[Gate-users] Fwd: The QGS software can read my files in Interfile format?
vieira.lina at sapo.pt
vieira.lina at sapo.pt
Sat Nov 14 14:19:28 CET 2009
Hello,
I used the digital phantom NURBS-based Cardiac-Torso (NCAT) and
Monte-Carlo simulations with GATE, to simulate the myocardium studies
Gated-SPECT. But I not able to read and process the myocardial studies
by Quantitative Gated SPECT (QGS) Cedars-Cinai, in order to
determine the end-diastolic volume (EDV), the end-systolic volume
(ESV) and the ejection fraction (EF), since I always get the
following message:
Please deselect un-necessary datasets to avoid such conflict.
Would you like to proceed with these datasets being discarded?
1. RGATE-1_03E (RGATE-1, 2009.10.23 – 12:39:52.0)
2. RGATE-1_04E (RGATE-1, 2009.10.23 – 12:39:52.0)
3. RGATE-1_05E (RGATE-1, 2009.10.23 – 12:39:52.0)
4. RGATE-1_06E (RGATE-1, 2009.10.23 – 12:39:52.0)
5. RGATE-1_07E (RGATE-1, 2009.10.23 – 12:39:52.0)
6. RGATE-1_08E (RGATE-1, 2009.10.23 – 12:39:52.0)
7. RGATE-1_01F (RGATE-1, 2009.10.23 – 12:39:52.0)
8. RGATE-1_02F (RGATE-1, 2009.10.23 – 12:39:52.0)
9. RGATE-1_03F (RGATE-1, 2009.10.23 – 12:39:52.0)
10. RGATE-1_04F (RGATE-1, 2009.10.23 – 12:39:52.0)
11. RGATE-1_05F (RGATE-1, 2009.10.23 – 12:39:52.0)
The conditions of the simulations were the following:
- Digital NCAT phantom where the heart cycle is divided into eight timeframes;
- 72 beats per minute (0,83333 cycle/sec);
- Equipment with two detectors;
- Detectors that make an angle of 101º;
- Each detector acquire a tomographic scan until 101,25º (201,5º with
both detectors);
- 18 projections per detector (36 projections with both detectors);
- 10 seconds for each projection (as the cycle is divided into 8
timeframes is the equivalent to having: 1,25 sec x 8 timeframes = 10
sec).
At the end of the simulations and to build my files to be read by QGS
I did the following:
- I added all the 1st timeframes of all the 18 projections of the
Detector 1 and I obtained RGATE-1_001.IMG
- I added all the 1st timeframes of all the 18 projections of the
Detector 2 and I obtained RGATE_009.IMG
- And so on ... RGATE-1_002.IMG ... until RGATE-1_016.IMG.
The File.HDR that I am using is the following:
RGATE-001.hdr
!INTERFILE :=
!imaging modality :=nucmed
!originating system :=GENIE
!version of keys :=3.3
date of keys :=1992:01:01
conversion program :=Genie
program author :=Raja .P
program version :=1.7
program date :=1997:03:05
!GENERAL DATA :=
original institution :=GATE simulation
contact person :=
data description :=xxGENIE:RGATE-1 xxGENIE:RGATE-1_01E
!data offset in bytes :=0
!name of data file :=RGATE-001.IMG
patient name :=vieira e vieira
!patient ID :=11111111
patient dob :=
patient sex :=M
!study ID :=Perf Miocardio
exam type :=TOMO
data compression :=none
data encode :=none
!GENERAL IMAGE DATA :=
!type of data :=Tomographic
!total number of images :=18
study date :=2009:10:23
study time :=12:39:52
imagedata byte order :=LITTLEENDIAN
number of energy windows :=1
energy window [1] :=Tc99m
energy window lower level [1] :=130.2
energy window upper level [1] :=158.2
flood corrected :=N
decay corrected :=N
!SPECT STUDY (general) :=
number of detector heads :=2
!number of images/energy window :=18
!process status :=Acquired
!matrix size [1] :=64
!matrix size [2] :=64
!number format :=SIGNED INTEGER
!number of bytes per pixel :=2
scaling factor (mm/pixel) [1] :=6.78
scaling factor (mm/pixel) [2] :=6.78
!number of projections :=18
!extent of rotation :=101.25
!time per projection (sec) :=10
study duration (sec) :=180
!maximum pixel count :=10
patient orientation :=feet_in
patient rotation :=supine
!SPECT STUDY (acquired data) :=
!direction of rotation :=CCW
start angle :=-303.7
first projection angle in data set :=-303.7
acquisition mode :=stepped
orbit :=Circular
preprocessed :=
!number of images/energy window :=18
!process status :=Acquired
!matrix size [1] :=64
!matrix size [2] :=64
!number format :=UNSIGNED INTEGER
!number of bytes per pixel :=2
scaling factor (mm/pixel) [1] :=6.78
scaling factor (mm/pixel) [2] :=6.78
!number of projections :=18
