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<div>Helen,</div>
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<div>This is a common problem with ANALYZE file format. Your data is not compliant with any standard (neither DICOM nor the Analyze 7.5 file format as defined by the developers of the Analyze^{TM} Program).</div>
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<div>Even the Analyze^{TM} main developers have moved away from using Analye 7.5 format over a decade ago because of its serious limitations, and because the community has been very bad about defining many different interpretations of those 348 bytes header
file to have vastly different meanings.</div>
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<div>I've come to the conclusion that what people call "Analyze" image data very seldom conforms to the original intent or definition of what that file is supposed to contain.</div>
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<div>In fact, the entire NIFTI file format initiative was centered around the massive difficulties that arise from different groups attempting to use data in a file formats (yes formats with an 's') that they called Analyze, but were completely in compatible.</div>
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<div>I work very closely with the Analyze^{TM} development team to ensure that ITK, and by extension brains2, respected the definition of Analyze7.5 file format as it was originally defined and intended to be used. If you data does not load properly, that
means that it is very likely not compliant with the Analyze7.5 standard.</div>
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<div>Hans</div>
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<div>-- </div>
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<div style="font-family:Calibri; font-size:15px"><font face="Arial" size="2"><span style="font-size:10pt">Hans J. Johnson, Ph.D.</span></font></div>
<div style="font-family:Calibri; font-size:15px"><font face="Arial" size="2"><span style="font-size:10pt"><a href="mailto:hans-johnson@uiowa.edu">hans-johnson@uiowa.edu</a></span></font></div>
<div style="font-family:Calibri; font-size:15px"><font face="Arial" size="2"><span style="font-size:10pt">Assistant Professor of Psychiatry</span></font></div>
<div style="font-family:Calibri; font-size:15px"><span class="Apple-style-span" style="font-size:13px; font-family:Arial">University of Iowa Carver College of Medicine</span></div>
<div style="font-family:Calibri; font-size:15px"><font face="Arial" size="2"><span style="font-size:10pt"><span class="Apple-style-span" style="font-family:Calibri; font-size:15px">
<div><span class="Apple-style-span" style="font-size:13px; font-family:Arial">W278 GH, 200 Hawkins Drive</span></div>
</span></span></font></div>
<div style="font-family:Calibri; font-size:15px"><font face="Arial" size="2"><span style="font-size:10pt">Iowa City, Iowa 52242</span></font></div>
<div style="font-family:Calibri; font-size:15px"><font face="Arial" size="2"><span style="font-size:10pt">Phone: 319-353-8587</span></font></div>
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<span style="font-weight:bold">From: </span>"Crawford, Helen" <<a href="mailto:helen.crawford@ucl.ac.uk">helen.crawford@ucl.ac.uk</a>><br>
<span style="font-weight:bold">Date: </span>Thu, 23 Feb 2012 10:46:44 +0000<br>
<span style="font-weight:bold">To: </span>"<a href="mailto:brains-users@www.nitrc.org">brains-users@www.nitrc.org</a>" <<a href="mailto:brains-users@public.nitrc.org">brains-users@public.nitrc.org</a>><br>
<span style="font-weight:bold">Subject: </span>[Brains-users] Getting started - image orientation<br>
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<div style="direction:ltr; font-family:Tahoma; color:#000000; font-size:10pt">Hi Brains Users,<br>
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My name is Helen Crawford and I work in England at University College London in the Huntington's Disease Research Group. I am new to the BRAINS software and have just installed BRAINS2. I seem to have fallen at the first hurdle, loading my images, and am hoping
there is a simple solution. When trying to view T1 scans in NIFTI format the sagittal image appears in the axial window, the axial image in coronal and coronal in sagittal. When trying a different format, ANALYZE (.hdr) files, the images appear in the correct
windows but are upside down in orientation. <br>
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Any help would be greatly appreciated.<br>
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Kind regards,<br>
<br>
Helen<br>
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<div style="font-family:Tahoma; font-size:13px"><span style="font-family:Helvetica"><font size="3"><span style="font-family:Helvetica; font-weight:bold"></span><span style="font-family:Helvetica"><br>
<span style="font-style:italic"><br>
</span><font size="2" style="font-weight:bold; font-style:italic">Helen Crawford</font></span><font size="2"><span style="font-family:Helvetica"><br>
Research Assistant</span><br style="font-family:Helvetica">
<span style="font-family:Helvetica">HD Research Group,</span><br style="font-family:Helvetica">
<span style="font-family:Helvetica">UCL Institue of Neurology,</span><br style="font-family:Helvetica">
<span style="font-family:Helvetica">2nd Floor, Ormond House,</span><br style="font-family:Helvetica">
<span style="font-family:Helvetica">27 Boswell Street,</span><br style="font-family:Helvetica">
<span style="font-family:Helvetica">London,</span><br style="font-family:Helvetica">
<span style="font-family:Helvetica">WC1N 3JZ</span><br style="font-family:Helvetica">
<br style="font-family:Helvetica">
<span style="font-family:Helvetica">Tel: 020 7242 0038</span></font> </font><br>
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