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><br><br><div class="gmail_quote">On 21 October 2012 12:22, Robert Smith <span dir="ltr"><<a 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 class="im"><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 href="http://www.florey.edu.au" target="_blank">www.florey.edu.au</a><div class="HOEnZb"><div class="h5"><br><br>
<br><br><div class="gmail_quote">On Fri, Oct 19, 2012 at 9:42 PM, Peter Neher <span dir="ltr"><<a 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 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 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 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>
_______________________________________________<br>
Mrtrix-discussion mailing list<br>
<a href="mailto:Mrtrix-discussion@www.nitrc.org" target="_blank">Mrtrix-discussion@www.nitrc.org</a><br>
<a href="http://www.nitrc.org/mailman/listinfo/mrtrix-discussion" target="_blank">http://www.nitrc.org/mailman/listinfo/mrtrix-discussion</a><br>
</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 value="+61390357024">+61 3 9035 7024</a></div>
</div>
<div><a value="+61390357024">www.florey.edu.au</a></div>
<br>
</div>
</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 href="mailto:p.neher@dkfz-heidelberg.de" target="_blank">p.neher@dkfz-heidelberg.de</a>, Web: <a 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 value="+61390357024">+61 3 9035 7024</a></div>
</div>
<div><a value="+61390357024">www.florey.edu.au</a></div>
<br>
</div>
</div>
</div>
<br>
_______________________________________________<br>
Mrtrix-discussion mailing list<br>
<a href="mailto:Mrtrix-discussion@www.nitrc.org" target="_blank">Mrtrix-discussion@www.nitrc.org</a><br>
<a href="http://www.nitrc.org/mailman/listinfo/mrtrix-discussion" target="_blank">http://www.nitrc.org/mailman/listinfo/mrtrix-discussion</a><br>
<br>
</blockquote>
</div>
<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 href="mailto:p.neher@dkfz-heidelberg.de" target="_blank">p.neher@dkfz-heidelberg.de</a>, Web: <a 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>
</div></div></div>
<br>_______________________________________________<br>
Mrtrix-discussion mailing list<br>
<a href="mailto:Mrtrix-discussion@www.nitrc.org" target="_blank">Mrtrix-discussion@www.nitrc.org</a><br>
<a href="http://www.nitrc.org/mailman/listinfo/mrtrix-discussion" target="_blank">http://www.nitrc.org/mailman/listinfo/mrtrix-discussion</a><br>
<br></blockquote></div><br>
</div></div><br>_______________________________________________<br>
Mrtrix-discussion mailing list<br>
<a href="mailto:Mrtrix-discussion@www.nitrc.org">Mrtrix-discussion@www.nitrc.org</a><br>
<a href="http://www.nitrc.org/mailman/listinfo/mrtrix-discussion" target="_blank">http://www.nitrc.org/mailman/listinfo/mrtrix-discussion</a><br>
<br></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 href="http://www.florey.edu.au" target="_blank">www.florey.edu.au</a></font></div>
<br><br>
</div>