Hi everyone,
I’m having some issues converting my DICOMs (DWI) into NIFTI using mri_convert. I looked for other topics with people having the same kind of problem but couldn’t find an answer.
Each time I run mri_convert on my DICOMs I get the following error : WARNING: file MR.1.3.12.2.1107.5.2.19.45306.2014091812330393354083931 does not contain a Siemens ASCII header has this file been anonymized? ERROR: cannot unpack mosiacs without ASCII header
Here are the following DICOMs informations : Identification NumarisVer syngo MR D13 ScannerModel Skyra PatientName xxxxx Date and time StudyDate 20140918 StudyTime 121037.203000 SeriesTime 123450.600000 AcqTime 123257.367500 Acquisition parameters PulseSeq ep_b0 Protocol AX DTI no angle MS NEX 4 2 PhEncDir COL EchoNo 1 FlipAngle 90 EchoTime 96 InversionTime -1 RepetitionTime 4700 PhEncFOV 0 ReadoutFOV 0 Image information RunNo 4 SeriesNo 5 ImageNo 1 NImageRows 990 NImageCols 990 NFrames 64 SliceArraylSize 0 IsMosaic 1 ImgPos 1075.1575 1069.8385 -48.6769 VolRes 2.1818 2.1818 2.0000 VolDim 0 0 0 Vc -1.0000 -0.0000 0.0000 Vr -0.0000 -1.0000 0.0000 Vs 0.0000 0.0000 0.0000 VolCenter 0.0000 0.0000 0.0000 TransferSyntaxUID 1.2.840.10008.1.2.1
Then I try using mri_convert -it dicom, it converts the files but not as it is expected, you could notice the difference when I run mri_info on my output : Volume information for output.nii.gz type: nii dimensions: 990 x 990 x 1 x 64 voxel sizes: 2.1818, 2.1818, 2.0000 type: SHORT (4) fov: 2160.000 dof: 0 xstart: -1080.0, xend: 1080.0 ystart: -1080.0, yend: 1080.0 zstart: -1.0, zend: 1.0 TR: 4700.00 msec, TE: 0.00 msec, TI: 0.00 msec, flip angle: 0.00 degrees nframes: 64 PhEncDir: UNKNOWN ras xform present xform info: x_r = -1.0000, y_r = -0.0000, z_r = -0.0000, c_r = -4.8425 : x_a = -0.0000, y_a = -1.0000, z_a = -0.0000, c_a = -10.1615 : x_s = 0.0000, y_s = 0.0000, z_s = 1.0000, c_s = -47.6769 Orientation : LPS Primary Slice Direction: axial
voxel to ras transform: -2.1818 -0.0000 -0.0000 1075.1575 -0.0000 -2.1818 -0.0000 1069.8385 0.0000 0.0000 2.0000 -48.6769 0.0000 0.0000 0.0000 1.0000
voxel-to-ras determinant 9.52066
ras to voxel transform: -0.4583 0.0000 0.0000 492.7805 0.0000 -0.4583 0.0000 490.3426 -0.0000 -0.0000 0.5000 24.3384 0.0000 0.0000 0.0000 1.0000
I would really appreciate your help, thank you.
Best,
Ismail
can you answer the question that it asks?
On 07/05/2016 10:52 AM, Koubiyr, Ismail wrote:
Hi everyone,
I’m having some issues converting my DICOMs (DWI) into NIFTI using mri_convert. I looked for other topics with people having the same kind of problem but couldn’t find an answer.
Each time I run mri_convert on my DICOMs I get the following error : WARNING: file MR.1.3.12.2.1107.5.2.19.45306.2014091812330393354083931 does not contain a Siemens ASCII header has this file been anonymized? ERROR: cannot unpack mosiacs without ASCII header
Here are the following DICOMs informations : Identification NumarisVer syngo MR D13 ScannerModel Skyra PatientName xxxxx Date and time StudyDate 20140918 StudyTime 121037.203000 SeriesTime 123450.600000 AcqTime 123257.367500 Acquisition parameters PulseSeq ep_b0 Protocol AX DTI no angle MS NEX 4 2 PhEncDir COL EchoNo 1 FlipAngle 90 EchoTime 96 InversionTime -1 RepetitionTime 4700 PhEncFOV 0 ReadoutFOV 0 Image information RunNo 4 SeriesNo 5 ImageNo 1 NImageRows 990 NImageCols 990 NFrames 64 SliceArraylSize 0 IsMosaic 1 ImgPos 1075.1575 1069.8385 -48.6769 VolRes 2.1818 2.1818 2.0000 VolDim 0 0 0 Vc -1.0000 -0.0000 0.0000 Vr -0.0000 -1.0000 0.0000 Vs 0.0000 0.0000 0.0000 VolCenter 0.0000 0.0000 0.0000 TransferSyntaxUID 1.2.840.10008.1.2.1
Then I try using mri_convert -it dicom, it converts the files but not as it is expected, you could notice the difference when I run mri_info on my output : Volume information for output.nii.gz type: nii dimensions: 990 x 990 x 1 x 64 voxel sizes: 2.1818, 2.1818, 2.0000 type: SHORT (4) fov: 2160.000 dof: 0 xstart: -1080.0, xend: 1080.0 ystart: -1080.0, yend: 1080.0 zstart: -1.0, zend: 1.0 TR: 4700.00 msec, TE: 0.00 msec, TI: 0.00 msec, flip angle: 0.00 degrees nframes: 64 PhEncDir: UNKNOWN ras xform present xform info: x_r = -1.0000, y_r = -0.0000, z_r = -0.0000, c_r = -4.8425 : x_a = -0.0000, y_a = -1.0000, z_a = -0.0000, c_a = -10.1615 : x_s = 0.0000, y_s = 0.0000, z_s = 1.0000, c_s = -47.6769 Orientation : LPS Primary Slice Direction: axial
voxel to ras transform: -2.1818 -0.0000 -0.0000 1075.1575 -0.0000 -2.1818 -0.0000 1069.8385 0.0000 0.0000 2.0000 -48.6769 0.0000 0.0000 0.0000 1.0000
voxel-to-ras determinant 9.52066
ras to voxel transform: -0.4583 0.0000 0.0000 492.7805 0.0000 -0.4583 0.0000 490.3426 -0.0000 -0.0000 0.5000 24.3384 0.0000 0.0000 0.0000 1.0000
I would really appreciate your help, thank you.
Best,
Ismail
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The file has not been anonymized.
Thanks,
Ismail
On Jul 5, 2016, at 11:20 AM, Douglas N Greve greve@nmr.mgh.harvard.edu wrote:
can you answer the question that it asks?
On 07/05/2016 10:52 AM, Koubiyr, Ismail wrote:
Hi everyone,
I’m having some issues converting my DICOMs (DWI) into NIFTI using mri_convert. I looked for other topics with people having the same kind of problem but couldn’t find an answer.
Each time I run mri_convert on my DICOMs I get the following error : WARNING: file MR.1.3.12.2.1107.5.2.19.45306.2014091812330393354083931 does not contain a Siemens ASCII header has this file been anonymized? ERROR: cannot unpack mosiacs without ASCII header
Here are the following DICOMs informations : Identification NumarisVer syngo MR D13 ScannerModel Skyra PatientName xxxxx Date and time StudyDate 20140918 StudyTime 121037.203000 SeriesTime 123450.600000 AcqTime 123257.367500 Acquisition parameters PulseSeq ep_b0 Protocol AX DTI no angle MS NEX 4 2 PhEncDir COL EchoNo 1 FlipAngle 90 EchoTime 96 InversionTime -1 RepetitionTime 4700 PhEncFOV 0 ReadoutFOV 0 Image information RunNo 4 SeriesNo 5 ImageNo 1 NImageRows 990 NImageCols 990 NFrames 64 SliceArraylSize 0 IsMosaic 1 ImgPos 1075.1575 1069.8385 -48.6769 VolRes 2.1818 2.1818 2.0000 VolDim 0 0 0 Vc -1.0000 -0.0000 0.0000 Vr -0.0000 -1.0000 0.0000 Vs 0.0000 0.0000 0.0000 VolCenter 0.0000 0.0000 0.0000 TransferSyntaxUID 1.2.840.10008.1.2.1
Then I try using mri_convert -it dicom, it converts the files but not as it is expected, you could notice the difference when I run mri_info on my output : Volume information for output.nii.gz type: nii dimensions: 990 x 990 x 1 x 64 voxel sizes: 2.1818, 2.1818, 2.0000 type: SHORT (4) fov: 2160.000 dof: 0 xstart: -1080.0, xend: 1080.0 ystart: -1080.0, yend: 1080.0 zstart: -1.0, zend: 1.0 TR: 4700.00 msec, TE: 0.00 msec, TI: 0.00 msec, flip angle: 0.00 degrees nframes: 64 PhEncDir: UNKNOWN ras xform present xform info: x_r = -1.0000, y_r = -0.0000, z_r = -0.0000, c_r = -4.8425 : x_a = -0.0000, y_a = -1.0000, z_a = -0.0000, c_a = -10.1615 : x_s = 0.0000, y_s = 0.0000, z_s = 1.0000, c_s = -47.6769 Orientation : LPS Primary Slice Direction: axial
voxel to ras transform: -2.1818 -0.0000 -0.0000 1075.1575 -0.0000 -2.1818 -0.0000 1069.8385 0.0000 0.0000 2.0000 -48.6769 0.0000 0.0000 0.0000 1.0000
voxel-to-ras determinant 9.52066
ras to voxel transform: -0.4583 0.0000 0.0000 492.7805 0.0000 -0.4583 0.0000 490.3426 -0.0000 -0.0000 0.5000 24.3384 0.0000 0.0000 0.0000 1.0000
I would really appreciate your help, thank you.
Best,
Ismail
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hi,
This is a repost. Would anyone have a solution to this problem ? Thanks for your help.
Best,
Ismail
On Jul 5, 2016, at 11:24 AM, Koubiyr, Ismail IKOUBIYR@BWH.HARVARD.EDU wrote:
The file has not been anonymized.
Thanks,
Ismail
On Jul 5, 2016, at 11:20 AM, Douglas N Greve greve@nmr.mgh.harvard.edu wrote:
can you answer the question that it asks?
On 07/05/2016 10:52 AM, Koubiyr, Ismail wrote:
Hi everyone,
I’m having some issues converting my DICOMs (DWI) into NIFTI using mri_convert. I looked for other topics with people having the same kind of problem but couldn’t find an answer.
