[MINC-users] dcm2mnc freezes at end on OS X

[Divya Bolar]

Hi all, 

I know dcm2mnc has been discussed ad nauseam, but I can't seem to find any solutions in my searches.  

No matter what I do, dcm2mnc appears to freeze at the end (i.e. when writing out the mnc, which ends up being "zero bytes").    I am able to load the images into other DICOM viewers including OsiriX, so the data seems intact.  Notably,  if I import then export these DICOMs from Osirix, dcm2mnc still fails.... It seems like it is having a problem outputting (writing out) the mnc, perhaps with micreate, but I have no idea how to debug.... 

I am using the version below on MacOS X 10.9.5 mavericks.   
program: 2.01.03 built Feb  5 2016 14:01:49
libminc: 2.3.01
netcdf : 4.3.3 of Feb  5 2016 12:15:31 $
HDF5   : 1.8.15

This the command line I use (I have also tried without the -usecoordinates and lots of other combinations)
dcm2mnc -usecoordinates ./DICOM/ ./


File ./DICOM/MoCoSeries-PASL-anon/0001-1.3.12.2.1107.5.2.32.35235.2016080612385213830244495.dcm appears to be DICOM (CD/Export).
Parsing 91 files     |<--------------------------------------------------->|
Sorting 91 files...   Done sorting files.
Processing files, one series at a time...
WARNING: Acquisition number is per scan.
WARNING: Image number is a mystery.
INFO: Acquisition number ranges from 1 to 91
INFO: Image number ranges from 1 to 91
-Parsing series info |<--First Slice at 1,18.478516,0.000000               |
First Echo at 1,0.011000,0.000000
First Time at 1,0.000000,0.000000
First Phase at 1,0.000000,0.000000
First ChmSh at 1,0.000000,0.000000
-------------------------------------------------->

And then it just hangs here!


I have also tried on a 3D data set (rather than 4D)

Parsing 64 files     |<--------------------------------------------------->|
Sorting 64 files...   Done sorting files.
Processing files, one series at a time...
WARNING: Acquisition number is not informative.
WARNING: Image number is per slice.
INFO: Acquisition number ranges from 1 to 1
INFO: Image number ranges from 1 to 64
-Parsing series info |<--First Slice at 1,-41.735644,0.000000              |
First Echo at 1,0.091000,0.000000
First Time at 1,-206.275000,0.000000
First Phase at 1,0.000000,0.000000
First ChmSh at 1,0.000000,0.000000
Warning: merging extra indices on Time axis:   1 2
->Warning: merging extra indices on Time axis:   1 3

.....

Warning: merging extra indices on Time axis:   1 60
->Warning: merging extra indices on Time axis:   1 61
->Warning: merging extra indices on Time axis:   1 62
->Warning: merging extra indices on Time axis:   1 63
->
Warning: merging extra indices on Time axis:   1 64

And then it just hangs here..... 


Any assistance would be greatly appreciated, thanks so much!
Div





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