Sorry, I gave you a slightly wrong tkmedit command-line, it should have
been -overlay-reg ...
As for tkmedit, the mask is probably too dark. Click in the window and
hit 'i'. This will turn on intensity normalization, which will probably
fix the problem. You may want to load in the volume that you traced the
mask on instead of the mask itself.
doug
Fornito, Alexander wrote:
Hi Doug,
I tried the tkmedit command and it loaded the volume with the mask, although I got a message saying:
Error: Parsing command line options
Option -reg not recognized
This option was not recognized and ignored.
Not sure why this occurred, as I loaded it from scratch through the GUI (File > Load Overlay Data, with the mask as the volume and register.dat as the registration file) and it produced the same with no error.
In any case, I can see from tkmedit that the mask is not where it should be (It's in the neck, where it should be in the cingulate, above the corpus callosum).
However, I tried running tkregister as you suggested to me, and although the GUI pops up, I'm unable to see the movable volume (ie., the mask). This has happened to me before when i tried something else in tkregister, and am not sure if I'm doing anything wrong. The output is below.
Thanks for your help,
Alex.
tkregister2 --s ./1000186 --mov ./186_corconv_mask.img --reg ./register.dat --regheader
INFO: no target volume specified, assuming FreeSurfer orig volume.
target volume orig
movable volume ./186_corconv_mask.img
reg file ./register.dat
LoadVol 1
$Id: tkregister2.c,v 1.22 2003/11/05 21:30:50 greve Exp $
Diagnostic Level -1
INFO: analyzeRead(): found 1 files for ./186_corconv_mask.img
-----------------------------------------------------------------
INFO: could not find ./186_corconv_mask.mat file for direction cosine info.
INFO: use Analyze 7.5 hdr->hist.orient value: 0, transverse unflipped (default).
INFO: if not valid, please provide the information in ./186_corconv_mask.mat file
-----------------------------------------------------------------
INFO: loading target /data/flanders/work/alex/freesurfer/subjects/./1000186/mri/orig
INFO: changing target type to float
Ttarg: --------------------
-1.000 0.000 0.000 128.000;
0.000 0.000 1.000 -128.000;
0.000 -1.000 0.000 128.000;
0.000 0.000 0.000 1.000;
INFO: loading movable ./186_corconv_mask.img
INFO: analyzeRead(): found 1 files for ./186_corconv_mask.img
-----------------------------------------------------------------
INFO: could not find ./186_corconv_mask.mat file for direction cosine info.
INFO: use Analyze 7.5 hdr->hist.orient value: 0, transverse unflipped (default).
INFO: if not valid, please provide the information in ./186_corconv_mask.mat file
-----------------------------------------------------------------
INFO: analyzeRead(): min = 0, max = 1
INFO: changing move type to float
Tmov: --------------------
-1.000 0.000 0.000 128.000;
0.000 0.000 1.000 -128.000;
0.000 -1.000 0.000 128.000;
0.000 0.000 0.000 1.000;
mkheaderreg = 1, float2int = 0
---- Input registration matrix (computed) --------
1.000 0.000 0.000 0.000;
0.000 0.000 1.000 -0.000;
0.000 -1.000 0.000 0.000;
0.000 0.000 0.000 1.000;
---------------------------------------
subject = ./1000186
Zoom Factor = 2
---- Input registration matrix --------
1.000 0.000 0.000 0.000;
0.000 0.000 1.000 -0.000;
0.000 -1.000 0.000 0.000;
0.000 0.000 0.000 1.000;
Opening window ./1000186
Setting scale
tkregister2: interface: /usr/local/freesurfer/lib/tcl/tkregister2.tcl
tkregister.tcl: startup done
tkregister.tcl: default macro interface (to change: macro,mini,micro)
tkregister.tcl: or: setenv tkregisterinterface {macro,mini,micro}
-----Original Message-----
From: Doug Greve [mailto:[EMAIL PROTECTED]]
Sent: Fri 7/1/2005 12:47 PM
To: Fornito, Alexander
Cc: Bruce Fischl; freesurfer@nmr.mgh.harvard.edu
Subject: RE: [Freesurfer] mri_vol2surf
The first thing that you should do is load your mask as an overlay in
tkmedit to make sure that it is actually falling where you think it
is:
tkmedit yoursubject orig -overlay ./mask.img -reg ./register.dat \
-fthresh 0.5
The fthresh is set assuming your mask is 0 or 1. You can even load
the surface to see if it actually inersects.
If this fails, then you need a new registration file. You can
create this with:
tkregiser2 --s yoursubject --mov mask.img --reg reg.dat --regheader
tkregiser2 allows you to interactively change the registration. Note
that you only use --regheader the first time you run it (ie, before
you have a reg.dat).
doug
On Fri, 1 Jul 2005, Fornito, Alexander wrote:
Sorry, I forgot to mention, I have the mask in analyze format (I traced it in another program). I ran mri_vol2surf using the register.dat file format that Doug provided, and got the output below. Although it creates a .w file, nothing happens when I load it in tksurfer, I'm gessing because the vertex values are zero (?). Have I done something wrong?
mri_vol2surf --src 186_corconv_mask --src_type analyze --srcreg register.dat --hemi lh --out ./186_mask_surf.w --out_type paint
INFO: output format is paint
srcvol = 186_corconv_mask
srctype = analyze
srcreg = register.dat
srcregold = 0
srcwarp unspecified
surf = white
hemi = lh
interp = nearest
float2int = round
INFO: float2int code = 0
INFO: analyzeRead(): found 1 files for /data/flanders/work/alex/freesurfer/subjects/186_corconv_mask
-----------------------------------------------------------------
INFO: could not find /data/flanders/work/alex/freesurfer/subjects/186_corconv_mask.mat file for direction cosine info.
INFO: use Analyze 7.5 hdr->hist.orient value: 0, transverse unflipped (default).
INFO: if not valid, please provide the information in /data/flanders/work/alex/freesurfer/subjects/186_corconv_mask.mat file
-----------------------------------------------------------------
INFO: analyzeRead(): min = 0, max = 1
INFO: chaning type to float
Done loading volume
Reading surface /data/flanders/work/alex/freesurfer/subjects/1000186/surf/lh.white
Done reading source surface
Mapping Source Volume onto Source Subject Surface
vol2surf_linear: nhits = 152789/152789
Done mapping volume to surface
Number of source voxels hit = 96553
Warning: all vertex values are zero
-----Original Message-----
From: Bruce Fischl [mailto:[EMAIL PROTECTED]]
Sent: Fri 7/1/2005 11:06 AM
To: Fornito, Alexander
Cc: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] mri_vol2surf
Hi Alex,
I think you can just load the label into tksurfer (file->label->load) and
it will sample it onto the surface, assuming that it was drawn on one of
the volumes that the surface was created from (or a coregistered one).
The 1st time you do this it may take a bit, but if you save it again it
will save the vertex #s.
cheers,
Bruce
On Fri, 1 Jul 2005, Fornito, Alexander wrote:
Hi,
I'm trying apply ROI masks that I've manually traced in volume space to the same image's surface using mri_vol2surf. mri_vol2surf seems to requires a register.dat file, and I'm unsure what needs to be registered, since the volume that I traced the masks on is exactly the same as the one that I began with to create the surface (so presumably they are in the same space?) . Any hints would be appreciated.
Thanks,
Alex
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--
Douglas N. Greve, Ph.D.
MGH-NMR Center
[EMAIL PROTECTED]
Phone Number: 617-724-2358
Fax: 617-726-7422
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