[Freesurfer] Re: Missing Dicom Fields (Revisted)
Hi Niels, I can't remember what the original problem was. Were the dicom fields missing or were they just wrong? We can handle wrong ones, but missing ones cause our 3rd party dicom reader to fail, which we can't really do anything about. doug Niels Bergsland wrote: Hi again, From the last time that I asked about this, the project was temporarily put on hold, but now it has started up again... When looking back at the responses from last time, I realized that I am not sure if I made it clear what I was proposing as a solution to the missing fields 0020,0032 (ImagePositionPatient) and 0020,0037 (ImageOrientationPatient). My original question was as follows: Is it possible to 'fake' the 20,37 field by inserting the values: 1\0\0\0\1\0 since we know they are acquired in the axial plane? 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? To which you said that you didn't have something to allow us to specify the fields ourselves. I realized that you thought I was asking if Freesurfer has the capability. What I actually meant though is if I can manually insert the values using, for example, dcmodify (part of the DCMTK) and then process the scans with Freesurfer. Hopefully this is a bit more clear! Thanks again, Niels Bergsland -- Douglas N. Greve, Ph.D. MGH-NMR Center [EMAIL PROTECTED] 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 mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] Re: Missing Dicom Fields (Revisted)
Hi Doug, Thanks for the response. The issue is that the fields are missing, but we know that the scans are acquired in the axial plane. Would it be a horrible idea to insert into 20,37 the following values since they correspond to a 'true' axial plane: 1\0\0\0\1\0 ? You mentioned before that Freesurfer uses 20,32 to calculate the order of the slices. Can we insert values into 20,32 in order to allow Freesurfer to work? (This would all be done prior to actually using Freesurfer by using dcmodify from the DCMTK package to manually insert the values, if this approach is feasible). Thanks again Doug. Regards, Niels On 10/3/06, Doug Greve [EMAIL PROTECTED] wrote: Hi Niels, I can't remember what the original problem was. Were the dicom fields missing or were they just wrong? We can handle wrong ones, but missing ones cause our 3rd party dicom reader to fail, which we can't really do anything about. doug Niels Bergsland wrote: Hi again, From the last time that I asked about this, the project was temporarily put on hold, but now it has started up again... When looking back at the responses from last time, I realized that I am not sure if I made it clear what I was proposing as a solution to the missing fields 0020,0032 (ImagePositionPatient) and 0020,0037 (ImageOrientationPatient). My original question was as follows: Is it possible to 'fake' the 20,37 field by inserting the values: 1\0\0\0\1\0 since we know they are acquired in the axial plane? 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? To which you said that you didn't have something to allow us to specify the fields ourselves. I realized that you thought I was asking if Freesurfer has the capability. What I actually meant though is if I can manually insert the values using, for example, dcmodify (part of the DCMTK) and then process the scans with Freesurfer. Hopefully this is a bit more clear! Thanks again, Niels Bergsland -- Douglas N. Greve, Ph.D. MGH-NMR Center [EMAIL PROTECTED] 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 mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] Re: Missing Dicom Fields (Revisted)
From a FreeSurfer stand-point it is fine. Your data integrity is, of course, your own business, but I would advise being very careful with it and putting a comment if you can into the dicom file indicating what you did. You might approach the manufacturer (or whoever is creating the dicoms) about including all the correct info from the start. doug Niels Bergsland wrote: Hi Doug, Thanks for the response. The issue is that the fields are missing, but we know that the scans are acquired in the axial plane. Would it be a horrible idea to insert into 20,37 the following values since they correspond to a 'true' axial plane: 1\0\0\0\1\0 ? You mentioned before that Freesurfer uses 20,32 to calculate the order of the slices. Can we insert values into 20,32 in order to allow Freesurfer to work? (This would all be done prior to actually using Freesurfer by using dcmodify from the DCMTK package to manually insert the values, if this approach is feasible). Thanks again Doug. Regards, Niels On 10/3/06, Doug Greve [EMAIL PROTECTED] wrote: Hi Niels, I can't remember what the original problem was. Were the dicom fields missing or were they just wrong? We can handle wrong ones, but missing ones cause our 3rd party dicom reader to fail, which we can't really do anything about. doug Niels Bergsland wrote: Hi again, From the last time that I asked about this, the project was temporarily put on hold, but now it has started up again... When looking back at the responses from last time, I realized that I am not sure if I made it clear what I was proposing as a solution to the missing fields 0020,0032 (ImagePositionPatient) and 0020,0037 (ImageOrientationPatient). My original question was as follows: Is it possible to 'fake' the 20,37 field by inserting the values: 1\0\0\0\1\0 since we know they are acquired in the axial plane? 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? To which you said that you didn't have something to allow us to specify the fields ourselves. I realized that you thought I was asking if Freesurfer has the capability. What I actually meant though is if I can manually insert the values using, for example, dcmodify (part of the DCMTK) and then process the scans with Freesurfer. Hopefully this is a bit more clear! Thanks again, Niels Bergsland -- Douglas N. Greve, Ph.D. MGH-NMR Center [EMAIL PROTECTED] 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 [EMAIL PROTECTED] 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 mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
