Hi everybody
Does anyone know if there is something that I can do to fix the follow error occurred in stage1 of recon-all?
Thnaks a lot
Massimiliano Calabrese Imaging Group Neuroimmunology Branch NINDS, NIH.
mri_fill: could not find corpus callosum No such file or directory INFO: Modifying dst c_(r,a,s), using the transform dst find_cutting_plane:seed point not in structure! Searching neighborhood... find_cutting_plane:seed point not in structure! Searching neighborhood... ERROR: mri_fill exited with non-zero status ------------------------------------------ Filesystem 1K-blocks Used Available Use% Mounted on apollo.ninds.nih.gov:/arena3 1372150372 1218678884 83770268 94% /net/apollo ------------------------------------------ recon-all exited with errors at Mon Nov 15 14:25:03 EST 2004
did you try specifying the cc point with mri_fill -cc <x> <y> <z> where the coords are in talairach?
Bruce
On Mon, 15 Nov 2004, Calabrese Massimiliano wrote:
Hi everybody
Does anyone know if there is something that I can do to fix the follow error occurred in stage1 of recon-all?
Thnaks a lot
Massimiliano Calabrese Imaging Group Neuroimmunology Branch NINDS, NIH.
mri_fill: could not find corpus callosum No such file or directory INFO: Modifying dst c_(r,a,s), using the transform dst find_cutting_plane:seed point not in structure! Searching neighborhood... find_cutting_plane:seed point not in structure! Searching neighborhood... ERROR: mri_fill exited with non-zero status
Filesystem 1K-blocks Used Available Use% Mounted on apollo.ninds.nih.gov:/arena3 1372150372 1218678884 83770268 94% /net/apollo
recon-all exited with errors at Mon Nov 15 14:25:03 EST 2004
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hi all,
Using mris_convert -p I converted a ?h.patch.flat file to ?h.patch.flat.asc
I am not sure I understand the file format correctly. Could some one please help?
Also is the vertex indexing of faces maintained througout in freesurfer.
For example if I have a ?h.pial which I convert to ?h.inflated and then to ?h.flat will the vertex numbers remain the same?
Will this hold true even if I export them asc.
Also what is the difference between ?h.sphere and ?h.qsphere ?
Ajay
Hi Ajay,
yes, the vertex indexing is the same for all surface configurations of a given surface (e.g. lh.inflated, lh.white, lh.pial, lh.sphere, etc...). The ascii patch file format is as follows:
#!ascii version of patch <surface_file_name> <num vertices> <num faces> <vno> <x> <y> <z> . . . <fno> <vno1> <vno2> <vno3> . . .
where there is one entry for each vertex in the patch, and one entry for each face in the patch.
cheers, Bruce
On Wed, 17 Nov 2004, Ajay Pillai wrote:
Hi all,
Using mris_convert -p I converted a ?h.patch.flat file to ?h.patch.flat.asc
I am not sure I understand the file format correctly. Could some one please help?
Also is the vertex indexing of faces maintained througout in freesurfer.
For example if I have a ?h.pial which I convert to ?h.inflated and then to ?h.flat will the vertex numbers remain the same?
Will this hold true even if I export them asc.
Also what is the difference between ?h.sphere and ?h.qsphere ?
Ajay
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hello all,
Does any one have a matlab routine to convert given coordinates from RAS to talarach space.
If not atleas give an indication of how to do it?
Ajay
If you have the RAS in a vector: v = [R A S 1]';
And the talairach.xfm matrix X, then MNI talairach cooridnates are:
vMNI = X*v;
These can be computed to something closer to true talairach coords using the attached mfile, originally from Matthew Brett.
doug
Ajay Pillai wrote:
Hello all,
Does any one have a matlab routine to convert given coordinates from RAS to talarach space.
If not atleas give an indication of how to do it?
Ajay _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Thank you Doug,
What I have is MEG data in RAS coordinates and I want to convert it to Talairach.
So I do not have a talairach.xfm file.So how does one do it. will the m file you gave work without the .xfm file
Ajay
Doug Greve wrote:
If you have the RAS in a vector: v = [R A S 1]';
And the talairach.xfm matrix X, then MNI talairach cooridnates are:
vMNI = X*v;
These can be computed to something closer to true talairach coords using the attached mfile, originally from Matthew Brett.
doug
Ajay Pillai wrote:
Hello all,
Does any one have a matlab routine to convert given coordinates from RAS to talarach space.
If not atleas give an indication of how to do it?
Ajay _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
function outpoints = mni2tal(inpoints) % Converts coordinates from MNI brain to best guess % for equivalent Talairach coordinates % FORMAT outpoints = mni2tal(inpoints) % Where inpoints is N by 3 or 3 by N matrix of coordinates % (N being the number of points) % outpoints is the coordinate matrix with Talairach points % Matthew Brett 10/8/99
dimdim = find(size(inpoints) == 3); if isempty(dimdim) error('input must be a N by 3 or 3 by N matrix') end if dimdim == 2 inpoints = inpoints'; %' end
% Transformation matrices, different zooms above/below AC upT = spm_matrix([0 0 0 0.05 0 0 0.99 0.97 0.92]); downT = spm_matrix([0 0 0 0.05 0 0 0.99 0.97 0.84]);
tmp = inpoints(3,:)<0; % 1 if below AC inpoints = [inpoints; ones(1, size(inpoints, 2))]; inpoints(:, tmp) = downT * inpoints(:, tmp); inpoints(:, ~tmp) = upT * inpoints(:, ~tmp); outpoints = inpoints(1:3, :); if dimdim == 2 outpoints = outpoints'; %' end
If you've done the freesurfer recon, then you should have one in yoursubject/mri/transforms.
