T-5: First steps for SPM analysis

First steps for SPM analysis¶

I'm doing most of my work remotely this summer, by using ssh to access my work computer.
So I'll be doing mostly everything using the command line. There were a few tools that
I did not know existed until fairly recently.

1. Open a window with ssh for viewing figures, gui's, ect. Uses XQuartz (Mac connecting to Ubuntu)

ssh -X username@remoteconnection

2. Use wget to download files (Ubuntu). Specifically, see the SPM dataset files below

# download the spm structural MRI data
wget http://www.fil.ion.ucl.ac.uk/spm/download/data/mmfaces/multimodal_smri.zip

# download the fMRI data
wget http://www.fil.ion.ucl.ac.uk/spm/download/data/mmfaces/multimodal_fmri.zip

# download the EEG data
wget http://www.fil.ion.ucl.ac.uk/spm/download/data/mmfaces/multimodal_eeg.zip

# download the MEG data
wget http://www.fil.ion.ucl.ac.uk/spm/download/data/mmfaces/multimodal_meg.zip

3. Unzip files from command line (Ubuntu)

# decompress the spm structural MRI data
unzip http://www.fil.ion.ucl.ac.uk/spm/download/data/mmfaces/multimodal_smri.zip

# decompress the fMRI data
unzip http://www.fil.ion.ucl.ac.uk/spm/download/data/mmfaces/multimodal_fmri.zip

# decompress the EEG data
unzip http://www.fil.ion.ucl.ac.uk/spm/download/data/mmfaces/multimodal_eeg.zip

# decompress the MEG data
unzip http://www.fil.ion.ucl.ac.uk/spm/download/data/mmfaces/multimodal_meg.zip

4. Perform reconstruction on sMRI data

# set subjects directory
export SUBJECTS_DIR=/data/users/alanData/SPM-face/subjects

# convert .img format to .mgz
recon-all -i /data/users/alanData/SPM-face/sMRI/smri.img -subject SPM

# perform segmentation
recon-all -subject SPM -all