T1 Pre Processing
sMRI data can be processed in a variety of ways, however in order to run to run Diffusion Analysis Mapping you will need to generate two things.
1)Tissue segmented image
2)Surface mesh for either the cortical surface or white matter.
Fortunately, FREESURFER has largely automated tools for running through your processing steps. Alternatively, you can process data through the LONI PIPELINE. Below are a few steps that will take raw siemens dicom data, convert it to .nii, and then run it through Freesurfer's recon-all using the LONI pipeline.
1)To convert Siemens dicom data to .nii or nii.gz format, use the following pipeline: Dicom_to_nii.pipe. Nii is a good format to use because it preserves the left right orientation of your scan. Hopefully, this will prevent any flipping down the line, however, please check the output and customize for your own data.
2)To run Recon-all on the LONI PIPELINE. You will have to edit a download recon-all.pipe. This will set up your data structure so that freesurfer can run correctly through the Pipeline and it will take it through autorecon1, 2, & 3. Note~ You will need to edit the executable path and input volume paths to fit your data. If you are new to the Pipeline, take a look at the website for some basic tutorials.