The matlab file just converts MNI talairach coordinates to "true" talairach coordinates. The MNI talairach atlas does not map to the true talairach atlas very well, and this attempts to fix it. The talairach.xfm maps from subject RAS to MNI talairach RAS.
doug
Ajay Pillai wrote:
Thank you Doug,
What I have is MEG data in RAS coordinates and I want to convert it to Talairach.
So I do not have a talairach.xfm file.So how does one do it. will the m file you gave work without the .xfm file
Ajay
Doug Greve wrote:
If you have the RAS in a vector: v = [R A S 1]';
And the talairach.xfm matrix X, then MNI talairach cooridnates are:
vMNI = X*v;
These can be computed to something closer to true talairach coords using the attached mfile, originally from Matthew Brett.
doug
Ajay Pillai wrote:
Hello all,
Does any one have a matlab routine to convert given coordinates from RAS to talarach space.
If not atleas give an indication of how to do it?
Ajay _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
function outpoints = mni2tal(inpoints) % Converts coordinates from MNI brain to best guess % for equivalent Talairach coordinates % FORMAT outpoints = mni2tal(inpoints) % Where inpoints is N by 3 or 3 by N matrix of coordinates % (N being the number of points) % outpoints is the coordinate matrix with Talairach points % Matthew Brett 10/8/99
dimdim = find(size(inpoints) == 3); if isempty(dimdim) error('input must be a N by 3 or 3 by N matrix') end if dimdim == 2 inpoints = inpoints'; %' end
% Transformation matrices, different zooms above/below AC upT = spm_matrix([0 0 0 0.05 0 0 0.99 0.97 0.92]); downT = spm_matrix([0 0 0 0.05 0 0 0.99 0.97 0.84]);
tmp = inpoints(3,:)<0; % 1 if below AC inpoints = [inpoints; ones(1, size(inpoints, 2))]; inpoints(:, tmp) = downT * inpoints(:, tmp); inpoints(:, ~tmp) = upT * inpoints(:, ~tmp); outpoints = inpoints(1:3, :); if dimdim == 2 outpoints = outpoints'; %' end
-- ..so long as the people do not care to exercise their freedom, those who wish to tyrannize will do so; for tyrants are active and ardent, and will devote themselves in the name of any number of gods, religious and otherwise, to put shackles upon sleeping men. -- Voltairine de Cleyre
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hi,
please find attached some matlab functions this transformation. All of my freesurfer_*.m files are available by anonymous cvs checkout, see http://eeg.sf.net for details.
Kind regards, Darren
Doug Greve wrote:
If you've done the freesurfer recon, then you should have one in yoursubject/mri/transforms.
The matlab file just converts MNI talairach coordinates to "true" talairach coordinates. The MNI talairach atlas does not map to the true talairach atlas very well, and this attempts to fix it. The talairach.xfm maps from subject RAS to MNI talairach RAS.
doug
Ajay Pillai wrote:
Thank you Doug,
What I have is MEG data in RAS coordinates and I want to convert it to Talairach.
So I do not have a talairach.xfm file.So how does one do it. will the m file you gave work without the .xfm file
Ajay
Doug Greve wrote:
If you have the RAS in a vector: v = [R A S 1]';
And the talairach.xfm matrix X, then MNI talairach cooridnates are:
vMNI = X*v;
These can be computed to something closer to true talairach coords using the attached mfile, originally from Matthew Brett.
doug
Ajay Pillai wrote:
Hello all,
Does any one have a matlab routine to convert given coordinates from RAS to talarach space.
If not atleas give an indication of how to do it?
Ajay _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
function outpoints = mni2tal(inpoints) % Converts coordinates from MNI brain to best guess % for equivalent Talairach coordinates % FORMAT outpoints = mni2tal(inpoints) % Where inpoints is N by 3 or 3 by N matrix of coordinates % (N being the number of points) % outpoints is the coordinate matrix with Talairach points % Matthew Brett 10/8/99
dimdim = find(size(inpoints) == 3); if isempty(dimdim) error('input must be a N by 3 or 3 by N matrix') end if dimdim == 2 inpoints = inpoints'; %' end
% Transformation matrices, different zooms above/below AC upT = spm_matrix([0 0 0 0.05 0 0 0.99 0.97 0.92]); downT = spm_matrix([0 0 0 0.05 0 0 0.99 0.97 0.84]);
tmp = inpoints(3,:)<0; % 1 if below AC inpoints = [inpoints; ones(1, size(inpoints, 2))]; inpoints(:, tmp) = downT * inpoints(:, tmp); inpoints(:, ~tmp) = upT * inpoints(:, ~tmp); outpoints = inpoints(1:3, :); if dimdim == 2 outpoints = outpoints'; %' end
-- ..so long as the people do not care to exercise their freedom, those who wish to tyrannize will do so; for tyrants are active and ardent, and will devote themselves in the name of any number of gods, religious and otherwise, to put shackles upon sleeping men. -- Voltairine de Cleyre
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hi,
You need a talairach.xfm which is a RAS-to-"MNI-Talairach" transform, which should be present in $subject/mri/transforms (this is the 4x4 affine transform).
The following site explains the difference between "MNI" talairach and the "real" talairach space: http://www.mrc-cbu.cam.ac.uk/Imaging/Common/mnispace.shtml
Tosa
Ajay Pillai wrote:
Hello all,
Does any one have a matlab routine to convert given coordinates from RAS to talarach space.
If not atleas give an indication of how to do it?
Ajay _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
freesurfer@nmr.mgh.harvard.edu
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Ajay Pillai -
Bruce Fischl -
Calabrese Massimiliano -
Darren Weber -
Doug Greve -
Yasunari Tosa