BOLDfold steps

  1. The following steps assume that the necessary data exist in the current directory in spr/sdt (stimulate) format.

  2. Start up the BOLDfold program by typing "bfold" at the Unix prompt.

  3. The BOLDfold program will ask you if you want to use the old parameters or new parameters. For the first dataset you analyze, select new parameters, by typing "2".

  4. For cluster type "1" for "unclustered"; the "clustered" option was (is) experimental and never produced anything useful (it tried to combine spatial correlation with temporal correlation).

  5. Next, BOLDfold will ask you if you want to specify an eta cutoff. Select "Specify an eta cutoff" (type "1"). Specify "0.6" as your eta cutoff.

  6. Next, BOLDfold will ask you what the first volume of the first period is. This corresponds to the amount of volumes at the beginning of the dataset that you do not need for the BOLDfold analysis. For most experimental designs, this will probably be a small number, almost always no less than 5. Recommended value is 5. Refer to your design specifications for the exact number. [See the BOLDfold preprint for a description of the repeated, event-related experimental design required by the BOLDfold program. Another example experimental design may also be found on the comparisons web page.]

  7. Next up is the length of the period, in volumes. This is the number of volumes of images that are taken during the stimulus and the rest period, as well as any warnings, such as fixation crosses. It is the block of volumes that repeats a number of times during the experiment. This number will be different for each experimental design.

  8. Next is the number of volumes between each period. Most often, this is zero (the periods are "shoulder to shoulder" with each other).

  9. The number of periods is the number of trials that each participant engaged in, during one session of scanning (one "run"). For instance, if the participant's task was to name numbers, and they did this 5 times while the magnet was acquiring images, the number of periods would be 5.

  10. The number of active volumes at the start of each period refers to the time, in volumes, that the participant was engaged in the experimental task.

  11. Lastly, the noise cutoff is the number above which, intensities are considered to be nothing more than noise. Choose "200", for standard experiments.

  12. Motion correction should be turned "off".

  13. Lastly, if your command shell is running off of a SPARC station and your data were acquired on the RUH MRI prior to February 2002, select "1" for computer combos, as the images were taken from a SPARC computer at the RUH facilities. (This is the case for the BioE 898 project data for 2002). If you are analyzing old (pre-February 2002) data on a linux Intel-based computer you may need to select option "2", depending on how the data were transfered (ftp, nfs, etc.). If you are analyzing new data on an old Sun workstation you may need to select option "3". For new MRI data (after February 2002) being analyzed on a linux workstation, option "4" (which is actually equivalent to "1") is to be used. This option can deal with the "big endian/little endian" mess if used correctly.

  14. When you repeat step 2 for the next sdt file in the same directory, you can use the design specifications that you just entered, if the experimental design for that next dataset is identical to the last one. To accomplish this, select "1" (old parameters) at the first prompt.