Re: [Freesurfer] custom templates and mris_make_template options

2008-08-24 Thread Jan Kalkus 

Thanks Bruce,

One more question, just to be sure, when using mris_register, the  
first time I use:


mris_register \
-curv \
$SUBJECTS_DIR/bu_edited/surf/lh.sphere \
lh.monk_temp_wreg1.tif \
$SUBJECTS_DIR/bu_edited/surf/lh.sphere.reg

Is this correct? I shouldn't be using *h.sphere.reg (instead of  
*h.sphere) for the input surface after the first round?


Thanks.


    - Jan Kalkus


On Aug 24, 2008, at 10:15 PM, Bruce Fischl wrote:


Hi Jan,

you should use the ?h.sphere.reg on the 2nd round. On our 1st round  
we use a single subject ?h.sphere to avoid blurring the folding  
patterns too much, then register all to that one, create the atlas  
from all the subjects (with the sphere.reg), then recreate all the  
sphere.reg by reregistering to the 2nd round atlas, then create a  
3rd round atlas from the new sphere.reg files.


let us know if you need more help.

Bruce


On Sun, 24 Aug 2008, Jan Kalkus wrote:


Hi everyone,

	We're making a template to register some monkey brain surfaces to.  
I've written a script based on instructions from the Surface  
Registration and Templates page ( http://surfer.nmr.mgh.harvard.edu/fswiki/SurfaceRegAndTemplates 
 ) on FreeSurfer wiki.
	I'm stuck at "Round 1" with the "mris_make_template" command. In  
the first step we used:


mris_make_template \
lh sphere \
bu_edited bs_edited vi_edited \
lh.monk_temp_all.tif

As there were no *h.sphere.reg files yes, we used the *h.phere  
surfaces. My question is, for the next "mris_make_template" should  
we use the same (*h.sphere) surface or use the newly created  
*h.sphere.reg surfaces to create the template?


mris_make_template \
lh sphere.reg \
bu_edited bs_edited vi_edited \
lh.monk_temp_all.tif


Has anyone else used this process to create their own templates/ 
registered surfaces? Does anyone have any suggestions? Thanks.



- Jan Kalkus

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[Freesurfer] custom templates and mris_make_template options

2008-08-24 Thread Jan Kalkus 

Hi everyone,

	We're making a template to register some monkey brain surfaces to.  
I've written a script based on instructions from the Surface  
Registration and Templates page ( http://surfer.nmr.mgh.harvard.edu/fswiki/SurfaceRegAndTemplates 
 ) on FreeSurfer wiki.
	I'm stuck at "Round 1" with the "mris_make_template" command. In the  
first step we used:


mris_make_template \
lh sphere \
bu_edited bs_edited vi_edited \
lh.monk_temp_all.tif

As there were no *h.sphere.reg files yes, we used the *h.phere  
surfaces. My question is, for the next "mris_make_template" should we  
use the same (*h.sphere) surface or use the newly created  
*h.sphere.reg surfaces to create the template?


mris_make_template \
lh sphere.reg \
bu_edited bs_edited vi_edited \
lh.monk_temp_all.tif


Has anyone else used this process to create their own templates/ 
registered surfaces? Does anyone have any suggestions? Thanks.



- Jan Kalkus

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Re: [Freesurfer] error message of mris_register

2008-07-09 Thread Jan Kalkus 

Thanks a lot. It's working so far.


On Jul 9, 2008, at 12:25 PM, Nick Schmansky wrote:


Jan,

I've put an updated mris_register here:


wget
ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/fsdev/nicks/stable/macintel/mris_register

there may be other problem binaries, just let me know.

