Sorry to send this twice, but I should have elaborated:
I am trying to convert files to mgz format. I was able to run mri_convert, but when I run csurf and attempt to open the orig volume, I get the error:
"First orig image: /freesurfer/subjects/2332/mri/orig/COR-001 not found"
Does anyone know why this may happen?
Here is the command and output:
[root@localhost /freesurfer]# cd subjects/2332/mri/orig [root@localhost orig]# ls 2332_analyze 2332_crsg [root@localhost orig]# mri_convert -it dicom -ot mgz 2332_crsg/001 001.mgz mri_convert -it dicom -ot mgz 2332_crsg/001 001.mgz reading from 2332_crsg/001... 124 DICOM 3.0 files in list Found 124 DICOM Files WARNING: NumberOfFrames 0 != Found Count of slices 124. reading DICOM image... ------------------------------------------------- DICOM meta-header
file name 2332_crsg/001 Date and time study date 20030630 study time 101639.0000 series time 104735.12 acquisition time 104735.12 Identification patient name ... manufacturer Philips Medical Systems Dimensions number of rows 256 number of columns 256 number of frames 124 pixel width 0.9375 pixel height 0.9375 slice thickness 1.5 field of view 240 image number 1 (might be not reliable) Acquisition parameters echo time 6.00003 repetition time 35 inversion time not found echo number 1 flip angle 0.785398 bits allocated 16 Spatial information first image position -114.756 -101.936 133.356 last image position -126.115 82.1994 135.698 image orientation 0.998088 0.0614863 0.00638348 0.00559035 0.0130627 -0.999899 -------------------------------------------------
TR=35.00, TE=6.00, TI=0.00, flip angle=45.00 i_ras = (-0.998088, -0.0614863, 0.00638348) j_ras = (-0.00559035, -0.0130627, -0.999899) k_ras = (0.0615663, -0.998022, 0.0126937) writing to 001.mgz... [root@localhost orig]# csurf
Thanks, Sasha
Sasha Wolosin Research Assistant Developmental Cognitive Neurology Kennedy Krieger Institute 707 N. Broadway Baltimore, MD 21205 ph: (443) 923-9270
Disclaimer: The materials in this e-mail are private and may contain Protected Health Information. Please note that e-mail is not necessarily confidential or secure. Your use of e-mail constitutes your acknowledgment of these confidentiality and security limitations. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying, distribution, or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this e-mail in error, please immediately notify the sender via telephone or return e-mail.
It looks like there's something "messed up" with your dicom file. We have success converting GE and Siemens, but I've never tried Philips before. Can you tar it up or put it some place where I can get it?
Sasha Wolosin wrote:
Sorry to send this twice, but I should have elaborated:
I am trying to convert files to mgz format. I was able to run mri_convert, but when I run csurf and attempt to open the orig volume, I get the error:
"First orig image: /freesurfer/subjects/2332/mri/orig/COR-001 not found"
Does anyone know why this may happen?
Here is the command and output:
[root@localhost /freesurfer]# cd subjects/2332/mri/orig [root@localhost orig]# ls 2332_analyze 2332_crsg [root@localhost orig]# mri_convert -it dicom -ot mgz 2332_crsg/001 001.mgz mri_convert -it dicom -ot mgz 2332_crsg/001 001.mgz reading from 2332_crsg/001... 124 DICOM 3.0 files in list Found 124 DICOM Files WARNING: NumberOfFrames 0 != Found Count of slices 124. reading DICOM image...
DICOM meta-header
file name 2332_crsg/001 Date and time study date 20030630 study time 101639.0000 series time 104735.12 acquisition time 104735.12 Identification patient name ... manufacturer Philips Medical Systems Dimensions number of rows 256 number of columns 256 number of frames 124 pixel width 0.9375 pixel height 0.9375 slice thickness 1.5 field of view 240 image number 1 (might be not reliable) Acquisition parameters echo time 6.00003 repetition time 35 inversion time not found echo number 1 flip angle 0.785398 bits allocated 16 Spatial information first image position -114.756 -101.936 133.356 last image position -126.115 82.1994 135.698 image orientation 0.998088 0.0614863 0.00638348 0.00559035 0.0130627 -0.999899
TR=35.00, TE=6.00, TI=0.00, flip angle=45.00 i_ras = (-0.998088, -0.0614863, 0.00638348) j_ras = (-0.00559035, -0.0130627, -0.999899) k_ras = (0.0615663, -0.998022, 0.0126937) writing to 001.mgz... [root@localhost orig]# csurf
Thanks, Sasha
Sasha Wolosin Research Assistant Developmental Cognitive Neurology Kennedy Krieger Institute 707 N. Broadway Baltimore, MD 21205 ph: (443) 923-9270
Disclaimer: The materials in this e-mail are private and may contain Protected Health Information. Please note that e-mail is not necessarily confidential or secure. Your use of e-mail constitutes your acknowledgment of these confidentiality and security limitations. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying, distribution, or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this e-mail in error, please immediately notify the sender via telephone or return e-mail.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Sasha,
You can securely upload files to us by following the instructions at this site:
https://www.nmr.mgh.harvard.edu/facility/filedrop/index.html
Nick
On Mon, 2005-08-29 at 17:45 -0400, Doug Greve wrote:
It looks like there's something "messed up" with your dicom file. We have success converting GE and Siemens, but I've never tried Philips before. Can you tar it up or put it some place where I can get it?
