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

[Divya Bolar]

Yes, apologies:

minc-toolkit-1.0.08-20160205-Darwin-10.7-x86_64.dmg

Thanks also for such a quick reply!
div

On Sep 9, 2016, at 12:49 PM, Vladimir S. FONOV <vladimir.fonov at gmail.com> wrote:

> Is it minc-toolkit binary installation ? If it is - which version did you
> install?
> 
> 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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> 
> 
> 
> -- 
> Best regards,
> 
> Vladimir S. Fonov ~ vladimir <dot> fonov <at> gmail <dot> com
> _______________________________________________
> MINC-users at bic.mni.mcgill.ca
> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
> 
>