Each time I run mri_convert on my DICOMs I get the following error : WARNING: file MR.1.3.12.2.1107.5.2.19.45306.2014091812330393354083931 does not contain a Siemens ASCII header has this file been anonymized? ERROR: cannot unpack mosiacs without ASCII header
Here are the following DICOMs informations : Identification NumarisVer syngo MR D13 ScannerModel Skyra PatientName xxxxx Date and time StudyDate 20140918 StudyTime 121037.203000 SeriesTime 123450.600000 AcqTime 123257.367500 Acquisition parameters PulseSeq ep_b0 Protocol AX DTI no angle MS NEX 4 2 PhEncDir COL EchoNo 1 FlipAngle 90 EchoTime 96 InversionTime -1 RepetitionTime 4700 PhEncFOV 0 ReadoutFOV 0 Image information RunNo 4 SeriesNo 5 ImageNo 1 NImageRows 990 NImageCols 990 NFrames 64 SliceArraylSize 0 IsMosaic 1 ImgPos 1075.1575 1069.8385 -48.6769 VolRes 2.1818 2.1818 2.0000 VolDim 0 0 0 Vc -1.0000 -0.0000 0.0000 Vr -0.0000 -1.0000 0.0000 Vs 0.0000 0.0000 0.0000 VolCenter 0.0000 0.0000 0.0000 TransferSyntaxUID 1.2.840.10008.1.2.1
Then I try using mri_convert -it dicom, it converts the files but not as it is expected, you could notice the difference when I run mri_info on my output : Volume information for output.nii.gz type: nii dimensions: 990 x 990 x 1 x 64 voxel sizes: 2.1818, 2.1818, 2.0000 type: SHORT (4) fov: 2160.000 dof: 0 xstart: -1080.0, xend: 1080.0 ystart: -1080.0, yend: 1080.0 zstart: -1.0, zend: 1.0 TR: 4700.00 msec, TE: 0.00 msec, TI: 0.00 msec, flip angle: 0.00 degrees nframes: 64 PhEncDir: UNKNOWN ras xform present xform info: x_r = -1.0000, y_r = -0.0000, z_r = -0.0000, c_r = -4.8425 : x_a = -0.0000, y_a = -1.0000, z_a = -0.0000, c_a = -10.1615 : x_s = 0.0000, y_s = 0.0000, z_s = 1.0000, c_s = -47.6769 Orientation : LPS Primary Slice Direction: axial
voxel to ras transform: -2.1818 -0.0000 -0.0000 1075.1575 -0.0000 -2.1818 -0.0000 1069.8385 0.0000 0.0000 2.0000 -48.6769 0.0000 0.0000 0.0000 1.0000
voxel-to-ras determinant 9.52066
ras to voxel transform: -0.4583 0.0000 0.0000 492.7805 0.0000 -0.4583 0.0000 490.3426 -0.0000 -0.0000 0.5000 24.3384 0.0000 0.0000 0.0000 1.0000
I would really appreciate your help, thank you.
Best,
Ismail
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Is this still a problem? If so, can you upload the dicom files to our file drop?
On 07/05/2016 11:24 AM, Koubiyr, Ismail wrote:
The file has not been anonymized.
Thanks,
Ismail
On Jul 5, 2016, at 11:20 AM, Douglas N Greve greve@nmr.mgh.harvard.edu wrote:
can you answer the question that it asks?
On 07/05/2016 10:52 AM, Koubiyr, Ismail wrote:
Hi everyone,
I’m having some issues converting my DICOMs (DWI) into NIFTI using mri_convert. I looked for other topics with people having the same kind of problem but couldn’t find an answer.
Each time I run mri_convert on my DICOMs I get the following error : WARNING: file MR.1.3.12.2.1107.5.2.19.45306.2014091812330393354083931 does not contain a Siemens ASCII header has this file been anonymized? ERROR: cannot unpack mosiacs without ASCII header
Here are the following DICOMs informations : Identification NumarisVer syngo MR D13 ScannerModel Skyra PatientName xxxxx Date and time StudyDate 20140918 StudyTime 121037.203000 SeriesTime 123450.600000 AcqTime 123257.367500 Acquisition parameters PulseSeq ep_b0 Protocol AX DTI no angle MS NEX 4 2 PhEncDir COL EchoNo 1 FlipAngle 90 EchoTime 96 InversionTime -1 RepetitionTime 4700 PhEncFOV 0 ReadoutFOV 0 Image information RunNo 4 SeriesNo 5 ImageNo 1 NImageRows 990 NImageCols 990 NFrames 64 SliceArraylSize 0 IsMosaic 1 ImgPos 1075.1575 1069.8385 -48.6769 VolRes 2.1818 2.1818 2.0000 VolDim 0 0 0 Vc -1.0000 -0.0000 0.0000 Vr -0.0000 -1.0000 0.0000 Vs 0.0000 0.0000 0.0000 VolCenter 0.0000 0.0000 0.0000 TransferSyntaxUID 1.2.840.10008.1.2.1
Then I try using mri_convert -it dicom, it converts the files but not as it is expected, you could notice the difference when I run mri_info on my output : Volume information for output.nii.gz type: nii dimensions: 990 x 990 x 1 x 64 voxel sizes: 2.1818, 2.1818, 2.0000 type: SHORT (4) fov: 2160.000 dof: 0 xstart: -1080.0, xend: 1080.0 ystart: -1080.0, yend: 1080.0 zstart: -1.0, zend: 1.0 TR: 4700.00 msec, TE: 0.00 msec, TI: 0.00 msec, flip angle: 0.00 degrees nframes: 64 PhEncDir: UNKNOWN ras xform present xform info: x_r = -1.0000, y_r = -0.0000, z_r = -0.0000, c_r = -4.8425 : x_a = -0.0000, y_a = -1.0000, z_a = -0.0000, c_a = -10.1615 : x_s = 0.0000, y_s = 0.0000, z_s = 1.0000, c_s = -47.6769 Orientation : LPS Primary Slice Direction: axial
voxel to ras transform: -2.1818 -0.0000 -0.0000 1075.1575 -0.0000 -2.1818 -0.0000 1069.8385 0.0000 0.0000 2.0000 -48.6769 0.0000 0.0000 0.0000 1.0000
voxel-to-ras determinant 9.52066
ras to voxel transform: -0.4583 0.0000 0.0000 492.7805 0.0000 -0.4583 0.0000 490.3426 -0.0000 -0.0000 0.5000 24.3384 0.0000 0.0000 0.0000 1.0000
I would really appreciate your help, thank you.
Best,
Ismail
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hi Doug,
It is still an issue. I uploaded the DICOMs to you. Hope it could be useful. Thanks.
Ismail
On Jul 18, 2016, at 6:14 PM, Douglas N Greve greve@nmr.mgh.harvard.edu wrote:
Is this still a problem? If so, can you upload the dicom files to our file drop?
On 07/05/2016 11:24 AM, Koubiyr, Ismail wrote:
The file has not been anonymized.
Thanks,
Ismail
On Jul 5, 2016, at 11:20 AM, Douglas N Greve greve@nmr.mgh.harvard.edu wrote:
can you answer the question that it asks?
On 07/05/2016 10:52 AM, Koubiyr, Ismail wrote:
Hi everyone,
I’m having some issues converting my DICOMs (DWI) into NIFTI using mri_convert. I looked for other topics with people having the same kind of problem but couldn’t find an answer.
Each time I run mri_convert on my DICOMs I get the following error : WARNING: file MR.1.3.12.2.1107.5.2.19.45306.2014091812330393354083931 does not contain a Siemens ASCII header has this file been anonymized? ERROR: cannot unpack mosiacs without ASCII header
Here are the following DICOMs informations : Identification NumarisVer syngo MR D13 ScannerModel Skyra PatientName xxxxx Date and time StudyDate 20140918 StudyTime 121037.203000 SeriesTime 123450.600000 AcqTime 123257.367500 Acquisition parameters PulseSeq ep_b0 Protocol AX DTI no angle MS NEX 4 2 PhEncDir COL EchoNo 1 FlipAngle 90 EchoTime 96 InversionTime -1 RepetitionTime 4700 PhEncFOV 0 ReadoutFOV 0 Image information RunNo 4 SeriesNo 5 ImageNo 1 NImageRows 990 NImageCols 990 NFrames 64 SliceArraylSize 0 IsMosaic 1 ImgPos 1075.1575 1069.8385 -48.6769 VolRes 2.1818 2.1818 2.0000 VolDim 0 0 0 Vc -1.0000 -0.0000 0.0000 Vr -0.0000 -1.0000 0.0000 Vs 0.0000 0.0000 0.0000 VolCenter 0.0000 0.0000 0.0000 TransferSyntaxUID 1.2.840.10008.1.2.1
Then I try using mri_convert -it dicom, it converts the files but not as it is expected, you could notice the difference when I run mri_info on my output : Volume information for output.nii.gz type: nii dimensions: 990 x 990 x 1 x 64 voxel sizes: 2.1818, 2.1818, 2.0000 type: SHORT (4) fov: 2160.000 dof: 0 xstart: -1080.0, xend: 1080.0 ystart: -1080.0, yend: 1080.0 zstart: -1.0, zend: 1.0 TR: 4700.00 msec, TE: 0.00 msec, TI: 0.00 msec, flip angle: 0.00 degrees nframes: 64 PhEncDir: UNKNOWN ras xform present xform info: x_r = -1.0000, y_r = -0.0000, z_r = -0.0000, c_r = -4.8425 : x_a = -0.0000, y_a = -1.0000, z_a = -0.0000, c_a = -10.1615 : x_s = 0.0000, y_s = 0.0000, z_s = 1.0000, c_s = -47.6769 Orientation : LPS Primary Slice Direction: axial
voxel to ras transform: -2.1818 -0.0000 -0.0000 1075.1575 -0.0000 -2.1818 -0.0000 1069.8385 0.0000 0.0000 2.0000 -48.6769 0.0000 0.0000 0.0000 1.0000
voxel-to-ras determinant 9.52066
ras to voxel transform: -0.4583 0.0000 0.0000 492.7805 0.0000 -0.4583 0.0000 490.3426 -0.0000 -0.0000 0.5000 24.3384 0.0000 0.0000 0.0000 1.0000
I would really appreciate your help, thank you.
Best,
Ismail
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
I was able to convert it fine with mri_convert MR.1.3.12.2.1107.5.2.19.45306.2014091812372179441003292 output.nii.gz If I included -it dicom, the conversion did not have an error, but the output had only one slice. Since these are mosaics, they need the Siemens ascii header which is ignored with -it dicom. So ... don't use -it dicom
On 07/19/2016 11:06 AM, Koubiyr, Ismail wrote:
Hi Doug,
It is still an issue. I uploaded the DICOMs to you. Hope it could be useful. Thanks.
Ismail
On Jul 18, 2016, at 6:14 PM, Douglas N Greve greve@nmr.mgh.harvard.edu wrote:
Is this still a problem? If so, can you upload the dicom files to our file drop?
On 07/05/2016 11:24 AM, Koubiyr, Ismail wrote:
The file has not been anonymized.
Thanks,
Ismail
On Jul 5, 2016, at 11:20 AM, Douglas N Greve greve@nmr.mgh.harvard.edu wrote:
can you answer the question that it asks?
On 07/05/2016 10:52 AM, Koubiyr, Ismail wrote:
Hi everyone,
I’m having some issues converting my DICOMs (DWI) into NIFTI using mri_convert. I looked for other topics with people having the same kind of problem but couldn’t find an answer.
Each time I run mri_convert on my DICOMs I get the following error : WARNING: file MR.1.3.12.2.1107.5.2.19.45306.2014091812330393354083931 does not contain a Siemens ASCII header has this file been anonymized? ERROR: cannot unpack mosiacs without ASCII header
Here are the following DICOMs informations : Identification NumarisVer syngo MR D13 ScannerModel Skyra PatientName xxxxx Date and time StudyDate 20140918 StudyTime 121037.203000 SeriesTime 123450.600000 AcqTime 123257.367500 Acquisition parameters PulseSeq ep_b0 Protocol AX DTI no angle MS NEX 4 2 PhEncDir COL EchoNo 1 FlipAngle 90 EchoTime 96 InversionTime -1 RepetitionTime 4700 PhEncFOV 0 ReadoutFOV 0 Image information RunNo 4 SeriesNo 5 ImageNo 1 NImageRows 990 NImageCols 990 NFrames 64 SliceArraylSize 0 IsMosaic 1 ImgPos 1075.1575 1069.8385 -48.6769 VolRes 2.1818 2.1818 2.0000 VolDim 0 0 0 Vc -1.0000 -0.0000 0.0000 Vr -0.0000 -1.0000 0.0000 Vs 0.0000 0.0000 0.0000 VolCenter 0.0000 0.0000 0.0000 TransferSyntaxUID 1.2.840.10008.1.2.1
Then I try using mri_convert -it dicom, it converts the files but not as it is expected, you could notice the difference when I run mri_info on my output : Volume information for output.nii.gz type: nii dimensions: 990 x 990 x 1 x 64 voxel sizes: 2.1818, 2.1818, 2.0000 type: SHORT (4) fov: 2160.000 dof: 0 xstart: -1080.0, xend: 1080.0 ystart: -1080.0, yend: 1080.0 zstart: -1.0, zend: 1.0 TR: 4700.00 msec, TE: 0.00 msec, TI: 0.00 msec, flip angle: 0.00 degrees nframes: 64 PhEncDir: UNKNOWN ras xform present xform info: x_r = -1.0000, y_r = -0.0000, z_r = -0.0000, c_r = -4.8425 : x_a = -0.0000, y_a = -1.0000, z_a = -0.0000, c_a = -10.1615 : x_s = 0.0000, y_s = 0.0000, z_s = 1.0000, c_s = -47.6769 Orientation : LPS Primary Slice Direction: axial
voxel to ras transform: -2.1818 -0.0000 -0.0000 1075.1575 -0.0000 -2.1818 -0.0000 1069.8385 0.0000 0.0000 2.0000 -48.6769 0.0000 0.0000 0.0000 1.0000
voxel-to-ras determinant 9.52066
ras to voxel transform: -0.4583 0.0000 0.0000 492.7805 0.0000 -0.4583 0.0000 490.3426 -0.0000 -0.0000 0.5000 24.3384 0.0000 0.0000 0.0000 1.0000
I would really appreciate your help, thank you.
Best,
Ismail
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hi Doug,
That’s weird because I can’t convert it using only mri_convert, here is the error I get :
WARNING: file /Users/ismailkoubiyr/Documents/PFE/Tracula/dti/3T2/MR.1.3.12.2.1107.5.2.19.45306.2014091812330393354083931 does not contain a Siemens ASCII header has this file been anonymized? ERROR: cannot unpack mosiacs without ASCII header
Any idea why ?
Best,
Ismail
On Jul 19, 2016, at 1:11 PM, Douglas N Greve <greve@nmr.mgh.harvard.edumailto:greve@nmr.mgh.harvard.edu> wrote:
I was able to convert it fine with mri_convert MR.1.3.12.2.1107.5.2.19.45306.2014091812372179441003292 output.nii.gz If I included -it dicom, the conversion did not have an error, but the output had only one slice. Since these are mosaics, they need the Siemens ascii header which is ignored with -it dicom. So ... don't use -it dicom
On 07/19/2016 11:06 AM, Koubiyr, Ismail wrote: Hi Doug,
It is still an issue. I uploaded the DICOMs to you. Hope it could be useful. Thanks.
Ismail
On Jul 18, 2016, at 6:14 PM, Douglas N Greve <greve@nmr.mgh.harvard.edumailto:greve@nmr.mgh.harvard.edu> wrote:
Is this still a problem? If so, can you upload the dicom files to our file drop?
On 07/05/2016 11:24 AM, Koubiyr, Ismail wrote: The file has not been anonymized.
Thanks,
Ismail
On Jul 5, 2016, at 11:20 AM, Douglas N Greve <greve@nmr.mgh.harvard.edumailto:greve@nmr.mgh.harvard.edu> wrote:
can you answer the question that it asks?
On 07/05/2016 10:52 AM, Koubiyr, Ismail wrote: Hi everyone,
I’m having some issues converting my DICOMs (DWI) into NIFTI using mri_convert. I looked for other topics with people having the same kind of problem but couldn’t find an answer.
Each time I run mri_convert on my DICOMs I get the following error : WARNING: file MR.1.3.12.2.1107.5.2.19.45306.2014091812330393354083931 does not contain a Siemens ASCII header has this file been anonymized? ERROR: cannot unpack mosiacs without ASCII header
Here are the following DICOMs informations : Identification NumarisVer syngo MR D13 ScannerModel Skyra PatientName xxxxx Date and time StudyDate 20140918 StudyTime 121037.203000 SeriesTime 123450.600000 AcqTime 123257.367500 Acquisition parameters PulseSeq ep_b0 Protocol AX DTI no angle MS NEX 4 2 PhEncDir COL EchoNo 1 FlipAngle 90 EchoTime 96 InversionTime -1 RepetitionTime 4700 PhEncFOV 0 ReadoutFOV 0 Image information RunNo 4 SeriesNo 5 ImageNo 1 NImageRows 990 NImageCols 990 NFrames 64 SliceArraylSize 0 IsMosaic 1 ImgPos 1075.1575 1069.8385 -48.6769 VolRes 2.1818 2.1818 2.0000 VolDim 0 0 0 Vc -1.0000 -0.0000 0.0000 Vr -0.0000 -1.0000 0.0000 Vs 0.0000 0.0000 0.0000 VolCenter 0.0000 0.0000 0.0000 TransferSyntaxUID 1.2.840.10008.1.2.1
Then I try using mri_convert -it dicom, it converts the files but not as it is expected, you could notice the difference when I run mri_info on my output : Volume information for output.nii.gz type: nii dimensions: 990 x 990 x 1 x 64 voxel sizes: 2.1818, 2.1818, 2.0000 type: SHORT (4) fov: 2160.000 dof: 0 xstart: -1080.0, xend: 1080.0 ystart: -1080.0, yend: 1080.0 zstart: -1.0, zend: 1.0 TR: 4700.00 msec, TE: 0.00 msec, TI: 0.00 msec, flip angle: 0.00 degrees nframes: 64 PhEncDir: UNKNOWN ras xform present xform info: x_r = -1.0000, y_r = -0.0000, z_r = -0.0000, c_r = -4.8425 : x_a = -0.0000, y_a = -1.0000, z_a = -0.0000, c_a = -10.1615 : x_s = 0.0000, y_s = 0.0000, z_s = 1.0000, c_s = -47.6769 Orientation : LPS Primary Slice Direction: axial
voxel to ras transform: -2.1818 -0.0000 -0.0000 1075.1575 -0.0000 -2.1818 -0.0000 1069.8385 0.0000 0.0000 2.0000 -48.6769 0.0000 0.0000 0.0000 1.0000
voxel-to-ras determinant 9.52066
ras to voxel transform: -0.4583 0.0000 0.0000 492.7805 0.0000 -0.4583 0.0000 490.3426 -0.0000 -0.0000 0.5000 24.3384 0.0000 0.0000 0.0000 1.0000
I would really appreciate your help, thank you.
Best,
Ismail
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edumailto:greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edumailto:greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edumailto:greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
What is your exact command line?
The version of the file that you gave me definitely has an ascii header, and I don't get that warning when I convert. What version of FS are you using on what platform? To check whether that file has an ascii header, run
mri_probedicom --i MR.1.3.12.2.1107.5.2.19.45306.2014091812330393354083931
There should be a line like below
### ASCCONV BEGIN
On 07/19/2016 01:16 PM, Koubiyr, Ismail wrote:
Hi Doug,
That’s weird because I can’t convert it using only mri_convert, here is the error I get :
WARNING: file /Users/ismailkoubiyr/Documents/PFE/Tracula/dti/3T2/MR.1.3.12.2.1107.5.2.19.45306.2014091812330393354083931 does not contain a Siemens ASCII header has this file been anonymized? ERROR: cannot unpack mosiacs without ASCII header
Any idea why ?
Best,
Ismail
On Jul 19, 2016, at 1:11 PM, Douglas N Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:
I was able to convert it fine with mri_convert MR.1.3.12.2.1107.5.2.19.45306.2014091812372179441003292 output.nii.gz If I included -it dicom, the conversion did not have an error, but the output had only one slice. Since these are mosaics, they need the Siemens ascii header which is ignored with -it dicom. So ... don't use -it dicom
On 07/19/2016 11:06 AM, Koubiyr, Ismail wrote:
Hi Doug,
It is still an issue. I uploaded the DICOMs to you. Hope it could be useful. Thanks.
Ismail
On Jul 18, 2016, at 6:14 PM, Douglas N Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:
Is this still a problem? If so, can you upload the dicom files to our file drop?
