the have.fsl command is true but i am facing the error of finding FSLDIR #12
Comments
|
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
—
You are receiving this because you are subscribed to this thread.
Reply to this email directly, view it on GitHub
<#12>, or unsubscribe
<https://github.com/notifications/unsubscribe-auth/AAIGPLQKPO52OE4XKYPZD3TUB34KNANCNFSM5D7QH62A>
.
Triage notifications on the go with GitHub Mobile for iOS
<https://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675>
or Android
<https://play.google.com/store/apps/details?id=com.github.android&referrer=utm_campaign%3Dnotification-email%26utm_medium%3Demail%26utm_source%3Dgithub>.
--
Best,
John
|
|
dear John thanks for your reply. |
|
when installing as I read in git hub apparently there is no way to solve this error |
|
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?
—
You are receiving this because you commented.
Reply to this email directly, view it on GitHub
<#12 (comment)>,
or unsubscribe
<https://github.com/notifications/unsubscribe-auth/AAIGPLQ7UQ32WHOY2Y4RNILUB5RE5ANCNFSM5D7QH62A>
.
Triage notifications on the go with GitHub Mobile for iOS
<https://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675>
or Android
<https://play.google.com/store/apps/details?id=com.github.android&referrer=utm_campaign%3Dnotification-email%26utm_medium%3Demail%26utm_source%3Dgithub>.
|
|
the codes i mentioned where picked from theme 3 of course and are designed for R |
|
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>
—
You are receiving this because you commented.
Reply to this email directly, view it on GitHub
<#12 (comment)>,
or unsubscribe
<https://github.com/notifications/unsubscribe-auth/AAIGPLSXDL7KCRMPTYX34RLUB5TATANCNFSM5D7QH62A>
.
Triage notifications on the go with GitHub Mobile for iOS
<https://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675>
or Android
<https://play.google.com/store/apps/details?id=com.github.android&referrer=utm_campaign%3Dnotification-email%26utm_medium%3Demail%26utm_source%3Dgithub>.
|
|
|
|
|
|
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
—
You are receiving this because you commented.
Reply to this email directly, view it on GitHub
<#12 (comment)>,
or unsubscribe
<https://github.com/notifications/unsubscribe-auth/AAIGPLSNC7V5LAM4S4NOHWTUB5ZNVANCNFSM5D7QH62A>
.
Triage notifications on the go with GitHub Mobile for iOS
<https://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675>
or Android
<https://play.google.com/store/apps/details?id=com.github.android&referrer=utm_campaign%3Dnotification-email%26utm_medium%3Demail%26utm_source%3Dgithub>.
|
|
Sorry John but i don't know how to run R in VMware virtual machine |
|
|
|
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
—
You are receiving this because you commented.
Reply to this email directly, view it on GitHub
<#12 (comment)>,
or unsubscribe
<https://github.com/notifications/unsubscribe-auth/AAIGPLRCLMXINPRYW4QUM2LUB6CN5ANCNFSM5D7QH62A>
.
Triage notifications on the go with GitHub Mobile for iOS
<https://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675>
or Android
<https://play.google.com/store/apps/details?id=com.github.android&referrer=utm_campaign%3Dnotification-email%26utm_medium%3Demail%26utm_source%3Dgithub>.
|
|
thanks a lot, John. my issue was resolved. I truly appreciate your help and dedication |
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
here is the code
Error in system(cmd, intern = TRUE) :
'FSLDIR="C:/Users/Asus/FSL/FSLVm7_64.vmwarevm";' not found
The text was updated successfully, but these errors were encountered: