Hello Bruce and Nick, Thank you, Bruce, for the clarification that FreeSurfer when reading my dicom files, it thinks the slice thickness is 0, and thank you Nick for your help as well. Just for your information, 3D Slicer was able to read in
the dicom files successfully. I find this perplexing. Anyways, I tried an alternate route with FreeSurfer which seemed to work reasonably well. The dicom files that I was using were derived from a nifti .nii file. So I used the original .nii file and everything worked with FreeSurfer, except when I tried to perform non-uniform intensity normalization (the program gave a segmentation crash) when I typed: mri_nu_correct.mni --i orig.mgz --o nu.mgz --n 2 So I did the talairach transformation without performing the non-uniform intensity normalization, and then I was able to calculate the total intercranial volume when I typed: talairach_avi --i orig.mgz --xfm transforms/talairach.auto.xfm cp transforms/talairach.auto.xfm transforms/talairach.xfm mri_segstats --subject subjid --etiv-only Now that I am able to calculate the total intercranial volume with FreeSurfer, I am interested in the details of the procedure that FreeSurfer uses to calculate the intercranial volume. Afterall, the pudding is in the details. I am interested in what components of the head FreeSurfer includes/excludes in its calculation of total intercranial volume. I am also interested in the details of the mathematical and computer algorithm used to calculate the total intercranial volume (as well as for calculating ventricle volume). I am performing image analysis for research on Alzheimer's Disease and I need to understand these calculations in detail. Can you recommend any good references that would provide me information on how FreeSurfer calculates the total intracranial volume and ventricle volume? Also, please let me know if the source code is available for my viewing if at all possible, which would be really handy. Thank you, John Drozd PostDoctoral Fellow Robarts Research Institute, Imaging Department, The University of Western Ontario London, Ontario, Canada On Wed, May 13, 2009 at 5:28 PM, Bruce Fischl <fis...@nmr.mgh.harvard.edu>wrote: > looks like it thinks the slice thickness is 0, which is probably bad.... > > On Wed, 13 May 2009, Nick Schmansky wrote: > > John, >> >> What does the file look like when its opened in tkmedit? ie >> >> tkmedit -f T1.mgz >> >> does it look like our sample subject data bert? ie, a full brain t1 >> anatomical scan? >> >> Nick >> >> On Wed, 2009-05-13 at 16:41 -0400, John Drozd wrote: >> >>> >>> Hello, >>> >>> Here is the ouput from bugr: >>> >>> FREESURFER_HOME: /trumpet/downloads/FreeSurfer/freesurfer >>> >>> Build stamp: freesurfer-Linux-centos4_x86_64-stable-pub-v4.3.0 >>> >>> RedHat release: Fedora release 10 (Cambridge) >>> >>> Kernel info: Linux 2.6.27.21-170.2.56.fc10.x86_64 x86_64 >>> >>> I have sets of dicom files such as: >>> >>> [jdr...