Issue with SIENA analysis

[nrqe19]

Dear all,

I´m new to linux and coding in general and any help will be appreciated. I download a VMware and I am running FSL now but I am unable to process SIENA. I already tried config a shared folder with Win10 via mng folder and also tried to process from a USB (ExFat format, I already installed the drive and the usb is read without issues) but the same error keeps appearing once a try to process siena:

[fsluser@localhost NMDA]$ siena avendano2.nii avendano1.nii
/usr/local/fsl/bin/bet2: error while loading shared libraries: libquadmath.so.0: cannot open shared object file: No such file or directory
/usr/local/fsl/bin/bet2: error while loading shared libraries: libquadmath.so.0: cannot open shared object file: No such file or directory
/usr/local/fsl/bin/fslstats: error while loading shared libraries: libquadmath.so.0: cannot open shared object file: No such file or directory
/usr/local/fsl/bin/fslmaths: error while loading shared libraries: libquadmath.so.0: cannot open shared object file: No such file or directory
/usr/local/fsl/bin/fslstats: error while loading shared libraries: libquadmath.so.0: cannot open shared object file: No such file or directory
/usr/local/fsl/bin/fslmaths: error while loading shared libraries: libquadmath.so.0: cannot open shared object file: No such file or directory
/usr/local/fsl/bin/fslstats: error while loading shared libraries: libquadmath.so.0: cannot open shared object file: No such file or directory
/usr/local/fsl/bin/overlay: error while loading shared libraries: libquadmath.so.0: cannot open shared object file: No such file or directory
/usr/local/fsl/bin/slicer: error while loading shared libraries: libquadmath.so.0: cannot open shared object file: No such file or directory
/usr/local/fsl/bin/fslstats: error while loading shared libraries: libquadmath.so.0: cannot open shared object file: No such file or directory
/usr/local/fsl/bin/overlay: error while loading shared libraries: libquadmath.so.0: cannot open shared object file: No such file or directory
/usr/local/fsl/bin/slicer: error while loading shared libraries: libquadmath.so.0: cannot open shared object file: No such file or directory
/usr/local/fsl/bin/fslhd: error while loading shared libraries: libquadmath.so.0: cannot open shared object file: No such file or directory
dc: stack empty
/usr/local/fsl/bin/fslhd: error while loading shared libraries: libquadmath.so.0: cannot open shared object file: No such file or directory
dc: stack empty
/usr/local/fsl/bin/fslhd: error while loading shared libraries: libquadmath.so.0: cannot open shared object file: No such file or directory
dc: stack empty
/usr/local/fsl/bin/fslmaths: error while loading shared libraries: libquadmath.so.0: cannot open shared object file: No such file or directory
/usr/local/fsl/bin/fslhd: error while loading shared libraries: libquadmath.so.0: cannot open shared object file: No such file or directory
dc: stack empty
/usr/local/fsl/bin/fslhd: error while loading shared libraries: libquadmath.so.0: cannot open shared object file: No such file or directory
dc: stack empty
/usr/local/fsl/bin/fslhd: error while loading shared libraries: libquadmath.so.0: cannot open shared object file: No such file or directory
dc: stack empty
/usr/local/fsl/bin/fslmaths: error while loading shared libraries: libquadmath.so.0: cannot open shared object file: No such file or directory
/usr/local/fsl/bin/flirt: error while loading shared libraries: libquadmath.so.0: cannot open shared object file: No such file or directory
/usr/local/fsl/bin/flirt: error while loading shared libraries: libquadmath.so.0: cannot open shared object file: No such file or directory
/usr/local/fsl/bin/fslmaths: error while loading shared libraries: libquadmath.so.0: cannot open shared object file: No such file or directory
/usr/local/fsl/bin/fslmaths: error while loading shared libraries: libquadmath.so.0: cannot open shared object file: No such file or directory
/usr/local/fsl/bin/overlay: error while loading shared libraries: libquadmath.so.0: cannot open shared object file: No such file or directory
/usr/local/fsl/bin/slicer: error while loading shared libraries: libquadmath.so.0: cannot open shared object file: No such file or directory
/usr/local/fsl/bin/overlay: error while loading shared libraries: libquadmath.so.0: cannot open shared object file: No such file or directory
/usr/local/fsl/bin/slicer: error while loading shared libraries: libquadmath.so.0: cannot open shared object file: No such file or directory
/usr/local/fsl/bin/fslhd: error while loading shared libraries: libquadmath.so.0: cannot open shared object file: No such file or directory
/usr/local/fsl/bin/fslhd: error while loading shared libraries: libquadmath.so.0: cannot open shared object file: No such file or directory
/usr/local/fsl/bin/fslhd: error while loading shared libraries: libquadmath.so.0: cannot open shared object file: No such file or directory
/usr/local/fsl/bin/fslhd: error while loading shared libraries: libquadmath.so.0: cannot open shared object file: No such file or directory
/usr/local/fsl/bin/fslhd: error while loading shared libraries: libquadmath.so.0: cannot open shared object file: No such file or directory
/usr/local/fsl/bin/fslhd: error while loading shared libraries: libquadmath.so.0: cannot open shared object file: No such file or directory
dc: stack empty
dc: stack empty
dc: stack empty
dc: stack empty
dc: stack empty
dc: stack empty
dc: stack empty
dc: stack empty
dc: stack empty
dc: stack empty
dc: stack empty
dc: stack empty
/usr/local/fsl/bin/siena_diff: error while loading shared libraries: libquadmath.so.0: cannot open shared object file: No such file or directory
dc: stack empty
/usr/local/fsl/bin/fslhd: error while loading shared libraries: libquadmath.so.0: cannot open shared object file: No such file or directory
/usr/local/fsl/bin/fslhd: error while loading shared libraries: libquadmath.so.0: cannot open shared object file: No such file or directory
/usr/local/fsl/bin/fslhd: error while loading shared libraries: libquadmath.so.0: cannot open shared object file: No such file or directory
/usr/local/fsl/bin/fslhd: error while loading shared libraries: libquadmath.so.0: cannot open shared object file: No such file or directory
/usr/local/fsl/bin/fslhd: error while loading shared libraries: libquadmath.so.0: cannot open shared object file: No such file or directory
/usr/local/fsl/bin/fslhd: error while loading shared libraries: libquadmath.so.0: cannot open shared object file: No such file or directory
dc: stack empty
dc: stack empty
dc: stack empty
dc: stack empty
dc: stack empty
dc: stack empty
dc: stack empty
dc: stack empty
dc: stack empty
dc: stack empty
dc: stack empty
dc: stack empty
/usr/local/fsl/bin/siena_diff: error while loading shared libraries: libquadmath.so.0: cannot open shared object file: No such file or directory
dc: stack empty
dc: dc: register 'd' (0144) is empty
dc: stack empty
dc: stack empty
dc: dc: stack empty
dc: stack empty
dc: stack empty
dc: stack empty
dc: stack empty
dc: stack empty
dc: stack empty
dc: stack empty
dc: stack empty
dc: dc: dc: stack empty
dc: stack empty
dc: register 'e' (0145) is empty
dc: dc: stack empty
dc: dc: dc: stack empty
dc: stack empty
dc: dc: stack empty
dc: stack empty
dc: dc: dc: input base must be a number between 2 and 16 (inclusive)
dc: dc: dc: dc: register 'd' (0144) is empty
dc: stack empty
dc: stack empty
dc: dc: stack empty
dc: stack empty
dc: stack empty
dc: stack empty
dc: stack empty
dc: stack empty
dc: stack empty
dc: stack empty
dc: stack empty
dc: dc: dc: stack empty
dc: stack empty
dc: register 'e' (0145) is empty
dc: dc: stack empty
dc: dc: dc: stack empty
dc: stack empty
dc: dc: stack empty
dc: stack empty
dc: dc: register 'i' (0151) is empty
dc: dc: dc: dc: dc: dc: dc: register 'd' (0144) is empty
dc: output base must be a number greater than 1
dc: dc: input base must be a number between 2 and 16 (inclusive)
dc: output base must be a number greater than 1
dc: stack empty
dc: dc: dc: register 'e' (0145) is empty
dc: dc: dc: dc: stack empty
dc: stack empty
dc: dc: stack empty
dc: stack empty
dc: dc: dc: input base must be a number between 2 and 16 (inclusive)
dc: dc: dc: dc: register 'd' (0144) is empty
dc: stack empty
dc: stack empty
dc: dc: stack empty
dc: stack empty
dc: stack empty
dc: stack empty
dc: stack empty
dc: stack empty
dc: stack empty
dc: stack empty
dc: stack empty
dc: dc: dc: stack empty
dc: stack empty
dc: register 'e' (0145) is empty
dc: dc: stack empty
dc: dc: dc: stack empty
dc: stack empty
dc: dc: stack empty
dc: stack empty
dc: dc: register 'i' (0151) is empty
dc: dc: dc: dc: dc: /usr/local/fsl/bin/siena_diff: error while loading shared libraries: libquadmath.so.0: cannot open shared object file: No such file or directory
/usr/local/fsl/bin/overlay: error while loading shared libraries: libquadmath.so.0: cannot open shared object file: No such file or directory
/usr/local/fsl/bin/slicer: error while loading shared libraries: libquadmath.so.0: cannot open shared object file: No such file or directory
/usr/local/fsl/bin/siena_diff: error while loading shared libraries: libquadmath.so.0: cannot open shared object file: No such file or directory
/usr/local/fsl/bin/overlay: error while loading shared libraries: libquadmath.so.0: cannot open shared object file: No such file or directory
/usr/local/fsl/bin/slicer: error while loading shared libraries: libquadmath.so.0: cannot open shared object file: No such file or directory
dc: stack empty
dc: stack empty
/usr/local/fsl/bin/fslmaths: error while loading shared libraries: libquadmath.so.0: cannot open shared object file: No such file or directory
/usr/local/fsl/bin/overlay: error while loading shared libraries: libquadmath.so.0: cannot open shared object file: No such file or directory
/usr/local/fsl/bin/slicer: error while loading shared libraries: libquadmath.so.0: cannot open shared object file: No such file or directory
/usr/local/fsl/bin/pngappend: error while loading shared libraries: libquadmath.so.0: cannot open shared object file: No such file or directory
/bin/rm: cannot remove 'grA_halfwayto_B?.???': No such file or directory

