Hi Bruce,
Here is the output from mri_info on both the mgz volume and dicom series.
Cheers,
Andy
On Mon, Apr 4, 2011 at 11:08 AM, Bruce Fischl <fis...@nmr.mgh.harvard.edu>wrote:
> Hi Andy
>
> can you run mri_info on the volume and see what it thinks the voxel
> dimensions are? Then also run it on the dicom series?
>
> cheers
> Bruce
>
>
>
> On Fri, 1 Apr 2011, Andrew R. Dykstra wrote:
>
> Hi all,
>>
>> I'm having problems either or converting a series of dicoms from a CT scan
>> obtained at MGH main. When viewing them in the standard hospital viewer,
>> they appear normal, but when viewing them in TKMEDIT (either the original
>> dicom series or converted mgz file), the scaling changes. Are there any
>> options in mri_convert I can use to overcome this problem? See attached
>> view of the mgz file.
>>
>> Cheers,
>> Andy
>>
>>
>
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--
Andrew R. Dykstra
PhD Candidate
Harvard-MIT Division of Health Sciences and Technology
Program in Speech and Hearing Bioscience and Technology
"How small the cosmos. How paltry and puny compared to human consciousness
. . . to a single individual recollection." - Vladimir Nabokov
[huygens:Cashlab] (nmr-std-env) mri_info iEEG/MG45_SURFER_OUTPUT/ct/ct.mgz
Volume information for iEEG/MG45_SURFER_OUTPUT/ct/ct.mgz
type: MGH
dimensions: 256 x 256 x 256
voxel sizes: 1.0000, 1.0000, 1.0000
type: UCHAR (0)
fov: 256.000
dof: 0
xstart: -128.0, xend: 128.0
ystart: -128.0, yend: 128.0
zstart: -128.0, zend: 128.0
TR: 0.00 msec, TE: 0.00 msec, TI: 0.00 msec, flip angle: 0.00
degrees
nframes: 1
PhEncDir: UNKNOWN
ras xform present
xform info: x_r = -1.0000, y_r = 0.0000, z_r = 0.0000, c_r = 16.1619
: x_a = 0.0000, y_a = 0.0000, z_a = 1.0000, c_a = -5.1820
: x_s = -0.0000, y_s = -1.0000, z_s = -0.0000, c_s = 55.6768
talairach xfm :
Orientation : LIA
Primary Slice Direction: coronal
voxel to ras transform:
-1.0000 0.0000 0.0000 144.1619
0.0000 0.0000 1.0000 -133.1820
-0.0000 -1.0000 -0.0000 183.6768
0.0000 0.0000 0.0000 1.0000
voxel-to-ras determinant -1
ras to voxel transform:
-1.0000 0.0000 0.0000 144.1619
0.0000 0.0000 -1.0000 183.6768
0.0000 1.0000 0.0000 133.1820
0.0000 0.0000 0.0000 1.0000
[huygens:Cashlab] (nmr-std-env) mri_info
iEEG/MG45_SURFER_OUTPUT/ct/1.2.840.113619.2.80.973217100.26943.1289361217.3.dcm
Starting DICOMRead2()
dcmfile =
iEEG/MG45_SURFER_OUTPUT/ct/1.2.840.113619.2.80.973217100.26943.1289361217.3.dcm
dcmdir = iEEG/MG45_SURFER_OUTPUT/ct
Ref Series No = 301
Found 83 files, checking for dicoms
Found 79 dicom files in series.
First Sorting
Computing Slice Direction
Vs: -105.559 33.8442 0.644257
Vs: -0.952237 0.305304 0.00581175
Second Sorting
Counting frames
nframes = 1
nslices = 79
ndcmfiles = 79
PE Dir = UNKNOWN (dicom read)
Segmentation fault
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