[MINC-users] 4d data with dcm2mnc

[Vladimir S. FONOV]

Hello,

it looks like dcm2mnc doesn't recognize that these is a time series and 
extracts only the first one ... Maybe you can try following things:

1. use -splitdynamic option - this probably will not work anyway , but 
worth trying

2. make a script which will run dcm2mnc with groups of 16 files, writing 
output in a separate minc files:

something like that (in bash):

for i in $(seq 1 160);do j in $(seq 1 37);do n=$((i*37+j));
printf 
"RestingState__160_Volumes37slices2sec_7/IM-0006-%04d.dcm\n">>/tmp/$i.lst
done
dcm2mnc -stdin -dname . -fname r112749_100_20111106_160551_`printf 
"%03d" $i`.mnc  rs_160_dcm2mnc < /tmp/$i.lst
rm /tmp/$i.lst
done

this will create series of 160 files with names
rs_160_dcm2mnc/r112749_100_20111106_160551_????.mnc  corresponding to 
the individual scans, which you can later concatenate using mincconcat 
to create a single 4D MINC file.

Hope this will help.

On 12-10-27 04:58 AM, R.L. Muetzel wrote:
> Dear Dr. Fonov,
>
> Thank you for your help!
>
> Below in the text, you'll find the screen output with the -debug flag turned off, and attached you'll find the output from both the -debug and from mincheader.
>
> We are using a clinical GE MR750 3T.  These are EPI fMRI data.  Each dicom file is a single slice (i.e., we're not using any kind of mosaic format, 37 slices, 160TRs = 5290 files).  I have also included the output from dcmtk /dcmdump for one of the dicom files, which includes some of the dicom headers.  Does this give you enough info about the dicom?  Let me know if there are other questions I can answer about the type of dicom.
>
> Thank you again for your time and help!
>
> All the best,
>
> Ryan
>
>
> lorisadmin at rietveld:~/sample_scans/R112749_100$ dcm2mnc RestingState__160_Volumes37slices2sec_7 ./rs_160_dcm2mnc
> Checking file types...
> File RestingState__160_Volumes37slices2sec_7/IM-0006-0906.dcm appears to be DICOM (CD/Export).
> Parsing 5920 files   |<--------------------------------------------------->|
> Sorting 5920 files...   Done sorting files.
> Processing files, one series at a time...
> -Parsing series info |<--------------------------------------------------->|
> WARNING: Coordinate spacing (-3.99999) differs from DICOM slice spacing (4)
>   (perhaps you should consider the -usecoordinates option)
>   Using -3.99999 for the slice spacing value.
> -Creating minc file  |<--------------------------------------------------->|
> Done processing files.
>
>
>
>
>
> lorisadmin at rietveld:~/sample_scans/R112749_100$ On Oct 26, 2012, at 9:30 PM, Vladimir S. FONOV wrote:
>
>> Hello Ryan,
>>
>> I suppose exact command line and the output of -debug would be useful. Also, can you describe what kind of dicom files you have got?
>>
>> On 12-10-26 09:13 AM, R.L. Muetzel wrote:
>>> Hello all,
>>>
>
>>>
>>> We are having trouble converting 4D data with dcm2mnc….basically, we get a 3D image out, and no error messages in the command line.
>>>
>>> We compiled this version (the tar.gz file):
>>>
>>> http://www.bic.mni.mcgill.ca/pipermail/minc-users/2012-September/003522.html
>>>
>>> The output from dcm2mnc -version:
>>>
>>> ~$ dcm2mnc -version
>>> program: 2.0.07 built Oct 25 2012 16:57:03
>>> libminc: 2.2.00
>>> netcdf : 4.1.1 of Nov  7 2011 11:35:16 $
>>> HDF5   : 1.8.4
>>>
>>> Any thoughts on what might be going on?  would it be helpful for us to send you the output from -debug?
>>>
>>> Thanks in advance for any help!
>>>
>>> (also, sorry if this is a duplicate post, as I'm not sure if it got sent through twice)
>>>
>>> Ryan Muetzel
>>> Generation R/Department of Child and Adolescent Psychiatry
>>> Erasmus MC - Sophia Children's Hospital
>>> Rotterdam, the Netherlands


-- 
Best regards,

  Vladimir S. FONOV ~ vladimir.fonov <at> gmail.com