Hi Darren,
This time, it's because you also have to recompile :
[log in to unmask]
using the same `mkoctfile --mex` command.
You probably also have to do the true/false change mentioned in the
previous email exchange.
Given that precompiled MEX files are only compatible with a single
Octave version, a solution would be to:
* remove all *.mex files
* remove spm_existfile.*
* provide a single script (bash, M-file, Makefile) for compilation of
all MEX files.
Best regards,
Guillaume.
On 20/03/2019 06:40, Darren Campbell wrote:
> Hi Guillaume and Others,
> Thanks again. I used the recompiling option and it worked for my
> subcortical analysis. But, when I tried a very similar analysis for the
> left and right cortices (see below), I receive the following errors.
>
> *Error using read_gifti_file
> ([log in to unmask]:17)*
> *[GIFTI] Loading of XML file ./HCP_subjects/L_midthickness.surf.gii failed.*
> *
> *
> *Error in gifti
> ([log in to unmask]:89->read_gifti_file)*
> *Error in palm_miscread
> (/home/brain/PALM-master/palm_miscread.m:243->gifti)*
> *Error in palm_takeargs
> (/home/brain/PALM-master/palm_takeargs.m:1565->palm_miscread)*
> *Error in palm_core (/home/brain/PALM-master/palm_core.m:33->palm_takeargs)*
> *Error in palm (/home/brain/PALM-master/palm.m:81->palm_core)*
> *
> *
> With an earlier version of PALM, I had a similar (not identical) gifti
> reading error which was fixed by changing Line 181 in a read_gifti_file
> from false to true.
> https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind1812&L=FSL&P=R8016&1=FSL&9=A&I=-3&J=on&X=FAA84569132B0FB091&Y=darrenc%40nipissingu.ca&d=No+Match%3BMatch%3BMatches&z=4
> <https://eur01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.jiscmail.ac.uk%2Fcgi-bin%2Fwebadmin%3FA2%3Dind1812%26L%3DFSL%26P%3DR8016%261%3DFSL%269%3DA%26I%3D-3%26J%3Don%26X%3DFAA84569132B0FB091%26Y%3Ddarrenc%2540nipissingu.ca%26d%3DNo%2BMatch%253BMatch%253BMatches%26z%3D4&data=02%7C01%7Cg.flandin%40UCL.AC.UK%7C2695fbb06cc14c9aa7f608d6acff22a6%7C1faf88fea9984c5b93c9210a11d9a5c2%7C0%7C0%7C636886609130316425&sdata=XOn0S7W9RXDgHqusrzyiEh8VmwwTQMqPwAgQnKrkT%2BA%3D&reserved=0>
> . However, this change did not work this time.
> Any suggestions? Thanks.
> Darren
>
> *More Details:*
> palm -i ./HCP_subjects/Y_left.func.gii -i
> ./HCP_subjects/Y_right.func.gii -d ./HCP_subjects/Progs/Design.mat -t
> ./HCP_subjects/Progs/DesignGrps.con -o L_R_cortical_CCU_Grps -n 5
> -corrcon -corrmod -logp -accel tail -nouncorrected -T -tfce2D -s
> ./HCP_subjects/L_midthickness.surf.gii -s
> ./HCP_subjects/R_midthickness.surf.gii
> =======================================================================
> Permutation Analysis of Linear Models
> =======================================================================
> Running PALM alpha115 using Octave 4.2.2 with the following options:
> -i ./HCP_subjects/Y_left.func.gii
> -i ./HCP_subjects/Y_right.func.gii
> -d ./HCP_subjects/Progs/Design.mat
> -t ./HCP_subjects/Progs/DesignGrps.con
> -o L_R_cortical_CCU_Grps
> -n 5
> -corrcon
> -corrmod
> -logp
> -accel tail
> -nouncorrected
> -T
> -tfce2D
> -s ./HCP_subjects/L_midthickness.surf.gii
> -s ./HCP_subjects/R_midthickness.surf.gii
> Found FSL in /usr/local/fsl
> Found FreeSurfer in /usr/local/freesurfer
> Found HCP Workbench executable in
> /home/brain/workbench/bin_linux64/wb_command
> Loading surface 1/2: ./HCP_subjects/L_midthickness.surf.gii
> Error using read_gifti_file
> ([log in to unmask]:17)
> [GIFTI] Loading of XML file ./HCP_subjects/L_midthickness.surf.gii failed.
>
> Error in gifti
> ([log in to unmask]:89->read_gifti_file)
> Error in palm_miscread (/home/brain/PALM-master/palm_miscread.m:243->gifti)
> Error in palm_takeargs
> (/home/brain/PALM-master/palm_takeargs.m:1565->palm_miscread)
> Error in palm_core (/home/brain/PALM-master/palm_core.m:33->palm_takeargs)
> Error in palm (/home/brain/PALM-master/palm.m:81->palm_core)
>
> Dr. Darren Campbell
> Associate Professor
> Department of Psychology
> Nipissing University
>
> On Tue, Mar 19, 2019 at 5:16 AM Flandin, Guillaume <[log in to unmask]
> <mailto:[log in to unmask]>> wrote:
>
> Hi Darren,
>
> The version of spm_existfile.mex from PALM is not compatible with your
> platform. You can either recompile it with:
> mkoctfile --mex spm_existfile.c
> or delete the file altogether:
> rm /home/brain/PALM-master/fileio/extras/spm_existfile.mex
> (a warning will be displayed when running palm but can be safely
> ignored).
>
> Best regards,
> Guillaume.
