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
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer