Never mind about the differences between tkmedit and tkregister - I
retained --regheader in the command line, even though the mask and the
volume were already correctly aligned, which caused them to move out of
alignment. However, I'm still unsure of what the correct file format is for
me to apply the image as an ROI to the surface to get regional anatomical
info.
Thanks,
Alex
-----Original Message-----
From: Bruce Fischl [mailto:[EMAIL PROTECTED]
Sent: Mon 7/4/2005 11:25 AM
To: Fornito, Alexander
Cc: Doug Greve; [email protected]
Subject: RE: [Freesurfer] mri_vol2surf
Hi Alex,
no, label files are text files with the extension .label that
usually
reside in the subject's label directory. .w files are "weight" files
(from EEG/MEG inverse solutions), and more generally, are a sparse
set of
floating point values. You can load them in tksurfer with file->load
overlay, and leave the register field blank. but they probably aren't
the
right format for a label, which is just a list of voxels. Maybe Doug
can
point you in the right direction for that (mri_vol2roi?)
cheers,
Bruce
On Mon, 4 Jul 2005, Fornito, Alexander wrote:
Hi,
I've managed to get the mask to a point where it's in the correct
position if I load it through tkmedit (as a binary in analyze format). I
then run mri_vol2surf, which seems to work (output below). However, If I
try to load the mask (now saved as a .w file) though tksurfer as file >
label > load, nothing happens (nothing happens if I try to load it as an
overlay with the register.dat file either). If I try to load it as a label
in tkmedit, I get the following:
Couldn't load the label.
Tkmedit couldn't read the label you specified. This could be
because the format wasn't valid or the file wasn't found.
Am I missing something? I though .w was the correct format for
labels of this type.
Here's the mri_vol2surf output. Thanks again!
mri_vol2surf --src 186_corconv_native_testmask_binary_y --src_type
analyze --srcreg register.dat --hemi lh --out
./186_native_flip_y_mask_surf.w --out_type paint
INFO: output format is paint
srcvol = 186_corconv_native_testmask_binary_y
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_native_testmask_binary_y
-----------------------------------------------------------------
INFO: could not find
/data/flanders/work/alex/freesurfer/subjects/186_corconv_native_testmask_binary_y.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_native_testmask_binary_y.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
avg = 1.000, stdev = 0.000, min = 1.000, max = 1.000
-----Original Message-----
From: Doug Greve [mailto:[EMAIL PROTECTED]
Sent: Fri 7/1/2005 10:11 PM
To: Fornito, Alexander
Cc: Bruce Fischl; [email protected]
Subject: Re: [Freesurfer] mri_vol2surf
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; [email protected]
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: [email protected]
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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