<div dir="ltr"><div><div><div>Hi Ulrike,<br><br></div>The problem looks to be specific to the use of compressed image formats with the shbasis command (though I suspect any command that modifies an image in-place will suffer a similar fate).<br></div>I'll dig into the problem when I get the chance, but for now the simplest fix is to convert to uncompressed NIfTI, run shbasis, then convert back to compressed format.<br><br></div>Thanks for the report<br>Rob<br></div><div class="gmail_extra"><br clear="all"><div><div class="gmail_signature"><div dir="ltr"><br>--<br><br><span style="color:rgb(255,102,0)"><b>Robert Smith, Ph.D</b><br>Research Officer, Imaging Division</span><br><br>The Florey Institute of Neuroscience and Mental Health<br>Melbourne Brain Centre - Austin Campus<br>245 Burgundy Street<br>Heidelberg Vic 3084<br>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><br></div></div></div>
<br><div class="gmail_quote">On Mon, Dec 15, 2014 at 11:31 PM, Ulrike Kuhl <span dir="ltr"><<a href="mailto:kuhl@cbs.mpg.de" target="_blank">kuhl@cbs.mpg.de</a>></span> wrote:<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">Dear MRtrix Team,<br>
<br>
First of all thank you for your great tools - they have been of great help to me during my tractography analysis so far. However, I've encountered a problem when trying to convert the SH basis of my CSD data computed with MRTrix 0.2 to the MRTrix3 version.<br>
As I eventually want to use SIFT implemented in MRTrix3, I followed the instructions in the wiki in order to convert the SH basis. Everything appears to work fine when running the 'shbasis -convert native' command (no warnings let alone error messages).<br>
However, I cannot use the resulting converted data as the NifTI format is not recognized anymore.<br>
Calling 'mrview' results in:<br>
<br>
mrview: image "./my_CSD.nii.gz" is not in NIfTI format (magic != "n+1\0")<br>
mrview: error opening image "my_CSD.nii.gz"<br>
<br>
Likewise I cannot open the resulting image in a differen viewer like fslview.<br>
<br>
This occurs when using the 'native' as well as the 'forced_oldtonew' choice.<br>
Did you come across this problem before and do you have a suggestion on how to overcome this issue?<br>
<br>
Thank you very much in advance!<br>
<br>
Best<br>
Ulrike<br>
<br>
--<br>
Max Planck Institute for Human Cognitive and Brain Sciences<br>
Department of Neuropsychology (A220)<br>
Stephanstraße 1a<br>
04103 Leipzig<br>
<br>
Phone: +49 (0) 341 9940 2586<br>
Mail: <a href="mailto:kuhl@cbs.mpg.de">kuhl@cbs.mpg.de</a><br>
Internet: <a href="http://www.cbs.mpg.de/staff/kuhl-12160" target="_blank">http://www.cbs.mpg.de/staff/kuhl-12160</a><br>
<br>
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</blockquote></div></div>