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syam.gadde
BIAC Staff

USA
421 Posts
Posted - Nov 20 2006 :  12:43:07 PM  Show Profile  Reply with Quote
Dharol,

Can you email me separately the location of this anatomical and I will see I can look at it.
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syam.gadde
BIAC Staff

USA
421 Posts
Posted - Nov 20 2006 :  1:48:13 PM  Show Profile  Reply with Quote
I think (hope) this problem will be resolved by using the standard version of MkFlirtInitMtx.pl (rather than the one that was [but is no longer] in my home directory). I posted to a new thread about this.
Edited by - syam.gadde on Nov 20 2006 1:49:11 PM
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tankersley
BIAC Alum

USA
143 Posts
Posted - Nov 28 2006 :  2:36:27 PM  Show Profile  Reply with Quote
I am continuing to have a problem registering the anatomicals for Exam 43044. The func registers fine to the normal brain, but the anat is inferior-superior flipped when registered to functionals as well as the normalized brain.
As far as I can tell, the headr file looks fine:

<?xml version="1.0"?>
<!-- This is a BXH (BIAC XML Header) file. -->
<bxh xmlns:bxh="http://www.biac.duke.edu/bxh" xmlns="http://www.biac.duke.edu/bxh" version="1.0">
<datarec type="image">
<!--AUTOGEN: Orientation is axial -->
<dimension type="x">
<units>mm</units>
<size>256</size>
<origin>119.53125</origin>
<gap>0</gap>
<spacing>0.9375</spacing>
<direction>-1 -0 0</direction>
</dimension>
<dimension type="y">
<units>mm</units>
<size>256</size>
<origin>119.53125</origin>
<gap>0</gap>
<spacing>0.9375</spacing>
<direction>-0 -1 -3.1e-05</direction>
</dimension>
<dimension type="z">
<units>mm</units>
<size>68</size>
<origin>-73.59635053125</origin>
<gap>0</gap>
<spacing>1.89999998507463</spacing>
<direction>0 0 1</direction>
</dimension>
<byteorder>lsbfirst</byteorder>
<elementtype>int16</elementtype>
<filename>mr5c_20040420_43044_002_00_00001.dcm</filename>
<fileoffset>9630</fileoffset>
<filerecordsize>131072</filerecordsize>
<filename>mr5c_20040420_43044_002_00_00002.dcm</filename>
<fileoffset>9630</fileoffset>
<filerecordsize>131072</filerecordsize>
<filename>mr5c_20040420_43044_002_00_00003.dcm</filename>
<fileoffset>9630</fileoffset>
<filerecordsize>131072</filerecordsize>
<filename>mr5c_20040420_43044_002_00_00004.dcm</filename>
<fileoffset>9630</fileoffset>
<filerecordsize>131072</filerecordsize>
<filename>mr5c_20040420_43044_002_00_00005.dcm</filename>
<fileoffset>9630</fileoffset>
<filerecordsize>131072</filerecordsize>
<filename>mr5c_20040420_43044_002_00_00006.dcm</filename>
<fileoffset>9630</fileoffset>
<filerecordsize>131072</filerecordsize>
<filename>mr5c_20040420_43044_002_00_00007.dcm</filename>
<fileoffset>9630</fileoffset>
<filerecordsize>131072</filerecordsize>
<filename>mr5c_20040420_43044_002_00_00008.dcm</filename>
<fileoffset>9630</fileoffset>
<filerecordsize>131072</filerecordsize>
<filename>mr5c_20040420_43044_002_00_00009.dcm</filename>
<fileoffset>9630</fileoffset>
<filerecordsize>131072</filerecordsize>
<filename>mr5c_20040420_43044_002_00_00010.dcm</filename>
<fileoffset>9630</fileoffset>
<filerecordsize>131072</filerecordsize>
<filename>mr5c_20040420_43044_002_00_00011.dcm</filename>
<fileoffset>9630</fileoffset>
