> > /Applications/freesurfer/subjects/10018/surf/lh.sphere.reg
> >
>  
> /Applications/freesurfer/average/lh.curvature.buckner40.filled.desikan_killiany.2010-03-25.gcs
> > /Applications/freesurfer/subjects/10018/label/lh.aparc.annot: Aborted
> >
> > ans =
> >
> >134
> >
> >
> >
> > I realized that this error has been previously reported
> > <
> https://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/2017-November/054961.html
> >
> > and, as Andrew said, one of the possible solutions could be to
> > disable the SIP (System Protection Integrity). I have disabled the
> > SIP following the instructions indicated here
> > <
> http://osxdaily.com/2015/10/05/disable-rootless-system-integrity-protection-mac-os-x/
> >
> > but unfortunately Matlab continues giving the same error.
> >
> >
> > How could I solve this problem?. Any help would be appreciated.
> >
> >
> > Thanks in advance.
> >
> > Best,
> >
> > --
> > *Miguel Ángel Rivas Fernández*
> >
> >
> >
> > --
> > *Miguel Ángel Rivas Fernández*
> >
> > ___
> > Freesurfer mailing list
> > Freesurfer@nmr.mgh.harvard.edu
> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer



-- 
*Miguel Ángel Rivas Fernández*
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Re: [Freesurfer] Matlab error in Freesurfer

2019-03-14 Thread Greve, Douglas N.,Ph.D. 
It looks like the library is not set up properly. Does freesurfer work 
outside of matlab?

On 3/14/19 1:46 PM, Miguel Ángel Rivas Fernández wrote:
>
> External Email - Use Caution
>
>
> Dear Freesurfer devs,
>
>
> Have you had occasion to review this error?. Could it be due to the 
> gcc version?
>
> Thank you very much for your help.
>
>
> Best regards,
>
> El mié., 13 mar. 2019 a las 16:09, Miguel Ángel Rivas Fernández 
> (mailto:miguelrivasf...@gmail.com>>) escribió:
>
>
> Dear Freesurfer experts,
>
> I am trying to run Freesurfer commands (eg. mri_ca_label) using
> Matlab in a Mac computer (macOS High Sierra 10.13.6 version)
> and I'm receiving the following error that I suspect are due to
> library incompatibilities:
>
>
> 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
>
> mris_ca_label -aseg
> /Applications/freesurfer/subjects/10018/mri/aseg.mgz -seed 1234
> 10018 lh
> /Applications/freesurfer/subjects/10018/surf/lh.sphere.reg
> 
> /Applications/freesurfer/average/lh.curvature.buckner40.filled.desikan_killiany.2010-03-25.gcs
> /Applications/freesurfer/subjects/10018/label/lh.aparc.annot: Aborted
>
> ans =
>
>    134
>
>
>
> I realized that this error has been previously reported
> 
> 
> and, as Andrew said, one of the possible solutions could be to
> disable the SIP (System Protection Integrity). I have disabled the
> SIP following the instructions indicated here
> 
> 
> but unfortunately Matlab continues giving the same error.
>
>
> How could I solve this problem?. Any help would be appreciated.
>
>
> Thanks in advance.
>
> Best,
>
> -- 
> *Miguel Ángel Rivas Fernández*
>
>
>
> -- 
> *Miguel Ángel Rivas Fernández*
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


___
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Re: [Freesurfer] Matlab error in Freesurfer

2019-03-14 Thread Miguel Ángel Rivas Fernández 
External Email - Use Caution

Dear Freesurfer devs,


Have you had occasion to review this error?. Could it be due to the gcc
version?

Thank you very much for your help.


Best regards,

El mié., 13 mar. 2019 a las 16:09, Miguel Ángel Rivas Fernández (<
miguelrivasf...@gmail.com>) escribió:

>
> Dear Freesurfer experts,
>
> I am trying to run Freesurfer commands (eg. mri_ca_label) using Matlab in
> a Mac computer (macOS High Sierra 10.13.6 version) and I'm receiving the
> following error that I suspect are due to library incompatibilities:
>
>
> 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
>
> mris_ca_label -aseg /Applications/freesurfer/subjects/10018/mri/aseg.mgz
> -seed 1234 10018 lh
> /Applications/freesurfer/subjects/10018/surf/lh.sphere.reg
> /Applications/freesurfer/average/lh.curvature.buckner40.filled.desikan_killiany.2010-03-25.gcs
> /Applications/freesurfer/subjects/10018/label/lh.aparc.annot: Aborted
>
> ans =
>
>134
>
>
>
> I realized that this error has been previously reported
> 
> and, as Andrew said, one of the possible solutions could be to disable the
> SIP (System Protection Integrity). I have disabled the SIP following the
> instructions indicated here
> 
> but unfortunately Matlab continues giving the same error.
>
>
> How could I solve this problem?. Any help would be appreciated.
>
>
> Thanks in advance.
>
> Best,
>
> --
> *Miguel Ángel Rivas Fernández*
>


-- 
*Miguel Ángel Rivas Fernández*
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

[Freesurfer] Matlab error in Freesurfer

2019-03-13 Thread Miguel Ángel Rivas Fernández 
External Email - Use Caution

Dear Freesurfer experts,

I am trying to run Freesurfer commands (eg. mri_ca_label) using Matlab in a
Mac computer (macOS High Sierra 10.13.6 version) and I'm receiving the
following error that I suspect are due to library incompatibilities:


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

mris_ca_label -aseg /Applications/freesurfer/subjects/10018/mri/aseg.mgz
-seed 1234 10018 lh
/Applications/freesurfer/subjects/10018/surf/lh.sphere.reg
/Applications/freesurfer/average/lh.curvature.buckner40.filled.desikan_killiany.2010-03-25.gcs
/Applications/freesurfer/subjects/10018/label/lh.aparc.annot: Aborted

ans =

   134



I realized that this error has been previously reported

and, as Andrew said, one of the possible solutions could be to disable the
SIP (System Protection Integrity). I have disabled the SIP following the
instructions indicated here

but unfortunately Matlab continues giving the same error.


How could I solve this problem?. Any help would be appreciated.


Thanks in advance.

Best,

-- 
*Miguel Ángel Rivas Fernández*
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer