Unfolding 

1. Setting up the files

• After the segmentation, you should have two files, entitled grayleft, and grayright.

• Create two separate directories on your UNIX machine in your segmentation directory, unfoldleft, and unfoldright, and put grayleft and grayright into the appropriate subdirectories:

cd HC-Subj/segment
mkdir unfoldleft
mv grayleft unfoldleft/.
mkdir unfoldright
mv grayright unfoldright/.
 
• You need to copy 3 additional files in each of the unfoldleft and unfoldright directories (DoMe6.m, UnfParams6.m, and runme6.m) ... these can be gotten from the HFM-unfoldingscripts tarfile/directory.
• Edit the file UnfParams6.m in both directories using nedit or emacs. You need to change two things:
• Make sure you specify the correct filename, that is, change the line:
graphFile='grayleft';
To say grayleft for the unfoldleft directory, and grayright for the unfoldright directory
• Make sure the following lines are present with the correct numbers:
xmmpix = 200/512; X field of view divided by the number of voxels in the structural image = mm per pixel
ymmpix = 200/512; Same for Y = mm per pixel
zmmpix = 3/7; Z thickness in mm divided by the number of interpolated slices = mm per interpolated slice
• Enter in the correct coordinates for the startpoint. You should have written down this number at the end of the segmentation. If not, go back to the segmentation, grow the gray matter, and find a gray matter start point near the center of the volume.
startPoint = [56 68 216];
Be sure to save the file!

2. Running the unfolding

• The best way to run the unfolding is overnight via the nohup command. It needs to run overnight because it will otherwise suck up a lot of processing power during the daytime (if needbe, though, you could theoretically run it during the day using the nice command, or if you have your own computer that no one else uses, just run it in the foreground by going to the unfoldleft directory, typing matlab6 -nojvm, and then runme6)
• Go to a mac or PC, and run telnet (not MacX, because it is better to have visual displays disabled) and cd into the unfoldleft directory.
cd unfoldleft
• You need about 30 megs free minimum for each hemisphere. Check this with the df command.
df -k .
• Start the process with a nohup command.
/usr/bin/nohup matlab6 -nojvm < runme6.m &
• The process will start and continue going even after you log out until it is done. It will output all text to the file nohup.out. After about 1 minute, check to make sure that it is doing OK by typing:
more nohup.out
You should see something like this:
                            < M A T L A B (R) >
                (c) Copyright 1984-03 The MathWorks, Inc.
                            All Rights Reserved
                               Version 6



Commands to get started: intro, demo, help help
Commands for more information: help, whatsnew, info, subscribe

>>
paramsFile =

UnfParams

Initializations
dimdist =
    0.3906    0.3906    0.4286

startNode =
       49641

Unfolding 96979 points; 150 mm from calcarine fundus.
Loading gray graph file: grayleft.
Read in unfList.
Calling unfoldDist ...
96979 unfold points out of 96980 gray nodes.
Subsampling layer 1 nodes at 1.50 mm

3. Making sure it worked

• The next morning, check to make sure the following files are all present
sampLocsF.mat, flat.mat, dist.mat
• Also, view the file nohup.out (or the log in your matlab window) and make sure there were no errors
  
• If sampLocsF.mat is not present, then more the nohup file:
more nohup.out
If you see the following lines, then there was a topological error in your segmentation:
Bad sample positions
You need to fix the segmentation, and unfold this fixed segmentation.
• After this hemisphere is verified to run correctly by all 3 files being present, run the opposite hemisphere.

4. Putting the appropriate links in place

• Go to the directory /usr/local/mri/anatomy (which you created beforehand)
cd /usr/local/mri/anatomy
• Make a directory for your subject, and create a directory structure as follows
mkdir HC-Subject
cd HC-Subject
mkdir left left/unfold right right/unfold
• Provide a link to the vAnatFSE512Crop106.dat anatomy file, calling it vAnatomy.dat
ln -s /f/d/zeineh/HC-Subject/segment/vAnatFSE512Crop106.dat vAnatomy.dat
• Provide links to the outputs of the unfolding algorithms in the left/unfold and right/unfold directories
cd left/unfold
ln -s /f/d/zeineh/HC-Subject/segment/unfoldleft/dist.mat
ln -s /f/d/zeineh/HC-Subject/segment/unfoldleft/flat.mat
ln -s /f/d/zeineh/HC-Subject/segment/unfoldleft/sampLocsF.mat
cd ../..
cd right/unfold
ln -s /f/d/zeineh/HC-Subject/segment/unfoldright/dist.mat
ln -s /f/d/zeineh/HC-Subject/segment/unfoldright/flat.mat
ln -s /f/d/zeineh/HC-Subject/segment/unfoldright/sampLocsF.mat

• You are now ready to run the HFM Module!
 

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