<filerecordsize>131072</filerecordsize>
<filename>mr5c_20040420_43044_002_00_00012.dcm</filename>
<fileoffset>9630</fileoffset>
<filerecordsize>131072</filerecordsize>
<filename>mr5c_20040420_43044_002_00_00013.dcm</filename>
<fileoffset>9630</fileoffset>
<filerecordsize>131072</filerecordsize>
<filename>mr5c_20040420_43044_002_00_00014.dcm</filename>
<fileoffset>9630</fileoffset>
<filerecordsize>131072</filerecordsize>
<filename>mr5c_20040420_43044_002_00_00015.dcm</filename>
<fileoffset>9630</fileoffset>
<filerecordsize>131072</filerecordsize>
<filename>mr5c_20040420_43044_002_00_00016.dcm</filename>
<fileoffset>9630</fileoffset>
<filerecordsize>131072</filerecordsize>
<filename>mr5c_20040420_43044_002_00_00017.dcm</filename>
<fileoffset>9630</fileoffset>
<filerecordsize>131072</filerecordsize>
<filename>mr5c_20040420_43044_002_00_00018.dcm</filename>
<fileoffset>9630</fileoffset>
<filerecordsize>131072</filerecordsize>
<filename>mr5c_20040420_43044_002_00_00019.dcm</filename>
<fileoffset>9630</fileoffset>
<filerecordsize>131072</filerecordsize>
<filename>mr5c_20040420_43044_002_00_00020.dcm</filename>
<fileoffset>9630</fileoffset>
<filerecordsize>131072</filerecordsize>
<filename>mr5c_20040420_43044_002_00_00021.dcm</filename>
<fileoffset>9630</fileoffset>
<filerecordsize>131072</filerecordsize>
<filename>mr5c_20040420_43044_002_00_00022.dcm</filename>
<fileoffset>9630</fileoffset>
<filerecordsize>131072</filerecordsize>
<filename>mr5c_20040420_43044_002_00_00023.dcm</filename>
<fileoffset>9630</fileoffset>
<filerecordsize>131072</filerecordsize>
<filename>mr5c_20040420_43044_002_00_00024.dcm</filename>
<fileoffset>9630</fileoffset>
<filerecordsize>131072</filerecordsize>
<filename>mr5c_20040420_43044_002_00_00025.dcm</filename>
<fileoffset>9630</fileoffset>
<filerecordsize>131072</filerecordsize>
<filename>mr5c_20040420_43044_002_00_00026.dcm</filename>
<fileoffset>9630</fileoffset>
<filerecordsize>131072</filerecordsize>
<filename>mr5c_20040420_43044_002_00_00027.dcm</filename>
<fileoffset>9630</fileoffset>
<filerecordsize>131072</filerecordsize>
<filename>mr5c_20040420_43044_002_00_00028.dcm</filename>
<fileoffset>9630</fileoffset>
<filerecordsize>131072</filerecordsize>
<filename>mr5c_20040420_43044_002_00_00029.dcm</filename>
<fileoffset>9630</fileoffset>
<filerecordsize>131072</filerecordsize>
<filename>mr5c_20040420_43044_002_00_00030.dcm</filename>
<fileoffset>9630</fileoffset>
<filerecordsize>131072</filerecordsize>
<filename>mr5c_20040420_43044_002_00_00031.dcm</filename>
<fileoffset>9630</fileoffset>
<filerecordsize>131072</filerecordsize>
<filename>mr5c_20040420_43044_002_00_00032.dcm</filename>
<fileoffset>9630</fileoffset>
<filerecordsize>131072</filerecordsize>
<filename>mr5c_20040420_43044_002_00_00033.dcm</filename>
<fileoffset>9630</fileoffset>
<filerecordsize>131072</filerecordsize>
<filename>mr5c_20040420_43044_002_00_00034.dcm</filename>
<fileoffset>9630</fileoffset>
<filerecordsize>131072</filerecordsize>
<filename>mr5c_20040420_43044_002_00_00035.dcm</filename>
<fileoffset>9630</fileoffset>
<filerecordsize>131072</filerecordsize>
<filename>mr5c_20040420_43044_002_00_00036.dcm</filename>
<fileoffset>9630</fileoffset>
<filerecordsize>131072</filerecordsize>
<filename>mr5c_20040420_43044_002_00_00037.dcm</filename>
<fileoffset>9630</fileoffset>
<filerecordsize>131072</filerecordsize>
<filename>mr5c_20040420_43044_002_00_00038.dcm</filename>
<fileoffset>9630</fileoffset>
<filerecordsize>131072</filerecordsize>
<filename>mr5c_20040420_43044_002_00_00039.dcm</filename>
<fileoffset>9630</fileoffset>
<filerecordsize>131072</filerecordsize>
<filename>mr5c_20040420_43044_002_00_00040.dcm</filename>
<fileoffset>9626</fileoffset>
<filerecordsize>131072</filerecordsize>
<filename>mr5c_20040420_43044_002_00_00041.dcm</filename>
<fileoffset>9626</fileoffset>
<filerecordsize>131072</filerecordsize>
<filename>mr5c_20040420_43044_002_00_00042.dcm</filename>
<fileoffset>9626</fileoffset>
<filerecordsize>131072</filerecordsize>
<filename>mr5c_20040420_43044_002_00_00043.dcm</filename>
<fileoffset>9626</fileoffset>
<filerecordsize>131072</filerecordsize>
<filename>mr5c_20040420_43044_002_00_00044.dcm</filename>
<fileoffset>9626</fileoffset>
<filerecordsize>131072</filerecordsize>
<filename>mr5c_20040420_43044_002_00_00045.dcm</filename>
<fileoffset>9630</fileoffset>
<filerecordsize>131072</filerecordsize>
<filename>mr5c_20040420_43044_002_00_00046.dcm</filename>
<fileoffset>9630</fileoffset>
<filerecordsize>131072</filerecordsize>
<filename>mr5c_20040420_43044_002_00_00047.dcm</filename>
<fileoffset>9630</fileoffset>
<filerecordsize>131072</filerecordsize>
<filename>mr5c_20040420_43044_002_00_00048.dcm</filename>
<fileoffset>9630</fileoffset>
<filerecordsize>131072</filerecordsize>
<filename>mr5c_20040420_43044_002_00_00049.dcm</filename>
<fileoffset>9630</fileoffset>
<filerecordsize>131072</filerecordsize>
<filename>mr5c_20040420_43044_002_00_00050.dcm</filename>
<fileoffset>9630</fileoffset>
<filerecordsize>131072</filerecordsize>
<filename>mr5c_20040420_43044_002_00_00051.dcm</filename>
<fileoffset>9630</fileoffset>
<filerecordsize>131072</filerecordsize>
<filename>mr5c_20040420_43044_002_00_00052.dcm</filename>
<fileoffset>9630</fileoffset>
<filerecordsize>131072</filerecordsize>
<filename>mr5c_20040420_43044_002_00_00053.dcm</filename>
<fileoffset>9630</fileoffset>
<filerecordsize>131072</filerecordsize>
<filename>mr5c_20040420_43044_002_00_00054.dcm</filename>
<fileoffset>9630</fileoffset>
<filerecordsize>131072</filerecordsize>
<filename>mr5c_20040420_43044_002_00_00055.dcm</filename>
<fileoffset>9630</fileoffset>
<filerecordsize>131072</filerecordsize>
<filename>mr5c_20040420_43044_002_00_00056.dcm</filename>
<fileoffset>9630</fileoffset>
<filerecordsize>131072</filerecordsize>
<filename>mr5c_20040420_43044_002_00_00057.dcm</filename>
<fileoffset>9630</fileoffset>
<filerecordsize>131072</filerecordsize>
<filename>mr5c_20040420_43044_002_00_00058.dcm</filename>
<fileoffset>9630</fileoffset>
<filerecordsize>131072</filerecordsize>
<filename>mr5c_20040420_43044_002_00_00059.dcm</filename>
<fileoffset>9630</fileoffset>
<filerecordsize>131072</filerecordsize>
<filename>mr5c_20040420_43044_002_00_00060.dcm</filename>
<fileoffset>9630</fileoffset>
<filerecordsize>131072</filerecordsize>
<filename>mr5c_20040420_43044_002_00_00061.dcm</filename>
<fileoffset>9630</fileoffset>
<filerecordsize>131072</filerecordsize>
<filename>mr5c_20040420_43044_002_00_00062.dcm</filename>
<fileoffset>9630</fileoffset>
<filerecordsize>131072</filerecordsize>