!extent of rotation :=101.25
!time per projection (sec) :=10
study duration (sec) :=180
!maximum pixel count :=10
patient orientation :=feet_in
patient rotation :=supine
!SPECT STUDY (acquired data) :=
!direction of rotation :=CCW
start angle :=-303.7
first projection angle in data set :=-303.7
acquisition mode :=stepped
orbit :=Circular
preprocessed :=
!GATED STUDY (general) :=
!matrix size [1] :=64
!matrix size [2] :=64
!number format :=SIGNED INTEGER
!number of bytes per pixel :=2
scaling factor (mm/pixel) [1] :=6.78
scaling factor (mm/pixel) [2] :=6.78
study duration (elapsed) sec :=180
number of cardiac cycles (observed) :=216
number of time windows :=1
!Gated Study (each time window) :=
!time window number :=1
!number of images in time window :=1
!image duration (sec) :=10
framing method :=Forward
time window lower limit (sec) :=0
time window upper limit (sec) :=0.833333
% R-R cycles acquired this window :=100
number of cardiac cycles (acquired) :=216
study duration (acquired) :=0
!maximum pixel count :=10
R-R histogram :=Y
!END OF INTERFILE :=
RGATE-009.hdr
!INTERFILE :=
!imaging modality :=nucmed
!originating system :=GENIE
!version of keys :=3.3
date of keys :=1992:01:01
program author :=Raja .P
program version :=1.7
program date :=1997:03:05
!GENERAL DATA :=
original institution :=GATE simulation
contact person :=
data description :=xxGENIE:RGATE-1 xxGENIE:RGATE-1_01F
!data offset in bytes :=0
!name of data file :=RGATE-009.IMG
patient name :=vieira e vieira
!patient ID :=11111111
patient dob :=
patient sex :=M
!study ID :=Perf Miocardio
exam type :=TOMO
data compression :=none
data encode :=none
!GENERAL IMAGE DATA :=
!type of data :=Tomographic
!total number of images :=18
study date :=2009:10:23
study time :=12:39:52
imagedata byte order :=LITTLEENDIAN
number of energy windows :=1
energy window [1] :=Tc99m
energy window lower level [1] :=130.2
energy window upper level [1] :=158.2
flood corrected :=N
decay corrected :=N
!SPECT STUDY (general) :=
number of detector heads :=2
!number of images/energy window :=18
!process status :=Acquired
!matrix size [1] :=64
!matrix size [2] :=64
!number format :=SIGNED INTEGER
!number of bytes per pixel :=2
scaling factor (mm/pixel) [1] :=6.78
scaling factor (mm/pixel) [2] :=6.78
!number of projections :=18
!extent of rotation :=101.25
!time per projection (sec) :=10
study duration (sec) :=180
!maximum pixel count :=11
patient orientation :=feet_in
patient rotation :=supine
!SPECT STUDY (acquired data) :=
!direction of rotation :=CCW
start angle :=-45
first projection angle in data set :=-45
acquisition mode :=stepped
orbit :=Circular
preprocessed :=
!number of images/energy window :=18
!process status :=Acquired
!matrix size [1] :=64
!matrix size [2] :=64
!number format :=SIGNED INTEGER
!number of bytes per pixel :=2
scaling factor (mm/pixel) [1] :=6.78
scaling factor (mm/pixel) [2] :=6.78
!number of projections :=18
!extent of rotation :=101.25
!time per projection (sec) :=10
study duration (sec) :=180
!maximum pixel count :=11
patient orientation :=feet_in
patient rotation :=supine
!SPECT STUDY (acquired data) :=
!direction of rotation :=CCW
start angle :=-45
first projection angle in data set :=-45
acquisition mode :=stepped
orbit :=Circular
preprocessed :=
!GATED STUDY (general) :=
!matrix size [1] :=64
!matrix size [2] :=64
!number format :=UNSIGNED INTEGER
!number of bytes per pixel :=2
scaling factor (mm/pixel) [1] :=6.78
scaling factor (mm/pixel) [2] :=6.78
study duration (elapsed) sec :=180
number of cardiac cycles (observed) :=216
number of time windows :=1
!Gated Study (each time window) :=
!time window number :=1
!number of images in time window :=1
!image duration (sec) :=10
framing method :=Forward
time window lower limit (sec) :=0
time window upper limit (sec) :=0.833333
% R-R cycles acquired this window :=100
number of cardiac cycles (acquired) :=216
study duration (acquired) :=0
!maximum pixel count :=11
R-R histogram :=Y
!END OF INTERFILE :=
What should I add/modify in my HDR file, so that the QGS software can
read my files in Interfile format?
