[Freesurfer] Errors on compiling FreeSurfer

[Aziz Nanthaamornphong]

Hi Experts,

I tried to compile FreeSurfer on Ubuntu 16. When I ran a command 'make
check', I got these error messages:






*/usr/bin/ld: warning: libtk8.4.so , needed by
/home/aziz/centos6-x86_64-packages/KWWidgets/current/lib/KWWidgets/libKWWidgets.so,
not found (try using -rpath or -rpath-link)/usr/bin/ld: IconLoaderTest.o:
undefined reference to symbol
'Tcl_GetStringResult'//usr/lib/x86_64-linux-gnu/libtcl8.4.so
: error adding symbols: DSO missing from command
linecollect2: error: ld returned 1 exit statusMakefile:947: recipe for
target 'IconLoaderTest' failedmake[2]: *** [IconLoaderTest] Error 1*

Best Wishes,
Aziz.
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[Freesurfer] Build Freeview on macOS

[Aziz Nanthaamornphong]

Hi Freesurfer experts,

Based on this link
https://surfer.nmr.mgh.harvard.edu/fswiki/freesurfer_mac_developers_page,
it mentions that "*As of the writing of this document (June 2016) freeview
is unable to build on macOS 10.11 platforms and higher (El Capitan and
higher)." *

Could we build Freeview on macOS now?

Best wishes,
Aziz.
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[Freesurfer] Compile problems

[Aziz Nanthaamornphong]

Hi Freesurfer experts,

I ran the commands to build Freesurfer (Yosemite based)  by following this
link
https://surfer.nmr.mgh.harvard.edu/fswiki/freesurfer_mac_developers_page

However, I got the error message when I ran *`make install'* command as
follows:


gunzip: can't stat: ../../distribution/average/cvs_avg35.tar.gz
(../../distribution/average/cvs_avg35.tar.gz.gz): No such file or directory

mv ../../distribution/average/cvs_avg35 \

/Users/azizn/fs_install_2/subjects

mv: rename ../../distribution/average/cvs_avg35 to
/Users/azizn/fs_install_2/subjects/cvs_avg35: No such file or directory

make[2]: *** [install] Error 1

make[1]: *** [install-recursive] Error 1

make: *** [install-recursive] Error 1


Please let me know how to solve this problem. I need to compile the
Freesurfer on my own Macbook.

Best Wishes,
Aziz
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[Freesurfer] Error when trying to compile the code

[Aziz Nanthaamornphong]

Dear FreeSurfer Experts,

I was trying to compile the FreeSurfer code by following steps shown in
https://surfer.nmr.mgh.harvard.edu/fswiki/freesurfer_mac_developers_page

However, I got this error message after I ran ./configure


configure: error: FATAL: netcdf lib not found. Set LDFLAGS or
--with-mni-dir.



I currently use  OS X El Capitan as the OS.

How can I solve this problem? Thank you in advance.

Aziz.
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[Freesurfer] Freesurfer commands

[Aziz Nanthaamornphong]

Hi Freesurfer Experts,

Currently, I am using these command excited in Matlab to extract the
coordinates of volume.


*mri = MRIread('aseg.mgz');pos = find(mri.vol == 17 | mri.vol == 53);*
*[i,j,k] = ind2sub(mri.volsize,pos);*

I would like to run these command in the Freesurfer itself rather than
using Matlab. Can I do that? Which command are qual?

Best Wishes,
Aziz
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Re: [Freesurfer] Specification of computer

[Aziz Nanthaamornphong]

Hi Bruce,

So, I am not sure if I understand correct. Suppose, I would like to run 4
subjects simultenously, I have to run the recon-all command of each subject
on each terminal with -openmp. Otherwise, is there any other options to run
4 subjects in one terminal.

Thank you,
Aziz.

On Sat, Feb 4, 2017 at 9:46 PM, Bruce Fischl 
wrote:

> yes it does, and it should significantly reduce execution time unless you
> don't have multiple cores
>
> cheers
> Bruce
>
> On Sat, 4 Feb 2017, Aziz Nanthaamornphong wrote:
>
> Hi Bruce,
>> Does FS6 support the 'openmp 8' flag? I tried to use this flag with
>> 'recon-all -all' on FS6, but it took
>> longer time for only one subject.
>>
>> Thank you,
>> Aziz.
>>
>> On Fri, Feb 3, 2017 at 10:16 PM, Bruce Fischl 
>> wrote:
>>   Hi Aziz
>>
>>   with multiple course you can specify -openmp 8 for exmaple to use 8
>> cores, which speeds
>>   things up a lot. It also depends how many recons you will be
>> running at the same time. A 16
>>   core machine with 64G of ram would be able to run 4 recons in a few
>> hours each.
>>
>>   cheers
>>   Bruce
>>
>>   On Fri, 3 Feb 2017, Aziz Nanthaamornphong wrote:
>>
>> Hi experts,
>> I would like to find a new high-performance computer to
>> run the reconstruction
>> process in Freesurfer.
>> Currently, I used a single computer (Intel core i7, RAM 8MB)
>> to run the commands
>> (e.g., 'recon-all -all'
>> ) that spent average time 7-9 hours per one subject data.
>>
>> Please let me know what the best spec of the computer that
>> can reduce the time
>> to 2-3 hours (if
>> possible).
>>
>> Thank you,
>> Aziz
>>
>>
>> ___
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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
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>> in error
>> but does not contain patient information, please contact the sender and
>> properly
>> dispose of the e-mail.
>>
>>
>>
>>
>> --
>>
>> Aziz Nanthaamornphong, Ph.D.,
>> Chair of Master of Science Program in Information Technology
>> Department of ICT
>> Faculty of Technology and Environment
>> Prince of Songkla University, Phuket Campus
>> +66 7627 6716 (v)
>> http://research.te.psu.ac.th/aziz
>>
>>
>>
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Re: [Freesurfer] Specification of computer

[Aziz Nanthaamornphong]

Hi Bruce,

Does FS6 support the 'openmp 8' flag? I tried to use this flag with
'recon-all -all' on FS6, but it took longer time for only one subject.

Thank you,
Aziz.

On Fri, Feb 3, 2017 at 10:16 PM, Bruce Fischl 
wrote:

> Hi Aziz
>
> with multiple course you can specify -openmp 8 for exmaple to use 8 cores,
> which speeds things up a lot. It also depends how many recons you will be
> running at the same time. A 16 core machine with 64G of ram would be able
> to run 4 recons in a few hours each.
>
> cheers
> Bruce
>
>
> On Fri, 3 Feb 2017, Aziz Nanthaamornphong wrote:
>
> Hi experts,
>> I would like to find a new high-performance computer to run the
>> reconstruction process in Freesurfer.
>> Currently, I used a single computer (Intel core i7, RAM 8MB) to run the
>> commands (e.g., 'recon-all -all'
>> ) that spent average time 7-9 hours per one subject data.
>>
>> Please let me know what the best spec of the computer that can reduce the
>> time to 2-3 hours (if
>> possible).
>>
>> Thank you,
>> Aziz
>>
>>
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>
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> is
> addressed. If you believe this e-mail was sent to you in error and the
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> dispose of the e-mail.
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>


-- 

Aziz Nanthaamornphong, Ph.D.,
Chair of Master of Science Program in Information Technology
Department of ICT
Faculty of Technology and Environment
Prince of Songkla University, Phuket Campus
+66 7627 6716 (v)
http://research.te.psu.ac.th/aziz
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[Freesurfer] Specification of computer

[Aziz Nanthaamornphong]

Hi experts,

I would like to find a new high-performance computer to run the
reconstruction process in Freesurfer.  Currently, I used a single computer
(Intel core i7, RAM 8MB) to run the commands (e.g., 'recon-all -all' ) that
spent average time 7-9 hours per one subject data.

Please let me know what the best spec of the computer that can reduce the
time to 2-3 hours (if possible).

Thank you,
Aziz
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Re: [Freesurfer] Freesurfer 6.0 link

[Aziz Nanthaamornphong]

Thank a lot.

