Hi, there,
I have a case_1.hdr file and case_1.img file, but no the corresponding .mat file which contains the necessary direction cosine info. So everytime when I try to register another nifti file case_2.nii to it using tkregister2 or mri_vol2vol, it always complains that
"INFO: could not find ../../case_1.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 ../../case_1.mat file"
Just want to know if there are other methods I can use to register case_1 and case_2? Any kinds of method!
Thanks a lot!
Guang
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Guang,
If you're 100% certain that case_2 is oriented the same way as case_1, for instance if they were from the same scanner, then you can do this:
mri_convert case_2.nii case_2.img
(this outputs case_2.mat)
cp case_2.mat case_1.mat
now tkregister2 should work. Keep in mind this is a hack accounting for the missing case_1 data. If the data is from different scanners, then there is a risk of L-R reversal, because the orientation info may not be the same.
Nick
On Fri, 2009-09-18 at 17:33 -0500, Guang Zeng wrote:
Hi, there,
I have a case_1.hdr file and case_1.img file, but no the corresponding .mat file which contains the necessary direction cosine info. So everytime when I try to register another nifti file case_2.nii to it using tkregister2 or mri_vol2vol, it always complains that
"INFO: could not find ../../case_1.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 ../../case_1.mat file"
Just want to know if there are other methods I can use to register case_1 and case_2? Any kinds of method!
Thanks a lot!
Guang
Bing™ brings you maps, menus, and reviews organized in one place. Try it now. _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hello, Nick,
Thanks a lot for your help. The bad thing is case_1&2 are not oriented the same way. Anything else I can do?
Guang
Subject: Re: [Freesurfer] tkregister2 question From: nicks@nmr.mgh.harvard.edu To: freesurfer_zg@hotmail.com CC: freesurfer@nmr.mgh.harvard.edu Date: Sat, 19 Sep 2009 11:51:28 -0400
Guang,
If you're 100% certain that case_2 is oriented the same way as case_1, for instance if they were from the same scanner, then you can do this:
mri_convert case_2.nii case_2.img
(this outputs case_2.mat)
cp case_2.mat case_1.mat
now tkregister2 should work. Keep in mind this is a hack accounting for the missing case_1 data. If the data is from different scanners, then there is a risk of L-R reversal, because the orientation info may not be the same.
Nick
On Fri, 2009-09-18 at 17:33 -0500, Guang Zeng wrote:
Hi, there,
I have a case_1.hdr file and case_1.img file, but no the corresponding .mat file which contains the necessary direction cosine info. So everytime when I try to register another nifti file case_2.nii to it using tkregister2 or mri_vol2vol, it always complains that
"INFO: could not find ../../case_1.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 ../../case_1.mat file"
Just want to know if there are other methods I can use to register case_1 and case_2? Any kinds of method!
Thanks a lot!
Guang
Bing™ brings you maps, menus, and reviews organized in one place. Try it now. _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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Guang,
You could use the freesurfer utility 'orient_mri'.
First open case_1:
orient_mri --volume case_1.img
then case_2:
orient_mri --volume case_2.nii
Then use the rotate icons to rotate case_1 so that its oriented the same as case_2, and save the case_1 volume (you can save as 'case_1.nii'). Then you can use tkregister2.
Again, without fudicial markers, its difficult to tell left from right, so there is no guarantee that your l-r orientation is correct.
Nick
On Sun, 2009-09-20 at 12:31 -0500, Guang Zeng wrote:
Hello, Nick,
Thanks a lot for your help. The bad thing is case_1&2 are not oriented the same way. Anything else I can do?
Guang
Subject: Re: [Freesurfer] tkregister2 question From: nicks@nmr.mgh.harvard.edu To: freesurfer_zg@hotmail.com CC: freesurfer@nmr.mgh.harvard.edu Date: Sat, 19 Sep 2009 11:51:28 -0400
Guang,
If you're 100% certain that case_2 is oriented the same way as
case_1,
for instance if they were from the same scanner, then you can do
this:
mri_convert case_2.nii case_2.img
(this outputs case_2.mat)
cp case_2.mat case_1.mat
now tkregister2 should work. Keep in mind this is a hack accounting
for
the missing case_1 data. If the data is from different scanners,
then
there is a risk of L-R reversal, because the orientation info may
not be
the same.
Nick
On Fri, 2009-09-18 at 17:33 -0500, Guang Zeng wrote:
Hi, there,
I have a case_1.hdr file and case_1.img file, but no the corresponding .mat file which contains the necessary direction
cosine
info. So everytime when I try to register another nifti file case_2.nii
to
it using tkregister2 or mri_vol2vol, it always complains that
"INFO: could not find ../../case_1.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 ../../case_1.mat
file"
Just want to know if there are other methods I can use to register case_1 and case_2? Any kinds of method!
Thanks a lot!
Guang
Bing™ brings you maps, menus, and reviews organized in one place.
Try
it now. _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Lauren found her dream laptop. Find the PC that’s right for you.
Hello, Nick,
Which version of orient_mri you are using? I read this from FreeSurfer Wiki "First, load up a volume either by passing one on the command line or by using the File menu command or toolbar button. You will see the volume in four views."
However when I call orient_mri, I only saw one view, not four. My version of orient_mri is 1.0.
Thanks a lot! Guang
From: nicks@nmr.mgh.harvard.edu To: freesurfer_zg@hotmail.com Date: Mon, 21 Sep 2009 10:58:15 -0400 CC: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] tkregister2 question
Guang,
You could use the freesurfer utility 'orient_mri'.
First open case_1:
orient_mri --volume case_1.img
then case_2:
orient_mri --volume case_2.nii
Then use the rotate icons to rotate case_1 so that its oriented the same as case_2, and save the case_1 volume (you can save as 'case_1.nii'). Then you can use tkregister2.
Again, without fudicial markers, its difficult to tell left from right, so there is no guarantee that your l-r orientation is correct.
Nick
On Sun, 2009-09-20 at 12:31 -0500, Guang Zeng wrote:
Hello, Nick,
Thanks a lot for your help. The bad thing is case_1&2 are not oriented the same way. Anything else I can do?
Guang
Subject: Re: [Freesurfer] tkregister2 question From: nicks@nmr.mgh.harvard.edu To: freesurfer_zg@hotmail.com CC: freesurfer@nmr.mgh.harvard.edu Date: Sat, 19 Sep 2009 11:51:28 -0400
Guang,
If you're 100% certain that case_2 is oriented the same way as
case_1,
for instance if they were from the same scanner, then you can do
this:
mri_convert case_2.nii case_2.img
(this outputs case_2.mat)
cp case_2.mat case_1.mat
now tkregister2 should work. Keep in mind this is a hack accounting
for
the missing case_1 data. If the data is from different scanners,
then
there is a risk of L-R reversal, because the orientation info may
not be
the same.
Nick
On Fri, 2009-09-18 at 17:33 -0500, Guang Zeng wrote:
Hi, there,
I have a case_1.hdr file and case_1.img file, but no the corresponding .mat file which contains the necessary direction
cosine
info. So everytime when I try to register another nifti file case_2.nii
to
it using tkregister2 or mri_vol2vol, it always complains that
"INFO: could not find ../../case_1.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 ../../case_1.mat
file"
Just want to know if there are other methods I can use to register case_1 and case_2? Any kinds of method!
Thanks a lot!
Guang
Bing™ brings you maps, menus, and reviews organized in one place.
Try
it now. _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Lauren found her dream laptop. Find the PC that’s right for you.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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freesurfer@nmr.mgh.harvard.edu
-
Guang Zeng -
Nick Schmansky