Hi, We have some old scans that were originally in ACR-NEMA format which we have converted to DICOM. The problem is that they are missing both the ImagePositionPatient and ImageOrientationPatient fields. Is there anyway to use freesurfer without having these two fields? Based on the post by Doug which I found at http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg03409.html , I am afraid not...
Thank you for any help. Regards, Niels Bergsland
Which diom tags do you mean? I think we can get away with not having the Patient Orientation (tag 20,20) -- I'm not sure why I required it in the first place. ImagePositionPatient (tag 20,32) is considerably more important as this is one of the ways the slices are sorted and the direction cosines estabilished. Are these for mosaics?
doug
Niels Bergsland wrote:
Hi, We have some old scans that were originally in ACR-NEMA format which we have converted to DICOM. The problem is that they are missing both the ImagePositionPatient and ImageOrientationPatient fields. Is there anyway to use freesurfer without having these two fields? Based on the post by Doug which I found at http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg03409.html , I am afraid not...
Thank you for any help. Regards, Niels Bergsland _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hi Doug, Thanks for the quick response. These are for single images. These older files are missing 0020,0032 (ImagePositionPatient) and 0020,0037 (ImageOrientationPatient). It is my understanding that 20,37 is used to establish the direction cosines. The scans were all acquired in the axial plane. Is it possible to 'fake' the 20,37 field by inserting the values: 1\0\0\0\1\0 ? We also know which way the slices are supposed to be sorted, is it possible to insert values into 20,32 in order to have freesurfer able to 'know' the proper sorting order? As I said in my first email, I am afraid not... But I figured it would not hurt to ask. Thanks! Cheers, Niels
On 8/28/06, Doug Greve greve@nmr.mgh.harvard.edu wrote:
Which diom tags do you mean? I think we can get away with not having the Patient Orientation (tag 20,20) -- I'm not sure why I required it in the first place. ImagePositionPatient (tag 20,32) is considerably more important as this is one of the ways the slices are sorted and the direction cosines estabilished. Are these for mosaics?
doug
Niels Bergsland wrote:
Hi, We have some old scans that were originally in ACR-NEMA format which we have converted to DICOM. The problem is that they are missing both the ImagePositionPatient and ImageOrientationPatient fields. Is there anyway to use freesurfer without having these two fields? Based on the post by Doug which I found at http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg03409.html , I am afraid not...
Thank you for any help. Regards, Niels Bergsland _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
In order to help us help you, please follow the steps in: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
No, I don't have anything which allows you to specify them yourself. On the other hand, you can work-around this with something like:
mri_probedicom --i slice1.dcm --o slice1.dat
slice1.dat will be a binary file of the pixel data from the file slice1.dcm. You can do this for each slice, then assemble the data into a real format. Not fun, but possible. Other tools out there might not require the direction cosines.
doug
Niels Bergsland wrote:
Hi Doug, Thanks for the quick response. These are for single images. These older files are missing 0020,0032 (ImagePositionPatient) and 0020,0037 (ImageOrientationPatient). It is my understanding that 20,37 is used to establish the direction cosines. The scans were all acquired in the axial plane. Is it possible to 'fake' the 20,37 field by inserting the values: 1\0\0\0\1\0 ? We also know which way the slices are supposed to be sorted, is it possible to insert values into 20,32 in order to have freesurfer able to 'know' the proper sorting order? As I said in my first email, I am afraid not... But I figured it would not hurt to ask. Thanks! Cheers, Niels
On 8/28/06, Doug Greve greve@nmr.mgh.harvard.edu wrote:
Which diom tags do you mean? I think we can get away with not having the Patient Orientation (tag 20,20) -- I'm not sure why I required it in the first place. ImagePositionPatient (tag 20,32) is considerably more important as this is one of the ways the slices are sorted and the direction cosines estabilished. Are these for mosaics?
doug
Niels Bergsland wrote:
Hi, We have some old scans that were originally in ACR-NEMA format which we have converted to DICOM. The problem is that they are missing both the ImagePositionPatient and ImageOrientationPatient fields. Is there anyway to use freesurfer without having these two fields? Based on the post by Doug which I found at
http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg03409.html
, I am afraid not...
Thank you for any help. Regards, Niels Bergsland _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
In order to help us help you, please follow the steps in: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
Thanks for the help Doug! I will let you know how it goes.
Niels
On 8/29/06, Doug Greve greve@nmr.mgh.harvard.edu wrote:
No, I don't have anything which allows you to specify them yourself. On the other hand, you can work-around this with something like:
mri_probedicom --i slice1.dcm --o slice1.dat
slice1.dat will be a binary file of the pixel data from the file slice1.dcm. You can do this for each slice, then assemble the data into a real format. Not fun, but possible. Other tools out there might not require the direction cosines.
doug
Niels Bergsland wrote:
Hi Doug, Thanks for the quick response. These are for single images. These older files are missing 0020,0032 (ImagePositionPatient) and 0020,0037 (ImageOrientationPatient). It is my understanding that 20,37 is used to establish the direction cosines. The scans were all acquired in the axial plane. Is it possible to 'fake' the 20,37 field by inserting the values: 1\0\0\0\1\0 ? We also know which way the slices are supposed to be sorted, is it possible to insert values into 20,32 in order to have freesurfer able to 'know' the proper sorting order? As I said in my first email, I am afraid not... But I figured it would not hurt to ask. Thanks! Cheers, Niels
On 8/28/06, Doug Greve greve@nmr.mgh.harvard.edu wrote:
Which diom tags do you mean? I think we can get away with not having the Patient Orientation (tag 20,20) -- I'm not sure why I required it in the first place. ImagePositionPatient (tag 20,32) is considerably more important as this is one of the ways the slices are sorted and the direction cosines estabilished. Are these for mosaics?
doug
Niels Bergsland wrote:
Hi, We have some old scans that were originally in ACR-NEMA format which we have converted to DICOM. The problem is that they are missing both the ImagePositionPatient and ImageOrientationPatient fields. Is there anyway to use freesurfer without having these two fields? Based on the post by Doug which I found at
http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg03409.html
, I am afraid not...
Thank you for any help. Regards, Niels Bergsland _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
In order to help us help you, please follow the steps in: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
In order to help us help you, please follow the steps in: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
freesurfer@nmr.mgh.harvard.edu
-
Doug Greve -
Niels Bergsland