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Hi<br>
<br>
thanks, output is attached, I see it has recognised the data as being
DTI which is good. On the other hand, it's a 32 directions scan with
one b=0, and I see<br>
dim: 112,112,60<b>,34</b><br>
<br>
could it be that it has fallen foul of the cheeky 34th dataset which
Philips add, an isotropic DW image? caused issues with quite a few of
our codes, ppl always forget about it.<br>
<br>
Ph<br>
<br>
On 04/06/10 05:54, Donald Tournier wrote:
<blockquote
cite="mid:AANLkTimzl1WRcRo9NuXpxvNv-Szkp_34Md42kNFaz1nk@mail.gmail.com"
type="cite">Hi Philip,
<div><br>
</div>
<div>Sounds a bit odd. To narrow things down a bit, could you post
the output of the following:</div>
<div><br>
</div>
<div>$ mrinfo dwi.mif</div>
<div>$ mrinfo sf.mif</div>
<div>
<div>$ awk '{ if ($0=="END") exit 0; print $0 }' dwi.mif</div>
</div>
<div>$ awk '{ if ($0=="END") exit 0; print $0 }' sf.mif</div>
<div>$ ls -l dwi.mif sf.mif</div>
<div><br>
</div>
<div>That should give me a bit more info...</div>
<div>Cheers,</div>
<div><br>
</div>
<div>Donald.</div>
<div>
<div><br>
</div>
<br>
<div class="gmail_quote">On 3 June 2010 01:49, Philip G Batchelor <span
dir="ltr"><<a moz-do-not-send="true"
href="mailto:philip.batchelor@kcl.ac.uk">philip.batchelor@kcl.ac.uk</a>></span>
wrote:<br>
<blockquote class="gmail_quote"
style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
<div bgcolor="#ffffff" text="#000000">On 12/03/10 00:38, Donald
Tournier wrote:
<blockquote type="cite">
<div>This message has been archived. Â <a moz-do-not-send="true"
href="https://kclev.kcl.ac.uk/EnterpriseVault/ViewMessage.asp?VaultId=1CFCE6957FBD5654F8CCD18F833B7A6301110000kcl-evsite01&SavesetId=730000000000000%7E201003120038120000%7E0%7EE7E2A350A97B45AD91183E4EEB3B887"
target="_blank">View
the original item </a></div>
<div class="im">
<div>Hi Philip, Sorry, there is currently
no documentation on that file format... It is quite simple, though. It
consists of a text header, followed by binary data. The first line of
the text header</div>
</div>
<div>Attachments:</div>
<table border="0" cellpadding="2" cellspacing="1" width="97%"
align="center">
<tbody>
<tr>
<td width="80%"><a moz-do-not-send="true"
href="https://kclev.kcl.ac.uk/EnterpriseVault/ViewMessage.asp?VaultId=1CFCE6957FBD5654F8CCD18F833B7A6301110000kcl-evsite01&SavesetId=730000000000000%7E201003120038120000%7E0%7EE7E2A350A97B45AD91183E4EEB3B887&AttachmentId=1"
target="_blank">read_mrtrix_tracks.m </a></td>
<td>(2 KB)</td>
</tr>
</tbody>
</table>
</blockquote>
<br>
<br>
Hi<br>
<br>
am trying to process some of the Philips DICOM we acquired, in order to
perform CSD. At the estimate_response stage it crashes, something went
wrong with 'axes specification' but nore sure what. Here is the
sequence of operation I go though:<br>
<br>
   $ mrconvert -info DICOM/ ./mrtrix-data/dwi.mif<br>
   [...]<br>
  <br>
   $ mrconvert dwi.mif -coord 3 0 - | threshold - - | median3D - - |
median3D - mask.mif<br>
    [...]<br>
  <br>
   $ dwi2tensor dwi.mif dti.mif<br>
  [...]<br>
   <br>
   $ tensor2FA dti.mif - | mrmult - mask.mif fa.mif<br>
   $ erode mask.mif - | erode - - | mrmult fa.mif - - | threshold -
-abs 0.6 sf.mif <br>
   $ estimate_response dwi.mif sf.mif response.txt<br>
<br>
     estimate_response: incorrect number of axes in axes specification
"-0,-1,+2,+3"<br>
     *** glibc detected *** estimate_response: free(): invalid next
size (fast): 0x000000000194c420 ***<br>
     ======= Backtrace: =========<br>
    /lib/libc.so.6(+0x775b6)[0x7f4f4d5065b6]<br>
   /lib/libc.so.6(cfree+0x73)[0x7f4f4d50ce53]<br>
   etc...<br>
<br>
Am trying to diagnose if I'm doing some basic error, or if there's a
problem with the way the axes are read from the DICOMS?<br>
Any suggestion?<br>
<br>
Ph<br>
</div>
</blockquote>
</div>
<br>
<br clear="all">
<br>
-- <br>
Jacques-Donald Tournier (PhD)<br>
Brain Research Institute, Melbourne, Australia<br>
Tel: +61 (0)3 9496 4078<br>
</div>
</blockquote>
<br>
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