Thus, most freesurfer functional commands will be run in dicomdir. In my case, the project directory is dicomdir. While freesurfer says to run commands in the project directory. What did you do in freesurfer? What folder structure did you create?įor anatomical scans, I filled the folder Jess/RAW_data with dicom scans and reconstructed them into a SUBJECTS_DIR called Jess/Subjects.įor functional scans, I created a new folder Jess/V1_REST_STUDY/dicomdir. Some important functions are implementation and manual correction of anatomical MRI data, the entire functional preprocessing pipeline from raw functional data to biologically meaningful extractable data, region definition, and time course extraction. Many things! But importantly, look through my lab manuals to get a sense of what (and more importantly how) I implemented freesurfer functions. I spend most of my work using the command line. There are some GUI operations in freesurfer but I mostly used the GUI freeview and tkmedit to visual scans. You can run commands in freesurfer from the command line using linux. Freesurfer is in fact used by the large neuroimaging compilation project (1200+ subject scans), the Human Connectome Project. If you're working with the Caramazza Lab, I still have my lab manuals for reference.įreesufer is a program created at Charles MGH that packages many functions in neuroimaging for widespread use. Look to the following document for an overview of these functions, my presentation, my weekly summaries for a sense of when I implemented what. In this document, along with a main focus on freesurfer, I mention important notes for operating the terminal (using bash scripts) along with some scripts in MATLAB.

Some analysis I implemented included dicom to NIFTI conversion, recon-all anatomical reconstruction and manual correction, functional scan preprocessing, region definition (segmentation transfer), and time course extraction.

Over the course of the summer, I worked largely with freesurfer to conduct preprocessing on a sample of blind and sighted subjects with structural and functional MRI scans. I worked at the Caramazza Lab with the postdoctoral fellow Ella Striem-Amit for summer of 2017.

How to open dicomdir file in matlab