Dear Freesurfer List,
I have used mri_convert as per the tutorial, to great the following mgz files from dicoms:
001/mri/orig/001.mgz and 002/mri/orig/002.mgz
They were created with the following call or the appropriate varient:
$mri_convert -it dicom -ot mgz 002/mri/orig/002/ 002.mgz There were no major errors that appeared during the conversion, and the files that were created are valid reconstructions. I have opened them both in Neurolens and they look exactly as they should.
However, when I try to tkmedit them, I get the following error: $ tkmedit 001 001.mgz mghRead(/Applications/freesurfer/subjects/001/mri/001.mgz, -1): read error
Error: Loading volume 001/mri/orig/001.mgz
Couldn't read the anatomical volume.
Tkmedit couldn't read the volume you specified. This could be because the image format wasn't recognized, or it couldn't find the proper header, or the file(s) were unreadable, or it was the wrong size.
A friend suggested that I use the COR format instead of going through the mgz intermediate, which I did with the commands:
$ mri_convert 002/mri/orig/002/IM-0001-0010.dcm 002 -ot cor
However, I get the same error.
These subjects-001 and 002-are in the default freesurfer/subjects folder. Tkmedit itself works, as I was able to run through the entire tutorial without a hitch.
These are T1-weighted structural images that I am just trying to take a look at, in my first FreeSurfer foray. Not trying anything fancy, I don't think.
Any help, guidance and/or suggestions would be appreciated.
Sincerely,
sgifford
you need to specify where they are. Try:
tkmedit 001 orig/001.mgz
On Tue, 17 Jul 2007, Sheyna Gifford wrote:
Dear Freesurfer List,
I have used mri_convert as per the tutorial, to great the following mgz files from dicoms:
001/mri/orig/001.mgz and 002/mri/orig/002.mgz
They were created with the following call or the appropriate varient:
$mri_convert -it dicom -ot mgz 002/mri/orig/002/ 002.mgz There were no major errors that appeared during the conversion, and the files that were created are valid reconstructions. I have opened them both in Neurolens and they look exactly as they should.
However, when I try to tkmedit them, I get the following error: $ tkmedit 001 001.mgz mghRead(/Applications/freesurfer/subjects/001/mri/001.mgz, -1): read error
Error: Loading volume 001/mri/orig/001.mgz
Couldn't read the anatomical volume.
Tkmedit couldn't read the volume you specified. This could be because the image format wasn't recognized, or it couldn't find the proper header, or the file(s) were unreadable, or it was the wrong size.
A friend suggested that I use the COR format instead of going through the mgz intermediate, which I did with the commands:
$ mri_convert 002/mri/orig/002/IM-0001-0010.dcm 002 -ot cor
However, I get the same error.
These subjects-001 and 002-are in the default freesurfer/subjects folder. Tkmedit itself works, as I was able to run through the entire tutorial without a hitch.
These are T1-weighted structural images that I am just trying to take a look at, in my first FreeSurfer foray. Not trying anything fancy, I don't think.
Any help, guidance and/or suggestions would be appreciated.
Sincerely,
sgifford
Sheyna,
In which directory was the mri_convert command executed? It is not clear to me where the files 001.mgz and 002.mgz were placed. They should be in the <subject>/mri/orig directory.
If they are in that directory, you can view them by:
cd /Applications/freesurfer/subjects/001/mri/orig tkmedit -f 001.mgz
and
tkmedit -f 002.mgz
Nick
On Tue, 2007-07-17 at 16:35 -0400, Sheyna Gifford wrote:
Dear Freesurfer List,
I have used mri_convert as per the tutorial, to great the following mgz files from dicoms:
001/mri/orig/001.mgz and 002/mri/orig/002.mgz
They were created with the following call or the appropriate varient:
$mri_convert -it dicom -ot mgz 002/mri/orig/002/ 002.mgz There were no major errors that appeared during the conversion, and the files that were created are valid reconstructions. I have opened them both in Neurolens and they look exactly as they should.
However, when I try to tkmedit them, I get the following error: $ tkmedit 001 001.mgz mghRead(/Applications/freesurfer/subjects/001/mri/001.mgz, -1): read error
Error: Loading volume 001/mri/orig/001.mgz
Couldn't read the anatomical volume.
Tkmedit couldn't read the volume you specified. This could be because the image format wasn't recognized, or it couldn't find the proper header, or the file(s) were unreadable, or it was the wrong size.
A friend suggested that I use the COR format instead of going through the mgz intermediate, which I did with the commands:
$ mri_convert 002/mri/orig/002/IM-0001-0010.dcm 002 -ot cor
However, I get the same error.
These subjects-001 and 002-are in the default freesurfer/subjects folder. Tkmedit itself works, as I was able to run through the entire tutorial without a hitch.
These are T1-weighted structural images that I am just trying to take a look at, in my first FreeSurfer foray. Not trying anything fancy, I don't think.
Any help, guidance and/or suggestions would be appreciated.
Sincerely,
sgifford
They are in their respective directories, yes.
$ tkmedit -f 001/mri/orig/001.mgz
Got us a pretty brain picture!
We're on the right track...
On 7/17/07 4:48 PM, "Nick Schmansky" nicks@nmr.mgh.harvard.edu wrote:
Sheyna,
In which directory was the mri_convert command executed? It is not clear to me where the files 001.mgz and 002.mgz were placed. They should be in the <subject>/mri/orig directory.
If they are in that directory, you can view them by:
cd /Applications/freesurfer/subjects/001/mri/orig tkmedit -f 001.mgz
and
tkmedit -f 002.mgz
Nick
On Tue, 2007-07-17 at 16:35 -0400, Sheyna Gifford wrote:
Dear Freesurfer List,
I have used mri_convert as per the tutorial, to great the following mgz files from dicoms:
001/mri/orig/001.mgz and 002/mri/orig/002.mgz
They were created with the following call or the appropriate varient:
$mri_convert -it dicom -ot mgz 002/mri/orig/002/ 002.mgz There were no major errors that appeared during the conversion, and the files that were created are valid reconstructions. I have opened them both in Neurolens and they look exactly as they should.
However, when I try to tkmedit them, I get the following error: $ tkmedit 001 001.mgz mghRead(/Applications/freesurfer/subjects/001/mri/001.mgz, -1): read error
Error: Loading volume 001/mri/orig/001.mgz
Couldn't read the anatomical volume.
Tkmedit couldn't read the volume you specified. This could be because the image format wasn't recognized, or it couldn't find the proper header, or the file(s) were unreadable, or it was the wrong size.
A friend suggested that I use the COR format instead of going through the mgz intermediate, which I did with the commands:
$ mri_convert 002/mri/orig/002/IM-0001-0010.dcm 002 -ot cor
However, I get the same error.
These subjects-001 and 002-are in the default freesurfer/subjects folder. Tkmedit itself works, as I was able to run through the entire tutorial without a hitch.
These are T1-weighted structural images that I am just trying to take a look at, in my first FreeSurfer foray. Not trying anything fancy, I don't think.
Any help, guidance and/or suggestions would be appreciated.
Sincerely,
sgifford
freesurfer@nmr.mgh.harvard.edu
-
Bruce Fischl -
Nick Schmansky -
Sheyna Gifford