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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