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Hi Donald and Rob,<br>
<br>
indeed didn't fix it but at least I have a better idea about how
MRtrix handles these things. And I found a (ugly) workaround for my
issue :)<br>
Thank you!<br>
<br>
Best,<br>
Peter<br>
<br>
<div class="moz-cite-prefix">On 10/22/2012 02:47 AM, Donald Tournier
wrote:<br>
</div>
<blockquote
cite="mid:CAPP9hqSr-AzR9FyKO7eg86+XNu8PSW11v1KH8h=apZgz8_812g@mail.gmail.com"
type="cite">Hi Peter,
<div><br>
</div>
<div>Sorry, just noticed you mention your images are LPS, in which
case the primary source of mismatch will probably be the data
layout, as suggested by Rob. The way this was handled for
overlays in FSL was to convert all of the images using mrconvert
(from NIfTI straight back to NIfTI), including the image that
you're tryiing to overlay onto. This will modify the sform/qform
as I mentioned previously, and convert all your data to RAS (as
per the NIfTI standard, and MRtrix's internal coordinate
system). I have no idea whether this will fix all the issues
(unlikely), but worth a shot...</div>
<div><br>
</div>
<div>Cheers,</div>
<div><br>
</div>
<div>Donald.</div>
<div><br>
<br>
<div class="gmail_quote">On 22 October 2012 11:37, Donald
Tournier <span dir="ltr"><<a moz-do-not-send="true"
href="mailto:d.tournier@brain.org.au" target="_blank">d.tournier@brain.org.au</a>></span>
wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0
.8ex;border-left:1px #ccc solid;padding-left:1ex">Hi Peter,
<div><br>
</div>
<div>Further to Rob's response, the issue really is that in
MRtrix, the directions are stored be with respect to
real/scanner coordinates (technically, the RAS equivalent
of the DICOM patient-centered coordinate system), not the
image axes as (I assume) they are in FSL. The directions
probably won't match unless the image transform is
identity - a straight non-oblique axial scan. To make
matters worse, as far as I know (someone correct me if I'm
wrong), FSL's coordinate system is LAS, whereas MRtrix is
RAS, so even for a straight axial scan the x-axis will
probably be flipped. </div>
<div><br>
</div>
<div>And then on top of that, there is a good chance that
the sform/qform of the original NIfTI data corresponds to
some other orientation (sagittal / coronal), in which case
Rob's comments about the data layout would also be
relevant. Note that MRtrix currently writes out NIfTI
images in a near-axial layout (the data layout will always
be +0,+1,+2,+3), regardless of the original qform/sform of
the original images, and will modify the transform (or the
new qform/sform for NIfTI) accordingly. You will only
notice a mismatch due to the data layout issue if trying
to overlay MRtrix-derived images/data onto your original
NIfTI data (in FSL only, MRtrix should handle this
appropriately). There was a discussion about the overlay
in FSL issue a while back on this mailing list. </div>
<div><br>
</div>
<div>Also, just to clarify: with MRtrix it's not possible to
produce NIfTI images with the volume contiguous in RAM
(Rob's '-layout +1,+2,+3,+0' suggestion), since this is
not generally supported by that format (technically that's
not quite correct, it is possible to specify the data type
as being a vector, in which case this particular scenario
could be supported, but since arbitrary strides (layout)
are not supported under NIfTI, it's not a special case
that I thought was worth the trouble to implement).</div>
<div><br>
</div>
<div>Essentially, this is the inverse problem to that of
using bvals/bvecs files with MRtrix: you need to convert
from scanner coordinates to image coordinates to view the
directions in FSL...</div>
<div><br>
</div>
<div>Not entirely sure this helps you, but at least you
should have a clearer understanding of why this is
happening.</div>
<div>Cheers,</div>
<div><br>
</div>
<div>Donald.</div>
<div>
<div>
<div class="h5"><br>
<br>
<div class="gmail_quote">
On 21 October 2012 12:22, Robert Smith <span
dir="ltr"><<a moz-do-not-send="true"
href="mailto:r.smith@brain.org.au"
target="_blank">r.smith@brain.org.au</a>></span>
wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0
.8ex;border-left:1px #ccc solid;padding-left:1ex">
<div>Peter<br clear="all">
</div>
<div><br>
</div>
<div>MRtrix is extremely flexible with regards to
how the image data are aligned in memory; if you
run the mrinfo command on your image and check
the 'data layout' field, you'll most likely see
that the ordering of the data in memory in those
