Dear Darren,
It seems that replacing false by true in this line of code:
https://github.com/andersonwinkler/PALM/blob/master/fileio/%40gifti/private/read_gifti_file.m#L181
should fix the issue for you.
Best regards,
Guillaume.
On 05/12/2018 21:33, Darren Campbell wrote:
> Hi
> I am attempting to conduct a basic group analyses with three groups (subsets) of HCP participants based on task fMRI data. I believe that I followed (imitated closely) the June 2018 HCP course instructions for the setup of palm group level (level 3) anlaysis. I also have followed the basic setup instructions for the various software programs (FSL, Freesurfer, workbench, palm, Octave), and the "which" command identifies each software programs from any directory in BASH.
> But, I am running into some unexpected (and uninterpretable to me) errors (see below). Although Anderson W. has helped me test and fix some preliminary issues, new errors keep emerging. I would appreciated any suggestions. My basic palm command and the feedback received is below. Thanks.
> Darren
>
> palm -i ./HCP_subjects/Y.dtseries.nii -transposedata -d ./HCP_subjects/Progs/Design.mat -t ./HCP_subjects/Progs/Design.con -o ResultsCifti -n 500 -corrcon -logp -accel tail -nouncorrected
> =======================================================================
> Permutation Analysis of Linear Models
> =======================================================================
> Running PALM alpha112 using Octave 4.2.2 with the following options:
> -i ./HCP_subjects/Y.dtseries.nii
> -transposedata
> -d ./HCP_subjects/Progs/Design.mat
> -t ./HCP_subjects/Progs/Design.con
> -o ResultsCifti
> -n 500
> -corrcon
> -logp
> -accel tail
> -nouncorrected
> 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/Y.dtseries.nii
> warning: xml_findstr is not compiled for your platform.
> This will result in a slowdown of the XML parsing.
> Error using permute ([log in to unmask]:10)
> file_array objects can not be permuted.
>
> Error in read_gifti_file>gifti_Data ([log in to unmask]:201->permute)
> Error in read_gifti_file>gifti_DataArray ([log in to unmask]:122->read_gifti_file>gifti_Data)
> Error in read_gifti_file ([log in to unmask]:45->read_gifti_file>gifti_DataArray)
> Error in gifti ([log in to unmask]:89->read_gifti_file)
> Error in palm_ciftiread (/home/brain/palm-alpha112/palm_ciftiread.m:84->gifti)
> Error in palm_miscread (/home/brain/palm-alpha112/palm_miscread.m:167->palm_ciftiread)
> Error in palm_ready (/home/brain/palm-alpha112/palm_ready.m:47->palm_miscread)
> Error in palm_takeargs (/home/brain/palm-alpha112/palm_takeargs.m:1644->palm_ready)
> Error in palm_core (/home/brain/palm-alpha112/palm_core.m:33->palm_takeargs)
> Error in palm (/home/brain/palm-alpha112/palm.m:81->palm_core)
>
> ########################################################################
>
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>
--
Guillaume Flandin, PhD
Wellcome Centre for Human Neuroimaging
UCL Queen Square Institute of Neurology
London WC1N 3BG
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