>
>
> On 18/03/2019 18:50, Darren Campbell wrote:
> > Hi
> > Previously, I have used PALM successfully on this specific data
> and design setup. After downloading (Mar 9th) and installing PALM
> alpha115 from GitHub (https://github.com/andersonwinkler/PALM), the
> first error line message was:
> >
> > Error using write_hdr_raw
> ([log in to unmask]:49) .
> >
> > Any suggestions? Thanks.
> >
> > Darren
> > P.S. If necessary, see below for more details.
> >
> > More Details:
> > To address some basic setup issues, I ensured that I have the
> latest build-essential and liboctave-dev packages. I ran the two
> compile commands:
> >
> > cd /home/brain/PALM-master/fileio/@file_array/private
> > ./compile.sh
> > cd /home/brain/PALM-master/fileio/@gifti/private
> > ./compile.sh
> >
> > My actual command:
> >
> > brain@brain-Tower:~$ palm -i ./HCP_subjects/Y192_subcortical.nii
> -d ./HCP_subjects/Progs/Design.mat -t
> ./HCP_subjects/Progs/DesignGrpContr.con -o subcort_1 -n 10 -corrcon
> -logp -accel tail -nouncorrected -T -cmcx
> > . . .
> > . . .
> >
> > Found FSL in /usr/local/fsl
> > Found FreeSurfer in /usr/local/freesurfer
> > Found HCP Workbench executable in
> /home/brain/workbench/bin_linux64/wb_command
> > Reading input 1/1: ./HCP_subjects/Y192_subcortical.nii
> > Reading design matrix and contrasts.
> > Elapsed time parsing inputs: ~ 18.9825 seconds.
> > Number of possible permutations is exp(820.987) = 192!.
> > Generating 10 shufflings (permutations only).
> > Building null distribution.
> > 3.33% [Shuffling 1/10, Design 1/1, Contrast 1/3, Modality 1/1]
> > Saving file: subcort_1_vox_tstat_c1
> > Error using write_hdr_raw
> ([log in to unmask]:49)
> > /home/brain/PALM-master/fileio/extras/spm_existfile.mex: failed to
> load: liboctinterp.so.6: cannot open shared object file: No such
> file or directory
> >
> > Error in create
> ([log in to unmask]:25->write_hdr_raw)
> > Error in palm_miscwrite
> (/home/brain/PALM-master/palm_miscwrite.m:101->create)
> > Error in palm_quicksave
> (/home/brain/PALM-master/palm_quicksave.m:163->palm_miscwrite)
> > Error in palm_core
> (/home/brain/PALM-master/palm_core.m:1569->palm_quicksave)
> > Error in palm (/home/brain/PALM-master/palm.m:81->palm_core)
> >
> >
> ########################################################################
> >
> > To unsubscribe from the FSL list, click the following link:
> >
> https://eur01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.jiscmail.ac.uk%2Fcgi-bin%2Fwebadmin%3FSUBED1%3DFSL%26A%3D1&data=02%7C01%7Cg.flandin%40UCL.AC.UK%7C5a16c6c6c2804ca4712f08d6abd42775%7C1faf88fea9984c5b93c9210a11d9a5c2%7C0%7C0%7C636885325023445224&sdata=GWz7fBTsOcXq%2BYmAW66Ysa4vXNWXIZvl%2B%2BHyrT6ALVs%3D&reserved=0
> <https://eur01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.jiscmail.ac.uk%2Fcgi-bin%2Fwebadmin%3FSUBED1%3DFSL%26A%3D1&data=02%7C01%7Cg.flandin%40UCL.AC.UK%7C2695fbb06cc14c9aa7f608d6acff22a6%7C1faf88fea9984c5b93c9210a11d9a5c2%7C0%7C0%7C636886609130316425&sdata=GuOTFbiFh2HZuOXWYtlNoqfq8J%2FrSeFWcy4cVOM5vmk%3D&reserved=0>
> >
>
> --
> Guillaume Flandin, PhD
> Wellcome Centre for Human Neuroimaging
> UCL Queen Square Institute of Neurology
> London WC1N 3BG
>
> ########################################################################
>
> To unsubscribe from the FSL list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=FSL&A=1
> <https://eur01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.jiscmail.ac.uk%2Fcgi-bin%2Fwebadmin%3FSUBED1%3DFSL%26A%3D1&data=02%7C01%7Cg.flandin%40UCL.AC.UK%7C2695fbb06cc14c9aa7f608d6acff22a6%7C1faf88fea9984c5b93c9210a11d9a5c2%7C0%7C0%7C636886609130326430&sdata=1FwCa3C%2B01jfa4n%2FV9l52NK1xvzMJZvd3AsoU5pRMjw%3D&reserved=0>
>
>
> ------------------------------------------------------------------------
>
> To unsubscribe from the FSL list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=FSL&A=1
> <https://eur01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.jiscmail.ac.uk%2Fcgi-bin%2Fwebadmin%3FSUBED1%3DFSL%26A%3D1&data=02%7C01%7Cg.flandin%40UCL.AC.UK%7C2695fbb06cc14c9aa7f608d6acff22a6%7C1faf88fea9984c5b93c9210a11d9a5c2%7C0%7C0%7C636886609130336439&sdata=MVxabcHYF%2BNFAyQdDY80iT%2Fuo%2F9KJ%2B%2BlnI6jaOnOve0%3D&reserved=0>
>
>
--
Guillaume Flandin, PhD
Wellcome Centre for Human Neuroimaging
UCL Queen Square Institute of Neurology
London WC1N 3BG
########################################################################
To unsubscribe from the FSL list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=FSL&A=1
|