Finished. The SIENA report can be viewed by pointing your web browser at:
file:/home/fsluser/Desktop/NMDA/avendano2_to_avendano1_siena/report.html
Estimated percentage brain volume change (PBVC) =

[muschellij2]

This is a question for FSL itself: https://www.jiscmail.ac.uk/cgi-bin/webadmin?A0=FSL Also, you may want to look at LD_LIBRARY_PATH and PATH variables: https://www.linuxquestions.org/questions/linux-newbie-8/error-while-loading-shared-libraries-libquadmath-so-0-a-4175526728/ John

…

On Thu, May 23, 2019 at 7:50 PM nrqe19 ***@***.***> wrote: Dear all, I´m new to linux and coding in general and any help will be appreciated. I download a VMware and I am running FSL now but I am unable to process SIENA. I already tried config a shared folder with Win10 via mng folder and also tried to process from a USB (ExFat format, I already installed the drive and the usb is read without issues) but the same error keeps appearing once a try to process siena: ***@***.*** NMDA]$ siena avendano2.nii avendano1.nii /usr/local/fsl/bin/bet2: error while loading shared libraries: libquadmath.so.0: cannot open shared object file: No such file or directory /usr/local/fsl/bin/bet2: error while loading shared libraries: libquadmath.so.0: cannot open shared object file: No such file or directory /usr/local/fsl/bin/fslstats: error while loading shared libraries: libquadmath.so.0: cannot open shared object file: No such file or directory /usr/local/fsl/bin/fslmaths: error while loading shared libraries: libquadmath.so.0: cannot open shared object file: No such file or directory /usr/local/fsl/bin/fslstats: error while loading shared libraries: libquadmath.so.0: cannot open shared object file: No such file or directory /usr/local/fsl/bin/fslmaths: error while loading shared libraries: libquadmath.so.0: cannot open shared object file: No such file or directory /usr/local/fsl/bin/fslstats: error while loading shared libraries: libquadmath.so.0: cannot open shared object file: No such file or directory /usr/local/fsl/bin/overlay: error while loading shared libraries: libquadmath.so.0: cannot open shared object file: No such file or directory /usr/local/fsl/bin/slicer: error while loading shared libraries: libquadmath.so.0: cannot open shared object file: No such file or directory /usr/local/fsl/bin/fslstats: error while loading shared libraries: libquadmath.so.0: cannot open shared object file: No such file or directory /usr/local/fsl/bin/overlay: error while loading shared libraries: libquadmath.so.0: cannot open shared object file: No such file or directory /usr/local/fsl/bin/slicer: error while loading shared libraries: libquadmath.so.0: cannot open shared object file: No such file or directory /usr/local/fsl/bin/fslhd: error while loading shared libraries: libquadmath.so.0: cannot open shared object file: No such file or directory dc: stack empty /usr/local/fsl/bin/fslhd: error while loading shared libraries: libquadmath.so.0: cannot open shared object file: No such file or directory dc: stack empty /usr/local/fsl/bin/fslhd: error while loading shared libraries: libquadmath.so.0: cannot open shared object file: No such file or directory dc: stack empty /usr/local/fsl/bin/fslmaths: error while loading shared libraries: libquadmath.so.0: cannot open shared object file: No such file or directory /usr/local/fsl/bin/fslhd: error while loading shared libraries: libquadmath.so.0: cannot open shared object file: No such file or directory dc: stack empty /usr/local/fsl/bin/fslhd: error while loading shared libraries: libquadmath.so.0: cannot open shared object file: No such file or directory dc: stack empty /usr/local/fsl/bin/fslhd: error while loading shared libraries: libquadmath.so.0: cannot open shared object