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