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

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.eduwrote:

...

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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