Re: [Freesurfer] Help with LGI pipeline output - Freeview

First, try using tksurferfv (this is the freeview version of tksurfer; tksurfer is obsolete) Second, you'll have to tell us more than "it did not work" (eg, send the terminal output or some other description) On 6/21/2021 3:03 PM, Lab of Autism and Developmental Neuroscience, Lab of Autism

[Freesurfer] Help with LGI pipeline output - Freeview

External Email - Use Caution Dear FreeSurfer experts, Hope that everyone is well and having a great Monday. I am having some trouble opening the outputs for the LGI pipeline via Freeview - could someone please help me with this? I tried using + editing the code available on the

Re: [Freesurfer] Help with LGI

External Email - Use Caution Dear Tim, 1) Here is the output after I type matlab: - Matlab does open, and the following appears on terminal: shell-init: error retrieving current directory: getcwd: cannot access parent directories: No such file or directory pwd: error retrieving

Re: [Freesurfer] Help with LGI

External Email - Use Caution Looks like something is wrong with the Matlab installation. It would be good to know: 1) What happens if you type 'matlab' in your shell? 2) What happens if you type '/Applications/MATLAB_R2020a/bin/matlab' in your shell? Best, Tim > On August 4,

Re: [Freesurfer] Help with LGI

External Email - Use Caution Dear Freesurfer experts, Just wanted to follow up my last email - does anyone know what might be wrong with my code? Thank you and stay safe, Alex On Sat, Aug 1, 2020 at 5:40 PM Lab of Autism and Developmental Neuroscience, Lab of Autism and

Re: [Freesurfer] Help with LGI

External Email - Use Caution Dear Douglas, Yes, now matlab is correctly set to my freesurfer path, but the following error occurs when I run localGI (please see below). Any ideas what might be wrong? Maybe there are some issues with the matlab version or image processing toolbox

Re: [Freesurfer] Help with LGI

If you type matlab at the command line, does matlab start? On 7/12/2020 10:42 PM, Lab of Autism and Developmental Neuroscience, Lab of Autism and Developmental Neuroscience wrote: External Email - Use Caution Dear Freesurfer experts, I have added Matlab my path and either the same

Re: [Freesurfer] Help with LGI

External Email - Use Caution Dear Freesurfer experts, I have added Matlab my path and either the same error (please see my first email) occurs, or recon-all -s (ID) -localGI command is said to 'not exist'. Any other ideas on how to properly solve this problem? Thank you and hope

Re: [Freesurfer] Help with LGI

External Email - Use Caution Dear Douglas, So to accomplish this, should I do the following through matlab? The following code has to be in matlab’s startup.m file: 1 2 3 4 5 6 7 8 9 % FreeSurfer -% fshome = getenv('FREESURFER_HOME');

Re: [Freesurfer] Help with LGI

You need to have matlab in your path so that when you type "matlab" it starts matlab On 7/9/2020 4:58 PM, Lab of Autism and Developmental Neuroscience, Lab of Autism and Developmental Neuroscience wrote: External Email - Use Caution Dear Freesurfer experts, I'm needing some simple

[Freesurfer] Help with LGI

External Email - Use Caution Dear Freesurfer experts, I'm needing some simple help running LGI. After downloading MATLAB + Image processing toolbox and double checking if the ?h.pial file is located in the SUBJECT_DIR, the recon-all -s (subject_ID) -localGI command still doesn't