Hi Bruce,
thanks for replying so fast. But somehow I still don't get this running. When I say:
"mri_convert avant/IM-0001-0001.dcm avant.mgz"
I get:
"mri_convert avant/IM-0001-0001.dcm avant.mgz unknown file type for file avant/IM-0001-0001.dcm"
when saying:
"mri_convert -it dicom -ot mgz avant/IM-0001-0001.dcm avant.mgz"
I get:
"mri_convert -it dicom -ot mgz avant/IM-0001-0001.dcm avant.mgz reading from avant/IM-0001-0001.dcm... no DICOM files found. Exit"
I don't have any idea what's wrong there.
Cheers, Birte
On Jul 12, 2007, at 9:02 PM, Bruce Fischl wrote:
Hi Birte, you need to specify the name of a single DICOM file that is in the series you want to use for building anatomical models, not just the directory name. cheers, Bruce On Thu, 12 Jul 2007, Birte Schrader wrote:
Hello, I just downloaded and installed the freesurfer and got up the step where I tested it by trying "recon-all -s bert -autorecon1". This works fine :-) Now I (thoroughly) followed the instructions "Getting started with your own data" in of https://surfer.nmr.mgh.harvard.edu/ fswiki/ TestingFreeSurfer. But unfortunately the mri_convert command does not work on (my?) dicom-files: "mri_convert -it dicom -ot mgz avant/ avant.mgz" is what I type in. I am really in mri/orig/ and in mri/orig/avant are 120 .dcm-files so I don't see what's wrong. I get the error message: "reading from avant/... no DICOM files found. Exit" Do you know if there are different types if dicom-files and not all of them are supported? Or do you see anything else that might be wrong? Thanks in advance. Birte PS: The FreeSurfer software was highly recommended to me by a friend of a friend of mine, so I am really looking forward to trying it on my data... PPS: tkmedit and tksurfer do not work yet for me. But that is some problem with displaying the windows. I get "GLUT: Fatal Error in tksurfer.bin: could not open display:". But this shouldn't alter the no-display-functions of freesurfer, no? Visualization I can do otherwise if I cannot fix it... _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Try -siemens_dicom instead of -dicom
On Thu, 2007-07-12 at 21:44 +0200, Birte Schrader wrote:
Hi Bruce,
thanks for replying so fast. But somehow I still don't get this running. When I say:
"mri_convert avant/IM-0001-0001.dcm avant.mgz"
I get:
"mri_convert avant/IM-0001-0001.dcm avant.mgz unknown file type for file avant/IM-0001-0001.dcm"
when saying:
"mri_convert -it dicom -ot mgz avant/IM-0001-0001.dcm avant.mgz"
I get:
"mri_convert -it dicom -ot mgz avant/IM-0001-0001.dcm avant.mgz reading from avant/IM-0001-0001.dcm... no DICOM files found. Exit"
I don't have any idea what's wrong there.
Cheers, Birte
On Jul 12, 2007, at 9:02 PM, Bruce Fischl wrote:
Hi Birte, you need to specify the name of a single DICOM file that is in the series you want to use for building anatomical models, not just the directory name. cheers, Bruce On Thu, 12 Jul 2007, Birte Schrader wrote:
Hello, I just downloaded and installed the freesurfer and got up the step where I tested it by trying "recon-all -s bert - autorecon1". This works fine :-) Now I (thoroughly) followed the instructions "Getting started with your own data" in of https://surfer.nmr.mgh.harvard.edu/fswiki/ TestingFreeSurfer. But unfortunately the mri_convert command does not work on (my?) dicom-files: "mri_convert -it dicom -ot mgz avant/ avant.mgz" is what I type in. I am really in mri/orig/ and in mri/orig/avant are 120 .dcm-files so I don't see what's wrong. I get the error message: "reading from avant/... no DICOM files found. Exit" Do you know if there are different types if dicom-files and not all of them are supported? Or do you see anything else that might be wrong? Thanks in advance. Birte PS: The FreeSurfer software was highly recommended to me by a friend of a friend of mine, so I am really looking forward to trying it on my data... PPS: tkmedit and tksurfer do not work yet for me. But that is some problem with displaying the windows. I get "GLUT: Fatal Error in tksurfer.bin: could not open display:". But this shouldn't alter the no-display-functions of freesurfer, no? Visualization I can do otherwise if I cannot fix it... _______________________________________________ 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
Thank you, Nick, But this doesn't work either. It then says:
"mri_convert -it siemens_dicom -ot mgz avant/IM-0001-0001.dcm avant.mgz reading from avant/IM-0001-0001.dcm... ERROR (ScanSiemensSeries): avant/IM-0001-0001.dcm is not a Siemens DICOM file ERROR: could not find any files (SeriesList==NULL)"
On Jul 12, 2007, at 9:52 PM, Nick Schmansky wrote:
Try -siemens_dicom instead of -dicom
On Thu, 2007-07-12 at 21:44 +0200, Birte Schrader wrote:
Hi Bruce,
thanks for replying so fast. But somehow I still don't get this running. When I say:
"mri_convert avant/IM-0001-0001.dcm avant.mgz"
I get:
"mri_convert avant/IM-0001-0001.dcm avant.mgz unknown file type for file avant/IM-0001-0001.dcm"
when saying:
"mri_convert -it dicom -ot mgz avant/IM-0001-0001.dcm avant.mgz"
I get:
"mri_convert -it dicom -ot mgz avant/IM-0001-0001.dcm avant.mgz reading from avant/IM-0001-0001.dcm... no DICOM files found. Exit"
I don't have any idea what's wrong there.