Nick

On Wed, 2008-07-09 at 11:14 -0400, Jan Kalkus wrote:

I have also been having similar trouble with mris_register:

[dynamic-oit-vapornet-c-124:Data/monkey_surface_data/bu_edited] work%
mris_register surf/rh.sphere $SUBJECTS_DIR/monk_temp0.tif surf/
rh.sphere.reg
$Id: mris_register.c,v 1.48 2007/07/19 15:58:50 fischl Exp $
  $Id: mrisurf.c,v 1.557.2.13 2008/05/23 00:06:05 nicks Exp $
reading surface from surf/rh.sphere...
reading template parameterization from /Volumes/Data/
monkey_surface_data/monk_temp0.tif...
/Volumes/Data/monkey_surface_data/monk_temp0.tif: Deflate compression
support is not configured.
TiffReadImage:  TIFFReadScanline returned error
No such file or directory
MRISPread(/Volumes/Data/monkey_surface_data/monk_temp0.tif): could  
not

open file
No such file or directory
mris_register: could not open template file /Volumes/Data/
monkey_surface_data/monk_temp0.tif
No such file or directory


    - Jan Kalkus

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Re: [Freesurfer] error message of mris_register

2008-07-09 Thread Jan Kalkus 

I have also been having similar trouble with mris_register:

[dynamic-oit-vapornet-c-124:Data/monkey_surface_data/bu_edited] work%  
mris_register surf/rh.sphere $SUBJECTS_DIR/monk_temp0.tif surf/ 
rh.sphere.reg

$Id: mris_register.c,v 1.48 2007/07/19 15:58:50 fischl Exp $
  $Id: mrisurf.c,v 1.557.2.13 2008/05/23 00:06:05 nicks Exp $
reading surface from surf/rh.sphere...
reading template parameterization from /Volumes/Data/ 
monkey_surface_data/monk_temp0.tif...
/Volumes/Data/monkey_surface_data/monk_temp0.tif: Deflate compression  
support is not configured.

TiffReadImage:  TIFFReadScanline returned error
No such file or directory
MRISPread(/Volumes/Data/monkey_surface_data/monk_temp0.tif): could not  
open file

No such file or directory
mris_register: could not open template file /Volumes/Data/ 
monkey_surface_data/monk_temp0.tif

No such file or directory


- Jan Kalkus

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Re: [Freesurfer] deflate compression support

2008-07-09 Thread Jan Kalkus 
Thank you very much, that solved my problem. However, though I can now  
write .tif files, freesurfer does not seem to want to read them (when  
using mris_register):


[Macintosh-10:/Volumes/Data/monkey_surface_data] work%  
mris_make_template rh sphere bu_edited monk_temp0.tif

creating new parameterization...

processing subject bu_edited (1 of 1)
reading spherical surface /Volumes/Data/monkey_surface_data/bu_edited/ 
surf/rh.sphere...

curvature mean = 0.000, std = 1.000
computing parameterization for surface /Volumes/Data/ 
monkey_surface_data/bu_edited/surf/rh.inflated.H...

curvature mean = 0.000, std = 0.592
computing parameterization for surface /Volumes/Data/ 
monkey_surface_data/bu_edited/surf/rh.sulc...

curvature mean = -0.100, std = 1.787
computing parameterization for surface /Volumes/Data/ 
monkey_surface_data/bu_edited/surf/rh.smoothwm...

writing updated template with 1 subjects to monk_temp0.tif...
[Macintosh-10:/Volumes/Data/monkey_surface_data] work% mris_register  
$SUBJECTS_DIR/bu_edited/surf/rh.sphere $SUBJECTS_DIR/monk_temp0.tif  
$SUBJECTS_DIR/bu_edited/surf/rh.sphere.reg

$Id: mris_register.c,v 1.48 2007/07/19 15:58:50 fischl Exp $
 $Id: mrisurf.c,v 1.557.2.13 2008/05/23 00:06:05 nicks Exp $
reading surface from /Volumes/Data/monkey_surface_data/bu_edited/surf/ 
rh.sphere...
reading template parameterization from /Volumes/Data/ 
monkey_surface_data/monk_temp0.tif...
/Volumes/Data/monkey_surface_data/monk_temp0.tif: Deflate compression  
support is not configured.