@trumpet orig]$ ls >>> 70731171155016_S32496_I63397_0.dcm* >>> 70731171155016_S32496_I63397_25.dcm* >>> 70731171155016_S32496_I63397_100.dcm* >>> 70731171155016_S32496_I63397_26.dcm* >>> 70731171155016_S32496_I63397_101.dcm* >>> 70731171155016_S32496_I63397_27.dcm* >>> 70731171155016_S32496_I63397_102.dcm* >>> 70731171155016_S32496_I63397_28.dcm* >>> 70731171155016_S32496_I63397_103.dcm* >>> 70731171155016_S32496_I63397_29.dcm* >>> 70731171155016_S32496_I63397_104.dcm* >>> 70731171155016_S32496_I63397_2.dcm* >>> 70731171155016_S32496_I63397_105.dcm* >>> 70731171155016_S32496_I63397_30.dcm* >>> 70731171155016_S32496_I63397_106.dcm* >>> 70731171155016_S32496_I63397_31.dcm* >>> 70731171155016_S32496_I63397_107.dcm* >>> 70731171155016_S32496_I63397_32.dcm* >>> 70731171155016_S32496_I63397_108.dcm* >>> 70731171155016_S32496_I63397_33.dcm* >>> 70731171155016_S32496_I63397_109.dcm* >>> 70731171155016_S32496_I63397_34.dcm* >>> 70731171155016_S32496_I63397_10.dcm* >>> 70731171155016_S32496_I63397_35.dcm* >>> 70731171155016_S32496_I63397_110.dcm* >>> 70731171155016_S32496_I63397_36.dcm* >>> 70731171155016_S32496_I63397_111.dcm* >>> 70731171155016_S32496_I63397_37.dcm* >>> 70731171155016_S32496_I63397_112.dcm* >>> 70731171155016_S32496_I63397_38.dcm* >>> 70731171155016_S32496_I63397_113.dcm* >>> 70731171155016_S32496_I63397_39.dcm* >>> 70731171155016_S32496_I63397_114.dcm* >>> 70731171155016_S32496_I63397_3.dcm* >>> 70731171155016_S32496_I63397_115.dcm* >>> 70731171155016_S32496_I63397_40.dcm* >>> 70731171155016_S32496_I63397_116.dcm* >>> 70731171155016_S32496_I63397_41.dcm* >>> 70731171155016_S32496_I63397_117.dcm* >>> 70731171155016_S32496_I63397_42.dcm* >>> 70731171155016_S32496_I63397_118.dcm* >>> 70731171155016_S32496_I63397_43.dcm* >>> 70731171155016_S32496_I63397_119.dcm* >>> 70731171155016_S32496_I63397_44.dcm* >>> 70731171155016_S32496_I63397_11.dcm* >>> 70731171155016_S32496_I63397_45.dcm* >>> 70731171155016_S32496_I63397_120.dcm* >>> 70731171155016_S32496_I63397_46.dcm* >>> 70731171155016_S32496_I63397_121.dcm* >>> 70731171155016_S32496_I63397_47.dcm* >>> 70731171155016_S32496_I63397_122.dcm* >>> 70731171155016_S32496_I63397_48.dcm* >>> 70731171155016_S32496_I63397_123.dcm* >>> 70731171155016_S32496_I63397_49.dcm* >>> 70731171155016_S32496_I63397_124.dcm* >>> 70731171155016_S32496_I63397_4.dcm* >>> 70731171155016_S32496_I63397_125.dcm* >>> 70731171155016_S32496_I63397_50.dcm* >>> 70731171155016_S32496_I63397_126.dcm* >>> 70731171155016_S32496_I63397_51.dcm* >>> 70731171155016_S32496_I63397_127.dcm* >>> 70731171155016_S32496_I63397_52.dcm* >>> 70731171155016_S32496_I63397_128.dcm* >>> 70731171155016_S32496_I63397_53.dcm* >>> 70731171155016_S32496_I63397_129.dcm* >>> 70731171155016_S32496_I63397_54.dcm* >>> 70731171155016_S32496_I63397_12.dcm* >>> 70731171155016_S32496_I63397_55.dcm* >>> 70731171155016_S32496_I63397_130.dcm* >>> 70731171155016_S32496_I63397_56.dcm* >>> 70731171155016_S32496_I63397_131.dcm* >>> 70731171155016_S32496_I63397_57.dcm* >>> 70731171155016_S32496_I63397_132.dcm* >>> 70731171155016_S32496_I63397_58.dcm* >>> 70731171155016_S32496_I63397_133.dcm* >>> 70731171155016_S32496_I63397_59.dcm* >>> 70731171155016_S32496_I63397_134.dcm* >>> 70731171155016_S32496_I63397_5.dcm* >>> 70731171155016_S32496_I63397_135.dcm* >>> 70731171155016_S32496_I63397_60.dcm* >>> 70731171155016_S32496_I63397_136.dcm* >>> 70731171155016_S32496_I63397_61.dcm* >>> 70731171155016_S32496_I63397_137.dcm* >>> 70731171155016_S32496_I63397_62.dcm* >>> 70731171155016_S32496_I63397_138.dcm* >>> 70731171155016_S32496_I63397_63.dcm* >>> 70731171155016_S32496_I63397_139.dcm* >>> 70731171155016_S32496_I63397_64.dcm* >>> 70731171155016_S32496_I63397_13.dcm* >>> 