Re: [Freesurfer] Re: zero determinant error in using mri_convert rawavg.mgz orig.mgz --conform

Hi John,

the method to compute the ICV (also called eTIV estimated total intracranial volume) is quite simple. It is taken from this paper A unified approach for morphometric and functional data analysis in young, old, and demented adults using automated atlas-based head size normalization: reliability and validation against manual measurement of total intracranial volume Buckner et al. (2004) NeuroImage 23:724-738.

What basically happens is this: the volume (with head) is aligned to a Tal space image consisting of several subjects with know TIV. Then the scaling factor of this transform (determinant) is used (together with a fixed scaling factor) to estimate the TIV of the current subject. Of course this is only approximate. We recently switched to the talairach.xfm which is more accurate than the map that was used before (therefore we had to adjust the fixed scaling factor).

You can also find some details on http://surfer.nmr.mgh.harvard.edu/fswiki/eTIV

Best, Martin

On Fri, 2009-05-15 at 07:35 -0400, John Drozd wrote:

Hello again,

I incorrectly used the term intercranial volume in my email below. I meant to type intracranial volume.

john

On Fri, May 15, 2009 at 7:29 AM, John Drozd john.drozd@gmail.com wrote: 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
    <fischl@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:

                                   [jdrozd@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:

                                   [jdrozd@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:

                                   [jdrozd@trumpet orig]$ cp
                            T1.mgz ../rawavg.mgz
                                   [jdrozd@trumpet orig]$ cd ..
                                   [jdrozd@trumpet mri]$ ls
                                   1.Bvq.Xml*  2.Bvq.Xml*
                             error.log  orig/  orig2/  rawavg.mgz
                                    transforms/
                                   [jdrozd@trumpet mri]$ pwd

                             /trumpet/downloads/FreeSurfer/freesurfer/subjects/buckner_data/tutorial_subjs/convertedfile/mri

                                   Then I tried to conform the
                            data using:

                                   [jdrozd@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

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