On 07/05/2016 11:24 AM, Koubiyr, Ismail wrote:
The file has not been anonymized.
Thanks,
Ismail
On Jul 5, 2016, at 11:20 AM, Douglas N Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:
can you answer the question that it asks?
On 07/05/2016 10:52 AM, Koubiyr, Ismail wrote: > Hi everyone, > > I’m having some issues converting my DICOMs (DWI) into NIFTI using > mri_convert. I looked for other topics with people having the same > kind of problem but couldn’t find an answer. > > Each time I run mri_convert on my DICOMs I get the following error : > WARNING: file > MR.1.3.12.2.1107.5.2.19.45306.2014091812330393354083931 > does not contain a Siemens ASCII header > has this file been anonymized? > ERROR: cannot unpack mosiacs without ASCII header > > Here are the following DICOMs informations : > Identification > NumarisVer syngo MR D13 > ScannerModel Skyra > PatientName xxxxx > Date and time > StudyDate 20140918 > StudyTime 121037.203000 > SeriesTime 123450.600000 > AcqTime 123257.367500 > Acquisition parameters > PulseSeq ep_b0 > Protocol AX DTI no angle MS NEX 4 2 > PhEncDir COL > EchoNo 1 > FlipAngle 90 > EchoTime 96 > InversionTime -1 > RepetitionTime 4700 > PhEncFOV 0 > ReadoutFOV 0 > Image information > RunNo 4 > SeriesNo 5 > ImageNo 1 > NImageRows 990 > NImageCols 990 > NFrames 64 > SliceArraylSize 0 > IsMosaic 1 > ImgPos 1075.1575 1069.8385 -48.6769 > VolRes 2.1818 2.1818 2.0000 > VolDim 0 0 0 > Vc -1.0000 -0.0000 0.0000 > Vr -0.0000 -1.0000 0.0000 > Vs 0.0000 0.0000 0.0000 > VolCenter 0.0000 0.0000 0.0000 > TransferSyntaxUID 1.2.840.10008.1.2.1 > > > Then I try using mri_convert -it dicom, it converts the files > but not > as it is expected, you could notice the difference when I run > mri_info > on my output : > Volume information for output.nii.gz > type: nii > dimensions: 990 x 990 x 1 x 64 > voxel sizes: 2.1818, 2.1818, 2.0000 > type: SHORT (4) > fov: 2160.000 > dof: 0 > xstart: -1080.0, xend: 1080.0 > ystart: -1080.0, yend: 1080.0 > zstart: -1.0, zend: 1.0 > TR: 4700.00 msec, TE: 0.00 msec, TI: 0.00 msec, flip > angle: 0.00 degrees > nframes: 64 > PhEncDir: UNKNOWN > ras xform present > xform info: x_r = -1.0000, y_r = -0.0000, z_r = -0.0000, c_r = > -4.8425 > : x_a = -0.0000, y_a = -1.0000, z_a = -0.0000, c_a = > -10.1615 > : x_s = 0.0000, y_s = 0.0000, z_s = 1.0000, c_s = > -47.6769 > Orientation : LPS > Primary Slice Direction: axial > > voxel to ras transform: > -2.1818 -0.0000 -0.0000 1075.1575 > -0.0000 -2.1818 -0.0000 1069.8385 > 0.0000 0.0000 2.0000 -48.6769 > 0.0000 0.0000 0.0000 1.0000 > > voxel-to-ras determinant 9.52066 > > ras to voxel transform: > -0.4583 0.0000 0.0000 492.7805 > 0.0000 -0.4583 0.0000 490.3426 > -0.0000 -0.0000 0.5000 24.3384 > 0.0000 0.0000 0.0000 1.0000 > > I would really appreciate your help, thank you. > > Best, > > Ismail > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > mailto:Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
I used the same command line as you did. And when I check with mri_probedicom I can see the ASCII header.
Here is the version of FS I am using : freesurfer-i386-apple-darwin11.4.2-stable5-20130514
Do you think it might be related ?
Thanks again.
Ismail
On Jul 19, 2016, at 1:27 PM, Douglas N Greve <greve@nmr.mgh.harvard.edumailto:greve@nmr.mgh.harvard.edu> wrote:
What is your exact command line?
The version of the file that you gave me definitely has an ascii header, and I don't get that warning when I convert. What version of FS are you using on what platform? To check whether that file has an ascii header, run
mri_probedicom --i MR.1.3.12.2.1107.5.2.19.45306.2014091812330393354083931
There should be a line like below
### ASCCONV BEGIN
On 07/19/2016 01:16 PM, Koubiyr, Ismail wrote: Hi Doug,
That’s weird because I can’t convert it using only mri_convert, here is the error I get :
WARNING: file /Users/ismailkoubiyr/Documents/PFE/Tracula/dti/3T2/MR.1.3.12.2.1107.5.2.19.45306.2014091812330393354083931 does not contain a Siemens ASCII header has this file been anonymized? ERROR: cannot unpack mosiacs without ASCII header
Any idea why ?
Best,
Ismail
On Jul 19, 2016, at 1:11 PM, Douglas N Greve <greve@nmr.mgh.harvard.edumailto:greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:
I was able to convert it fine with mri_convert MR.1.3.12.2.1107.5.2.19.45306.2014091812372179441003292 output.nii.gz If I included -it dicom, the conversion did not have an error, but the output had only one slice. Since these are mosaics, they need the Siemens ascii header which is ignored with -it dicom. So ... don't use -it dicom
On 07/19/2016 11:06 AM, Koubiyr, Ismail wrote: Hi Doug,
It is still an issue. I uploaded the DICOMs to you. Hope it could be useful. Thanks.
Ismail
On Jul 18, 2016, at 6:14 PM, Douglas N Greve <greve@nmr.mgh.harvard.edumailto:greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:
Is this still a problem? If so, can you upload the dicom files to our file drop?
On 07/05/2016 11:24 AM, Koubiyr, Ismail wrote: The file has not been anonymized.
Thanks,
Ismail
On Jul 5, 2016, at 11:20 AM, Douglas N Greve <greve@nmr.mgh.harvard.edumailto:greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:
can you answer the question that it asks?
On 07/05/2016 10:52 AM, Koubiyr, Ismail wrote: Hi everyone,
I’m having some issues converting my DICOMs (DWI) into NIFTI using mri_convert. I looked for other topics with people having the same kind of problem but couldn’t find an answer.
Each time I run mri_convert on my DICOMs I get the following error : WARNING: file MR.1.3.12.2.1107.5.2.19.45306.2014091812330393354083931 does not contain a Siemens ASCII header has this file been anonymized? ERROR: cannot unpack mosiacs without ASCII header
Here are the following DICOMs informations : Identification NumarisVer syngo MR D13 ScannerModel Skyra PatientName xxxxx Date and time StudyDate 20140918 StudyTime 121037.203000 SeriesTime 123450.600000 AcqTime 123257.367500 Acquisition parameters PulseSeq ep_b0 Protocol AX DTI no angle MS NEX 4 2 PhEncDir COL EchoNo 1 FlipAngle 90 EchoTime 96 InversionTime -1 RepetitionTime 4700 PhEncFOV 0 ReadoutFOV 0 Image information RunNo 4 SeriesNo 5 ImageNo 1 NImageRows 990 NImageCols 990 NFrames 64 SliceArraylSize 0 IsMosaic 1 ImgPos 1075.1575 1069.8385 -48.6769 VolRes 2.1818 2.1818 2.0000 VolDim 0 0 0 Vc -1.0000 -0.0000 0.0000 Vr -0.0000 -1.0000 0.0000 Vs 0.0000 0.0000 0.0000 VolCenter 0.0000 0.0000 0.0000 TransferSyntaxUID 1.2.840.10008.1.2.1
Then I try using mri_convert -it dicom, it converts the files but not as it is expected, you could notice the difference when I run mri_info on my output : Volume information for output.nii.gz type: nii dimensions: 990 x 990 x 1 x 64 voxel sizes: 2.1818, 2.1818, 2.0000 type: SHORT (4) fov: 2160.000 dof: 0 xstart: -1080.0, xend: 1080.0 ystart: -1080.0, yend: 1080.0 zstart: -1.0, zend: 1.0 TR: 4700.00 msec, TE: 0.00 msec, TI: 0.00 msec, flip angle: 0.00 degrees nframes: 64 PhEncDir: UNKNOWN ras xform present xform info: x_r = -1.0000, y_r = -0.0000, z_r = -0.0000, c_r = -4.8425 : x_a = -0.0000, y_a = -1.0000, z_a = -0.0000, c_a = -10.1615 : x_s = 0.0000, y_s = 0.0000, z_s = 1.0000, c_s = -47.6769 Orientation : LPS Primary Slice Direction: axial
voxel to ras transform: -2.1818 -0.0000 -0.0000 1075.1575 -0.0000 -2.1818 -0.0000 1069.8385 0.0000 0.0000 2.0000 -48.6769 0.0000 0.0000 0.0000 1.0000
voxel-to-ras determinant 9.52066
ras to voxel transform: -0.4583 0.0000 0.0000 492.7805 0.0000 -0.4583 0.0000 490.3426 -0.0000 -0.0000 0.5000 24.3384 0.0000 0.0000 0.0000 1.0000
I would really appreciate your help, thank you.
Best,
Ismail
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edumailto:greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReportinghttp://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.htmlhttp://www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edumailto:greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReportinghttp://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.htmlhttp://www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
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-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edumailto:greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReportinghttp://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.htmlhttp://www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
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-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edumailto:greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReportinghttp://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.htmlhttp://www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
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I used the same version, but I used it on linux. Do you have a linux box with FS installed that you can try it on?
On 7/19/16 1:57 PM, Koubiyr, Ismail wrote:
I used the same command line as you did. And when I check with mri_probedicom I can see the ASCII header.
Here is the version of FS I am using : freesurfer-i386-apple-darwin11.4.2-stable5-20130514
Do you think it might be related ?
Thanks again.
Ismail
On Jul 19, 2016, at 1:27 PM, Douglas N Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:
What is your exact command line?
