Yea, that should work. Use the filedrop at the end of this email On 10/23/2014 04:13 PM, Flavin, John wrote: > We only have a few examples of the multi frame dicom, and they’re all > of humans. We can anonymize one and email it to you directly. > > Flavin > >> On Oct 23, 2014, at 1:18 PM, Douglas N Greve >> <gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu>> wrote: >> >> >> I doubt that it will work. I've never actually seen a multi-frame dicom >> myself. Can you upload one to me? It should be of a phantom, not a >> human, so we can avoid privacy issues. >> doug >> >> >> On 10/23/2014 01:07 PM, Flavin, John wrote: >>> >>>> Hi Timothy >>>> >>>> you should be able to. You can use the -nth <frame #> switch to convert >>>> each frame individually >>>> cheers >>>> Bruce >>>> >>>> >>>> On Mon, 11 Jul 2011, Timothy Brown wrote: >>>> >>>>> Hi All, >>>>> >>>>> Can mri_convert be used with multiframe dicom? >>> >>> >>> Is this advice still valid? I tried converting a multi frame DICOM >>> (176 frames in one file) using the -nth flag in mri_convert in >>> Freesurfer 5.3 and it did not work as I expected. >>> >>>> $ $FREESURFER_HOME/bin/mri_convert -i RAW/301/foo.dcm -o >>>> PROCESSED/subj/mri/orig/001.mgz -nth 0 >>>> /path/to/bin/mri_convert -i RAW/301/foo.dcm -o >>>> PROCESSED/subj/mri/orig/001.mgz -nth 0 >>>> $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ >>>> reading from RAW/301/foo.dcm... >>>> Starting DICOMRead2() >>>> dcmfile = RAW/301/foo.dcm >>>> dcmdir = RAW/301 >>>> WARNING: tag image orientation not found in RAW/301/foo.dcm >>>> Ref Series No = 301 >>>> Found 3 files, checking for dicoms >>>> WARNING: tag image orientation not found in RAW/301/foo.dcm >>>> Found 1 dicom files in series. >>>> WARNING: tag image orientation not found in RAW/301/foo.dcm >>>> First Sorting >>>> Computing Slice Direction >>>> >>>> >>>> WARNING: it appears that the image position for all slices is the same. >>>> This is a problem with the DICOM file. Using direction cosines from >>>> col and row >>>> to compute slice direction, but the output may be misoriented. >>>> >>>> Vs: 0 0 0 >>>> Vs: -nan -nan -nan >>>> Second Sorting >>>> Counting frames >>>> nframes = 1 >>>> nslices = 1 >>>> ndcmfiles = 1 >>>> PE Dir = UNKNOWN (dicom read) >>>> /usr/pubsw/packages/vxl/1.13.0/src/core/vnl/algo/vnl_qr.txx: >>>> vnl_qr<T>::solve() : matrix is rank-deficient by 2 >>>> /usr/pubsw/packages/vxl/1.13.0/src/core/vnl/algo/vnl_qr.txx: >>>> vnl_qr<T>::solve() : matrix is rank-deficient by 2 >>>> /usr/pubsw/packages/vxl/1.13.0/src/core/vnl/algo/vnl_qr.txx: >>>> vnl_qr<T>::solve() : matrix is rank-deficient by 2 >>>> /usr/pubsw/packages/vxl/1.13.0/src/core/vnl/algo/vnl_qr.txx: >>>> vnl_qr<T>::solve() : matrix is rank-deficient by 2 >>>> TransferSyntaxUID: --1.2.840.10008.1.2.1-- >>>> Loading pixel data >>>> /usr/pubsw/packages/vxl/1.13.0/src/core/vnl/algo/vnl_qr.txx: >>>> vnl_qr<T>::solve() : matrix is rank-deficient by 2 >>>> /usr/pubsw/packages/vxl/1.13.0/src/core/vnl/algo/vnl_qr.txx: >>>> vnl_qr<T>::solve() : matrix is rank-deficient by 2 >>>> /usr/pubsw/packages/vxl/1.13.0/src/core/vnl/algo/vnl_qr.txx: >>>> vnl_qr<T>::solve() : matrix is rank-deficient by 2 >>>> /usr/pubsw/packages/vxl/1.13.0/src/core/vnl/algo/vnl_qr.txx: >>>> vnl_qr<T>::solve() : matrix is rank-deficient by 2 >>>> TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 >>>> i_ras = (-0, -0, 0) >>>> j_ras = (-0, -0, 0) >>>> k_ras = (nan, nan, -nan) >>>> Reslicing using trilinear interpolation >>>> /usr/pubsw/packages/vxl/1.13.0/src/core/vnl/algo/vnl_qr.txx: >>>> vnl_qr<T>::solve() : matrix is rank-deficient by 2 >>>> /usr/pubsw/packages/vxl/1.13.0/src/core/vnl/algo/vnl_qr.txx: >>>> vnl_qr<T>::solve() : matrix is rank-deficient by 2 >>>> /usr/pubsw/packages/vxl/1.13.0/src/core/vnl/algo/vnl_qr.txx: >>>> vnl_qr<T>::solve() : matrix is rank-deficient by 2 >>>> /usr/pubsw/packages/vxl/1.13.0/src/core/vnl/algo/vnl_qr.txx: >>>> vnl_qr<T>::solve() : matrix is rank-deficient by 2 >>>> MRIresample(): error inverting matrix; determinant is -nan, matrix is: >>>> -0.000 -0.000 nan nan; >>>> -0.000 -0.000 nan nan; >>>> 0.000 0.000 -nan -nan; >>>> 0.000 0.000 0.000 1.000; >>> >>> I get the exact same output running with -nth 0 as I do not using >>> the -nth flag at all. If I try using -nth 1 (or -nth i for any >>> integer i > 0) I get >>>> mri_read(): start frame (1) is out of range (1 frames in volume) >>> >>> mri_convert reports nframes = 1. I can look in the DICOM headers of >>> the file and find >>>> (0028, 0008) Number of Frames IS: ‘176’ >>> and >>>> (2001, 1018) [Number of Slices MR] SL: 176 >>> >>> Anything I can do to tell mri_convert the correct number of frames? >>> >>> Flavin >>> >>> >>> ------------------------------------------------------------------------ >>> >>> The material in this message is private and may contain Protected >>> Healthcare Information (PHI). If you are not the intended recipient, >>> be advised that any unauthorized use, disclosure, copying or the >>> taking of any action in reliance on the contents of this information >>> is strictly prohibited. If you have received this email in error, >>> please immediately notify the sender via telephone or return mail. >>> >>> >>> _______________________________________________ >>> 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 >> gr...@nmr.mgh.harvard.edu <mailto:gr...@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 >> >> >> The information in this e-mail is intended only for the person to >> whom it is >> addressed. If you believe this e-mail was sent to you in error and >> the e-mail >> contains patient information, please contact the Partners Compliance >> HelpLine at >> http://www.partners.org/complianceline . If the e-mail was sent to >> you in error >> but does not contain patient information, please contact the sender >> and properly >> dispose of the e-mail. > > > ------------------------------------------------------------------------ > > The material in this message is private and may contain Protected > Healthcare Information (PHI). If you are not the intended recipient, > be advised that any unauthorized use, disclosure, copying or the > taking of any action in reliance on the contents of this information > is strictly prohibited. If you have received this email in error, > please immediately notify the sender via telephone or return mail. > > > _______________________________________________ > 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 gr...@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