70731171155016_S32496_I63397_65.dcm* >>> 70731171155016_S32496_I63397_140.dcm* >>> 70731171155016_S32496_I63397_66.dcm* >>> 70731171155016_S32496_I63397_141.dcm* >>> 70731171155016_S32496_I63397_67.dcm* >>> 70731171155016_S32496_I63397_142.dcm* >>> 70731171155016_S32496_I63397_68.dcm* >>> 70731171155016_S32496_I63397_143.dcm* >>> 70731171155016_S32496_I63397_69.dcm* >>> 70731171155016_S32496_I63397_144.dcm* >>> 70731171155016_S32496_I63397_6.dcm* >>> 70731171155016_S32496_I63397_145.dcm* >>> 70731171155016_S32496_I63397_70.dcm* >>> 70731171155016_S32496_I63397_146.dcm* >>> 70731171155016_S32496_I63397_71.dcm* >>> 70731171155016_S32496_I63397_147.dcm* >>> 70731171155016_S32496_I63397_72.dcm* >>> 70731171155016_S32496_I63397_148.dcm* >>> 70731171155016_S32496_I63397_73.dcm* >>> 70731171155016_S32496_I63397_149.dcm* >>> 70731171155016_S32496_I63397_74.dcm* >>> 70731171155016_S32496_I63397_14.dcm* >>> 70731171155016_S32496_I63397_75.dcm* >>> 70731171155016_S32496_I63397_150.dcm* >>> 70731171155016_S32496_I63397_76.dcm* >>> 70731171155016_S32496_I63397_151.dcm* >>> 70731171155016_S32496_I63397_77.dcm* >>> 70731171155016_S32496_I63397_152.dcm* >>> 70731171155016_S32496_I63397_78.dcm* >>> 70731171155016_S32496_I63397_153.dcm* >>> 70731171155016_S32496_I63397_79.dcm* >>> 70731171155016_S32496_I63397_154.dcm* >>> 70731171155016_S32496_I63397_7.dcm* >>> 70731171155016_S32496_I63397_155.dcm* >>> 70731171155016_S32496_I63397_80.dcm* >>> 70731171155016_S32496_I63397_156.dcm* >>> 70731171155016_S32496_I63397_81.dcm* >>> 70731171155016_S32496_I63397_157.dcm* >>> 70731171155016_S32496_I63397_82.dcm* >>> 70731171155016_S32496_I63397_158.dcm* >>> 70731171155016_S32496_I63397_83.dcm* >>> 70731171155016_S32496_I63397_159.dcm* >>> 70731171155016_S32496_I63397_84.dcm* >>> 70731171155016_S32496_I63397_15.dcm* >>> 70731171155016_S32496_I63397_85.dcm* >>> 70731171155016_S32496_I63397_160.dcm* >>> 70731171155016_S32496_I63397_86.dcm* >>> 70731171155016_S32496_I63397_161.dcm* >>> 70731171155016_S32496_I63397_87.dcm* >>> 70731171155016_S32496_I63397_162.dcm* >>> 70731171155016_S32496_I63397_88.dcm* >>> 70731171155016_S32496_I63397_163.dcm* >>> 70731171155016_S32496_I63397_89.dcm* >>> 70731171155016_S32496_I63397_164.dcm* >>> 70731171155016_S32496_I63397_8.dcm* >>> 70731171155016_S32496_I63397_165.dcm* >>> 70731171155016_S32496_I63397_90.dcm* >>> 70731171155016_S32496_I63397_16.dcm* >>> 70731171155016_S32496_I63397_91.dcm* >>> 70731171155016_S32496_I63397_17.dcm* >>> 70731171155016_S32496_I63397_92.dcm* >>> 70731171155016_S32496_I63397_18.dcm* >>> 70731171155016_S32496_I63397_93.dcm* >>> 70731171155016_S32496_I63397_19.dcm* >>> 70731171155016_S32496_I63397_94.dcm* >>> 70731171155016_S32496_I63397_1.dcm* >>> 70731171155016_S32496_I63397_95.dcm* >>> 70731171155016_S32496_I63397_20.dcm* >>> 70731171155016_S32496_I63397_96.dcm* >>> 70731171155016_S32496_I63397_21.dcm* >>> 70731171155016_S32496_I63397_97.dcm* >>> 70731171155016_S32496_I63397_22.dcm* >>> 70731171155016_S32496_I63397_98.dcm* >>> 70731171155016_S32496_I63397_23.dcm* >>> 70731171155016_S32496_I63397_99.dcm* >>> 70731171155016_S32496_I63397_24.dcm* >>> 70731171155016_S32496_I63397_9.dcm* >>> >>> I first converted these files to an mgz file using: >>> >>> [jdr...