Dear Sir / madam,
I'm a last year student of Medical Imaging (from Hoge school Universiteit Brussel, HUB). In January i'm defending my thesis. My subject is MRI and Alzheimer's disease. With volumetry I want to show that the Hippocampi have a smaller volume then normal patients.
I used the program: SPM, VBM and IBASPM previous year, but I got weird results from those software. My supervisors said that it's probably the best to use a new software, so i'm trying to use Freesurfer.
I'm not used to programming with Linux (Xbuntu), so it's a bit difficult for me personally. Also the physicist (who i colaborate with) isn't used to programming.
This is my problem: When i open Virtualbox (installed with freesurfer-Virtualbox-linux-x86-stable-pub-v5.3-full) I go to
file-system -> usr -> local -> freesurfer -> subjects (the map where also the subject"Bert" is in it). In the subject-folder is paste a folder with only T1-Dicom images.
After i copied & pasted the DICOM-files in the subjects folder, i go to the "terminal". There I type: "tcsh" to setup freesurfer (I read it on the Freesurfer wiki site).
After that I type:
recon-all -s <new folder where the new made files are putted in> \ -i $SUBJECTS_DIR/<name of the folder where my DICOM-files are in (here i made an archive of the DICOM-files, extented with .mgz) > \ -autorecon1
When i hit Enter, i get a message that says: "tcsh v6.17.06 has an exit code bug! Please update tcsh!"
There is also a new folder created, with some subfolders (BEM, label, scripts , MRI ,etc.). But there is nothing to see in those folders.
My question is how can I update tcsh so I can do the recon-all procedure?
Hopefully you can help me,
Thank you in advance, Kind regards,
Philippe Blaes (3rd year Medical Imaging)