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muschellij2 / Neurohacking

Neurohacking Coursera Course
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the have.fsl command is true but i am facing the error of finding FSLDIR #12

Open amirka1379 opened 3 years ago

amirka1379 commented 3 years ago

here is the code

have.fsl() [1] TRUE getOption("fsl.path") [1] "C:/Users/Asus/FSL/FSLVm7_64.vmwarevm"

options(fsl.path = "C:/Users/Asus/FSL/FSLVm7_64.vmwarevm")

setwd("/Users/Asus/Desktop/Neurohacking_data-0.0/kirby21/visit_1/113") nim = readNIfTI("113-01-MPRAGE.nii.gz", reorient = F) mean(nim) [1] 143789.2 fslstats("113-01-MPRAGE.nii.gz", opts= "-m") FSLDIR="C:/Users/Asus/FSL/FSLVm7_64.vmwarevm"; PATH=${FSLDIR}/bin:${PATH};export PATH FSLDIR; FSLOUTPUTTYPE=NIFTI_GZ; export FSLOUTPUTTYPE; ${FSLDIR}/bin/fslstats "C:\Users\Asus\Desktop\Neurohacking_data-0.0\kirby21\visit_1\113\113-01-MPRAGE.nii.gz" -m

Error in system(cmd, intern = TRUE) : 'FSLDIR="C:/Users/Asus/FSL/FSLVm7_64.vmwarevm";' not found

muschellij2 commented 3 years ago

You need to run the commands inside the VM.

On Tue, Sep 14, 2021 at 3:43 AM amirka1379 @.***> wrote:

here is the code

have.fsl() [1] TRUE getOption("fsl.path") [1] "C:/Users/Asus/FSL/FSLVm7_64.vmwarevm"

options(fsl.path = "C:/Users/Asus/FSL/FSLVm7_64.vmwarevm")

setwd("/Users/Asus/Desktop/Neurohacking_data-0.0/kirby21/visit_1/113") nim = readNIfTI("113-01-MPRAGE.nii.gz", reorient = F) mean(nim) [1] 143789.2 fslstats("113-01-MPRAGE.nii.gz", opts= "-m") FSLDIR="C:/Users/Asus/FSL/FSLVm7_64.vmwarevm"; PATH=${FSLDIR}/bin:${PATH};export PATH FSLDIR; FSLOUTPUTTYPE=NIFTI_GZ; export FSLOUTPUTTYPE; ${FSLDIR}/bin/fslstats "C:\Users\Asus\Desktop\Neurohacking_data-0.0\kirby21\visit_1\113\113-01-MPRAGE.nii.gz" -m

Error in system(cmd, intern = TRUE) : 'FSLDIR="C:/Users/Asus/FSL/FSLVm7_64.vmwarevm";' not found

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-- Best, John

amirka1379 commented 3 years ago

dear John thanks for your reply. I was entering the code in Rstudio and R and the FSLDIR error kept popping up. after your reply, I tried running the same command in fsl terminal in VMware16 in windows 10 because you said I should enter it in virtualmachine and this is what appears for every command syntax error near unexpected token `"113-01-MPRAGE.nii.gz",'

amirka1379 commented 3 years ago

when installing devtools::install_github("muschellij2/fslr") this appears Skipping install of 'fslr' from a github remote, the SHA1 (0c588287) has not changed since last install. Use force = TRUE to force installation

as I read in git hub apparently there is no way to solve this error I ran the force command do you think it is the cause?

muschellij2 commented 3 years ago

What is the path that is coming up when you are running the command inside the VM? FSL does not run on Windows so you need the virtual machine. Best, John

On Tue, Sep 14, 2021 at 11:14 AM amirka1379 @.***> wrote:

when installing devtools::install_github("muschellij2/fslr") this appears Skipping install of 'fslr' from a github remote, the SHA1 (0c588287) has not changed since last install. Use force = TRUE to force installation

as I read in git hub apparently there is no way to solve this error I ran the force command do you think it is the cause?

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amirka1379 commented 3 years ago

the codes i mentioned where picked from theme 3 of course and are designed for R so when I run them in VM ware syntax error appears image

muschellij2 commented 3 years ago

You need to run that command within R. The code above is within bash. Please run R first. Best, John

On Tue, Sep 14, 2021 at 11:30 AM amirka1379 @.***> wrote:

the codes i mentioned where picked from theme 3 of course and are designed for R so when I run them in VM ware syntax error appears [image: image] https://user-images.githubusercontent.com/90680284/133287453-9fc69d26-cf14-4079-b0b9-7c337ef62a4e.png

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amirka1379 commented 3 years ago

image this the error

amirka1379 commented 3 years ago

image and this is R I really appreciate your help and sorry if this is going long

muschellij2 commented 3 years ago

Sorry - you need to run this in R inside the VM. So in a VM Terminal, run the command R. Now that you're in R, try the fslstats command. Best, John

On Tue, Sep 14, 2021 at 12:24 PM amirka1379 @.***> wrote:

[image: image] https://user-images.githubusercontent.com/90680284/133296319-93f49fa8-b535-4b4f-986a-feffd6f3a56d.png and this is R I really appreciate your help and sorry if this is going long

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amirka1379 commented 3 years ago

Sorry John but i don't know how to run R in VMware virtual machine image

amirka1379 commented 3 years ago

image this is ubuntu linux terminal

muschellij2 commented 3 years ago

To be clear you're using the VM provided by the course https://smart-stats-tools.org/mooc-2015? It seems as though you're using FSL's VM, which we do not support.

Best, John

On Tue, Sep 14, 2021 at 1:41 PM amirka1379 @.***> wrote:

[image: image] https://user-images.githubusercontent.com/90680284/133307140-b093cc57-5215-4a95-a102-91922e4f1283.png this is ubuntu linux terminal

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amirka1379 commented 3 years ago

thanks a lot, John. my issue was resolved. I truly appreciate your help and dedication