TiffReadImage:  TIFFReadScanline returned error
No such file or directory
MRISPread(/Volumes/Data/monkey_surface_data/monk_temp0.tif): could not  
open file

No such file or directory
mris_register: could not open template file /Volumes/Data/ 
monkey_surface_data/monk_temp0.tif

No such file or directory

Is there an updated 'mris_register' binary too that I could get a hold  
of? Thanks.



    - Jan Kalkus



On Jul 8, 2008, at 6:51 PM, Nick Schmansky wrote:


Jan,

It appears that the libtiff used to build mris_make_template did not
have deflate (zip) support.  An updated binary can be downloaded from
here:

wget
ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/fsdev/nicks/stable/macintel/mris_make_template


the wget command is one line.  run this command in
the /Applications/freesurfer/bin directory, then type:
chmod a+x /Applications/freesurfer/bin/mris_make_template

Nick




On Tue, 2008-07-01 at 11:27 -0400, Jan Kalkus wrote:

Hi everyone,

I'm trying to make a monkey template using mris_make_template. So
far, every time I run the mris_make_template, I get this error:

[jkalkus:~] work% /Volumes/Data/monkey_surface_data/mris_make
creating new parameterization...

processing subject bu_edited (1 of 1)
reading spherical surface /Volumes/Data/monkey_surface_data// 
bu_edited/

surf/rh.sphere...
curvature mean = 0.000, std = 1.000
computing parameterization for surface /Volumes/Data/
monkey_surface_data//bu_edited/surf/rh.inflated.H...
curvature mean = 0.000, std = 0.592
computing parameterization for surface /Volumes/Data/
monkey_surface_data//bu_edited/surf/rh.sulc...
curvature mean = -0.100, std = 1.787
computing parameterization for surface /Volumes/Data/
monkey_surface_data//bu_edited/surf/rh.smoothwm...
writing updated template with 1 subjects to monk_temp0.tif...
monk_temp0.tif: Deflate compression support is not configured.
TiffWrite: TIFFWriteScanline returned error

I am working on an intel MacBook with OS X 10.5.4 and I'm running
freesurfer-Darwin-leopard-i686-stable-pub-v4.0.5. Has anyone else
encountered this problem? Does anyone have any suggestions? Thanks

- Jan Kalkus
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On Jul 8, 2008, at 6:51 PM, Nick Schmansky wrote:


Jan,

It appears that the libtiff used to build mris_make_template did not
have deflate (zip) support.  An updated binary can be downloaded from
here:

wget
ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/fsdev/nicks/stable/macintel/mris_make_template


the wget command is one line.  run this command in
the /Applications/freesurfer/bin directory, then type:
chmod a+x /Applications/freesurfer/bin/mris_make_template

Nick




On Tue, 2008-07-01 at 11:27 -0400, Jan Kalkus wrote:

Hi everyone,

I'm trying to make a monkey template using mris_make_template. So
far, every time I run the mris_make_template, I get this error:

[jkalkus:~] work% /Volumes/Data/monkey_surface_data/mris_make
creating new parameterization...

processing subject bu_edited (1 of 1)
reading spherical surface /Volumes/Data/monkey_surface_data// 
bu_edited/

surf/rh.sphere...
curvature mean = 0.000, std = 1.000
computing parameterization for surface /Volumes/Data/
monkey_surface_data//bu_edited/surf/rh.inflated.H...
curvature mean = 0.000, std = 0.592
computing parameterization

Re: [Freesurfer] deflate compression support

2008-07-01 Thread Jan Kalkus 
I've tried reinstalling libtiff with darwinports, but unfortunately I  
still get the same error.



On Jul 1, 2008, at 12:20 PM, Pedro Paulo de Magalhães Oliveira Junior  
wrote:



The problem is if the libtiff was compiled with zlib or not.

I think it would be nice to rebuild your libtiff from ports: 
http://tiff.darwinports.com/

2008/7/1 Jan Kalkus <[EMAIL PROTECTED]>:
I have libtiff 3.8.2.