The version of the file that you gave me definitely has an ascii header, and I don't get that warning when I convert. What version of FS are you using on what platform? To check whether that file has an ascii header, run
mri_probedicom --i MR.1.3.12.2.1107.5.2.19.45306.2014091812330393354083931
There should be a line like below
### ASCCONV BEGIN
On 07/19/2016 01:16 PM, Koubiyr, Ismail wrote:
Hi Doug,
That’s weird because I can’t convert it using only mri_convert, here is the error I get :
WARNING: file /Users/ismailkoubiyr/Documents/PFE/Tracula/dti/3T2/MR.1.3.12.2.1107.5.2.19.45306.2014091812330393354083931 does not contain a Siemens ASCII header has this file been anonymized? ERROR: cannot unpack mosiacs without ASCII header
Any idea why ?
Best,
Ismail
On Jul 19, 2016, at 1:11 PM, Douglas N Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edumailto:greve@nmr.mgh.harvard.edu> wrote:
I was able to convert it fine with mri_convert MR.1.3.12.2.1107.5.2.19.45306.2014091812372179441003292 output.nii.gz If I included -it dicom, the conversion did not have an error, but the output had only one slice. Since these are mosaics, they need the Siemens ascii header which is ignored with -it dicom. So ... don't use -it dicom
On 07/19/2016 11:06 AM, Koubiyr, Ismail wrote:
Hi Doug,
It is still an issue. I uploaded the DICOMs to you. Hope it could be useful. Thanks.
Ismail
On Jul 18, 2016, at 6:14 PM, Douglas N Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edumailto:greve@nmr.mgh.harvard.edu> wrote:
Is this still a problem? If so, can you upload the dicom files to our file drop?
On 07/05/2016 11:24 AM, Koubiyr, Ismail wrote: > The file has not been anonymized. > > Thanks, > > Ismail > >> On Jul 5, 2016, at 11:20 AM, Douglas N Greve >> <greve@nmr.mgh.harvard.edu >> mailto:greve@nmr.mgh.harvard.edumailto:greve@nmr.mgh.harvard.edu> >> wrote: >> >> can you answer the question that it asks? >> >> On 07/05/2016 10:52 AM, Koubiyr, Ismail wrote: >>> Hi everyone, >>> >>> I’m having some issues converting my DICOMs (DWI) into NIFTI using >>> mri_convert. I looked for other topics with people having the same >>> kind of problem but couldn’t find an answer. >>> >>> Each time I run mri_convert on my DICOMs I get the following >>> error : >>> WARNING: file >>> MR.1.3.12.2.1107.5.2.19.45306.2014091812330393354083931 >>> does not contain a Siemens ASCII header >>> has this file been anonymized? >>> ERROR: cannot unpack mosiacs without ASCII header >>> >>> Here are the following DICOMs informations : >>> Identification >>> NumarisVer syngo MR D13 >>> ScannerModel Skyra >>> PatientName xxxxx >>> Date and time >>> StudyDate 20140918 >>> StudyTime 121037.203000 >>> SeriesTime 123450.600000 >>> AcqTime 123257.367500 >>> Acquisition parameters >>> PulseSeq ep_b0 >>> Protocol AX DTI no angle MS NEX 4 2 >>> PhEncDir COL >>> EchoNo 1 >>> FlipAngle 90 >>> EchoTime 96 >>> InversionTime -1 >>> RepetitionTime 4700 >>> PhEncFOV 0 >>> ReadoutFOV 0 >>> Image information >>> RunNo 4 >>> SeriesNo 5 >>> ImageNo 1 >>> NImageRows 990 >>> NImageCols 990 >>> NFrames 64 >>> SliceArraylSize 0 >>> IsMosaic 1 >>> ImgPos 1075.1575 1069.8385 -48.6769 >>> VolRes 2.1818 2.1818 2.0000 >>> VolDim 0 0 0 >>> Vc -1.0000 -0.0000 0.0000 >>> Vr -0.0000 -1.0000 0.0000 >>> Vs 0.0000 0.0000 0.0000 >>> VolCenter 0.0000 0.0000 0.0000 >>> TransferSyntaxUID 1.2.840.10008.1.2.1 >>> >>> >>> Then I try using mri_convert -it dicom, it converts the files >>> but not >>> as it is expected, you could notice the difference when I run >>> mri_info >>> on my output : >>> Volume information for output.nii.gz >>> type: nii >>> dimensions: 990 x 990 x 1 x 64 >>> voxel sizes: 2.1818, 2.1818, 2.0000 >>> type: SHORT (4) >>> fov: 2160.000 >>> dof: 0 >>> xstart: -1080.0, xend: 1080.0 >>> ystart: -1080.0, yend: 1080.0 >>> zstart: -1.0, zend: 1.0 >>> TR: 4700.00 msec, TE: 0.00 msec, TI: 0.00 msec, flip >>> angle: 0.00 degrees >>> nframes: 64 >>> PhEncDir: UNKNOWN >>> ras xform present >>> xform info: x_r = -1.0000, y_r = -0.0000, z_r = -0.0000, c_r = >>> -4.8425 >>> : x_a = -0.0000, y_a = -1.0000, z_a = -0.0000, c_a = >>> -10.1615 >>> : x_s = 0.0000, y_s = 0.0000, z_s = 1.0000, c_s = >>> -47.6769 >>> Orientation : LPS >>> Primary Slice Direction: axial >>> >>> voxel to ras transform: >>> -2.1818 -0.0000 -0.0000 1075.1575 >>> -0.0000 -2.1818 -0.0000 1069.8385 >>> 0.0000 0.0000 2.0000 -48.6769 >>> 0.0000 0.0000 0.0000 1.0000 >>> >>> voxel-to-ras determinant 9.52066 >>> >>> ras to voxel transform: >>> -0.4583 0.0000 0.0000 492.7805 >>> 0.0000 -0.4583 0.0000 490.3426 >>> -0.0000 -0.0000 0.5000 24.3384 >>> 0.0000 0.0000 0.0000 1.0000 >>> >>> I would really appreciate your help, thank you. >>> >>> Best, >>> >>> Ismail >>> >>> >>> >>> _______________________________________________ >>> Freesurfer mailing list >>> Freesurfer@nmr.mgh.harvard.edu >>> mailto:Freesurfer@nmr.mgh.harvard.edu >>> mailto:Freesurfer@nmr.mgh.harvard.edu >>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> -- >> Douglas N. Greve, Ph.D. >> MGH-NMR Center >> greve@nmr.mgh.harvard.edu >> mailto:greve@nmr.mgh.harvard.edumailto:greve@nmr.mgh.harvard.edu >> Phone Number: 617-724-2358 >> Fax: 617-726-7422 >> >> Bugs:surfer.nmr.mgh.harvard.edu/fswiki/BugReporting >> http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting >> FileDrop:https://gate.nmr.mgh.harvard.edu/filedrop2 >> www.nmr.mgh.harvard.edu/facility/filedrop/index.html >> http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html >> Outgoing: >> ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> mailto:Freesurfer@nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > mailto:Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >
>
Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edumailto:greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs:surfer.nmr.mgh.harvard.edu/fswiki/BugReporting http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop:https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
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-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edumailto:greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs:surfer.nmr.mgh.harvard.edu/fswiki/BugReporting http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop:https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing:ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
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-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs:surfer.nmr.mgh.harvard.edu/fswiki/BugReporting http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop:https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing:ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
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Hi Doug,
I tried it on the cluster and it worked, which is weird because it was not working before … Any idea what might be the problem on my system ? Thanks again.
Ismail
On Jul 19, 2016, at 10:32 PM, Douglas Greve <greve@nmr.mgh.harvard.edumailto:greve@nmr.mgh.harvard.edu> wrote:
I used the same version, but I used it on linux. Do you have a linux box with FS installed that you can try it on?
On 7/19/16 1:57 PM, Koubiyr, Ismail wrote: I used the same command line as you did. And when I check with mri_probedicom I can see the ASCII header.
Here is the version of FS I am using : freesurfer-i386-apple-darwin11.4.2-stable5-20130514
Do you think it might be related ?
Thanks again.
Ismail
On Jul 19, 2016, at 1:27 PM, Douglas N Greve <greve@nmr.mgh.harvard.edumailto:greve@nmr.mgh.harvard.edu> wrote:
What is your exact command line?
The version of the file that you gave me definitely has an ascii header, and I don't get that warning when I convert. What version of FS are you using on what platform? To check whether that file has an ascii header, run
mri_probedicom --i MR.1.3.12.2.1107.5.2.19.45306.2014091812330393354083931
There should be a line like below
### ASCCONV BEGIN
On 07/19/2016 01:16 PM, Koubiyr, Ismail wrote: Hi Doug,
That’s weird because I can’t convert it using only mri_convert, here is the error I get :
WARNING: file /Users/ismailkoubiyr/Documents/PFE/Tracula/dti/3T2/MR.1.3.12.2.1107.5.2.19.45306.2014091812330393354083931 does not contain a Siemens ASCII header has this file been anonymized? ERROR: cannot unpack mosiacs without ASCII header
Any idea why ?
Best,
Ismail
On Jul 19, 2016, at 1:11 PM, Douglas N Greve <greve@nmr.mgh.harvard.edumailto:greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:
I was able to convert it fine with mri_convert MR.1.3.12.2.1107.5.2.19.45306.2014091812372179441003292 output.nii.gz If I included -it dicom, the conversion did not have an error, but the output had only one slice. Since these are mosaics, they need the Siemens ascii header which is ignored with -it dicom. So ... don't use -it dicom
On 07/19/2016 11:06 AM, Koubiyr, Ismail wrote: Hi Doug,
It is still an issue. I uploaded the DICOMs to you. Hope it could be useful. Thanks.
Ismail
On Jul 18, 2016, at 6:14 PM, Douglas N Greve <greve@nmr.mgh.harvard.edumailto:greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:
Is this still a problem? If so, can you upload the dicom files to our file drop?
On 07/05/2016 11:24 AM, Koubiyr, Ismail wrote: The file has not been anonymized.
Thanks,
Ismail
On Jul 5, 2016, at 11:20 AM, Douglas N Greve <greve@nmr.mgh.harvard.edumailto:greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:
can you answer the question that it asks?
On 07/05/2016 10:52 AM, Koubiyr, Ismail wrote: Hi everyone,
I’m having some issues converting my DICOMs (DWI) into NIFTI using mri_convert. I looked for other topics with people having the same kind of problem but couldn’t find an answer.
