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

[Robert D. Vincent]

Hi,

Sorry, I've not heard this one before. I'll try to reproduce the problem on
OS X today. Is there any chance you can share a sample dataset that
exhibits the problem?

    -bert

On Fri, Sep 9, 2016 at 12:46 PM, Divya Bolar <dbolar at nmr.mgh.harvard.edu>
wrote:

> 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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