Can you drop 1.3.12.2.1107.5.2.7.20409.30000007030804425018700002322.dcm to me at the file drop below?
doug Myriam Siefert wrote: > Hi everybody, > > We're doing a structural VBM bicentric cross cultural study, using > Freesurfer v5.0.0. on 2 computers : > FREESURFER_HOME: /Applications/freesurfer > Build stamp: freesurfer-Darwin-leopard-i686-stable-pub-v5.0.0 > Kernel info: Darwin 9.8.0 i386 > > FREESURFER_HOME: /home/scnlab/Desktop/ > freesurfer > Build stamp: freesurfer-Linux-centos4-stable-pub-v5.0.0 > Debian version: squeeze/sid > Kernel info: Linux 2.6.32-29-generic i686 > > <mailto:freesurfer@nmr.mgh.harvard.edu> > > Successful reconstructions have been realized for some of the subjects > from one of the 2 centers, using their DICOMS (Siemens Trio), but we > seem to be unable to use any DICOM from the other center (Siemens > Allegra). > It seems that the same problem has already been submitted to the > mailing list, without any available solution : > http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg01354.html > > We get the following error messages (same on both computers): > > [wireless-XXX-XXX-XXX-XXX:/OK-J-01/structural] SPLab% mri_convert > 1.3.12.2.1107.5.2.7.20409.30000007030804425018700002322.dcm 001.mgz > mri_convert > 1.3.12.2.1107.5.2.7.20409.30000007030804425018700002322.dcm 001.mgz > file not found or unknown file type for file > 1.3.12.2.1107.5.2.7.20409.30000007030804425018700002322.dcm > > [wireless-XXX-XXX-XXX-XXX:/OK-J-01/structural] SPLab% mri_convert > --in_type siemens_dicom > 1.3.12.2.1107.5.2.7.20409.30000007030804425018700002322.dcm 001.mgz > mri_convert --in_type siemens_dicom > 1.3.12.2.1107.5.2.7.20409.30000007030804425018700002322.dcm 001.mgz > $Id: mri_convert.c,v 1.166.2.2 2010/08/10 19:11:50 greve Exp $ > reading from > 1.3.12.2.1107.5.2.7.20409.30000007030804425018700002322.dcm... > ERROR (ScanSiemensSeries): > /Users/SPLab/Desktop/OK-J-01/structural/1.3.12.2.1107.5.2.7.20409.30000007030804425018700002322.dcm > > is not a Siemens DICOM file > ERROR: could not find any files (SeriesList==NULL) > > [wireless-XXX-XXX-XXX-XXX:fMRI/OK-J-01/structural] SPLab% mri_convert > --in_type dicom > 1.3.12.2.1107.5.2.7.20409.30000007030804425018700002322.dcm > 001.mgzmri_convert --in_type dicom > 1.3.12.2.1107.5.2.7.20409.30000007030804425018700002322.dcm 001.mgz > $Id: mri_convert.c,v 1.166.2.2 2010/08/10 19:11:50 greve Exp $ > reading from > 1.3.12.2.1107.5.2.7.20409.30000007030804425018700002322.dcm... > Starting DICOMRead2() > dcmfile = > /Users/SPLab/Desktop/OK-J-01/structural/1.3.12.2.1107.5.2.7.20409.30000007030804425018700002322.dcm > dcmdir = /Users/SPLab/Desktop/OK-J-01/structural > ERROR: > /Users/SPLab/Desktop/OK-J-01/structural/1.3.12.2.1107.5.2.7.20409.30000007030804425018700002322.dcm > > is not a dicom file > > > [wireless-XXX-XXX-XXX-XXX:fMRI/OK-J-01/structural] SPLab% mri_convert > --in_type siemens --out_type mgz > 1.3.12.2.1107.5.2.7.20409.30000007030804425018700002322.dcm 001.mgz > mri_convert --in_type siemens --out_type mgz > 1.3.12.2.1107.5.2.7.20409.30000007030804425018700002322.dcm 001.mgz > $Id: mri_convert.c,v 1.166.2.2 2010/08/10 19:11:50 greve Exp $ > reading from > 1.3.12.2.1107.5.2.7.20409.30000007030804425018700002322.dcm... > ERROR: could not parse > /Users/SPLab/Desktop/OK-J-01/structural/1.3.12.2.1107.5.2.7.20409.30000007030804425018700002322.dcm > ERROR: siemensRead(): > /Users/SPLab/Desktop/OK-J-01/structural/1.3.12.2.1107.5.2.7.20409.30000007030804425018700002322.dcm > > - When trying to convert them with the MRI Convert software I get > the following error message : "Unable to find series UID" > - I can however convert them to nifti using SPM8 and MIPAV, and then > successfully run mri_convert and auto-recon1. I also tried to "save as > dicoms" in MIPAV, but it didn't change anything. > > Here are headers as given by MIPAV : > > Dimension 256 > > Dimension 256 > > Dimension 192 > > Type Unsigned Short > > Min 0.0 > > Max 1654.0 > > Orientation Axial > > Pixel resolution 0 0.75 > > Pixel resolution 1 0.75 > > Pixel resolution 2 1.0 > > Unit of measure Millimeters per pixel > > > > Transformation Matrix > > 1.0000 0.0000 0.0000 0.0000 > > 0.0000 1.0000 0.0000 0.0000 > > 0.0000 0.0000 1.0000 0.0000 > > 0.0000 0.0000 0.0000 1.0000 > > > > (0002,0000) File Meta Information Group Length 206 > (0002,0001) File Meta Information Version 1 > (0002,0002) Media Storage SOP Class UID 1.2.840.10008.5.1.4.1.1.4 > (0002,0003) Media Storage SOP Instance UID > 1.3.12.2.1107.5.2.7.20409.30000007030804425018700002322 > (0002,0010) Transfer Syntax UID 1.2.840.10008.1.2 > (0002,0012) Implementation Class UID 1.2.804.114118.3 > (0002,0013) Implementation Version Name eFilm/UCDavisLib > (0002,0016) Source Application Entity Title > (0008,0005) Specific Character Set ISO_IR 100 > (0008,0008) Image Type ORIGINAL, PRIMARY, M, ND > (0008,0016) SOP Class UID 1.2.840.10008.5.1.4.1.1.4 > (0008,0018) SOP Instance UID > 1.3.12.2.1107.5.2.7.20409.30000007030804425018700002322 > (0008,0020) Study Date 20070308 > (0008,0021) Series Date 20070308 > (0008,0022) Acquisition Date 20070308 > (0008,0023) Content (formerly Image) Date 20070308 > (0008,0030) Study Time 142430.328000 > (0008,0031) Series Time 153343.484000 > (0008,0032) Acquisition Time 152244.074999 > (0008,0033) Content (formerly Image) Time 153344.937000 > (0008,0050) Accession Number 06H17 > (0008,0060) Modality MAGNETIC_RESONANCE > (0008,0064) Conversion Type Workstation > (0008,0070) Manufacturer SIEMENS > (0008,1010) Station Name MRC20409 > (0008,1030) Study Description Research001^affiliates > (0008,103E) Series Description MPRAGE_high_resolution > (0008,1090) Manufacturer's Model Name Allegra > (0008,1140) Referenced Image Sequence > (0008,1140) (0008,1150): Referenced SOP Class UID > 1.2.840.10008.5.1.4.1.1.4 > (0008,1140) (0008,1155): Referenced SOP Instance UID > 1.3.12.2.1107.5.2.7.20409.30000007030804425018700001053 > (0008,1140) (0008,1150): Referenced SOP Class UID > 1.2.840.10008.5.1.4.1.1.4 > (0008,1140) (0008,1155): Referenced SOP Instance UID > 1.3.12.2.1107.5.2.7.20409.30000007030804425018700001054 > (0008,1140) (0008,1150): Referenced SOP Class UID > 1.2.840.10008.5.1.4.1.1.4 > (0008,1140) (0008,1155): Referenced SOP Instance UID > 1.3.12.2.1107.5.2.7.20409.30000007030804425018700001055 > (0018,0000) Acquisition Group Length 472 > (0018,0020) Scanning Sequence IR, GR > (0018,0021) Sequence Variant SP, MP > (0018,0022) Scan Options IR > (0018,0023) MR Acquisition Type 3D > (0018,0024) Sequence Name *tfl3d1 > (0018,0025) Angio Flag N > (0018,0050) Slice Thickness 1 > (0018,0080) Repetition Time 2500 > (0018,0081) Echo Time 4.38 > (0018,0082) Inversion Time 1100 > (0018,0083) Number of Averages 1 > (0018,0084) Imaging Frequency 123.075312 > (0018,0085) Imaged Nucleus 1H > (0018,0086) Echo Number(s) 0 > (0018,0087) Magnetic Field Strength 2.8936200141907 > (0018,0089) Number of Phase Encoding Steps 256 > (0018,0091) Echo Train Length 1 > (0018,0093) Percent Sampling 100 > (0018,0094) Percent Phase Field of View 100 > (0018,0095) Pixel Bandwidth 130 > (0018,1000) Device Serial Number 20409 > (0018,1012) Date of Secondary Capture 20110311 > (0018,1014) Time of Secondary Capture 163150 > (0018,1016) Secondary Capture Device Manufacturer National Institutes > of Health, Center for Information Technology > (0018,1018) Secondary Capture Device Manufacturer's Model Name Medical > Image Processing, Analysis and Visualization (MIPAV) > (0018,1019) Secondary Capture Device Software