Fls tools

[MRI]

Hi

I am new to Mac as I use Linux most of the time. I was wondering how to set a working directory using the terminal. For example, I use fslmaths, which is one of the fsl software tools, on my MRI datasets in a specific directory. However, it complains that no such file. I think fslmaths searchs for the file outside the current working directory. any hint please?

One example:
Image Exception : #63 :: No image files match: aseg-in-rawavg_lower_thresholded_CC_Whole.img

I am using it in Mac OS (bash shell).

The fsl setup is as follows:
# FSL Setup
FSLDIR=/Users/imaging/fsl
PATH=${FSLDIR}/share/fsl/bin:${PATH}
export FSLDIR PATH
. ${FSLDIR}/etc/fslconf/fsl.sh


Thanks in advance,

 

[deliriouscat]

When using the terminal, you can change your working directory using the 'cd' (change directory) command followed by the path of the directory you want to navigate to.

If you are unsure about the absolute path of your file, you can use the 'pwd' command (Print Working Directory) to show the full path of the current directory. Then, you can provide this full path to your file while running fslmaths.

Here is a guide on how to use Terminal on a Mac that might be helpful.

 

[MRI]

When using the terminal, you can change your working directory using the 'cd' (change directory) command followed by the path of the directory you want to navigate to.

If you are unsure about the absolute path of your file, you can use the 'pwd' command (Print Working Directory) to show the full path of the current directory. Then, you can provide this full path to your file while running fslmaths.

Here is a guide on how to use Terminal on a Mac that might be helpful.

Thanks alot.
I run the fslmaths in the directory (folder) of my files. Do I have to also to repoint the fslmaths to the directory of my files??

 

[deliriouscat]

When using 'fslmaths' or any other command line tool, you usually need to either be in the same directory as your files or provide the full path to your files. So if your MRI dataset is in a specific directory, you should 'cd' into that directory first before running 'fslmaths'. If the files are in another directory, you should provide the full path to the files when you run 'fslmaths'.

 

[MRI]

When using 'fslmaths' or any other command line tool, you usually need to either be in the same directory as your files or provide the full path to your files. So if your MRI dataset is in a specific directory, you should 'cd' into that directory first before running 'fslmaths'. If the files are in another directory, you should provide the full path to the files when you run 'fslmaths'.

Hi,
I am not sure if you did get my question right. I don't need to know how to change a directory. Thank you