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.htm l), but I can't seem to find an answer in the archives.
Thanks, -Adam
[adamt@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@master 004]$
--- Adam Thomas adamt@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
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.htm l), but I can't seem to find an answer in the archives.
Thanks, -Adam
[adamt@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@master 004]$
Adam Thomas adamt@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
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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@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@nmr.mgh.harvard.edu] Sent: Thursday, July 06, 2006 12:41 PM To: Thomas, Adam (NIH/NIMH) [E] Cc: freesurfer@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@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@master 004]$
Adam Thomas adamt@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
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
OK, I've downloaded your files and replicated the error. It might take a few days for me to actually figure out what's going wrong. I'll let you know when I do.
doug
ps. I'm not sure about the source of the file drop system. Feel free to ask our sys admins by sending email to help@nmr...
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@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@nmr.mgh.harvard.edu] Sent: Thursday, July 06, 2006 12:41 PM To: Thomas, Adam (NIH/NIMH) [E] Cc: freesurfer@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@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@master 004]$
Adam Thomas adamt@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
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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@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@nmr.mgh.harvard.edu] Sent: Thursday, July 06, 2006 12:41 PM To: Thomas, Adam (NIH/NIMH) [E] Cc: freesurfer@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@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@master 004]$
Adam Thomas adamt@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
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hi Adam,
I've created a new version of mri_convert which should hangle multi-frame GE dicom data properly. You can get it from here:
ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_convert
Run it as you would ordinarily, but add -dicomread2 to the cmd line.
I want to stress that this is experimental and that you are practically alpha testing it. Do you have other data sets that you can test it on?
It should really be tested on several acquisitions collected with various orientations. The volumes should have fiducials to make sure that we are getting right right, but it might take me a while to drum up such data sets.
doug
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@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@nmr.mgh.harvard.edu] Sent: Thursday, July 06, 2006 12:41 PM To: Thomas, Adam (NIH/NIMH) [E] Cc: freesurfer@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@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@master 004]$
Adam Thomas adamt@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
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
freesurfer@nmr.mgh.harvard.edu
-
Bruce Fischl -
Doug Greve -
Thomas, Adam (NIH/NIMH) [E]