Version(s) 5.2.1 > (0018,1020) Software Version(s) syngo MR 2004A 4VA25A > (0018,1030) Protocol Name MPRAGE_high_resolution > (0018,1200) Date of Last Calibration 20070216 > (0018,1201) Time of Last Calibration 124353.000000 > (0018,1251) Transmit Coil Name Head_3T > (0018,1310) Acquisition Matrix 256, 0, 0, 256 > (0018,1312) In-plane Phase Encoding Direction COL > (0018,1314) Flip Angle 8 > (0018,1315) Variable Flip Angle Flag N > (0018,1316) SAR 0.01545061543584 > (0018,1318) dB/dt 0 > (0018,5100) Patient Position Head First-Supine > (0020,0000) Relationship Group Length 336 > (0020,000D) Study Instance UID > 1.3.12.2.1107.5.2.7.20409.30000007030804422681200000004 > (0020,000E) Series Instance UID > 1.3.12.2.1107.5.2.7.20409.30000007030804425018700002321 > (0020,0010) Study ID 1 > (0020,0011) Series Number 9 > (0020,0012) Acquisition Number 1 > (0020,0013) Instance (formerly Image) Number 95 > (0020,0032) Image Position (Patient) -100.06779670715, > -96.722891569138, 2.4289360046387 > (0020,0037) Image Orientation (Patient) 1, 0, 0, 0, 1, 0 > (0020,0052) Frame of Reference UID > 1.3.12.2.1107.5.2.7.20409.20070308142804656.0.0.0 > (0020,1040) Position Reference Indicator > (0020,1041) Slice Location 2.4289360046387 > (0028,0000) Image Presentation Group Length 166 > (0028,0002) Samples per Pixel 1 > (0028,0004) Photometric Interpretation MONOCHROME2 > (0028,0010) Rows 256 > (0028,0011) Columns 256 > (0028,0030) Pixel Spacing 0.75, 0.75 > (0028,0100) Bits Allocated 16 > (0028,0101) Bits Stored 12 > (0028,0102) High Bit 11 > (0028,0103) Pixel Representation 0 > (0028,0106) Smallest Image Pixel Value 0 > (0028,0107) Largest Image Pixel Value 752 > (0028,1050) Window Center 460 > (0028,1051) Window Width 898 > (0028,1055) Window Center & Width Explanation Algo1 > (0029,0000) Private Tag -118 > (0029,0010) Private Tag SIEMENS CSA HEADER > (0029,0011) Private Tag SIEMENS MEDCOM HEADER > (0029,0012) Private Tag SIEMENS MEDCOM HEADER2 > (0029,1008) Private Tag IMAGE NUM 4 > (0029,1009) Private Tag 20070308 > (0029,1010) Private Tag SV10 8MEchoLinePositionB?a… > (0029,1131) Private Tag 4.0.204078339 > (0029,1132) Private Tag 131072 > (0029,1133) Private Tag 0 > (0029,1134) Private Tag DB TO DICOM > (0029,1260) Private Tag com > (0032,0000) Study Group Length 30 > (0032,1060) Requested Procedure Description Research001 affiliates > (0040,0000) Private Tag \ > (0040,0244) Performed Procedure Step Start Date 20070308 > (0040,0245) Performed Procedure Step Start Time 142430.328000 > (0040,0253) Performed Procedure Step ID MR20070308142430 > (0040,0254) Performed Procedure Step Description Research001^affiliates > (7FE0,0000) Pixel Data Group Length 131080 > > > > So here are my questions : > 1) Is there something wrong with the command lines I wrote? > 2) Is there maybe something wrong in the files headers that I should > edit so that Freesurfer would recognize them as dicoms? or any other > solution in order to use those dicoms? > 3) If we were to use the nifti files : > - what would be the disadvantages? > - is there a risk of orientation problems with single nifti files? > with dual nifti files? should we check for L-R inversion for each > subject after mri-convert? > - are there any concerns with comparing these subjects to our other > groups subjects (for whom we used the dicoms)? > > Thank you very much in advance, > > Myriam Siefert > > > > > > > > > ------------------------------------------------------------------------ > > _______________________________________________ > 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: www.nmr.mgh.harvard.edu/facility/filedrop/index.html _______________________________________________ Freesurfer mailing list 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.