Aziz.

On Wed, Jan 25, 2017 at 9:38 PM, Z K  wrote:

> https://surfer.nmr.mgh.harvard.edu/fswiki/DownloadAndInstall
>
> On 01/25/2017 05:44 AM, Aziz Nanthaamornphong wrote:
> > Hi experts,
> >
> > How can I download Freesurfer version 6.0? Is there an available URL
> link?
> >
> > Thank you,
> > Aziz
> > --
> >
> > Aziz Nanthaamornphong, Ph.D.,
> > Chair of Master of Science Program in Information Technology
> > Department of ICT
> > Faculty of Technology and Environment
> > Prince of Songkla University, Phuket Campus
> > +66 7627 6716 (v)
> > http://research.te.psu.ac.th/aziz
> >
> >
> >
> > ___
> > Freesurfer mailing list
> > Freesurfer@nmr.mgh.harvard.edu
> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> >
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[Freesurfer] Freesurfer 6.0 link

[Aziz Nanthaamornphong]

Hi experts,

How can I download Freesurfer version 6.0? Is there an available URL link?

Thank you,
Aziz
-- 

Aziz Nanthaamornphong, Ph.D.,
Chair of Master of Science Program in Information Technology
Department of ICT
Faculty of Technology and Environment
Prince of Songkla University, Phuket Campus
+66 7627 6716 (v)
http://research.te.psu.ac.th/aziz
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Re: [Freesurfer] Cannot allocate memory error

[Aziz Nanthaamornphong]

Hi Bruce,

So, I  should run the freeview after got those error messages. I will try.

Thank you,
Aziz.

On Thu, Jan 12, 2017 at 10:32 PM, Bruce Fischl 
wrote:

> Hi Aziz
>
> it will be in the subject's surf dir. You can visualize it via:
>
> freeview -f $SUBJECTS_DIR//surf/lh.inflated.nofix
>
>
>
> cheers
> Bruce
>
>
> On Thu, 12 Jan 2017, Aziz Nanthaamornphong wrote:
>
> Hi Bruce,
>> How can I look at inflated.nofix as you mentioned? I think I ran recon-all
>> for the 001.mgz without other files.
>>
>> Best Regards,
>> Aziz.
>>
>> On Thu, Jan 12, 2017 at 8:55 PM, Bruce Fischl > >
>> wrote:
>>   Hi Aziz
>>
>>   yes, you ran out of RAM. That said, a defect with 66K vertices
>>   is pretty big - more than 1/3 of a typical surface. You should
>>   check to make sure nothing big is wrong (hemis attached, skull
>>   left around, etc). Look at the inflated.nofix surface and it
>>   should be obvious what the defect is
>>
>>   cheers
>>   Bruce
>>   On Thu, 12 Jan 2017, Aziz Nanthaamornphong wrote:
>>
>> Hi experts,
>>
>> I ran the command
>>
>> $recon-all -all  -subjid 0696
>>
>> I have got these error messages
>>
>> CORRECTING DEFECT 46 (vertices=66623, convex
>> hull=8931)
>> Excessive topologic defect encountered: could not
>> allocate 322592700 edges
>> for retessellation
>> Cannot allocate memory
>>
>> Linux xubuntu-VirtualBox 3.2.0-23-generic #36-Ubuntu
>> SMP Tue Apr 10 20:41:14
>> UTC 2012 i686 i686 i386 GNU/Linux
>>
>> I am not sure if this problem came from the
>>  insufficient memory on my
>> computer. Otherwise, please let me suggestions for
>> solving this problem.
>>
>> Thank you,
>> Aziz.
>>
>>
>>
>> ___
>> 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.
>>
>>
>>
>>
>> --
>>
>> Aziz Nanthaamornphong, Ph.D.,
>> Chair of Master of Science Program in Information Technology
>> Department of ICT
>> Faculty of Technology and Environment
>> Prince of Songkla University, Phuket Campus
>> +66 7627 6716 (v)
>> http://research.te.psu.ac.th/aziz
>>
>>
>>
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>
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> is
> addressed. If you believe this e-mail was sent to you in error and the
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> properly
> dispose of the e-mail.
>
>