Cheers, Birte
On Jul 12, 2007, at 9:02 PM, Bruce Fischl wrote:
Hi Birte, you need to specify the name of a single DICOM file that is in the series you want to use for building anatomical models, not just the directory name. cheers, Bruce On Thu, 12 Jul 2007, Birte Schrader wrote:
Hello, I just downloaded and installed the freesurfer and got up the step where I tested it by trying "recon-all -s bert - autorecon1". This works fine :-) Now I (thoroughly) followed the instructions "Getting started with your own data" in of https://surfer.nmr.mgh.harvard.edu/fswiki/ TestingFreeSurfer. But unfortunately the mri_convert command does not work on (my?) dicom-files: "mri_convert -it dicom -ot mgz avant/ avant.mgz" is what I type in. I am really in mri/orig/ and in mri/orig/avant are 120 .dcm-files so I don't see what's wrong. I get the error message: "reading from avant/... no DICOM files found. Exit" Do you know if there are different types if dicom-files and not all of them are supported? Or do you see anything else that might be wrong? Thanks in advance. Birte PS: The FreeSurfer software was highly recommended to me by a friend of a friend of mine, so I am really looking forward to trying it on my data... PPS: tkmedit and tksurfer do not work yet for me. But that is some problem with displaying the windows. I get "GLUT: Fatal Error in tksurfer.bin: could not open display:". But this shouldn't alter the no-display-functions of freesurfer, no? Visualization I can do otherwise if I cannot fix it... _______________________________________________ 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
what kind of dicoms are these? What version of freesurfer/mri_convert are you using?
Birte Schrader wrote:
Thank you, Nick, But this doesn't work either. It then says:
"mri_convert -it siemens_dicom -ot mgz avant/IM-0001-0001.dcm avant.mgz reading from avant/IM-0001-0001.dcm... ERROR (ScanSiemensSeries): avant/IM-0001-0001.dcm is not a Siemens DICOM file ERROR: could not find any files (SeriesList==NULL)"
On Jul 12, 2007, at 9:52 PM, Nick Schmansky wrote:
Try -siemens_dicom instead of -dicom
On Thu, 2007-07-12 at 21:44 +0200, Birte Schrader wrote:
Hi Bruce,
thanks for replying so fast. But somehow I still don't get this running. When I say:
"mri_convert avant/IM-0001-0001.dcm avant.mgz"
I get:
"mri_convert avant/IM-0001-0001.dcm avant.mgz unknown file type for file avant/IM-0001-0001.dcm"
when saying:
"mri_convert -it dicom -ot mgz avant/IM-0001-0001.dcm avant.mgz"
I get:
"mri_convert -it dicom -ot mgz avant/IM-0001-0001.dcm avant.mgz reading from avant/IM-0001-0001.dcm... no DICOM files found. Exit"
I don't have any idea what's wrong there.
