***UCF Files

Background Images

CSPM can create background images using the "Anatomical" section. These images should then be copied somewhere else, and a good idea is to make them read-only. If you are using CSPM, here is a Document Icon video that explains how the files should be moved from the analysis results to the Study Data folders.

Tracing Protocols

Iowa
Several structures

Caudate
caudate, Iowa; bipolar paper; pediatric depression

Hippocampus
Ammar developed his protocol based on talking with Jennifer, and referring to the following protocols, and the atlases.
Iowa and Mayo, recommend by LONI
LONI Hippocampus
Japanese

Using MRIcroN

You can now open nifti (*.nii) files as VOI files, and you can save the voi as nifti files, so you no longer need to save the voi files.

Previously, the VOI had to be saved as voi files, then exported each time they were changed:
Once you have created and saved a VOI, export it to a Nifti file (Draw => Convert => "VOI->NII"). Name the file something like "SUB106_hippocampus_left_Christiane."

Storing VOI Images

Once you have drawn the VOI and saved (no longer exported) it as a Nifti file, you can save it to a subject structure folder. The naming convention is "[structure name]_[optional "left_" / "right_" for bilateral structures]_[tracer name]."

Examples:

...\hippocampus_right_Ammar
...\caudate_left_Kasein
...\corpuscallosum_JoePae

If you are not blinded, use the folders within "MRI Study Data" on the W: drive. Each subject's folder has a "VOI" subfolder, and within that there are subfolders for all image sets on which VOI are drawn, labeled "imageset1," imageset2," etc. Often there will only be one image set. The image set folder contains the high-reslution anatomical file for tracing, usually rigid-body registered to the template space. There will also be segmented gray, white and CSG, and the spatial normalization parameters. All VOI go in subfolders of the imageset folders.

Example:
W:\MRI Study Data\CCHS\CCHSC101\VOI\imageset1\hippocampus_left_JoePae

If you are blinded, create a subject folder (e.g., ...\SUB101), and place the structure folder there.

Example:
Y:\Ammar\Tracing\SUB101\hippocampus_left_Ammar

Scaling for head size

Affine is an alternative to TIV scaling - both affine and TIV are ways of attempting to account for differences in head size. Here are three ways I can think of account for head size:

As a reminder, TIV = total intracranial volume = volume of areas of brain + CSF.

Use the raw values with TIV as a covariate
TIV - better than affine in my opinion - simply put, the each subject's VOI's are zoomed in or out so that the TIV of that subject matches the mean TIV - so the shape of the VOI is unchanged, even though it is expanded/shrunk.
Aaffine - this is a traditional version used by LONI; affine is a type of transformation (normalization) based on simple calculations; in this case it's a 9-parameter transformation (there are 6, 9, 12, and 15 versions); 6 parameters are a rigid body shift = shift in space (x/y/z changes) + rotation (yaw/pitch/roll), and the extra 3 parameters are scaling in the x/y/z direction. The problem with affine I see is that you get different scaling in the x/y/z directions, which means the VOI changes shape. Another problem is that, unlike TIV, it is based on normalizing the whole head, and the skulls can be pretty different - fat deposits, thickness of bone, etc.

Visualizing

1) ShapeViewer for UCF files

The LONI ShapeViewer comes with CSPM (CSPM GUI, Shape menu, view UCF). You will need to install java jre and java3d before it will run.
java jre
If you have a 64-bit system, open a 64-bit browser, typically "internet explorer (64-bit)" under Programs in the Start menu. Google java jre, and download and install. If you have a 32-bit system, just use any browser. You should end up with folder "C:\Program Files\java\jre7", which has folders "bin" and "lib"; you will need this to install java 3d.
java 3d
Google java3d api se desktop technologies, and download the appropriate version for your operating system. You will download a zipped file with a couple of subfolders in it ("bin" and "lib"). Unzip these subfolders, and copy them into the java jre folder (above), so that the "bin" files from the java3d go with the "bin" files for java jre (ditto for "lib"). You should now be able to open and view ucf files in the ShapeViewer.
Tip: once you have opend the ShapeViewer, you can drag UCF a file from an explorer window into the ShapeViewer to open it.

2) MRICROGL for nii and voi files

Chris Rorden, who wrote MRIcroN, also has a 3D viewer which can be useful for viewing *.voi or *.nii files. Google mricrogl, and you'll download a zipped file. Unzip this file, and I'd suggest putting it into into "C:\Program Files\mricrogl" (or "C:\Program Files (x86)\mricrogl" for 64-bit systems). Make a link to the executable "mricrogl" (right-click, Send to Desktop (create shortcut).

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