Sasha Wolosin wrote:
Sorry to send this twice, but I should have elaborated:
I am trying to convert files to mgz format. I was able to run mri_convert, but when I run csurf and attempt to open the orig volume, I get the error:
"First orig image: /freesurfer/subjects/2332/mri/orig/COR-001 not found"
Does anyone know why this may happen?
Here is the command and output:
[root@localhost /freesurfer]# cd subjects/2332/mri/orig [root@localhost orig]# ls 2332_analyze 2332_crsg [root@localhost orig]# mri_convert -it dicom -ot mgz 2332_crsg/001 001.mgz mri_convert -it dicom -ot mgz 2332_crsg/001 001.mgz reading from 2332_crsg/001... 124 DICOM 3.0 files in list Found 124 DICOM Files WARNING: NumberOfFrames 0 != Found Count of slices 124. reading DICOM image...
DICOM meta-header
file name 2332_crsg/001 Date and time study date 20030630 study time 101639.0000 series time 104735.12 acquisition time 104735.12 Identification patient name ... manufacturer Philips Medical Systems Dimensions number of rows 256 number of columns 256 number of frames 124 pixel width 0.9375 pixel height 0.9375 slice thickness 1.5 field of view 240 image number 1 (might be not reliable) Acquisition parameters echo time 6.00003 repetition time 35 inversion time not found echo number 1 flip angle 0.785398 bits allocated 16 Spatial information first image position -114.756 -101.936 133.356 last image position -126.115 82.1994 135.698 image orientation 0.998088 0.0614863 0.00638348 0.00559035 0.0130627 -0.999899
TR=35.00, TE=6.00, TI=0.00, flip angle=45.00 i_ras = (-0.998088, -0.0614863, 0.00638348) j_ras = (-0.00559035, -0.0130627, -0.999899) k_ras = (0.0615663, -0.998022, 0.0126937) writing to 001.mgz... [root@localhost orig]# csurf
Thanks, Sasha
Sasha Wolosin Research Assistant Developmental Cognitive Neurology Kennedy Krieger Institute 707 N. Broadway Baltimore, MD 21205 ph: (443) 923-9270
Disclaimer: The materials in this e-mail are private and may contain Protected Health Information. Please note that e-mail is not necessarily confidential or secure. Your use of e-mail constitutes your acknowledgment of these confidentiality and security limitations. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying, distribution, or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this e-mail in error, please immediately notify the sender via telephone or return e-mail.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hi Sasha,
try:
tkmedit 2332 orig/001.mgz
On Mon, 29 Aug 2005, Sasha Wolosin wrote:
Sorry to send this twice, but I should have elaborated:
I am trying to convert files to mgz format. I was able to run mri_convert, but when I run csurf and attempt to open the orig volume, I get the error:
"First orig image: /freesurfer/subjects/2332/mri/orig/COR-001 not found"
Does anyone know why this may happen?
Here is the command and output:
[root@localhost /freesurfer]# cd subjects/2332/mri/orig [root@localhost orig]# ls 2332_analyze 2332_crsg [root@localhost orig]# mri_convert -it dicom -ot mgz 2332_crsg/001 001.mgz mri_convert -it dicom -ot mgz 2332_crsg/001 001.mgz reading from 2332_crsg/001... 124 DICOM 3.0 files in list Found 124 DICOM Files WARNING: NumberOfFrames 0 != Found Count of slices 124. reading DICOM image...
DICOM meta-header
file name 2332_crsg/001 Date and time study date 20030630 study time 101639.0000 series time 104735.12 acquisition time 104735.12 Identification patient name ... manufacturer Philips Medical Systems Dimensions number of rows 256 number of columns 256 number of frames 124 pixel width 0.9375 pixel height 0.9375 slice thickness 1.5 field of view 240 image number 1 (might be not reliable) Acquisition parameters echo time 6.00003 repetition time 35 inversion time not found echo number 1 flip angle 0.785398 bits allocated 16 Spatial information first image position -114.756 -101.936 133.356 last image position -126.115 82.1994 135.698 image orientation 0.998088 0.0614863 0.00638348 0.00559035 0.0130627 -0.999899
TR=35.00, TE=6.00, TI=0.00, flip angle=45.00 i_ras = (-0.998088, -0.0614863, 0.00638348) j_ras = (-0.00559035, -0.0130627, -0.999899) k_ras = (0.0615663, -0.998022, 0.0126937) writing to 001.mgz... [root@localhost orig]# csurf
Thanks, Sasha
Sasha Wolosin Research Assistant Developmental Cognitive Neurology Kennedy Krieger Institute 707 N. Broadway Baltimore, MD 21205 ph: (443) 923-9270
Disclaimer: The materials in this e-mail are private and may contain Protected Health Information. Please note that e-mail is not necessarily confidential or secure. Your use of e-mail constitutes your acknowledgment of these confidentiality and security limitations. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying, distribution, or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this e-mail in error, please immediately notify the sender via telephone or return e-mail.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
freesurfer@nmr.mgh.harvard.edu
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Nick Schmansky -
Sasha Wolosin