<div dir="ltr"><div dir="ltr"><div dir="ltr"><div dir="ltr"><div dir="ltr"><div dir="ltr"><div dir="ltr"><div dir="ltr"><div dir="ltr"><div dir="ltr"><div dir="ltr"><div dir="ltr"><div>Hi Morgan,</div><div><br></div><div>topup is located in the same directory as fslino (/usr/bin), but if I open the topup file, I see a 1 line command (../lib/fsl/5.0/fsl_app_wrapper). the topup command does return a log file (see attached) although it reports "Segmentation fault (core dumped)".</div><div>fslinfo runs with no problem (see below). In fact, all other fsl functions I have tested so far run very well. I have uninstalled and reinstalled fsl-complete. I still get the same errors. </div><div>echo $FSLDIR returns nothing. </div><div><br></div><div>$ which fslinfo<br>/usr/bin/fslinfo</div><div><div>$ which topup</div><div>/usr/bin/topup</div><div><br></div><b></b><i></i><u></u><sub></sub><sup></sup><strike></strike>$ topup --imain=rrpEPI_fsl_swap.nii.gz --datain=datain_topup.txt --config=EPI_topup_HLL_fix.cnf --out=test<br>Segmentation fault (core dumped)</div><div><br></div><div>$ fslinfo EPI_fsl_swap.nii.gz<br>data_type FLOAT32<br>dim1 64<br>dim2 32<br>dim3 16<br>dim4 2<br>datatype 16<br>pixdim1 3.000000<br>pixdim2 3.000000<br>pixdim3 6.000000<br>pixdim4 2.000000<br>cal_max 201.1975<br>cal_min 0.0025<br>file_type NIFTI-1+<br></div><div><br></div><div>$echo $FSLDIR</div><div><b></b><i></i><u></u><sub></sub><sup></sup><strike></strike><br></div></div></div></div></div></div></div></div></div></div></div></div></div><br><div class="gmail_quote"><div class="gmail_attr" dir="ltr">On Mon, Feb 3, 2020 at 1:36 AM Morgan Hough <<a href="mailto:morgan.hough@gmail.com">morgan.hough@gmail.com</a>> wrote:<br></div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;padding-left:1ex;border-left-color:rgb(204,204,204);border-left-width:1px;border-left-style:solid"><div><div dir="auto">Hey Nan,</div><div dir="auto"><br></div><div dir="auto">Hmm. And “which topup” gives you the same path? I forget if topup is a script or a binary. You can less `which topup` and see.<br></div></div><div dir="auto"><br></div><div dir="auto">Never hurts to check the input files with other binaries. Fslinfo the 4D nifti. cat the text file. If you are getting a core dump, that is still my guess from what you have told me. </div><div dir="auto"><br></div><div dir="auto">You can remove with the same command you installed with. Check first you have fsl-complete installed. You want to check what is happening with your .bashrc/.profile. Echo $FSLDIR or something like that. </div><div dir="auto"><br></div><div dir="auto">Cheers,</div><div dir="auto"><br></div><div dir="auto">-Morgan</div><div><br><div class="gmail_quote"><div class="gmail_attr" dir="ltr">On Sun, Feb 2, 2020 at 21:53 Nan Xu <<a href="mailto:nxu@u.rochester.edu" target="_blank">nxu@u.rochester.edu</a>> wrote:<br></div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;padding-left:1ex;border-left-color:rgb(204,204,204);border-left-width:1px;border-left-style:solid"><div dir="auto">Hi Morgan,<div><br></div><div>Here’re what I have.</div><div>1. topup without arguments returns the usage output without problems.</div><div>2. input text file and the file paths should all be good because the same command works fine in a different Linux system which installed the FSL without using neurodebian.</div><div><br></div><div>So, I’m wondering if it’s a installation problem, how to uninstall fsl and reinstall fsl with neurodebian?