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 <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
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