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====== V. Setting up Second-Level Analyses ====== | ====== V. Setting up Second-Level Analyses ====== | ||
- | * Bring up a Golgi window in F-Secure SSH. | ||
- | * **cd / | ||
* Type **fsl**. Click **FEAT**. | * Type **fsl**. Click **FEAT**. | ||
* Change the top left pull-down menu to **Higher-level analysis**. | * Change the top left pull-down menu to **Higher-level analysis**. | ||
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There is a good description of concepts behind higher-level analyses on the [[http:// | There is a good description of concepts behind higher-level analyses on the [[http:// | ||
- | ======= VI.Remaining Questions & Problems ======= | ||
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- | Intermittent crashes on golgi, often suggesting an "out of memory" | ||
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- | ===== Registration ===== | ||
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- | Registration is very poor for many of the spiral images | ||
- | * Should we correct for maximum image intensity in some way? | ||
- | * Do we use ORIENT files? Registration seems dubious. | ||
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- | It may be the case that if there is less than 120mm in any direction, then it will pop up the " | ||
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- | ===== Using ORIENT Files ===== | ||
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- | The ORIENT file created by Syam Gyadde seems to give better registration results for data acquired with both spiral and EPI sequences. The file is a .mat file located in / | ||
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- | == ORIENT in template.fsf == | ||
- | The last section of the template.fsf should read as follows: | ||
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- | < | ||
- | # Alternative example_func image (not derived from input 4D dataset) | ||
- | set fmri(alternative_example_func) "" | ||
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- | # Delete GLM residuals? | ||
- | set fmri(cleanup_residuals_yn) 1 | ||
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- | # Initial structural space registration initialisation transform | ||
- | set fmri(init_initial_highres) "" | ||
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- | # Structural space registration initialisation transform | ||
- | set fmri(init_highres) "" | ||
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- | # Standard space registration initialisation transform | ||
- | set fmri(init_standard) " | ||
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- | == ORIENT in batchFSL == | ||
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- | * Before the **for** loop in the batch script begins, paste the following line: | ||
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- | < | ||
- | / | ||
- | ORIENT=$FSLDATADIR/ | ||
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- | * You will also need to define the variable name **ORIENT** in your sed list: | ||
- | < | ||
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- | ===== MELODIC ICA ===== | ||
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- | ===== Second-level Analyses ===== | ||
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- | ====== Troubleshooting ====== | ||
- | === Registration problems: === | ||
- | * Problem: the data is being registered as a large, stretched-out brain, going way beyond the bounds of a normal brain | ||
- | * Solution: check the .bxh header files for your original functional data. The scanner has recently been putting out functional images with voxel sizes for anatomical images. | ||
- | * Problem: the brain is being flipped so that the frontal lobe is near the cerebellum | ||
- | * Solution: run a BET brain extraction on the anatomical data. See step 5 in the [[biac: | ||
- | === FEAT errors === | ||
- | * Problem: while running a batch script, all of the FEAT windows pop up at once even though the script is supposed to run them sequencially | ||
- | * Solution: open the script using nedit and find the line that starts with **feat** followed by some input files. | ||
- | * Problem: when running a batch script, the FEAT Watcher says that the number of volumes is 0 | ||
- | * Solution: your script is pointing to a file that doesn' | ||
- | * Problem: when running a batch script, the FEAT Watcher says that the number of volumes is incorrect (not 0, see above) | ||
- | * Solution: the batch script is most likely using a template file that assumes that all of your runs have the same number of time points. | ||
- | * Problem: the run stopped, saying the problem was possibly golgi ran out of memory | ||
- | * Solution: |