At the beginning of each section, there are some notes in RED about what the section covers. It may be that you have a certain understanding of what the section contains. If this is the case, feel free to skip ahead to a more relevant section. Sections are outlined in BLUE. AFNI buttons are presented in FUCHSIA.

A) the first step is to click on the Load. You may now choose the anatomical orientation from which to view further images. Commonly the axial orientation is chosen and click on SDT to change into the correct format. Then click Load and the slices will load. Often only the dirst slice will load and one will have to either click the up arrow to the right of Number Planes or manually enter a number...usually 10.

B) R click on Load and then click on Map from the pop-down menu. Then choose the map of interest. If wishing to view a BoldFold map choose the BF mag map as it is most useful. Make sure the format remains sdt and then click Load.

The most important of these is Pos as it is by L clicking on this button that activations will show up.

After clicking Pos the two areas Ceiling: and Floor: control the conditions that a given voxel must meet in order to be coloured. Increasing the floor (by clicking on the number to its right and entering a value) will generally reduce the number of voxels which will show up activated. How much activation is reduced depends on the type of map that was calculated. If a correlation map was calculated at 0.6 and you move the floor from 0.01 to 0.5 nothing will happen because no values below 0.6 will show up. Changing the floor and the floor in a % change map to 0.05 will remove activations for all voxels that did not show an intensity change of 5%.

ALWAYS REMEMBER IN STIMULATE THAT WHENEVER YOU ALTER A CRTIERIA ie Floor YOU MUST L CLICK ON Update Map FOR THE CHANGES TO BE SHOWN!!!

The buttons Map Max. and Map Min in the upper right hand corner of the interface control the colour pallette that will be displayed in the voxels. There is no right or wrong range for these values. The default range is from 0.01-0.10 which gives a map that has mostly yellow activations. Increasing the max value to a number like 0.3 or so should give a map with a "hot" colour scheme similar to Afni. This is all preference so if you have values that make you smile then by all means do not feel guilty by applying them.

The first step that is needed when calculating a map is to load a stim file. This is done by R clicking Load and L clicking stim. Next choose a stim file. Theese files are named by the task involved followed by the sdt suffix. For instance if one wanted to do map on case...pick case.sdt and make sure the format at the bottom of the window is in sdt. then click load.

There are several load options for sdt format. Important ones for making maps include First Time: the default for this is 0. In many instances when calculating a map you want to ignore the first few slices because the machine is equilibrating the hydrogen nuclei of the individual in the scanner and this is neither a control or stimulation period. Thus setting this to another number will ignore these equilibration scans. In many cases there are 5 scans so the first time should be 5. The first and last plane lines control the number of planes loaded. This is generally 10. When happy with the parameters selected hit Do It!

T-TEST

1) Once the stim file has been loaded you are now able to calculate a map. First, R click Calc Map. Then L click t Test.

2) Click on either Cntl or Stim depending on what the first period is.

Now fill in the Start and End lines with relevant numbers. For instance if the first period of stim or cntl is 18 scans enter 0 in start and 17 for end. Remember so much of fMRI starts at 0 so when adding it is often neccessary to add N-1. To beat this point into your head if the first period was 10 scans start would be 0 and end 9. I am not trying to mock the readers but only protect them from botched analyses that I made for this very samw reason

When done click Plot to see a graph of the parameters. This is a good check to see that the graph looks equal...a misrepresented stim or cntl period will be very obvious in this display.

3) Next L click Add under the box headed by T Tests.

L click All which is under the box that says T Test Periods.

4) BckGnd Thresh: limits evaluation to voxels that have a signal greater than the number entered in this space. By convention we choose 200.00 which removes any small activations that are outside the brain.

5) Confidence: voxels whose t-test values are below this threshold will be given a map value of zero. A very high confidencs level will work well and thus a confidence of 0.999 or greater is the norm.

6) There are two types of maps. Confidence...uses the t-test confidence values whereas Percent Change employs the ration of ave. intensity change to the mean intensity of the control period.

PZMV: period zero mean variance can be used to correct a baseline drift if suspected.

