Sorry, there's no way to change the resolution of the TIFF
images. However, we don't supersample when taking screen shots, so
just make the window as big as you can, take the TIFF, and then you
can use an image conversion program to change the DPI.
I don't think you want to use read_binary_surf. If you're just trying
to load a single vertex set in addition to the ones you've already
loaded, use this function:
read_surface_vertex_set field fileName
Reads a set of vertices from the fle in fileName. field should
be one of the following:
0 Main vertices
1 Inflated vertices
2 White vertices
3 Pial vertices
4 Orig vertices
I was having your problem until I replaced read_binary_surf with
read_surface_vertex_set, then labl_load works as expected.
On Sun, Feb 26, 2006 at 07:19:22PM -0800, Darren Weber wrote:
>
> Hi Daniel et al.,
>
> thanks for the rotate and save_tiff script. I've installed the dev
> version (redhat 9 download onto Debian sarge) and the script works
> well. I would like to set the resolution of the .tif output files (eg,
> 600 dpi), can we do that?
>
> I have a problem when using a label in the tcl script (see example.tcl
> below). I can startup tksurfer from the csh prompt, create a label,
> save it, exit, start again, load the label, and it displays correctly.
> So I assume all the label tools are working. When I restart with -tcl
> example.tcl, tksurfer draws an entirely blue surface after loading the
> label (any label). Have you seen this before? Am I doing something
> wrong? Should I source the tksurfer.tcl script, at the beginning of
> this script, to get all the lighting etc. correct? I tried to startup
> tksurfer normally, with no explicit -tcl option, and then "source
> example.tcl" at the tcl prompt, but the entire surface turns blue after
> the script loads a label. Can you replicate this or advise me how to
> avoid it?
>
> Is it possible to create a shell script or a tcl script that can startup
> tksurfer and run a specific tcl script across a group of subjects?
>
> Thanks, Darren
>
>
>
> ##################################################################
> # START EXAMPLE.TCL SCRIPT
>
> set SUBJECTS_DIR "/usr/local/freesurfer/subjects"
>
> set subjID "ucsf_cj"
> set subjPath [ file join ${SUBJECTS_DIR} ${subjID} ]
>
> set subjSurfPath [ file join ${subjPath} surf ]
> set subjLabelPath [ file join ${subjPath} label ]
> set subjTiffPath [ file join ${subjPath} rgb ]
>
> foreach h {lh} {
>
> # -----------------------------------------------
> # load the inflated surface, with curvature
>
> set insurf [file join ${subjSurfPath} ${h}.inflated]
> read_binary_surf
>
> set curv [file join ${subjSurfPath} ${h}.curv]
> read_binary_curv
>
> UpdateAndRedraw
>
> # -----------------------------------------------
> # load and display relevant .label files
>
> set labels [ glob -directory ${subjLabelPath} "${h}_test.label" ]
> foreach l $labels {
> puts "loading label: $l"
> labl_load "$l"
> # AT THIS POINT WE HAVE AN ENTIRELY BLUE SURFACE
> }
>
> # now rotate and save the views ...
> }
> # END TCL SCRIPT
> ##################################################################
>
>
>
> Best, Darren
>
>
>
> Daniel Goldenholz wrote:
>
> >Hi Darren and other Freesurfers
> >
> >I wrote a tcl script to do just what was described. The one I made
> >gives the flexibility to name the tiff files based on a prefix that
> >you specify before
> >running the script. This way you run the same exact script for as many
> >pictures as you like, simply changing the prefix before running the
> >script.
> >
> >
> >
> >Here is what you do. In tksurfer, after you have set up whatever
> >overlays and/or labels and/or surfaces etc that you like, you enter at
> >the command prompt
> >set pre <whatever-you-want>
> >
> >(where the stuff inside the < > is any file prefix... for instance,
> >set pre bold_contrast1 )
> >
> >then you run the following tcl script via the menu for running a
> >script...
> >
> >
> >UpdateAndRedraw
> >puts "Taking Snapshots..."
> >make_lateral_view
> >rotate_brain_y 90
> >redraw
> >set tiff "${pre}_bck.tif"
> >save_tiff $tiff
> >make_lateral_view
> >redraw
> >set tiff "${pre}_lat.tif"
> >save_tiff $tiff
> >rotate_brain_y 180
> >redraw
> >set tiff "${pre}_med.tif"
> >save_tiff $tiff
> >make_lateral_view
> >rotate_brain_x 90
> >redraw
> >set tiff "${pre}_inf.tif"
> >save_tiff $tiff
> >rotate_brain_x 180
> >redraw
> >set tiff "${pre}_sup.tif"
> >save_tiff $tiff
> >make_lateral_view
> >rotate_brain_y 270
> >redraw
> >set tiff "${pre}_front.tif"
> >save_tiff $tiff
> >
> >
> >
> >Darren Weber wrote:
> >
> >>Hi Bruce etal,
> >>
> >>I would like a short tcl script to rotate each hemisphere through all
> >>the main views (lateral, medial, dorsal, ventral, anterior,
> >>posterior) and output a graphics file with the name of the subject
> >>and the view in the file name. I've found rotate_brain_[xyz] and
> >>save_rgb, but the latter does not permit a file name for the output
> >>graphics. I would like high-resolution graphics for publications,
> >>but the save_rgb outputs about 85-90 dpi images. Is there an option
> >>for vector graphics or high resolution tiff or png images?
> >>
> >>Best, Darren
> >>_______________________________________________
> >>Freesurfer mailing list
> >>Freesurfer@nmr.mgh.harvard.edu
> >>https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> >>
> >>
> >
>
> --
>
> Darren L. Weber, Ph.D.
> Visiting Postdoctoral Scholar
>
> Dynamic Neuroimaging Laboratory, Department of Radiology,
> University of California, San Francisco,
> 185 Berry Street, Suite 350, Box 0946,
> San Francisco, CA 94107, USA.
>
> Tel: +1 415 353-9444
> Fax: +1 415 353-9421
> www: http://dnl.ucsf.edu/users/dweber
>
> "To explicate the uses of the brain seems as difficult
> a task as to paint the soul, of which it is commonly
> said, that it understands all things but itself."
> --Thomas Willis (The Anatomy of the Brain and Nerves, 1664)
>
>
> _______________________________________________
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
--
Kevin Teich
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