-- 

Aziz Nanthaamornphong, Ph.D.,
Chair of Master of Science Program in Information Technology
Department of ICT
Faculty of Technology and Environment
Prince of Songkla University, Phuket Campus
+66 7627 6716 (v)
http://research.te.psu.ac.th/aziz
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Re: [Freesurfer] Cannot allocate memory error

[Aziz Nanthaamornphong]

Hi Bruce,

How can I look at inflated.nofix as you mentioned? I think I ran recon-all
for the 001.mgz without other files.

Best Regards,
Aziz.

On Thu, Jan 12, 2017 at 8:55 PM, Bruce Fischl 
wrote:

> Hi Aziz
>
> yes, you ran out of RAM. That said, a defect with 66K vertices is pretty
> big - more than 1/3 of a typical surface. You should check to make sure
> nothing big is wrong (hemis attached, skull left around, etc). Look at
> the inflated.nofix surface and it should be obvious what the defect is
>
> cheers
> Bruce
>
> On Thu, 12 Jan 2017, Aziz Nanthaamornphong wrote:
>
> Hi experts,
>>
>> I ran the command
>>
>> $recon-all -all  -subjid 0696
>>
>> I have got these error messages
>>
>> CORRECTING DEFECT 46 (vertices=66623, convex hull=8931)
>> Excessive topologic defect encountered: could not allocate 322592700 edges
>> for retessellation
>> Cannot allocate memory
>>
>> Linux xubuntu-VirtualBox 3.2.0-23-generic #36-Ubuntu SMP Tue Apr 10
>> 20:41:14
>> UTC 2012 i686 i686 i386 GNU/Linux
>>
>> I am not sure if this problem came from the  insufficient memory on my
>> computer. Otherwise, please let me suggestions for solving this problem.
>>
>> Thank you,
>> Aziz.
>>
>>
>>
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>


-- 

Aziz Nanthaamornphong, Ph.D.,
Chair of Master of Science Program in Information Technology
Department of ICT
Faculty of Technology and Environment
Prince of Songkla University, Phuket Campus
+66 7627 6716 (v)
http://research.te.psu.ac.th/aziz
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[Freesurfer] Cannot allocate memory error

[Aziz Nanthaamornphong]

Hi experts,

I ran the command

$recon-all -all  -subjid 0696

I have got these error messages

*CORRECTING DEFECT 46 (vertices=66623, convex hull=8931)*
*Excessive topologic defect encountered: could not allocate 322592700 edges
for retessellation*
*Cannot allocate memory*

*Linux xubuntu-VirtualBox 3.2.0-23-generic #36-Ubuntu SMP Tue Apr 10
20:41:14 UTC 2012 i686 i686 i386 GNU/Linux*

I am not sure if this problem came from the  insufficient memory on my
computer. Otherwise, please let me suggestions for solving this problem.

Thank you,
Aziz.
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Re: [Freesurfer] Coordinates of particular volumes

[Aziz Nanthaamornphong]

I have tried to get the coordinates with following commands:


*mri = MRIread('aseg.mgz');pos = find(mri.vol == 17);*
*[i,j,k] = ind2sub(10213,pos);*

However, I found that all values of 'j' are 1. is there something wrongs
with my strategy?

Best Regards,
Aziz.

On Mon, Sep 12, 2016 at 8:40 PM, Bruce Fischl 
wrote:

> Hi Aziz,
>
> make sure $FREESURFER_HOME/matlab is in your matlab path.
>
> cheers
> Bruce
>
> On Mon, 12 Sep 2016, Aziz Nanthaamornphong wrote:
>
>
>> Which the version of Matlab has a 'MRIread' function? I got this error
>> message from my installed Matlab (v. 8.4.0).
>> "Undefined function 'MRIread' for input arguments of type 'char'."
>>
>> Best Regards,
>> Aziz.
>>
>> On Mon, Sep 5, 2016 at 6:46 AM, Bruce Fischl 
>> wrote:
>>   yup, or mri_Info called form the command line. If you use
>>   MRIread on the aseg.mgz you can extract e.g. the left
>>   hippocampus using matlab via:
>>
>>
>>   mri = MRIread('aseg.mgz');
>>   find(mri.vol == 17);
>>   then compute the ras coords of those indices using ind2sub
>>
>>   cheers
>>   Bruce
>>
>>   On Sun, 4 Sep 2016, Ruyuan Zhang wrote:
>>
>>
>> Hi, Aziz
>>
>>  You can use MRIread function to read in a
>> volume (i.e. brainmask.mgz).
>> You will get a structure, which contains a field
>> called ras2vox.
>>
>> cheers
>>
>> ruyuan
>>
>> On 9/4/16 6:23 PM, Aziz Nanthaamornphong wrote:
>>   Hi,
>> For example, I want to know the list of x, y, z
>> coordinates of a left
>> hippocampus volume.
>>
>> As you mentioned "ras2vox" matrices, hoe can I see
>> or get these
>> matrices?
>>
>> Thank you.
>> Aziz
>>
>> On Monday, 5 September 2016, Bruce Fischl
>> 
>> wrote:
>>   Hi Aziz
>>
>>   can you elaborate? What coordinates do you
>> want? What are
>>   you trying to do with them? The .mgz format
>> contains
>>   ras2vox matrices that let you go from voxel
>> indices to RAS
>>   coordinates and such.
>>
>>
>>   cheers
>>   Bruce
>>
>>
>>   On Sun, 4 Sep 2016, Aziz Nanthaamornphong
>> wrote:
>>
>> Dear Freesurfer experts,
>> How can we get the coordinates (X, Y, Z)
>> of a
>> particular volume? I couldn't
>> find any functions or command to do
>> that.
>>
>> Thank you in advance.
>>
>> Aziz.
>>
>>
>>
>>
>> --
>>
>> Aziz Nanthaamornphong, Ph.D.,
>> Chair of Master of Science Program in Information
>> Technology
>> Department of ICT
>> Faculty of Technology and Environment
>> Prince of Songkla University, Phuket Campus
>> +66 7627 6716 (v)
>> http://research.te.psu.ac.th/aziz
>>
>>
>>
>>
>> ___
>> 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-mai
>> l
>> contains patient information, please contact the
>> Partners Compliance HelpLin
>> e at
>> http://www.partners.org/complianceline . If the
>> e-mail was sent to you in er
>> ror
>> but does not contain patient information, please
>> contact the sender and prop
>> erly
>> dispose of the e-mail.
>>
>>
>>
>>
>> __

Re: [Freesurfer] Coordinates of particular volumes

[Aziz Nanthaamornphong]

Which the version of Matlab has a 'MRIread' function? I got this error
message from my installed Matlab (v. 8.4.0).

"Undefined function 'MRIread' for input arguments of type 'char'."

Best Regards,
Aziz.

On Mon, Sep 5, 2016 at 6:46 AM, Bruce Fischl 
wrote:

> yup, or mri_Info called form the command line. If you use MRIread on the
> aseg.mgz you can extract e.g. the left hippocampus using matlab via:
>
>
> mri = MRIread('aseg.mgz');
> find(mri.vol == 17);
> then compute the ras coords of those indices using ind2sub
>
> cheers
> Bruce
>
>
> On Sun, 4 Sep 2016, Ruyuan Zhang wrote:
>
>
>> Hi, Aziz
>>
>>  You can use MRIread function to read in a volume (i.e.
>> brainmask.mgz).
>> You will get a structure, which contains a field called ras2vox.
>>
>> cheers
>>
>> ruyuan
>>
>> On 9/4/16 6:23 PM, Aziz Nanthaamornphong wrote:
>>   Hi,
>> For example, I want to know the list of x, y, z coordinates of a left
>> hippocampus volume.
>>
>> As you mentioned "ras2vox" matrices, hoe can I see or get these
>> matrices?
>>
>> Thank you.
>> Aziz
>>
>> On Monday, 5 September 2016, Bruce Fischl 
>> wrote:
>>   Hi Aziz
>>
>>   can you elaborate? What coordinates do you want? What are
>>   you trying to do with them? The .mgz format contains
>>   ras2vox matrices that let you go from voxel indices to RAS
>>   coordinates and such.
>>
>>
>>   cheers
>>   Bruce
>>
>>
>>   On Sun, 4 Sep 2016, Aziz Nanthaamornphong wrote:
>>
>> Dear Freesurfer experts,
>> How can we get the coordinates (X, Y, Z) of a
>> particular volume? I couldn't
>> find any functions or command to do that.
>>
>> Thank you in advance.
>>
>> Aziz.
>>
>>
>>
>>
>> --
>>
>> Aziz Nanthaamornphong, Ph.D.,
>> Chair of Master of Science Program in Information Technology
>> Department of ICT
>> Faculty of Technology and Environment
>> Prince of Songkla University, Phuket Campus
>> +66 7627 6716 (v)
>> http://research.te.psu.ac.th/aziz
>>
>>
>>
>>
>> ___
>> 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-mai
>> l
>> contains patient information, please contact the Partners Compliance
>> HelpLin
>> e at
>> http://www.partners.org/complianceline . If the e-mail was sent to you
>> in er
>> ror
>> but does not contain patient information, please contact the sender and
>> prop
>> erly
>> dispose of the e-mail.
>>
>>
>>
>>
> ___
> 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.
>
>


-- 

Aziz Nanthaamornphong, Ph.D.,
Chair of Master of Science Program in Information Technology
Department of ICT
Faculty of Technology and Environment
Prince of Songkla University, Phuket Campus
+66 7627 6716 (v)
http://research.te.psu.ac.th/aziz
___
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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.

Re: [Freesurfer] Coordinates of particular volumes

[Aziz Nanthaamornphong]

Hi,

For example, I want to know the list of x, y, z coordinates of a left
hippocampus volume.

As you mentioned "ras2vox" matrices, hoe can I see or get these matrices?

Thank you.
Aziz

On Monday, 5 September 2016, Bruce Fischl 
wrote:

> Hi Aziz
>
> can you elaborate? What coordinates do you want? What are you trying to do
> with them? The .mgz format contains ras2vox matrices that let you go from
> voxel indices to RAS coordinates and such.
>
>
> cheers
> Bruce
>
>
> On Sun, 4 Sep 2016, Aziz Nanthaamornphong wrote:
>
> Dear Freesurfer experts,
>> How can we get the coordinates (X, Y, Z) of a particular volume? I
>> couldn't
>> find any functions or command to do that.
>>
>> Thank you in advance.
>>
>> Aziz.
>>
>>
>>

-- 

Aziz Nanthaamornphong, Ph.D.,
Chair of Master of Science Program in Information Technology
Department of ICT
Faculty of Technology and Environment
Prince of Songkla University, Phuket Campus
+66 7627 6716 (v)
http://research.te.psu.ac.th/aziz
___
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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.

[Freesurfer] Coordinates of particular volumes

[Aziz Nanthaamornphong]

Dear Freesurfer experts,

How can we get the coordinates (X, Y, Z) of a particular volume? I couldn't
find any functions or command to do that.

Thank you in advance.

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

[Freesurfer] All coordinates of volume of interest

[Aziz Nanthaamornphong]

Hi,

Is there a way to get all coordinates (x,y,z) of the particular volume of
interest (e.g., left-insula, left-thalamus)?

Best,
Aziz.
-- 

Aziz Nanthaamornphong, Ph.D.,
Faculty of Technology and Environment
Prince of Songkla University, Phuket Campus
+66 7627 6716 (v)
http://research.te.psu.ac.th/aziz
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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
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but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

[Freesurfer] Compile and Install on El Capitan

[Aziz Nanthaamornphong]

Hi,

Can we compile & install Freesurfer on El Capitan? Unfortunately, I found
the document for Lion (
https://surfer.nmr.mgh.harvard.edu/fswiki/freesurfer_mac_developers_page).

Thank you,
Aziz
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