7) When all the parameters for the t-test have been entered you must save the parameters. Thus, if doing a t-test on data of the same form one is able to load these parameters without having to re- enter them.

8) Finally hit Do Map Calc and the map will calculate see section 2 for info on how to view the map if needed.

PXC: correlates data with a box car waveform.

1) R click Calc Map

2) L click PXC

4) Enter Stim Cntl periods by typing numbers beside start and end. Periods do not have to encompass the entire time course. A smaller waveform can cover the entire time frame by shifting that wave.

5) Use Plot to view the boxcar waveform at any time. The wave can have sloping sides if you do not have consecutive periods. IE if the first ten scans are Stim and the next 10 Cntl one could for the first period enter start 0 end 7 and then start 11 end 18. The program will slop the waveform between 7 and 11 etc.

6) BckGnd Thres: see T-test section

Corr. Thres: ditto

7) Corr Start and Corr End are used to shift a waveform. Use the arrows or enter a number manually to shift a waveform so that multiple identical correlations are calculated.

8) When done entering waveform L click Save and then save the parameters remembering that the same file can be loaded if a similar calculation is need in the future.

9) MAX: gives map of each voxels greatest correlation over all shifts

Shift: map of correlations at the maximally correlated waveform.

% change: maps the % change from Stim to Cntl

10) Click Do map calc

TXC: period cross correlation

1) R click Calc Map

2) L click TXC

3) R click Load

Txc parms...for previously saved parameters

ascii text...for manually entered waveforms from the text editor.

c) Choose a regino of inerest (ROI) under Mouse Fnc: I find that the best one for this task is Poly...that is a preference as the others will also work. If choosing poly find an area on the brain that has significant activations that you are interested in and then hold down L button on the mouse as the encircle these pixels.

d) Under Time Course L click Full

e) L click Plot...

f) R click Save choose ASCII Avg TC if ROI is a box or polygon.

choose ASCII Rax TC if ROI is a point.

4) Once a waveform has been specified from a ROI or enter manually choose the saved waveform which will be in the ascii tc in the TXC menu. Alter the parameters as discussed previously and then save it as txc parms. All other options have been explained previously so when finished hit Do Map Calc!

a) Load the given anatomical...eg ax.sdt (discussed previously)

b) R click Save

c) L click Anat

d) L click Real (4 byte float)

e) L click Save..before saving ensure to change the name to something memorable i.e. axfloat.sdt

2) L click Tala Coord...

3) R click Load

5) If you would like a better view of the detail of the scan the magnification can be altered by adjusting the number in the lower right hand corner. Default mag. is set to 256 = 2^8 and increasing this to 2^9 or even 10 will allow better detail especially helpful in picking the AC (anterior commissure) or PC.

6) Next pick out the AC and PC points in the sagittal section. To pick the AC first click AC and then find the point on the scan and L click. Next click PC then find the posterior commisure. The best sag slice for this is Sag Idx: 9.

7) In the axial slice next pick the AP, PP, RM and LM in the same fashion. Adjust magnification if needed. Remember to first click thich point you are picking ie AP and then find that point of the scan and click. One thing to keep in mind that is important is on the AP and PP ensure that they are in the midline. This means that you find the farthest anterior or posterior extent of the brain and then shift this point into the longitudinal fissure. The reason to do this is you want the axis for these two to run parrallel and through the longitudinal fissure.

8) Next surprise surprise one moves onto the coronal section. For a alisting of what the abbreviations for each point are check Stimulate Manual pg 67. Choose these points in the same fashion. First click either SP, IP or IC and then find the correspondeing point on the scan...shift it into the midline and then click there. This is again to ensure that the Z axis lines up with the long. fissure.

9) When all points have been set click on Proj and Pts in the bottom right hand corner to check that the axes line up reasonalby and that you have not called the inferior cerebellum the antrior commisure etc.

10) Next click Grid in order to see the grid on the brain

11) L click Dims... then L click apply. This normalizes the dimensions of the brain in question to the dimensions of the Talairach brain.

12) Lastly L click Save and then name and save your co-ordinates so that they can be loaded at a later time.