Each time I run mri_convert on my DICOMs I get the following error : WARNING: file MR.1.3.12.2.1107.5.2.19.45306.2014091812330393354083931 does not contain a Siemens ASCII header has this file been anonymized? ERROR: cannot unpack mosiacs without ASCII header
Here are the following DICOMs informations : Identification NumarisVer syngo MR D13 ScannerModel Skyra PatientName xxxxx Date and time StudyDate 20140918 StudyTime 121037.203000 SeriesTime 123450.600000 AcqTime 123257.367500 Acquisition parameters PulseSeq ep_b0 Protocol AX DTI no angle MS NEX 4 2 PhEncDir COL EchoNo 1 FlipAngle 90 EchoTime 96 InversionTime -1 RepetitionTime 4700 PhEncFOV 0 ReadoutFOV 0 Image information RunNo 4 SeriesNo 5 ImageNo 1 NImageRows 990 NImageCols 990 NFrames 64 SliceArraylSize 0 IsMosaic 1 ImgPos 1075.1575 1069.8385 -48.6769 VolRes 2.1818 2.1818 2.0000 VolDim 0 0 0 Vc -1.0000 -0.0000 0.0000 Vr -0.0000 -1.0000 0.0000 Vs 0.0000 0.0000 0.0000 VolCenter 0.0000 0.0000 0.0000 TransferSyntaxUID 1.2.840.10008.1.2.1
Then I try using mri_convert -it dicom, it converts the files but not as it is expected, you could notice the difference when I run mri_info on my output : Volume information for output.nii.gz type: nii dimensions: 990 x 990 x 1 x 64 voxel sizes: 2.1818, 2.1818, 2.0000 type: SHORT (4) fov: 2160.000 dof: 0 xstart: -1080.0, xend: 1080.0 ystart: -1080.0, yend: 1080.0 zstart: -1.0, zend: 1.0 TR: 4700.00 msec, TE: 0.00 msec, TI: 0.00 msec, flip angle: 0.00 degrees nframes: 64 PhEncDir: UNKNOWN ras xform present xform info: x_r = -1.0000, y_r = -0.0000, z_r = -0.0000, c_r = -4.8425 : x_a = -0.0000, y_a = -1.0000, z_a = -0.0000, c_a = -10.1615 : x_s = 0.0000, y_s = 0.0000, z_s = 1.0000, c_s = -47.6769 Orientation : LPS Primary Slice Direction: axial
voxel to ras transform: -2.1818 -0.0000 -0.0000 1075.1575 -0.0000 -2.1818 -0.0000 1069.8385 0.0000 0.0000 2.0000 -48.6769 0.0000 0.0000 0.0000 1.0000
voxel-to-ras determinant 9.52066
ras to voxel transform: -0.4583 0.0000 0.0000 492.7805 0.0000 -0.4583 0.0000 490.3426 -0.0000 -0.0000 0.5000 24.3384 0.0000 0.0000 0.0000 1.0000
I would really appreciate your help, thank you.
Best,
Ismail
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edumailto:greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReportinghttp://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.htmlhttp://www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edumailto:greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReportinghttp://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.htmlhttp://www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
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-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edumailto:greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReportinghttp://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.htmlhttp://www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
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-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edumailto:greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReportinghttp://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.htmlhttp://www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
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There was an obscure error having to do with the ascii header when unpacking skyra data on the mac, that might be it. Zeke, can you get Ismail a version of mri_convert appropriate for his OS?
doug
On 7/20/16 10:34 AM, Koubiyr, Ismail wrote:
Hi Doug,
I tried it on the cluster and it worked, which is weird because it was not working before … Any idea what might be the problem on my system ? Thanks again.
Ismail
On Jul 19, 2016, at 10:32 PM, Douglas Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:
I used the same version, but I used it on linux. Do you have a linux box with FS installed that you can try it on?
On 7/19/16 1:57 PM, Koubiyr, Ismail wrote:
I used the same command line as you did. And when I check with mri_probedicom I can see the ASCII header.
Here is the version of FS I am using : freesurfer-i386-apple-darwin11.4.2-stable5-20130514
Do you think it might be related ?
Thanks again.
Ismail
On Jul 19, 2016, at 1:27 PM, Douglas N Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:
What is your exact command line?
The version of the file that you gave me definitely has an ascii header, and I don't get that warning when I convert. What version of FS are you using on what platform? To check whether that file has an ascii header, run
mri_probedicom --i MR.1.3.12.2.1107.5.2.19.45306.2014091812330393354083931
There should be a line like below
### ASCCONV BEGIN
On 07/19/2016 01:16 PM, Koubiyr, Ismail wrote:
Hi Doug,
That’s weird because I can’t convert it using only mri_convert, here is the error I get :
WARNING: file /Users/ismailkoubiyr/Documents/PFE/Tracula/dti/3T2/MR.1.3.12.2.1107.5.2.19.45306.2014091812330393354083931 does not contain a Siemens ASCII header has this file been anonymized? ERROR: cannot unpack mosiacs without ASCII header
Any idea why ?
Best,
Ismail
On Jul 19, 2016, at 1:11 PM, Douglas N Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edumailto:greve@nmr.mgh.harvard.edu> wrote:
I was able to convert it fine with mri_convert MR.1.3.12.2.1107.5.2.19.45306.2014091812372179441003292 output.nii.gz If I included -it dicom, the conversion did not have an error, but the output had only one slice. Since these are mosaics, they need the Siemens ascii header which is ignored with -it dicom. So ... don't use -it dicom
On 07/19/2016 11:06 AM, Koubiyr, Ismail wrote: > Hi Doug, > > It is still an issue. I uploaded the DICOMs to you. Hope it could be > useful. > Thanks. > > Ismail > >> On Jul 18, 2016, at 6:14 PM, Douglas N Greve >> <greve@nmr.mgh.harvard.edu >> mailto:greve@nmr.mgh.harvard.edumailto:greve@nmr.mgh.harvard.edu> >> wrote: >> >> Is this still a problem? If so, can you upload the dicom files >> to our >> file drop? >> >> On 07/05/2016 11:24 AM, Koubiyr, Ismail wrote: >>> The file has not been anonymized. >>> >>> Thanks, >>> >>> Ismail >>> >>>> On Jul 5, 2016, at 11:20 AM, Douglas N Greve >>>> <greve@nmr.mgh.harvard.edu >>>> mailto:greve@nmr.mgh.harvard.edumailto:greve@nmr.mgh.harvard.edu> >>>> wrote: >>>> >>>> can you answer the question that it asks? >>>> >>>> On 07/05/2016 10:52 AM, Koubiyr, Ismail wrote: >>>>> Hi everyone, >>>>> >>>>> I’m having some issues converting my DICOMs (DWI) into NIFTI >>>>> using >>>>> mri_convert. I looked for other topics with people having >>>>> the same >>>>> kind of problem but couldn’t find an answer. >>>>> >>>>> Each time I run mri_convert on my DICOMs I get the following >>>>> error : >>>>> WARNING: file >>>>> MR.1.3.12.2.1107.5.2.19.45306.2014091812330393354083931 >>>>> does not contain a Siemens ASCII header >>>>> has this file been anonymized? >>>>> ERROR: cannot unpack mosiacs without ASCII header >>>>> >>>>> Here are the following DICOMs informations : >>>>> Identification >>>>> NumarisVer syngo MR D13 >>>>> ScannerModel Skyra >>>>> PatientName xxxxx >>>>> Date and time >>>>> StudyDate 20140918 >>>>> StudyTime 121037.203000 >>>>> SeriesTime 123450.600000 >>>>> AcqTime 123257.367500 >>>>> Acquisition parameters >>>>> PulseSeq ep_b0 >>>>> Protocol AX DTI no angle MS NEX 4 2 >>>>> PhEncDir COL >>>>> EchoNo 1 >>>>> FlipAngle 90 >>>>> EchoTime 96 >>>>> InversionTime -1 >>>>> RepetitionTime 4700 >>>>> PhEncFOV 0 >>>>> ReadoutFOV 0 >>>>> Image information >>>>> RunNo 4 >>>>> SeriesNo 5 >>>>> ImageNo 1 >>>>> NImageRows 990 >>>>> NImageCols 990 >>>>> NFrames 64 >>>>> SliceArraylSize 0 >>>>> IsMosaic 1 >>>>> ImgPos 1075.1575 1069.8385 -48.6769 >>>>> VolRes 2.1818 2.1818 2.0000 >>>>> VolDim 0 0 0 >>>>> Vc -1.0000 -0.0000 0.0000 >>>>> Vr -0.0000 -1.0000 0.0000 >>>>> Vs 0.0000 0.0000 0.0000 >>>>> VolCenter 0.0000 0.0000 0.0000 >>>>> TransferSyntaxUID 1.2.840.10008.1.2.1 >>>>> >>>>> >>>>> Then I try using mri_convert -it dicom, it converts the files >>>>> but not >>>>> as it is expected, you could notice the difference when I run >>>>> mri_info >>>>> on my output : >>>>> Volume information for output.nii.gz >>>>> type: nii >>>>> dimensions: 990 x 990 x 1 x 64 >>>>> voxel sizes: 2.1818, 2.1818, 2.0000 >>>>> type: SHORT (4) >>>>> fov: 2160.000 >>>>> dof: 0 >>>>> xstart: -1080.0, xend: 1080.0 >>>>> ystart: -1080.0, yend: 1080.0 >>>>> zstart: -1.0, zend: 1.0 >>>>> TR: 4700.00 msec, TE: 0.00 msec, TI: 0.00 msec, flip >>>>> angle: 0.00 degrees >>>>> nframes: 64 >>>>> PhEncDir: UNKNOWN >>>>> ras xform present >>>>> xform info: x_r = -1.0000, y_r = -0.0000, z_r = -0.0000, >>>>> c_r = >>>>> -4.8425 >>>>> : x_a = -0.0000, y_a = -1.0000, z_a = -0.0000, >>>>> c_a = >>>>> -10.1615 >>>>> : x_s = 0.0000, y_s = 0.0000, z_s = 1.0000, >>>>> c_s = >>>>> -47.6769 >>>>> Orientation : LPS >>>>> Primary Slice Direction: axial >>>>> >>>>> voxel to ras transform: >>>>> -2.1818 -0.0000 -0.0000 1075.1575 >>>>> -0.0000 -2.1818 -0.0000 1069.8385 >>>>> 0.0000 0.0000 2.0000 -48.6769 >>>>> 0.0000 0.0000 0.0000 1.0000 >>>>> >>>>> voxel-to-ras determinant 9.52066 >>>>> >>>>> ras to voxel transform: >>>>> -0.4583 0.0000 0.0000 492.7805 >>>>> 0.0000 -0.4583 0.0000 490.3426 >>>>> -0.0000 -0.0000 0.5000 24.3384 >>>>> 0.0000 0.0000 0.0000 1.0000 >>>>> >>>>> I would really appreciate your help, thank you. >>>>> >>>>> Best, >>>>> >>>>> Ismail >>>>> >>>>> >>>>> >>>>> _______________________________________________ >>>>> Freesurfer mailing list >>>>> Freesurfer@nmr.mgh.harvard.edu >>>>> mailto:Freesurfer@nmr.mgh.harvard.edu >>>>> mailto:Freesurfer@nmr.mgh.harvard.edu >>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>>> -- >>>> Douglas N. Greve, Ph.D. >>>> MGH-NMR Center >>>> greve@nmr.mgh.harvard.edu >>>> mailto:greve@nmr.mgh.harvard.edumailto:greve@nmr.mgh.harvard.edu >>>> Phone Number: 617-724-2358 >>>> Fax: 617-726-7422 >>>> >>>> Bugs:surfer.nmr.mgh.harvard.edu/fswiki/BugReporting >>>> http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting >>>> FileDrop:https://gate.nmr.mgh.harvard.edu/filedrop2 >>>> www.nmr.mgh.harvard.edu/facility/filedrop/index.html >>>> http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html >>>> Outgoing: >>>> ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ >>>> >>>> _______________________________________________ >>>> Freesurfer mailing list >>>> Freesurfer@nmr.mgh.harvard.edu >>>> mailto:Freesurfer@nmr.mgh.harvard.edu >>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>> _______________________________________________ >>> Freesurfer mailing list >>> Freesurfer@nmr.mgh.harvard.edu >>> mailto:Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu >>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>> >>> >> -- >> Douglas N. Greve, Ph.D. >> MGH-NMR Center >> greve@nmr.mgh.harvard.edu >> mailto:greve@nmr.mgh.harvard.edumailto:greve@nmr.mgh.harvard.edu >> Phone Number: 617-724-2358 >> Fax: 617-726-7422 >> >> Bugs:surfer.nmr.mgh.harvard.edu/fswiki/BugReporting >> http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting >> FileDrop:https://gate.nmr.mgh.harvard.edu/filedrop2 >> www.nmr.mgh.harvard.edu/facility/filedrop/index.html >> http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html >> Outgoing: >> ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> mailto:Freesurfer@nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > mailto:Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > >
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edumailto:greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs:surfer.nmr.mgh.harvard.edu/fswiki/BugReporting http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop:https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing:ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs:surfer.nmr.mgh.harvard.edu/fswiki/BugReporting http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop:https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing:ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Current versions of the Mac freesurfer binaries are not compatible with the v5.3 release. Too much has changed since then. If you wanted to use the newest version on the code you will need to download the latest dev version of freesurfer from this page (see "Development Version"):
https://surfer.nmr.mgh.harvard.edu/fswiki/DownloadAndInstall#Download
Hope this helps.