</div><div><br></div><div>Thanks,</div><div>Nan</div><div><br></div><div><br></div><div><div dir="ltr"><blockquote type="cite">On Feb 2, 2020, at 11:27 PM, Morgan Hough <<a href="mailto:morgan.hough@gmail.com" target="_blank">morgan.hough@gmail.com</a>> wrote:<br><br></blockquote></div><blockquote type="cite"><div dir="ltr"></div></blockquote></div></div><div dir="auto"><div><blockquote type="cite"><div dir="ltr"><div><div dir="auto">Ok. So try topup without arguments. You should get the usage output. If that works for you, check your input text file the acquisition parameters. Make sure it’s UNIX text friendly. Then check the paths are OK? </div><div dir="auto"><br></div><div dir="auto">You can test your install with FEEDS. Hope this helps.</div></div><div dir="auto"><br></div><div dir="auto">Cheers,</div><div dir="auto"><br></div><div dir="auto">-Morgan</div><div><br><div class="gmail_quote"><div class="gmail_attr" dir="ltr">On Sun, Feb 2, 2020 at 13:11 Nan Xu <<a href="mailto:nxu@u.rochester.edu" target="_blank">nxu@u.rochester.edu</a>> wrote:<br></div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;padding-left:1ex;border-left-color:rgb(204,204,204);border-left-width:1px;border-left-style:solid"><div dir="ltr">Hi Morgan,<div><br></div><div>Yes, "which fslinfo" returns /user/bin/fslinfo</div><div><br></div><div>Thanks,</div><div>Nan</div></div><br><div class="gmail_quote"><div class="gmail_attr" dir="ltr">On Fri, Jan 31, 2020 at 2:41 PM Morgan Hough <<a href="mailto:morgan.hough@gmail.com" target="_blank">morgan.hough@gmail.com</a>> wrote:<br></div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;padding-left:1ex;border-left-color:rgb(204,204,204);border-left-width:1px;border-left-style:solid"><div><div dir="auto">Hi Nan,</div></div><div dir="auto"><br></div><div dir="auto">Did you add the install directory to your shell’s path? What about “which fslinfo”?</div><div dir="auto"><br></div><div dir="auto">Cheers,</div><div dir="auto"><br></div><div dir="auto">-Morgan</div><div><br><div class="gmail_quote"><div class="gmail_attr" dir="ltr">On Fri, Jan 31, 2020 at 11:37 Nan Xu <<a href="mailto:nxu@u.rochester.edu" target="_blank">nxu@u.rochester.edu</a>> wrote:<br></div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;padding-left:1ex;border-left-color:rgb(204,204,204);border-left-width:1px;border-left-style:solid"><div dir="ltr"><p class="MsoNormal"><a name="m_-5009090751811392274_m_746048170098337265_m_-4635091858041979071_m_5004809198632023978_m_-6046226554258725372_m_7116741943697188252_m_7143552538376495530__olk_signature">Hi,</a></p><p class="MsoNormal"><u></u> <u></u></p><p class="MsoNormal">I have a ubuntu 18.04 WSL system. I installed the neurodebian before install the fsl by using the command "sudo apt-get install fsl”. However, I received the following error message when running fsl topup:</p><p class="MsoNormal">$ topup --imain=EPI_fsl_swap --config=EPI_topup_HLL_fix.cnf --datain=datain_topup.txt --out=tu_g --iout=tus_g -v</p><p class="MsoNormal">Segmentation fault (core dumped)</p><p class="MsoNormal"><u></u> <u></u></p><p class="MsoNormal">Does anyone know how to fix this problem?<u></u><u></u></p><p class="MsoNormal"><u></u> <u></u></p><p class="MsoNormal">Thanks,<u></u><u></u></p><p class="MsoNormal">Nan</p></div>
_______________________________________________<br>
Neurodebian-users mailing list<br>
<a href="mailto:Neurodebian-users@alioth-lists.debian.net" target="_blank">Neurodebian-users@alioth-lists.debian.net</a><br>
<a href="https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/neurodebian-users" target="_blank" rel="noreferrer">https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/neurodebian-users</a></blockquote></div></div>
</blockquote></div>
</blockquote></div></div>
</div></blockquote></div></div></blockquote></div></div>
</blockquote></div>