Using DESPOT T1 and PD maps to create synthetic T1-weighted volume

command TR FA TE Path_to_T1Map Path_to_PDmap Path_to_output
- I have followed example give by freesurfer to achieve optimal contrast
TR= 20ms
Flip angle = 30 degrees
TE = 5ms

% mri_synthesize 20 30 5 /home/../T1_map.mgz /home/../PD_map.mgz /home/...synth_output.mgh

Freesurfer vertex-wise ROI analysis using Desikan atlas annotation

# Use mri_annotation2label to create labels from the annotations of the Desikan atlas. Apply this to fsaverage, so that the label is in common space.
# If freesurfer is run on a network you might have fsaverage in your project directory, but this might just be a link. So you may need to delete the link, and copy the directory 'fsaverage' from the source e.g. /software/system/.../freesurfer/fsaverage into your project directory - this will mean that it will be editable.

% mri_annotation2label --subject fsaverage \
--hemi lh \
--outdir fsaverage/label

or

% mri_annotation2label --subject fsaverage \
--hemi lh \
--annotation aparc.a2009s \
--outdir fsaverage/label


# You can also apply this command to individual subjects, but it will be in subject space not common space.

# You then need set up your environment for analysis - see GroupAnalysis page.
# Following the steps for resampling and smoothing but instead of using the --cortex option you will need to specify the label you'd like to use. - It is important not to smooth the whole brain here, you only want to smooth the region that you are interested in analysing. for example,

% mris_preproc --fsgd YOURFILE.fsgd \
  --target fsaverage --hemi lh \
  --meas thickness \
  --out lh.YOURFILE.thickness.00.mgh
% mri_surf2surf  --hemi lh \
  --s fsaverage \
  --sval lh.YOURFILE.thickness.00.mgh \
  --fwhm 10 \
  --label-trg /path/to/fsaverage/label
  --tval lh.YOURFILE.thickness.10B.mgh

# You can then run your analysis remembering to specify that you only want to analyse the region specified.

% mri_glmfit \

  --y lh.YOURFILE.thickness.10.mgh \

  --fsgd YOURFILE.fsgd dods\

  --C lh-Avg-thickness-age-Cor.mtx \

  --surf fsaverage lh \

  --label /path/to/fsaverage/label

  --glmdir lh.YOURFILE.glmdir

# Overlaying just the labels onto an inflated brain.
% tksurfer fsaverage lh inflated

Then go to File - Label - Load label
Repeat for all labels necessary
Save tiff.