On Jul 1, 2008, at 12:06 PM, Pedro Paulo de Magalhães Oliveira  
Junior wrote:



Some versions of LibTiff have the zlib compression support disabled.

Do you have an older version of LibTiff in your Mac?

2008/7/1 Jan Kalkus <[EMAIL PROTECTED]>:
Hi everyone,

   I'm trying to make a monkey template using  
mris_make_template. So far, every time I run the  
mris_make_template, I get this error:


[jkalkus:~] work% /Volumes/Data/monkey_surface_data/mris_make
creating new parameterization...

processing subject bu_edited (1 of 1)
reading spherical surface /Volumes/Data/monkey_surface_data// 
bu_edited/surf/rh.sphere...

curvature mean = 0.000, std = 1.000
computing parameterization for surface /Volumes/Data/ 
monkey_surface_data//bu_edited/surf/rh.inflated.H...

curvature mean = 0.000, std = 0.592
computing parameterization for surface /Volumes/Data/ 
monkey_surface_data//bu_edited/surf/rh.sulc...

curvature mean = -0.100, std = 1.787
computing parameterization for surface /Volumes/Data/ 
monkey_surface_data//bu_edited/surf/rh.smoothwm...

writing updated template with 1 subjects to monk_temp0.tif...
monk_temp0.tif: Deflate compression support is not configured.
TiffWrite: TIFFWriteScanline returned error

I am working on an intel MacBook with OS X 10.5.4 and I'm running  
freesurfer-Darwin-leopard-i686-stable-pub-v4.0.5. Has anyone else  
encountered this problem? Does anyone have any suggestions? Thanks


   - Jan Kalkus
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[Freesurfer] deflate compression support

2008-07-01 Thread Jan Kalkus 

Hi everyone,

	I'm trying to make a monkey template using mris_make_template. So  
far, every time I run the mris_make_template, I get this error:


[jkalkus:~] work% /Volumes/Data/monkey_surface_data/mris_make
creating new parameterization...

processing subject bu_edited (1 of 1)
reading spherical surface /Volumes/Data/monkey_surface_data//bu_edited/ 
surf/rh.sphere...

curvature mean = 0.000, std = 1.000
computing parameterization for surface /Volumes/Data/ 
monkey_surface_data//bu_edited/surf/rh.inflated.H...

curvature mean = 0.000, std = 0.592
computing parameterization for surface /Volumes/Data/ 
monkey_surface_data//bu_edited/surf/rh.sulc...

curvature mean = -0.100, std = 1.787
computing parameterization for surface /Volumes/Data/ 
monkey_surface_data//bu_edited/surf/rh.smoothwm...

writing updated template with 1 subjects to monk_temp0.tif...
monk_temp0.tif: Deflate compression support is not configured.
TiffWrite: TIFFWriteScanline returned error

I am working on an intel MacBook with OS X 10.5.4 and I'm running  
freesurfer-Darwin-leopard-i686-stable-pub-v4.0.5. Has anyone else  
encountered this problem? Does anyone have any suggestions? Thanks


    - Jan Kalkus
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[Freesurfer] Deflate compression support

2008-06-25 Thread Jan Kalkus 

Hi,

	I'm using mris_make_template to create a template with some monkey  
data. At the very end I get this message:


Deflate compression support is not configured.
TiffWrite: TIFFWriteScanline returned error

I've recompiled libtiff with the #define COMPRESSION_SUPPORT option in  
the tifconf.h file, but I keep getting the same message. Does anyone  
have any suggestions?



    - Jan Kalkus

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[Freesurfer] monkey template

2008-06-25 Thread Jan Kalkus 

Hi,

	I'm trying to construct a surface registration template with some  
monkey data and I was wondering if anyone could clear up some  
confusion I had. Can anyone tell me what the difference between  
mri_make_template and mris_make_template is?


Thanks,

        Jan Kalkus
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