[MINC-users] please disregard Philips dcm2mnc problem

[Audette, Michel]

Hi gents, 

please disregard my previous messages on dcm2mnc problems with the Philips format. 

I've discovered the virtues of dicom3_to_minc, which works like a charm. 

Thanks also to Jonathan Harlap for saving my bacon. 

Cheers, 

Michel


-----Original Message-----
From: minc-users-bounces at bic.mni.mcgill.ca on behalf of Audette, Michel
Sent: Tue 12/12/2006 11:27 AM
To: MINC users mailing list; minc-users at bic.mni.mcgill.ca
Subject: Re: [MINC-users] dcm2mnc: "Error parsing file during 2nd pass" (butnot1st...)
 
Hi again, 

sorry about the confusion, but I have downloaded the latest minc code (2.0.12), and the errors that I am seeing are somewhat different than in the previous message. 

Whether this information is relevant to anyone able to help me remains to be seen. The following text features snippets of the messages that I am seeing: 

Checking file types...
File Schlossmacher_Marita/Schlossmacher_Marita_0.dcm appears to be DICOM (CD/Export).
WARNING: Failed to find image position
...
WARNING: Failed to find image position
Skipping file Schlossmacher_Marita/Schlossmacher_Marita_88.dcm, which is not in the expected format.
...
WARNING: Failed to find image position
Using 478 files
Sorting 478 files...   
num  filename                         studyid        serialno acq      nec  iec  ndy  idy  nsl  isl  acol rcol mrow img#  seq             
   0 arita/Schlossmacher_Marita_0.dcm       0.000000       -1        0   -1   -1   -1   -1   -1   -1   -1   -1   -1    -1                 
 477 rita/Schlossmacher_Marita_99.dcm       0.000000       -1        0   -1   -1   -1   -1   -1   -1   -1   -1   -1    -1                 
Done sorting files.
Processing files, one series at a time...
Using directory 'Schlossmacher_Marita_mnc/'
file_prefix:  [Schlossmacher_Marita_mnc/]

Series    0                                           ( 478 files):
     Schlossmacher_Marita/Schlossmacher_Marita_0.dcm
...
     Schlossmacher_Marita/Schlossmacher_Marita_99.dcm
WARNING: Image coordinates absent or incomplete.
WARNING: Slice location is untrustworthy.

File Schlossmacher_Marita/Schlossmacher_Marita_0.dcm
ERROR: Needed values missing, marking invalid  nrows 0 ncolumns 0 bits_stored 0 bits_alloc 0 
(I made the error message a little more descriptive...)
...
File Schlossmacher_Marita/Schlossmacher_Marita_99.dcm
ERROR: Needed values missing, marking invalid  nrows 0 ncolumns 0 bits_stored 0 bits_alloc 0 
Not sorting Slice dimension
Not sorting Echo dimension
Not sorting Time dimension
Not sorting Phase dimension
Not sorting ChmSh dimension
Done processing files.

I should add that my Linux machine is 64-bit. Please advise. 

Best regards, 

Michel


-----Original Message-----
From: minc-users-bounces at bic.mni.mcgill.ca on behalf of Audette, Michel
Sent: Mon 12/11/2006 6:09 PM
To: minc-users at bic.mni.mcgill.ca
Subject: [MINC-users] dcm2mnc: "Error parsing file during 2nd pass" (but not1st...)
 
Hi everyone, 

I am returning to an old dcm2mnc problem that has become urgent. I am trying to convert what appears to be Philips DICOM files to a minc file, and using the debugger and some printfs, I see the following... 

The first call to read_numa4_dicom() seems to go fine, for all dicom files, although I get warnings: 
WARNING: Can't find Philips slice count
WARNING: Can't find Philips slice index

as well as the following in the final stages of that 1st pass...
WARNING: Can't find Philips private creator ID.
 file list 1st pass... file_list[ifile] Schlossmacher_Marita/Schlossmacher_Marita_478.dcm (this is a printf statement I put in)
WARNING: calculated slice width (0.4499999490) disagrees with file's slice width (0.4499512000)

Error parsing file 'Schlossmacher_Marita/Schlossmacher_Marita_0.dcm' during 2nd pass.

In the 2nd pass, read_std_dicom() and  acr_input_group_list() return NULL, and within acr_input_group_list(), one call to acr_input_group_with_max() apparently returns status = ACR_PROTOCOL_ERROR...

Can anyone suggest the cause of this error in the 2nd pass, or a means to better pinpoint it? 
Also, can anyone suggest a workaround? Is the varying slice width the issue here? 

Cheers, 

Michel

Michel Audette, Ph.D.
Innovation Center Computer Assisted Surgery (ICCAS)
Philipp-Rosenthal-Strasse 55
Leipzig, Germany
Phone: ++49 (0) 341 / 97 - 1 20 13
Fax: ++49 (0) 341 / 97 - 1 20 09

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