-Zeke
There was an obscure error having to do with the ascii header when unpacking skyra data on the mac, that might be it. Zeke, can you get Ismail a version of mri_convert appropriate for his OS?
doug
On 7/20/16 10:34 AM, Koubiyr, Ismail wrote:
Hi Doug,
I tried it on the cluster and it worked, which is weird because it was not working before Any idea what might be the problem on my system ? Thanks again.
Ismail
On Jul 19, 2016, at 10:32 PM, Douglas Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:
I used the same version, but I used it on linux. Do you have a linux box with FS installed that you can try it on?
On 7/19/16 1:57 PM, Koubiyr, Ismail wrote:
I used the same command line as you did. And when I check with mri_probedicom I can see the ASCII header.
Here is the version of FS I am using : freesurfer-i386-apple-darwin11.4.2-stable5-20130514
Do you think it might be related ?
Thanks again.
Ismail
On Jul 19, 2016, at 1:27 PM, Douglas N Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:
What is your exact command line?
The version of the file that you gave me definitely has an ascii header, and I don't get that warning when I convert. What version of FS are you using on what platform? To check whether that file has an ascii header, run
mri_probedicom --i MR.1.3.12.2.1107.5.2.19.45306.2014091812330393354083931
There should be a line like below
### ASCCONV BEGIN
On 07/19/2016 01:16 PM, Koubiyr, Ismail wrote:
Hi Doug,
Thats weird because I cant convert it using only mri_convert, here is the error I get :
WARNING: file /Users/ismailkoubiyr/Documents/PFE/Tracula/dti/3T2/MR.1.3.12.2.1107.5.2.19.45306.2014091812330393354083931 does not contain a Siemens ASCII header has this file been anonymized? ERROR: cannot unpack mosiacs without ASCII header
Any idea why ?
Best,
Ismail
> On Jul 19, 2016, at 1:11 PM, Douglas N Greve > <greve@nmr.mgh.harvard.edu > mailto:greve@nmr.mgh.harvard.edumailto:greve@nmr.mgh.harvard.edu> > wrote: > > I was able to convert it fine with > mri_convert MR.1.3.12.2.1107.5.2.19.45306.2014091812372179441003292 > output.nii.gz > If I included -it dicom, the conversion did not have an error, > but the > output had only one slice. Since these are mosaics, they need the > Siemens ascii header which is ignored with -it dicom. So ... > don't use > -it dicom > > > On 07/19/2016 11:06 AM, Koubiyr, Ismail wrote: >> Hi Doug, >> >> It is still an issue. I uploaded the DICOMs to you. Hope it could >> be >> useful. >> Thanks. >> >> Ismail >> >>> On Jul 18, 2016, at 6:14 PM, Douglas N Greve >>> <greve@nmr.mgh.harvard.edu >>> mailto:greve@nmr.mgh.harvard.edumailto:greve@nmr.mgh.harvard.edu> >>> wrote: >>> >>> Is this still a problem? If so, can you upload the dicom files >>> to our >>> file drop? >>> >>> On 07/05/2016 11:24 AM, Koubiyr, Ismail wrote: >>>> The file has not been anonymized. >>>> >>>> Thanks, >>>> >>>> Ismail >>>> >>>>> On Jul 5, 2016, at 11:20 AM, Douglas N Greve >>>>> <greve@nmr.mgh.harvard.edu >>>>> mailto:greve@nmr.mgh.harvard.edumailto:greve@nmr.mgh.harvard.edu> >>>>> wrote: >>>>> >>>>> can you answer the question that it asks? >>>>> >>>>> On 07/05/2016 10:52 AM, Koubiyr, Ismail wrote: >>>>>> Hi everyone, >>>>>> >>>>>> Im having some issues converting my DICOMs (DWI) into NIFTI >>>>>> using >>>>>> mri_convert. I looked for other topics with people having >>>>>> the same >>>>>> kind of problem but couldnt find an answer. >>>>>> >>>>>> Each time I run mri_convert on my DICOMs I get the following >>>>>> error : >>>>>> WARNING: file >>>>>> MR.1.3.12.2.1107.5.2.19.45306.2014091812330393354083931 >>>>>> does not contain a Siemens ASCII header >>>>>> has this file been anonymized? >>>>>> ERROR: cannot unpack mosiacs without ASCII header >>>>>> >>>>>> Here are the following DICOMs informations : >>>>>> Identification >>>>>> NumarisVer syngo MR D13 >>>>>> ScannerModel Skyra >>>>>> PatientName xxxxx >>>>>> Date and time >>>>>> StudyDate 20140918 >>>>>> StudyTime 121037.203000 >>>>>> SeriesTime 123450.600000 >>>>>> AcqTime 123257.367500 >>>>>> Acquisition parameters >>>>>> PulseSeq ep_b0 >>>>>> Protocol AX DTI no angle MS NEX 4 2 >>>>>> PhEncDir COL >>>>>> EchoNo 1 >>>>>> FlipAngle 90 >>>>>> EchoTime 96 >>>>>> InversionTime -1 >>>>>> RepetitionTime 4700 >>>>>> PhEncFOV 0 >>>>>> ReadoutFOV 0 >>>>>> Image information >>>>>> RunNo 4 >>>>>> SeriesNo 5 >>>>>> ImageNo 1 >>>>>> NImageRows 990 >>>>>> NImageCols 990 >>>>>> NFrames 64 >>>>>> SliceArraylSize 0 >>>>>> IsMosaic 1 >>>>>> ImgPos 1075.1575 1069.8385 -48.6769 >>>>>> VolRes 2.1818 2.1818 2.0000 >>>>>> VolDim 0 0 0 >>>>>> Vc -1.0000 -0.0000 0.0000 >>>>>> Vr -0.0000 -1.0000 0.0000 >>>>>> Vs 0.0000 0.0000 0.0000 >>>>>> VolCenter 0.0000 0.0000 0.0000 >>>>>> TransferSyntaxUID 1.2.840.10008.1.2.1 >>>>>> >>>>>> >>>>>> Then I try using mri_convert -it dicom, it converts the files >>>>>> but not >>>>>> as it is expected, you could notice the difference when I run >>>>>> mri_info >>>>>> on my output : >>>>>> Volume information for output.nii.gz >>>>>> type: nii >>>>>> dimensions: 990 x 990 x 1 x 64 >>>>>> voxel sizes: 2.1818, 2.1818, 2.0000 >>>>>> type: SHORT (4) >>>>>> fov: 2160.000 >>>>>> dof: 0 >>>>>> xstart: -1080.0, xend: 1080.0 >>>>>> ystart: -1080.0, yend: 1080.0 >>>>>> zstart: -1.0, zend: 1.0 >>>>>> TR: 4700.00 msec, TE: 0.00 msec, TI: 0.00 msec, flip >>>>>> angle: 0.00 degrees >>>>>> nframes: 64 >>>>>> PhEncDir: UNKNOWN >>>>>> ras xform present >>>>>> xform info: x_r = -1.0000, y_r = -0.0000, z_r = -0.0000, >>>>>> c_r = >>>>>> -4.8425 >>>>>> : x_a = -0.0000, y_a = -1.0000, z_a = -0.0000, >>>>>> c_a = >>>>>> -10.1615 >>>>>> : x_s = 0.0000, y_s = 0.0000, z_s = 1.0000, >>>>>> c_s = >>>>>> -47.6769 >>>>>> Orientation : LPS >>>>>> Primary Slice Direction: axial >>>>>> >>>>>> voxel to ras transform: >>>>>> -2.1818 -0.0000 -0.0000 1075.1575 >>>>>> -0.0000 -2.1818 -0.0000 1069.8385 >>>>>> 0.0000 0.0000 2.0000 -48.6769 >>>>>> 0.0000 0.0000 0.0000 1.0000 >>>>>> >>>>>> voxel-to-ras determinant 9.52066 >>>>>> >>>>>> ras to voxel transform: >>>>>> -0.4583 0.0000 0.0000 492.7805 >>>>>> 0.0000 -0.4583 0.0000 490.3426 >>>>>> -0.0000 -0.0000 0.5000 24.3384 >>>>>> 0.0000 0.0000 0.0000 1.0000 >>>>>> >>>>>> I would really appreciate your help, thank you. >>>>>> >>>>>> Best, >>>>>> >>>>>> Ismail >>>>>> >>>>>> >>>>>> >>>>>> _______________________________________________ >>>>>> Freesurfer mailing list >>>>>> Freesurfer@nmr.mgh.harvard.edu >>>>>> mailto:Freesurfer@nmr.mgh.harvard.edu >>>>>> mailto:Freesurfer@nmr.mgh.harvard.edu >>>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>>>> -- >>>>> Douglas N. Greve, Ph.D. >>>>> MGH-NMR Center >>>>> greve@nmr.mgh.harvard.edu >>>>> mailto:greve@nmr.mgh.harvard.edumailto:greve@nmr.mgh.harvard.edu >>>>> Phone Number: 617-724-2358 >>>>> Fax: 617-726-7422 >>>>> >>>>> Bugs:surfer.nmr.mgh.harvard.edu/fswiki/BugReporting >>>>> http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting >>>>> FileDrop:https://gate.nmr.mgh.harvard.edu/filedrop2 >>>>> www.nmr.mgh.harvard.edu/facility/filedrop/index.html >>>>> http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html >>>>> Outgoing: >>>>> ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ >>>>> >>>>> _______________________________________________ >>>>> Freesurfer mailing list >>>>> Freesurfer@nmr.mgh.harvard.edu >>>>> mailto:Freesurfer@nmr.mgh.harvard.edu >>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>>> _______________________________________________ >>>> Freesurfer mailing list >>>> Freesurfer@nmr.mgh.harvard.edu >>>> mailto:Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu >>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>>> >>>> >>> -- >>> Douglas N. Greve, Ph.D. >>> MGH-NMR Center >>> greve@nmr.mgh.harvard.edu >>> mailto:greve@nmr.mgh.harvard.edumailto:greve@nmr.mgh.harvard.edu >>> Phone Number: 617-724-2358 >>> Fax: 617-726-7422 >>> >>> Bugs:surfer.nmr.mgh.harvard.edu/fswiki/BugReporting >>> http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting >>> FileDrop:https://gate.nmr.mgh.harvard.edu/filedrop2 >>> www.nmr.mgh.harvard.edu/facility/filedrop/index.html >>> http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html >>> Outgoing: >>> ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ >>> >>> _______________________________________________ >>> Freesurfer mailing list >>> Freesurfer@nmr.mgh.harvard.edu >>> mailto:Freesurfer@nmr.mgh.harvard.edu >>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> mailto:Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> > > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > greve@nmr.mgh.harvard.edu > mailto:greve@nmr.mgh.harvard.edumailto:greve@nmr.mgh.harvard.edu > Phone Number: 617-724-2358 > Fax: 617-726-7422 > > Bugs:surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > FileDrop:https://gate.nmr.mgh.harvard.edu/filedrop2 > www.nmr.mgh.harvard.edu/facility/filedrop/index.html > http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html > Outgoing:ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > mailto:Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
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Doug, Zeke,
Thank you very much for your help.
Best,
Ismail
On Jul 21, 2016, at 1:15 AM, zkaufman@nmr.mgh.harvard.edumailto:zkaufman@nmr.mgh.harvard.edu wrote:
Current versions of the Mac freesurfer binaries are not compatible with the v5.3 release. Too much has changed since then. If you wanted to use the newest version on the code you will need to download the latest dev version of freesurfer from this page (see "Development Version"):
https://surfer.nmr.mgh.harvard.edu/fswiki/DownloadAndInstall#Download
Hope this helps.
-Zeke
There was an obscure error having to do with the ascii header when unpacking skyra data on the mac, that might be it. Zeke, can you get Ismail a version of mri_convert appropriate for his OS?
doug
On 7/20/16 10:34 AM, Koubiyr, Ismail wrote: Hi Doug,
I tried it on the cluster and it worked, which is weird because it was not working before . Any idea what might be the problem on my system ? Thanks again.
Ismail
On Jul 19, 2016, at 10:32 PM, Douglas Greve <greve@nmr.mgh.harvard.edumailto:greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:
I used the same version, but I used it on linux. Do you have a linux box with FS installed that you can try it on?
On 7/19/16 1:57 PM, Koubiyr, Ismail wrote: I used the same command line as you did. And when I check with mri_probedicom I can see the ASCII header.
Here is the version of FS I am using : freesurfer-i386-apple-darwin11.4.2-stable5-20130514
Do you think it might be related ?
Thanks again.
Ismail
On Jul 19, 2016, at 1:27 PM, Douglas N Greve <greve@nmr.mgh.harvard.edumailto:greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:
What is your exact command line?
The version of the file that you gave me definitely has an ascii header, and I don't get that warning when I convert. What version of FS are you using on what platform? To check whether that file has an ascii header, run
mri_probedicom --i MR.1.3.12.2.1107.5.2.19.45306.2014091812330393354083931
There should be a line like below
### ASCCONV BEGIN
On 07/19/2016 01:16 PM, Koubiyr, Ismail wrote: Hi Doug,
That's weird because I can't convert it using only mri_convert, here is the error I get :
WARNING: file /Users/ismailkoubiyr/Documents/PFE/Tracula/dti/3T2/MR.1.3.12.2.1107.5.2.19.45306.2014091812330393354083931 does not contain a Siemens ASCII header has this file been anonymized? ERROR: cannot unpack mosiacs without ASCII header
Any idea why ?
Best,
Ismail
On Jul 19, 2016, at 1:11 PM, Douglas N Greve <greve@nmr.mgh.harvard.edumailto:greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edumailto:greve@nmr.mgh.harvard.edu> wrote:
I was able to convert it fine with mri_convert MR.1.3.12.2.1107.5.2.19.45306.2014091812372179441003292 output.nii.gz If I included -it dicom, the conversion did not have an error, but the output had only one slice. Since these are mosaics, they need the Siemens ascii header which is ignored with -it dicom. So ... don't use -it dicom
On 07/19/2016 11:06 AM, Koubiyr, Ismail wrote: Hi Doug,
It is still an issue. I uploaded the DICOMs to you. Hope it could be useful. Thanks.
Ismail
On Jul 18, 2016, at 6:14 PM, Douglas N Greve <greve@nmr.mgh.harvard.edumailto:greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edumailto:greve@nmr.mgh.harvard.edu> wrote:
Is this still a problem? If so, can you upload the dicom files to our file drop?
On 07/05/2016 11:24 AM, Koubiyr, Ismail wrote: The file has not been anonymized.
Thanks,
Ismail
On Jul 5, 2016, at 11:20 AM, Douglas N Greve <greve@nmr.mgh.harvard.edumailto:greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edumailto:greve@nmr.mgh.harvard.edu> wrote:
can you answer the question that it asks?
On 07/05/2016 10:52 AM, Koubiyr, Ismail wrote: Hi everyone,
I'm having some issues converting my DICOMs (DWI) into NIFTI using mri_convert. I looked for other topics with people having the same kind of problem but couldn't find an answer.
Each time I run mri_convert on my DICOMs I get the following error : WARNING: file MR.1.3.12.2.1107.5.2.19.45306.2014091812330393354083931 does not contain a Siemens ASCII header has this file been anonymized? ERROR: cannot unpack mosiacs without ASCII header
Here are the following DICOMs informations : Identification NumarisVer syngo MR D13 ScannerModel Skyra PatientName xxxxx Date and time StudyDate 20140918 StudyTime 121037.203000 SeriesTime 123450.600000 AcqTime 123257.367500 Acquisition parameters PulseSeq ep_b0 Protocol AX DTI no angle MS NEX 4 2 PhEncDir COL EchoNo 1 FlipAngle 90 EchoTime 96 InversionTime -1 RepetitionTime 4700 PhEncFOV 0 ReadoutFOV 0 Image information RunNo 4 SeriesNo 5 ImageNo 1 NImageRows 990 NImageCols 990 NFrames 64 SliceArraylSize 0 IsMosaic 1 ImgPos 1075.1575 1069.8385 -48.6769 VolRes 2.1818 2.1818 2.0000 VolDim 0 0 0 Vc -1.0000 -0.0000 0.0000 Vr -0.0000 -1.0000 0.0000 Vs 0.0000 0.0000 0.0000 VolCenter 0.0000 0.0000 0.0000 TransferSyntaxUID 1.2.840.10008.1.2.1
Then I try using mri_convert -it dicom, it converts the files but not as it is expected, you could notice the difference when I run mri_info on my output : Volume information for output.nii.gz type: nii dimensions: 990 x 990 x 1 x 64 voxel sizes: 2.1818, 2.1818, 2.0000 type: SHORT (4) fov: 2160.000 dof: 0 xstart: -1080.0, xend: 1080.0 ystart: -1080.0, yend: 1080.0 zstart: -1.0, zend: 1.0 TR: 4700.00 msec, TE: 0.00 msec, TI: 0.00 msec, flip angle: 0.00 degrees nframes: 64 PhEncDir: UNKNOWN ras xform present xform info: x_r = -1.0000, y_r = -0.0000, z_r = -0.0000, c_r = -4.8425 : x_a = -0.0000, y_a = -1.0000, z_a = -0.0000, c_a = -10.1615 : x_s = 0.0000, y_s = 0.0000, z_s = 1.0000, c_s = -47.6769 Orientation : LPS Primary Slice Direction: axial
voxel to ras transform: -2.1818 -0.0000 -0.0000 1075.1575 -0.0000 -2.1818 -0.0000 1069.8385 0.0000 0.0000 2.0000 -48.6769 0.0000 0.0000 0.0000 1.0000
voxel-to-ras determinant 9.52066
ras to voxel transform: -0.4583 0.0000 0.0000 492.7805 0.0000 -0.4583 0.0000 490.3426 -0.0000 -0.0000 0.5000 24.3384 0.0000 0.0000 0.0000 1.0000
I would really appreciate your help, thank you.
Best,
Ismail
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edumailto:greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edumailto:greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
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