axes is reversed (i.e. has a '-' sign).</div>
<div>Unfortunately FSL doesn't always interpret
this in the same way as MRtrix does. There is
also some ambiguity in the Nifti file format
regarding how the image transform should be
stored/interpreted.</div>
<div>In my experience, when using MRtrix and FSL
in conjunction, the safest option is to run the
mrconvert command on your image, with the
following option: '-layout +0,+1,+2'. This makes
the data layout as unambiguous as possible.</div>
<div>In your case with a 4D image, I would try
'-layout +1,+2,+3,+0'; this makes the 4th
dimension (the fibre orientations) contiguous in
memory, so reading the image data for a single
voxel is as fast as possible.</div>
<div><br>
</div>
<div>Hope this fixes your problem; if not let me
know.<br clear="all">
</div>
<div>Rob</div>
<br>
--<br>
<br>
Robert Smith<br>
PhD Candidate <br>
<div><br>
The Florey Institute of Neuroscience and Mental
Health<br>
Melbourne Brain Centre - Austin Campus<br>
245 Burgundy Street<br>
Heidelberg Vic 3084<br>
</div>
Ph: +61 3 9035 7128<br>
Fax: +61 3 9035 7301<br>
<a moz-do-not-send="true"
href="http://www.florey.edu.au" target="_blank">www.florey.edu.au</a>
<div>
<div><br>
<br>
<br>
<br>
<div class="gmail_quote">On Fri, Oct 19, 2012
at 9:42 PM, Peter Neher <span dir="ltr"><<a
moz-do-not-send="true"
href="mailto:p.neher@dkfz-heidelberg.de"
target="_blank">p.neher@dkfz-heidelberg.de</a>></span>
wrote:<br>
<blockquote class="gmail_quote"
style="margin:0 0 0 .8ex;border-left:1px
#ccc solid;padding-left:1ex">
<div bgcolor="#FFFFFF" text="#000000"> One
more problem. If i apply the peak
extraction to my image file the output
nifti peaks seem to have two inverted
dimensions. Do you internally change the
image geometry somehow? My image has a
left-posterior-superior orientation.<br>
<br>
Best<span><font color="#888888"><br>
Peter</font></span>
<div><br>
<br>
<div>On 10/18/2012 10:22 PM, Luis
Concha wrote:<br>
</div>
</div>
<div>
<div>
<blockquote type="cite">Once you get
your peaks image, you can use
fslroi to extract each set of
peaks. For example, if you found
tree peaks per voxel, the 4th
dimension of your file should have
9 elements (3 peaks, each with xyz
components). So, to get the first
peak, you would invoke:<br>
<br>
fslroi my_peaks.nii first_peak 0 3<br>
<br>
and to get the second largest
peak:<br>
fslroi my_peaks.nii second_peak 2
3<br>
<br>
and finally the third:<br>
fslroi my_peaks.nii third_peak 6 3<br>
<br>
(I am sure you can substitute
fslroi for mrcat for similar
operations)<br>
<br>
You can visualize them as lines in
fslview.<br>
<br>
Luis<br>
<br>
<br>
<br>
<div class="gmail_quote">On Thu,
Oct 18, 2012 at 3:11 PM, David
Raffelt <span dir="ltr"><<a
moz-do-not-send="true"
href="mailto:d.raffelt@brain.org.au"
target="_blank">d.raffelt@brain.org.au</a>></span>
wrote:<br>
<blockquote class="gmail_quote"
style="margin:0 0 0
.8ex;border-left:1px #ccc
solid;padding-left:1ex">Hi
Peter,
<div>I would suggest using
more directions than SH
coefficients in your FOD
image. Check out the
find_SH_peaks help for more
information on how the peaks
are saved. What it does not
mention though is that the
output peaks are ordered by
size (largest first). Sorry
I'm not familiar with the
FSL peak file format,
however I'm sure it would be
fairly trial to code
a conversion tool up. A good
place to start would be
dir2amp, since this code
reads in the directions file
and loops over each peak.</div>
<div>Cheers,</div>
<div>Dave
<div>
<div><br>
<br>
<div class="gmail_quote">On
19 October 2012 00:43,
Peter Neher <span
dir="ltr"><<a
moz-do-not-send="true"
href="mailto:p.neher@dkfz-heidelberg.de" target="_blank">p.neher@dkfz-heidelberg.de</a>></span>
wrote:<br>
<blockquote
class="gmail_quote"
style="margin:0 0 0
.8ex;border-left:1px
#ccc
solid;padding-left:1ex">
<div
bgcolor="#FFFFFF"
text="#000000"> Hi
Dave,<br>
<br>
seems to work
fine. Do you have
any recommendation
how many
directions to
generate using
gendir? And can
you give me the
exact
specification of
the find_SH_peaks
output image so
that I can read it
somehow using my
own code? Or is
there a conversion
to the FSL peak
file format?<br>
<br>
Best,<br>
Peter
<div>
<div><br>
<br>
<br>
<div>On
10/18/2012
11:37 AM,
David Raffelt
wrote:<br>
</div>
<blockquote
type="cite">Hi
Peter,
<div>You can
use the
find_SH_peaks
command. Note
that you also
have to supply
a set of
directions as
input, which
are used as
seeds for the
peak finding.
