Dear Yu,
The fix described in the following post should solve the issue for you:
https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=fsl;82701fac.1812
Best regards,
Guillaume.
On 09/04/2019 02:11, Yu Han wrote:
> Dear Expert,
>
> I am running a PALM analysis with two groups. A represents group with autism, N represents group without autism. I currently have four subjects from the N group and 1 subject from the A group. Below I listed my contrast and design etc. I am running into the following error. I searched the FSL blog, some people say it is the version of PALM, and recommended to use an older version of PALM instead. Any suggestions/feedbacks would be much appreciated. Thank you for your help in advance!
>
> Best,
> Yu
>
> Yu Han
> Ph.D. Candidate
> Neuroscience Graduate Program
> The Vermont Complex Systems Center
> University of Vermont
>
>
> The contrast.csv file looks like this:
>
> 1,0
> 0,1
> 1,-1
> -1,1
>
> The design.csv file looks like this:
>
> 1 0
> 0 1
> 0 1
> 0 1
> 0 1
>
> The command I ran looks like this:
>
> palm -i tfMRI_EmoRec_ES_vs_HS_s5_beta.dscalar.nii -n 0 -transposedata -o EmoRec_ES_vs_HS_PALM -logp -d design.csv -t contrast.csv -ise -saveglm
>
> And I got this error.
>
> Found FSL in /gpfs1/arch/x86_64-rhel7/fsl-5.0.11/fsl
> Found FreeSurfer in /gpfs1/arch/x86_64-rhel7/freesurfer-5.3.0-HCP
> Found HCP Workbench executable in /gpfs1/home/y/h/yhan8/tools/workbench/bin_rh_linux64/wb_command
> Reading input 1/1: tfMRI_EmoRec_ES_vs_HS_s5_beta.dscalar.nii
> Error using permute ([log in to unmask]:10)
> file_array objects can not be permuted.
>
> Error in gifti_Data ([log in to unmask]:201->permute)
> Error in gifti_DataArray ([log in to unmask]:122->gifti_Data)
> Error in read_gifti_file ([log in to unmask]:45->gifti_DataArray)
> Error in gifti ([log in to unmask]:89->read_gifti_file)
> Error in palm_ciftiread (/users/y/h/yhan8/PALM/palm-alpha114/palm_ciftiread.m:84->gifti)
> Error in palm_miscread (/users/y/h/yhan8/PALM/palm-alpha114/palm_miscread.m:181->palm_ciftiread)
> Error in palm_ready (/users/y/h/yhan8/PALM/palm-alpha114/palm_ready.m:47->palm_miscread)
> Error in palm_takeargs (/users/y/h/yhan8/PALM/palm-alpha114/palm_takeargs.m:1645->palm_ready)
> Error in palm_core (/users/y/h/yhan8/PALM/palm-alpha114/palm_core.m:33->palm_takeargs)
> Error in palm (/users/y/h/yhan8/PALM/palm-alpha114/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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