I look forward to hearing from you.
Sincerely yours,
Lina Vieira
----- Finalizar mensagem encaminhada -----
-------------- next part --------------
A non-text attachment was scrubbed...
Name: RGATE-001.IMG
Type: application/x-executable-file
Size: 147456 bytes
Desc: not available
URL: <http://lists.opengatecollaboration.org/mailman/private/gate-users/attachments/20091114/65429e9f/attachment.bin>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: RGATE-002.IMG
Type: application/x-executable-file
Size: 147456 bytes
Desc: not available
URL: <http://lists.opengatecollaboration.org/mailman/private/gate-users/attachments/20091114/65429e9f/attachment-0001.bin>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: RGATE-003.IMG
Type: application/x-executable-file
Size: 147456 bytes
Desc: not available
URL: <http://lists.opengatecollaboration.org/mailman/private/gate-users/attachments/20091114/65429e9f/attachment-0002.bin>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: RGATE-004.IMG
Type: application/x-executable-file
Size: 147456 bytes
Desc: not available
URL: <http://lists.opengatecollaboration.org/mailman/private/gate-users/attachments/20091114/65429e9f/attachment-0003.bin>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: RGATE-005.IMG
Type: application/x-executable-file
Size: 147456 bytes
Desc: not available
URL: <http://lists.opengatecollaboration.org/mailman/private/gate-users/attachments/20091114/65429e9f/attachment-0004.bin>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: RGATE-006.IMG
Type: application/x-executable-file
Size: 147456 bytes
Desc: not available
URL: <http://lists.opengatecollaboration.org/mailman/private/gate-users/attachments/20091114/65429e9f/attachment-0005.bin>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: RGATE-007.IMG
Type: application/x-executable-file
Size: 147456 bytes
Desc: not available
URL: <http://lists.opengatecollaboration.org/mailman/private/gate-users/attachments/20091114/65429e9f/attachment-0006.bin>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: RGATE-008.IMG
Type: application/x-executable-file
Size: 147456 bytes
Desc: not available
URL: <http://lists.opengatecollaboration.org/mailman/private/gate-users/attachments/20091114/65429e9f/attachment-0007.bin>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: RGATE-009.IMG
Type: application/x-executable-file
Size: 147456 bytes
Desc: not available
URL: <http://lists.opengatecollaboration.org/mailman/private/gate-users/attachments/20091114/65429e9f/attachment-0008.bin>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: RGATE-010.IMG
Type: application/x-executable-file
Size: 147456 bytes
Desc: not available
URL: <http://lists.opengatecollaboration.org/mailman/private/gate-users/attachments/20091114/65429e9f/attachment-0009.bin>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: RGATE-011.IMG
Type: application/x-executable-file
Size: 147456 bytes
Desc: not available
URL: <http://lists.opengatecollaboration.org/mailman/private/gate-users/attachments/20091114/65429e9f/attachment-0010.bin>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: RGATE-012.IMG
Type: application/x-executable-file
Size: 147456 bytes
Desc: not available
URL: <http://lists.opengatecollaboration.org/mailman/private/gate-users/attachments/20091114/65429e9f/attachment-0011.bin>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: RGATE-013.IMG
Type: application/x-executable-file
Size: 147456 bytes
Desc: not available
URL: <http://lists.opengatecollaboration.org/mailman/private/gate-users/attachments/20091114/65429e9f/attachment-0012.bin>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: RGATE-014.IMG
Type: application/x-executable-file
Size: 147456 bytes
Desc: not available
URL: <http://lists.opengatecollaboration.org/mailman/private/gate-users/attachments/20091114/65429e9f/attachment-0013.bin>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: RGATE-015.IMG
Type: application/x-executable-file
Size: 147456 bytes
Desc: not available
URL: <http://lists.opengatecollaboration.org/mailman/private/gate-users/attachments/20091114/65429e9f/attachment-0014.bin>
More information about the Gate-users
mailing list