<div dir="ltr">Thank you very much.</div><div class="gmail_extra"><br><br><div class="gmail_quote">2013/9/21 <span dir="ltr"><<a href="mailto:mrtrix-discussion-request@www.nitrc.org" target="_blank">mrtrix-discussion-request@www.nitrc.org</a>></span><br>
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Today's Topics:<br>
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1. Open ROI with fslview or freeview (Arnaud Bor?)<br>
2. Re: Open ROI with fslview or freeview (Thijs Dhollander)<br>
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<br>
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<br>
Message: 1<br>
Date: Fri, 20 Sep 2013 15:33:39 -0400<br>
From: Arnaud Bor? <<a href="mailto:arnaud.bore@gmail.com">arnaud.bore@gmail.com</a>><br>
Subject: [Mrtrix-discussion] Open ROI with fslview or freeview<br>
To: <a href="mailto:mrtrix-discussion@www.nitrc.org">mrtrix-discussion@www.nitrc.org</a><br>
Message-ID:<br>
<<a href="mailto:CAPA8YjZ487AuSeECyPvfHeZUgueY2m2WhCTa8TX9sm-qAPUbxw@mail.gmail.com">CAPA8YjZ487AuSeECyPvfHeZUgueY2m2WhCTa8TX9sm-qAPUbxw@mail.gmail.com</a>><br>
Content-Type: text/plain; charset="iso-8859-1"<br>
<br>
Dear Mrtrix experts,<br>
<br>
I've got an error when I create and save a ROI and then try to load it in<br>
FSL fslview (4.0.1) .<br>
<br>
This is the error message:<br>
nifti_convert_nhdr2nim: bad datatype<br>
<br>
I've got the same kind of problem when I try to load it with freeview<br>
unsupported datatype 1 with scl_slope !=0<br>
<br>
I'm using mrview 0.2.12 (revision 393)<br>
<br>
I tried the patch here :<br>
<a href="http://www.nitrc.org/pipermail/mrtrix-discussion/2012-April/000398.html" target="_blank">http://www.nitrc.org/pipermail/mrtrix-discussion/2012-April/000398.html</a> but<br>
didn't fix anything or maybe I've done it wrong<br>
<br>
Thank you for your help<br>
<br>
Arnaud<br>
<br>
--<br>
Arnaud BORE<br>
Research assistant<br>
Cellulaire : (001) <a href="tel:514-647-8649" value="+15146478649">514-647-8649</a><br>
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Message: 2<br>
Date: Fri, 20 Sep 2013 21:56:37 +0200<br>
From: Thijs Dhollander <<a href="mailto:thijs.dhollander@gmail.com">thijs.dhollander@gmail.com</a>><br>
Subject: Re: [Mrtrix-discussion] Open ROI with fslview or freeview<br>
To: <a href="mailto:mrtrix-discussion@www.nitrc.org">mrtrix-discussion@www.nitrc.org</a><br>
Message-ID:<br>
<<a href="mailto:CAK9H7Ns3yBDX83cVzz0Ye1o9ZOggQv0Po%2BRWvtCB3_s5849CNg@mail.gmail.com">CAK9H7Ns3yBDX83cVzz0Ye1o9ZOggQv0Po+RWvtCB3_s5849CNg@mail.gmail.com</a>><br>
Content-Type: text/plain; charset="iso-8859-1"<br>
<br>
Hi Arnaud,<br>
<br>
The reason this tends to happen when trying to use ROIs created with MRtrix<br>
in another software package, is the fact that the latter does not support<br>
the bitwise datatype that MRtrix creates its ROIs with.<br>
The solution is easy: just convert your ROIs to another datatype using<br>
mrconvert with the "-datatype" option (see<br>
<a href="http://www.brain.org.au/software/mrtrix/commands/mrconvert.html" target="_blank">http://www.brain.org.au/software/mrtrix/commands/mrconvert.html</a> ). The<br>
available datatypes and the accompanying specifiers that should be used<br>
with the "-datatype" option, can be found at<br>
<a href="http://www.brain.org.au/software/mrtrix/general/formats.html" target="_blank">http://www.brain.org.au/software/mrtrix/general/formats.html</a> .<br>
You could run, e.g.:<br>
<br>
mrconvert -datatype Int8 myROIcreatedwithMRtrix.mif myROItobeusedwithFSL.nii<br>
<br>
Hope that's somewhat clear and solves your problem!<br>
<br>
Cheers,<br>
Thijs<br>
<br>
*Thijs Dhollander<br>
<a href="mailto:thijs.dhollander@gmail.com">thijs.dhollander@gmail.com</a><br>
Tel. <a href="tel:%2B32%20475%2036%2044%2027" value="+32475364427">+32 475 36 44 27</a>*<br>
Medical Image Computing (MIC), ESAT-PSI, Department of Electrical<br>
Engineering, KU Leuven<br>
<br>
<br>
On Fri, Sep 20, 2013 at 9:33 PM, Arnaud Boré <<a href="mailto:arnaud.bore@gmail.com">arnaud.bore@gmail.com</a>> wrote:<br>
<br>
> Dear Mrtrix experts,<br>
><br>
> I've got an error when I create and save a ROI and then try to load it in<br>
> FSL fslview (4.0.1) .<br>
><br>
> This is the error message:<br>
> nifti_convert_nhdr2nim: bad datatype<br>
><br>
> I've got the same kind of problem when I try to load it with freeview<br>
> unsupported datatype 1 with scl_slope !=0<br>
><br>
> I'm using mrview 0.2.12 (revision 393)<br>
><br>
> I tried the patch here :<br>
> <a href="http://www.nitrc.org/pipermail/mrtrix-discussion/2012-April/000398.htmlbut" target="_blank">http://www.nitrc.org/pipermail/mrtrix-discussion/2012-April/000398.htmlbut</a> didn't fix anything or maybe I've done it wrong<br>
><br>
> Thank you for your help<br>
><br>
> Arnaud<br>
><br>
> --<br>
> Arnaud BORE<br>
> Research assistant<br>
> Cellulaire : (001) <a href="tel:514-647-8649" value="+15146478649">514-647-8649</a><br>
><br>
><br>
> _______________________________________________<br>
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End of Mrtrix-discussion Digest, Vol 56, Issue 7<br>
************************************************<br>
</blockquote></div><br><br clear="all"><div><br></div>-- <br>Arnaud BORE<br>Research assistant <br>Cellulaire : (001) 514-647-8649<br><br>
</div>