Cheers, Birte
On Jul 12, 2007, at 9:02 PM, Bruce Fischl wrote:
Hi Birte, you need to specify the name of a single DICOM file that is in the series you want to use for building anatomical models, not just the directory name. cheers, Bruce On Thu, 12 Jul 2007, Birte Schrader wrote:
Hello, I just downloaded and installed the freesurfer and got up the step where I tested it by trying "recon-all -s bert - autorecon1". This works fine :-) Now I (thoroughly) followed the instructions "Getting started with your own data" in of https://surfer.nmr.mgh.harvard.edu/fswiki/ TestingFreeSurfer. But unfortunately the mri_convert command does not work on (my?) dicom-files: "mri_convert -it dicom -ot mgz avant/ avant.mgz" is what I type in. I am really in mri/orig/ and in mri/orig/avant are 120 .dcm-files so I don't see what's wrong. I get the error message: "reading from avant/... no DICOM files found. Exit" Do you know if there are different types if dicom-files and not all of them are supported? Or do you see anything else that might be wrong? Thanks in advance. Birte PS: The FreeSurfer software was highly recommended to me by a friend of a friend of mine, so I am really looking forward to trying it on my data... PPS: tkmedit and tksurfer do not work yet for me. But that is some problem with displaying the windows. I get "GLUT: Fatal Error in tksurfer.bin: could not open display:". But this shouldn't alter the no-display-functions of freesurfer, no? Visualization I can do otherwise if I cannot fix it... _______________________________________________ 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
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hello all. Thanks for the numerous replies and tips, none of them solved the problem though. Another strange thing (maybe this is the reason why it doesn't work): Though I have rwx-permits for all users in my directory and on the dcm-files, the error message I get when trying to convert the files is different when I precede it with a "sudo".
Without "sudo" it's:
"mri_convert -it dicom -ot mgz avant/IM-0001-0001.dcm avant.mgz reading from avant/IM-0001-0001.dcm... no DICOM files found. Exit"
and with "sudo" it is
"dyld: Library not loaded: /sw/lib/libgsl.0.dylib Referenced from: /Applications/freesurfer/bin//mri_convert Reason: image not found Trace/BPT trap"
So I will follow this trace now... Did anyone have the same problem? I am working on an Intel Mac (OS 10.4).
Cheers, Birte
On Jul 12, 2007, at 9:52 PM, Nick Schmansky wrote:
Try -siemens_dicom instead of -dicom
On Thu, 2007-07-12 at 21:44 +0200, Birte Schrader wrote:
Hi Bruce,
thanks for replying so fast. But somehow I still don't get this running. When I say:
"mri_convert avant/IM-0001-0001.dcm avant.mgz"
I get:
"mri_convert avant/IM-0001-0001.dcm avant.mgz unknown file type for file avant/IM-0001-0001.dcm"
when saying:
"mri_convert -it dicom -ot mgz avant/IM-0001-0001.dcm avant.mgz"
I get:
"mri_convert -it dicom -ot mgz avant/IM-0001-0001.dcm avant.mgz reading from avant/IM-0001-0001.dcm... no DICOM files found. Exit"
I don't have any idea what's wrong there.
Cheers, Birte
On Jul 12, 2007, at 9:02 PM, Bruce Fischl wrote:
Hi Birte, you need to specify the name of a single DICOM file that is in the series you want to use for building anatomical models, not just the directory name. cheers, Bruce On Thu, 12 Jul 2007, Birte Schrader wrote:
Hello, I just downloaded and installed the freesurfer and got up the step where I tested it by trying "recon-all -s bert - autorecon1". This works fine :-) Now I (thoroughly) followed the instructions "Getting started with your own data" in of https://surfer.nmr.mgh.harvard.edu/fswiki/ TestingFreeSurfer. But unfortunately the mri_convert command does not work on (my?) dicom-files: "mri_convert -it dicom -ot mgz avant/ avant.mgz" is what I type in. I am really in mri/orig/ and in mri/orig/avant are 120 .dcm-files so I don't see what's wrong. I get the error message: "reading from avant/... no DICOM files found. Exit" Do you know if there are different types if dicom-files and not all of them are supported? Or do you see anything else that might be wrong? Thanks in advance. Birte PS: The FreeSurfer software was highly recommended to me by a friend of a friend of mine, so I am really looking forward to trying it on my data... PPS: tkmedit and tksurfer do not work yet for me. But that is some problem with displaying the windows. I get "GLUT: Fatal Error in tksurfer.bin: could not open display:". But this shouldn't alter the no-display-functions of freesurfer, no? Visualization I can do otherwise if I cannot fix it... _______________________________________________ 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
freesurfer@nmr.mgh.harvard.edu
-
Birte Schrader -
Doug Greve -
Nick Schmansky