file: No such file or directory dc: stack empty /usr/local/fsl/bin/fslmaths: error while loading shared libraries: libquadmath.so.0: cannot open shared object file: No such file or directory /usr/local/fsl/bin/flirt: error while loading shared libraries: libquadmath.so.0: cannot open shared object file: No such file or directory /usr/local/fsl/bin/flirt: error while loading shared libraries: libquadmath.so.0: cannot open shared object file: No such file or directory /usr/local/fsl/bin/fslmaths: error while loading shared libraries: libquadmath.so.0: cannot open shared object file: No such file or directory /usr/local/fsl/bin/fslmaths: error while loading shared libraries: libquadmath.so.0: cannot open shared object file: No such file or directory /usr/local/fsl/bin/overlay: error while loading shared libraries: libquadmath.so.0: cannot open shared object file: No such file or directory /usr/local/fsl/bin/slicer: error while loading shared libraries: libquadmath.so.0: cannot open shared object file: No such file or directory /usr/local/fsl/bin/overlay: error while loading shared libraries: libquadmath.so.0: cannot open shared object file: No such file or directory /usr/local/fsl/bin/slicer: error while loading shared libraries: libquadmath.so.0: cannot open shared object file: No such file or directory /usr/local/fsl/bin/fslhd: error while loading shared libraries: libquadmath.so.0: cannot open shared object file: No such file or directory /usr/local/fsl/bin/fslhd: error while loading shared libraries: libquadmath.so.0: cannot open shared object file: No such file or directory /usr/local/fsl/bin/fslhd: error while loading shared libraries: libquadmath.so.0: cannot open shared object file: No such file or directory /usr/local/fsl/bin/fslhd: error while loading shared libraries: libquadmath.so.0: cannot open shared object file: No such file or directory /usr/local/fsl/bin/fslhd: error while loading shared libraries: libquadmath.so.0: cannot open shared object file: No such file or directory /usr/local/fsl/bin/fslhd: error while loading shared libraries: libquadmath.so.0: cannot open shared object file: No such file or directory dc: stack empty dc: stack empty dc: stack empty dc: stack empty dc: stack empty dc: stack empty dc: stack empty dc: stack empty dc: stack empty dc: stack empty dc: stack empty dc: stack empty /usr/local/fsl/bin/siena_diff: error while loading shared libraries: libquadmath.so.0: cannot open shared object file: No such file or directory dc: stack empty /usr/local/fsl/bin/fslhd: error while loading shared libraries: libquadmath.so.0: cannot open shared object file: No such file or directory /usr/local/fsl/bin/fslhd: error while loading shared libraries: libquadmath.so.0: cannot open shared object file: No such file or directory /usr/local/fsl/bin/fslhd: error while loading shared libraries: libquadmath.so.0: cannot open shared object file: No such file or directory /usr/local/fsl/bin/fslhd: error while loading shared libraries: libquadmath.so.0: cannot open shared object file: No such file or directory /usr/local/fsl/bin/fslhd: error while loading shared libraries: libquadmath.so.0: cannot open shared object file: No such file or directory /usr/local/fsl/bin/fslhd: error while loading shared libraries: libquadmath.so.0: cannot open shared object file: No such file or directory dc: stack empty dc: stack empty dc: stack empty dc: stack empty dc: stack empty dc: stack empty dc: stack empty dc: stack empty dc: stack empty dc: stack empty dc: stack empty dc: stack empty /usr/local/fsl/bin/siena_diff: error while loading shared libraries: libquadmath.so.0: cannot open shared object file: No such file or directory dc: stack empty dc: dc: register 'd' (0144) is empty dc: stack empty dc: stack empty dc: dc: stack empty dc: stack empty dc: stack empty dc: stack empty dc: stack empty dc: stack empty dc: stack empty dc: stack empty dc: stack empty dc: dc: dc: stack empty dc: stack empty dc: register 'e' (0145) is empty dc: dc: stack empty dc: dc: dc: stack empty dc: stack empty dc: dc: stack empty dc: stack empty dc: dc: dc: input base must be a number between 2 and 16 (inclusive) dc: dc: dc: dc: register 'd' (0144) is empty dc: stack empty dc: stack empty dc: dc: stack empty dc: stack empty dc: stack empty dc: stack empty dc: stack empty dc: stack empty dc: stack empty dc: stack empty dc: stack empty dc: dc: dc: stack empty dc: stack empty dc: register 'e' (0145) is empty dc: dc: stack empty dc: dc: dc: stack empty dc: stack empty dc: dc: stack empty dc: stack empty dc: dc: register 'i' (0151) is empty dc: dc: dc: dc: dc: dc: dc: register 'd' (0144) is empty dc: output base must be a number greater than 1 dc: dc: input base must be a number between 2 and 16 (inclusive) dc: output base must be a number greater than 1 dc: stack empty dc: dc: dc: register 'e' (0145) is empty dc: dc: dc: dc: stack empty dc: stack empty dc: dc: stack empty dc: stack empty dc: dc: dc: input base must be a number between 2 and 16 (inclusive) dc: dc: dc: dc: register 'd' (0144) is empty dc: stack empty dc: stack empty dc: dc: stack empty dc: stack empty dc: stack empty dc: stack empty dc: stack empty dc: stack empty dc: stack empty dc: stack empty dc: stack empty dc: dc: dc: stack empty dc: stack empty dc: register 'e' (0145) is empty dc: dc: stack empty dc: dc: dc: stack empty dc: stack empty dc: dc: stack empty dc: stack empty dc: dc: register 'i' (0151) is empty dc: dc: dc: dc: dc: /usr/local/fsl/bin/siena_diff: error while loading shared libraries: libquadmath.so.0: cannot open shared object file: No such file or directory /usr/local/fsl/bin/overlay: error while loading shared libraries: libquadmath.so.0: cannot open shared object file: No such file or directory /usr/local/fsl/bin/slicer: error while loading shared libraries: libquadmath.so.0: cannot open shared object file: No such file or directory /usr/local/fsl/bin/siena_diff: error while loading shared libraries: libquadmath.so.0: cannot open shared object file: No such file or directory /usr/local/fsl/bin/overlay: error while loading shared libraries: libquadmath.so.0: cannot open shared object file: No such file or directory /usr/local/fsl/bin/slicer: error while loading shared libraries: libquadmath.so.0: cannot open shared object file: No such file or directory dc: stack empty dc: stack empty /usr/local/fsl/bin/fslmaths: error while loading shared libraries: libquadmath.so.0: cannot open shared object file: No such file or directory /usr/local/fsl/bin/overlay: error while loading shared libraries: libquadmath.so.0: cannot open shared object file: No such file or directory /usr/local/fsl/bin/slicer: error while loading shared libraries: libquadmath.so.0: cannot open shared object file: No such file or directory /usr/local/fsl/bin/pngappend: error while loading shared libraries: libquadmath.so.0: cannot open shared object file: No such file or directory /bin/rm: cannot remove 'grA_halfwayto_B?.???': No such file or directory Finished. The SIENA report can be viewed by pointing your web browser at: file:/home/fsluser/Desktop/NMDA/avendano2_to_avendano1_siena/report.html Estimated percentage brain volume change (PBVC) = — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub <#21?email_source=notifications&email_token=AAIGPLSOHZ7WUSKKJZDZACDPW4UVVA5CNFSM4HPLD3L2YY3PNVWWK3TUL52HS4DFUVEXG43VMWVGG33NNVSW45C7NFSM4GVSW7ZA>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AAIGPLQGTDW2NEGHVHFDIHTPW4UVVANCNFSM4HPLD3LQ> .