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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