You can
generate these
using the
gendir
command.</div>
<div> <br>
</div>
<div>Note that
dir2amp can be
used to
convert these
directions to
peak
amplitudes.</div>
<div>Cheers,</div>
<div>Dave</div>
<div><br>
</div>
<div><br>
</div>
<div><br>
<br>
<div
class="gmail_quote">On
18 October
2012 19:06,
Peter Neher <span
dir="ltr"><<a
moz-do-not-send="true" href="mailto:p.neher@dkfz-heidelberg.de"
target="_blank">p.neher@dkfz-heidelberg.de</a>></span>
wrote:<br>
<blockquote
class="gmail_quote"
style="margin:0
0 0
.8ex;border-left:1px
#ccc
solid;padding-left:1ex">Hi
all, I
wondered if it
is possible to
directly
output the
fiber
directions and
not only the
SH
representation
of the ODFs.
If this is not
possible, can
anyone tell me
how the SH
file looks
like so that I
can read it
and extract
the peaks
myself?<br>
<br>
Best<br>
Peter<br>
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<br>
<br
clear="all">
<div><br>
</div>
-- <br>
<div><b><font
color="#ff6600">Dr David Raffelt</font></b></div>
<div><font
color="#ff6600">Post
Doctoral
Fellow</font></div>
<div><br>
</div>
<div>The
Florey
Institute of
Neuroscience
and Mental
Health</div>
<div>Melbourne
Brain Centre -
Austin Campus</div>
<div>245
Burgundy
Street</div>
<div>Heidelberg
Vic 3084
<div>Ph: <a
moz-do-not-send="true"
value="+61390357024">+61 3 9035 7024</a></div>
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moz-do-not-send="true"
value="+61390357024">www.florey.edu.au</a></div>
<br>
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</blockquote>
<br>
</div>
</div>
<span><font
color="#888888">
<pre cols="72">--
Dipl.-Inform. Peter Neher
German Cancer Research Center
(DKFZ, Deutsches Krebsforschungszentrum in der Helmholtz-Gemeinschaft, Stiftung des öffentlichen Rechts)
Division of Medical and Biological Informatics
Im Neuenheimer Feld 280, D-69120 Heidelberg
Phone: 49-(0)6221-42-3552, Fax: 49-(0)6221-42-2345
E-Mail: <a moz-do-not-send="true" href="mailto:p.neher@dkfz-heidelberg.de" target="_blank">p.neher@dkfz-heidelberg.de</a>, Web: <a moz-do-not-send="true" href="http://www.dkfz.de" target="_blank">www.dkfz.de</a>
The information contained in this message may be confidential and legally protected under applicable law. The message is intended solely for the addressee(s). If you are not the intended recipient, you are hereby notified that any use, forwarding, dissemination, or reproduction of this message is strictly prohibited and may be unlawful. If you are not the intended recipient, please contact the sender by return e-mail and destroy all copies of the original message.</pre>
</font></span></div>
</blockquote>
</div>
<br>
<br clear="all">
<div><br>
</div>
-- <br>
<div><b><font
color="#ff6600">Dr
David Raffelt</font></b></div>
<div><font
color="#ff6600">Post
Doctoral Fellow</font></div>
<div><br>
</div>
<div>The Florey
Institute of
Neuroscience and
Mental Health</div>
<div>Melbourne Brain
Centre - Austin Campus</div>
<div>245 Burgundy Street</div>
<div>Heidelberg Vic 3084
<div>Ph: <a
moz-do-not-send="true"
value="+61390357024">+61 3 9035 7024</a></div>
</div>
<div><a
moz-do-not-send="true"
value="+61390357024">www.florey.edu.au</a></div>
<br>
</div>
</div>
</div>
<br>
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<br>
