[Freesurfer] mri_convert: dicom to nifti 4D

Bruce Fischl fischl at nmr.mgh.harvard.edu
Thu Jul 6 21:29:52 EDT 2006
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it's something Paul Raines wrote.

On Thu, 6 Jul 2006, Thomas, Adam 
(NIH/NIMH) [E] wrote:

>
> Looks like the machine I was running it on before was still running a
> dev version from February, but I just tried it again with the latest
> stable version (see below) and got the same thing.
>
> I've uploaded a tar file with all of the dicom files. It also includes a
> script of how afni does the conversion and the nifti output from it.
>
> Thanks,
> -Adam
>
> PS. I like your filedrop utility. Is it freeware or something you wrote
> in house?
>
>
> [adamt at master ~]$ mri_convert --all-info
> mri_convert --all-info
> ProgramName: mri_convert ProgramArguments: --all-info ProgramVersion:
> $Name: stable3 $ TimeStamp: 06/07/06-17:12:35-GMT CVS: $Id:
> mri_convert.c,v 1.121 2006/02/22 05:39:36 greve Exp $ User: adamt
> Machine: master Platform: Linux PlatformVersion:
> 2.6.12-1.1387_FC4.rootsmp CompilerName: GCC CompilerVersion: 30400
>
>
>
> -----Original Message-----
> From: Doug Greve [mailto:greve at nmr.mgh.harvard.edu]
> Sent: Thursday, July 06, 2006 12:41 PM
> To: Thomas, Adam (NIH/NIMH) [E]
> Cc: freesurfer at nmr.mgh.harvard.edu
> Subject: Re: [Freesurfer] mri_convert: dicom to nifti 4D
>
> I'm not sure what's going on with this -- I don't have too much
> experience with GE functionals. Can you tar it up and put it somewhere I
>
> can get or send it thru our file drop system? The file drop is at:
> https://www.nmr.mgh.harvard.edu/facility/filedrop/index.html.
>
> Also, what version of mri_convert are you using? You can check with
> mri_convet --all-info
>
> doug
>
> Thomas, Adam (NIH/NIMH) [E] wrote:
>
>> I seem to be having some trouble converting a 4D time series from dicom
>> to nifti format using mri_convert. Rather than outputting 144 frames of
>> 38 slices each, it creates a volume with a single frame of 5472 slices
>> (see below). Is there an argument I should be using to specify number
> of
>> frames?
>>
>> I think there was a post on this back in April
>> (http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg02656.ht
> m
>> l), but I can't seem to find an answer in the archives.
>>
>> Thanks,
>> -Adam
>>
>>
>> [adamt at master 004]$ mri_convert axialepi-00001.dcm test.nii
>> mri_convert axialepi-00001.dcm test.nii
>> reading from axialepi-00001.dcm...
>> 5472 DICOM 3.0 files in list
>> Found 5472 DICOM Files
>> WARNING: NumberOfFrames 0 != Found Count of slices 5472.
>> reading DICOM image...
>> -------------------------------------------------
>> DICOM meta-header
>>
>> file name
>> /misc/radium0/adamt/mirrorTracking/XX/2006-02-11-S2/XXXXXXXX/2006_02_11
> -
>> 15667/004/axialepi-00001.dcm
>> Date and time
>>        study date              20060211
>>        study time              170403
>>        series time             172558
>>        acquisition time        172558
>> Identification
>>        patient name            XXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
>>        manufacturer            GE MEDICAL SYSTEMS
>> Dimensions
>>        number of rows          64
>>        number of columns       64
>>        number of frames        5472
>>        pixel width             3.28125
>>        pixel height            3.28125
>>        slice thickness         3.2
>>        field of view           210
>>        image number            1 (might be not reliable)
>>        transfer syntax UID     1.2.840.10008.1.2.1
>> Acquisition parameters
>>        echo time               30
>>        repetition time         2500
>>        inversion time          0
>>        echo number             1
>>        flip angle              1.5708
>>        bits allocated          16
>> Spatial information
>>        first image position    -103.359 -132.14 75.59
>>        last image position     -103.359 -132.14 -42.81
>>        image orientation       1 -0 0 -0 1 0
>> -------------------------------------------------
>>
>> TR=2500.00, TE=30.00, TI=0.00, flip angle=90.00
>> i_ras = (-1, 0, 0)
>> j_ras = (0, -1, 0)
>> k_ras = (0, 0, -1)
>> writing to test.nii...
>> [adamt at master 004]$
>>
>>
>>
>>
>> ---
>> Adam Thomas             adamt at nih.gov
>> Functional MRI Facility, NIMH/NIH/DHHS
>> 10 Center Dr, Room B1D708A
>> Bethesda MD. 20892-1148
>> Phone:301-402-6351    Fax:  301-402-1370
>>
>>
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>>
>>
>
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