@trumpet orig]$ mri_convert -it dicom >>> 70731171155016_S32496_I63397_0.dcm T1.mgz >>> mri_convert -it dicom 70731171155016_S32496_I63397_0.dcm >>> T1.mgz >>> $Id: mri_convert.c,v 1.146.2.4 2009/01/30 02:30:42 nicks Exp $ >>> reading from 70731171155016_S32496_I63397_0.dcm... >>> Starting DICOMRead2() >>> dcmfile >>> = >>> /trumpet/downloads/FreeSurfer/freesurfer/subjects/buckner_data/tutorial_subjs/convertedfile/mri/orig/70731171155016_S32496_I63397_0.dcm >>> dcmdir >>> = >>> /trumpet/downloads/FreeSurfer/freesurfer/subjects/buckner_data/tutorial_subjs/convertedfile/mri/orig >>> WARNING: tag ImageNumber not found >>> Ref Series No = 63443 >>> Found 168 files, checking for dicoms >>> WARNING: tag ImageNumber not found >>> Found 166 dicom files in series. >>> WARNING: tag ImageNumber not found >>> First Sorting >>> WARNING: files are not found to be different and cannot be >>> sorted >>> File1: >>> /trumpet/downloads/FreeSurfer/freesurfer/subjects/buckner_data/tutorial_subjs/convertedfile/mri/orig/70731171155016_S32496_I63397_0.dcm >>> File2: >>> /trumpet/downloads/FreeSurfer/freesurfer/subjects/buckner_data/tutorial_subjs/convertedfile/mri/orig/70731171155016_S32496_I63397_1.dcm >>> Computing Slice Direction >>> Vs: 1.2024 0 0 >>> Vs: 1 0 0 >>> Second Sorting >>> Counting frames >>> nframes = 1 >>> nslices = 166 >>> ndcmfiles = 166 >>> PE Dir = UNKNOWN (dicom read) >>> TransferSyntaxUID: --1.2.840.10008.1.2-- >>> jpegUID: --1.2.840.10008.1.2.4-- >>> Loading pixel data >>> TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 >>> i_ras = (-0, -0, -1) >>> j_ras = (-0, -1, 0) >>> k_ras = (-1, -0, 0) >>> writing to T1.mgz... >>> >>> Then I copied the outputted T1.mgz file using: >>> >>> [jdr...@trumpet orig]$ cp T1.mgz ../rawavg.mgz >>> [jdr...@trumpet orig]$ cd .. >>> [jdr...@trumpet mri]$ ls >>> 1.Bvq.Xml* 2.Bvq.Xml* error.log orig/ orig2/ rawavg.mgz >>> transforms/ >>> [jdr...@trumpet mri]$ pwd >>> >>> >>> /trumpet/downloads/FreeSurfer/freesurfer/subjects/buckner_data/tutorial_subjs/convertedfile/mri >>> >>> Then I tried to conform the data using: >>> >>> [jdr...@trumpet mri]$ mri_convert rawavg.mgz orig.mgz -- >>> conform >>> mri_convert rawavg.mgz orig.mgz --conform >>> $Id: mri_convert.c,v 1.146.2.4 2009/01/30 02:30:42 nicks Exp $ >>> reading from rawavg.mgz... >>> TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 >>> i_ras = (-0, -0, -1) >>> j_ras = (-0, -1, 0) >>> k_ras = (-1, -0, 0) >>> Original Data has (0.93905, 0.93905, 0) mm size and (256, 256, >>> 166) voxels. >>> Data is conformed to 1 mm size and 256 voxels for all >>> directions >>> changing data type from 4 to 0 (noscale = 0)... >>> MRIchangeType: Building histogram >>> Reslicing using trilinear interpolation >>> MRIresample(): source matrix has zero determinant; matrix is: >>> -0.000 -0.000 -0.000 0.000; >>> -0.000 -0.939 -0.000 0.000; >>> -0.939 0.000 0.000 0.000; >>> 0.000 0.000 0.000 1.000; >>> >>> Do you know why I get this error? >>> MRIresample(): source matrix has zero determinant; matrix is: >>> -0.000 -0.000 -0.000 0.000; >>> -0.000 -0.939 -0.000 0.000; >>> -0.939 0.000 0.000 0.000; >>> 0.000 0.000 0.000 1.000; >>> >>> Any help would be appreciated. >>> >>> John Drozd >>> PostDoctorate Fellow >>> >>> _______________________________________________ >>> 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 >> >> >> >>
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