</blockquote>
<br>
<pre cols="72">--
Dipl.-Inform. Peter Neher
German Cancer Research Center
(DKFZ, Deutsches Krebsforschungszentrum in der Helmholtz-Gemeinschaft, Stiftung des öffentlichen Rechts)
Division of Medical and Biological Informatics
Im Neuenheimer Feld 280, D-69120 Heidelberg
Phone: 49-(0)6221-42-3552, Fax: 49-(0)6221-42-2345
E-Mail: <a moz-do-not-send="true" href="mailto:p.neher@dkfz-heidelberg.de" target="_blank">p.neher@dkfz-heidelberg.de</a>, Web: <a moz-do-not-send="true" href="http://www.dkfz.de" target="_blank">www.dkfz.de</a>
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<br>
<br clear="all">
<div><br>
</div>
-- <br>
</div>
</div>
<font color="#ff6600" size="1"><b>Dr Jacques-Donald
Tournier<br>
</b></font>
<div><font color="#ff6600" size="1">Research Fellow</font></div>
<div class="im">
<div><font size="1"><br>
</font></div>
<div><font size="1">The Florey Institute of Neuroscience
and Mental Health</font></div>
<div><font size="1">Melbourne Brain Centre - Austin
Campus</font></div>
<div><font size="1">245 Burgundy Street</font></div>
<div><font size="1">Heidelberg Vic 3084</font></div>
</div>
<div><font size="1">Ph: +61 3 9035 7033</font></div>
<div><font size="1">Fax: +61 3 9035 7307</font></div>
<div><font size="1"><a moz-do-not-send="true"
href="http://www.florey.edu.au" target="_blank">www.florey.edu.au</a></font></div>
<br>
<br>
</div>
</blockquote>
</div>
<br>
<br clear="all">
<div><br>
</div>
-- <br>
<font color="#ff6600" size="1"><b>Dr Jacques-Donald Tournier<br>
</b></font>
<div><font color="#ff6600" size="1">Research Fellow</font></div>
<div><font size="1"><br>
</font></div>
<div><font size="1">The Florey Institute of Neuroscience and
Mental Health</font></div>
<div><font size="1">Melbourne Brain Centre - Austin Campus</font></div>
<div><font size="1">245 Burgundy Street</font></div>
<div><font size="1">Heidelberg Vic 3084</font></div>
<div><font size="1">Ph: +61 3 9035 7033</font></div>
<div><font size="1">Fax: +61 3 9035 7307</font></div>
<div><font size="1"><a moz-do-not-send="true"
href="http://www.florey.edu.au" target="_blank">www.florey.edu.au</a></font></div>
<br>
<br>
</div>
</blockquote>
<br>
<pre class="moz-signature" cols="72">--
Dipl.-Inform. Peter Neher
German Cancer Research Center
(DKFZ, Deutsches Krebsforschungszentrum in der Helmholtz-Gemeinschaft, Stiftung des öffentlichen Rechts)
Division of Medical and Biological Informatics
Im Neuenheimer Feld 280, D-69120 Heidelberg
Phone: 49-(0)6221-42-3552, Fax: 49-(0)6221-42-2345
E-Mail: <a class="moz-txt-link-abbreviated" href="mailto:p.neher@dkfz-heidelberg.de">p.neher@dkfz-heidelberg.de</a>, Web: <a class="moz-txt-link-abbreviated" href="http://www.dkfz.de">www.dkfz.de</a>
The information contained in this message may be confidential and legally protected under applicable law. The message is intended solely for the addressee(s). If you are not the intended recipient, you are hereby notified that any use, forwarding, dissemination, or reproduction of this message is strictly prohibited and may be unlawful. If you are not the intended recipient, please contact the sender by return e-mail and destroy all copies of the original message.</pre>
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