<filename>mr5c_20040420_43044_002_00_00063.dcm</filename>
<fileoffset>9630</fileoffset>
<filerecordsize>131072</filerecordsize>
<filename>mr5c_20040420_43044_002_00_00064.dcm</filename>
<fileoffset>9630</fileoffset>
<filerecordsize>131072</filerecordsize>
<filename>mr5c_20040420_43044_002_00_00065.dcm</filename>
<fileoffset>9630</fileoffset>
<filerecordsize>131072</filerecordsize>
<filename>mr5c_20040420_43044_002_00_00066.dcm</filename>
<fileoffset>9630</fileoffset>
<filerecordsize>131072</filerecordsize>
<filename>mr5c_20040420_43044_002_00_00067.dcm</filename>
<fileoffset>9630</fileoffset>
<filerecordsize>131072</filerecordsize>
<filename>mr5c_20040420_43044_002_00_00068.dcm</filename>
<fileoffset>9630</fileoffset>
<filerecordsize>131072</filerecordsize>
</datarec>
<acquisitiondata>
<examnumber>43044</examnumber>
<studyid>ExecInfo04</studyid>
<seriesnumber>2</seriesnumber>
<runnumber>0</runnumber>
<institution>Duke University BIAC 4T</institution>
<scanningsequence>GR</scanningsequence>
<sequencevariant>SS/SP/SK</sequencevariant>
<magneticfield>4</magneticfield>
<description>Head,Obl,3D,SPGR,Fast</description>
<examdescription>ExecInfo04</examdescription>
<scandate>2004-04-20</scandate>
<scantime>16:21:55</scantime>
<scanner>mr5cmr5c</scanner>
<fieldofview>240 240</fieldofview>
<tr>12.300000</tr>
<ti>300.000000</ti>
<te>5.400000</te>
<operator>jt</operator>
<flipangle>20</flipangle>
<prescribedslicespacing>1.9</prescribedslicespacing>
<frequencydirection>1</frequencydirection>
<acquisitionmatrix>256 256</acquisitionmatrix>
<bandwidth>31.26</bandwidth>
<receivecoilname>HEAD</receivecoilname>
<transmitcoilname>HEAD</transmitcoilname>
<psdname>efgre3d</psdname>
<psdinternalname>EFGRE3D</psdinternalname>
<psddate>2002-05-16</psddate>
<psdtime>00:15:11</psdtime>
</acquisitiondata>
<subject>
<name>3820</name>
<age>0</age>
<sex>M</sex>
<weight>72.575000</weight>
</subject>
<history>
<entry>
<date>2004-04-20 17:01:56</date>
<description>
Generated on fourier.biac.duke.edu by '/usr/local/bin/dicom2bxh' from 68 input files (first is 'mr5c_20040420_43044_002_00_00001.dcm').
-VERSIONSTR-isf2b:1.8,x2b:1.14,bSI:1.36,p2b:1.48,d2b:1.32,bDI:1.47,m2b:1.7,bab:1.21,a2b:1.17,sf2b:1.14</description>
</entry>
</history>
</bxh>

In MATLAB I used flipdim and saved the brain, but had to save the structure as .img files instead of .dcm files. I can convert the new header file to nifti format, but when I try to run BET on the nifti, FSL tells me that it is not equipped for this kind of file.

Any other suggestions?

Thanks,

Dharol
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syam.gadde
BIAC Staff

USA
421 Posts
Posted - Nov 29 2006 :  12:01:21 PM  Show Profile  Reply with Quote
Dharol,

It looks like in your case the anatomical and functional brains do not match in the slice direction (I->S vs. S->I) and the orientation labels do correctly describe the data as they are. However, FSL doesn't do too well with this scenario without some help. Did the flipdim you introduced have something to do with this, or is that an independent issue?

In any case, you can start FSL in the right direction for this situation by specifying a functional-to-highres initial matrix. I will mail you separately on this.
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