help
help > RE: Computing first-level results
Nov 16, 2015 06:11 PM | Alfonso Nieto-Castanon - Boston University
RE: Computing first-level results
Dear Ruth,
Regarding the ROI-to-ROI results, the only reason I can think of that may cause the GUI to simply switch you to ROI-to-ROI results without warning would be if either: a) in the corresponding first-level analysis tab the analysis options contain the 'ROI-to-ROI only' field (instead of the 'ROI-to-ROI and seed-to-voxel' field); or b) in the Setup.Options tab, the 'Seed-to-Voxel' analysis checkbox is unchecked. Could you please check if any of these is the case here? (and if not please send me you conn*.mat file and I will take a quick look to see if I can figure out the source of this issue)
And regarding the dynamic analyses, could you please send me the file named 'dyn_Base.mat' in the conn*/results/preprocessing folder to see if that helps me figure out the missing-second-run issue as well? The folder structure that you describe sounds perfectly fine, the additional BETA_* files in the Dynamic factor_01 folder would indicate that you have re-run those analyses to include seed-to-voxel analyses as well. Those "Dynamic factor #" folders contain the 'factor loading' analyses (PPI analyses where each temporal factor estimated in the dynamic FC step is used as a modulatory term). These are re-run automatically by the dynFC step if the 'Estimate dynamic loadings' checkbox is checked (and by default it will only run ROI-to-ROI analyses), but it is perfectly fine to re-run them manually later to also include the 'seed-to-voxel' results.
Hope this helps
Alfonso
Originally posted by Ruth Shaffer:
Regarding the ROI-to-ROI results, the only reason I can think of that may cause the GUI to simply switch you to ROI-to-ROI results without warning would be if either: a) in the corresponding first-level analysis tab the analysis options contain the 'ROI-to-ROI only' field (instead of the 'ROI-to-ROI and seed-to-voxel' field); or b) in the Setup.Options tab, the 'Seed-to-Voxel' analysis checkbox is unchecked. Could you please check if any of these is the case here? (and if not please send me you conn*.mat file and I will take a quick look to see if I can figure out the source of this issue)
And regarding the dynamic analyses, could you please send me the file named 'dyn_Base.mat' in the conn*/results/preprocessing folder to see if that helps me figure out the missing-second-run issue as well? The folder structure that you describe sounds perfectly fine, the additional BETA_* files in the Dynamic factor_01 folder would indicate that you have re-run those analyses to include seed-to-voxel analyses as well. Those "Dynamic factor #" folders contain the 'factor loading' analyses (PPI analyses where each temporal factor estimated in the dynamic FC step is used as a modulatory term). These are re-run automatically by the dynFC step if the 'Estimate dynamic loadings' checkbox is checked (and by default it will only run ROI-to-ROI analyses), but it is perfectly fine to re-run them manually later to also include the 'seed-to-voxel' results.
Hope this helps
Alfonso
Originally posted by Ruth Shaffer:
Dear Alfonso,
Thank you for your reply! Unfortunately, the problem occurs when I select the correct analysis name. When I select an analysis name for which the first level ROI-to-ROI results were not run, it warns me that the results have not been run. However, when I select the analysis name for which the first level ROI-to-ROI results have been run (along with the seed-to-voxel results), it simply defaults to the Seed-to-voxel tab, rather than showing the ROI-to-ROI results.
Additionally, for the second question, in the "explore factors" tab, the plot that appears shows factor scores for the first session, and, although an area is present denoting the second session, there are no factor scores/lines reporting the information, it simply appears blank. (I also tried running session 2 separately (and did not select both conditions), and the first session is still the only session present. (However, for other analyses such as voxel-to-voxel and seed-to-voxel, the second session is present/working fine.)
One thing I just noticed is that when I look in the first level results folder, there appear to be folders called "Dynamic factor _01" with folders for 01 through 10. Inside the first folder (01) there are files called BETA_Subject#_Condition#_Source# where both conditions 001 and 002 are present for each subject (additional files in this folder include corr, p_corr, pFDR_corr, and se). The rest of the Dynamic factor folders (02-10) have different contents with files named resultsROI_Subject#_Condition#.mat where condition # is 001 and 002. I wonder if the first folder contains ROI-to-ROI information, rather than Dynamic FC information.
One last thing of note is that the first level folder (that contains the analysis folders and the Dynamic factor folders 01-10) also contains files (not in any folder) called BETA_Subject#_Condition#_Measure#_Componenet#.nii with conditions 001 and 002, and additional files named PCAcov_Measure#_Component#.nii, and finally a mat file called TEMPORAL1_Measure001. Is it possible that the information is all there but that the folders / files somehow got in the wrong place, or should these folders be arranged in this way?
Thank you again so much for your help on this!
Ruth
Thank you for your reply! Unfortunately, the problem occurs when I select the correct analysis name. When I select an analysis name for which the first level ROI-to-ROI results were not run, it warns me that the results have not been run. However, when I select the analysis name for which the first level ROI-to-ROI results have been run (along with the seed-to-voxel results), it simply defaults to the Seed-to-voxel tab, rather than showing the ROI-to-ROI results.
Additionally, for the second question, in the "explore factors" tab, the plot that appears shows factor scores for the first session, and, although an area is present denoting the second session, there are no factor scores/lines reporting the information, it simply appears blank. (I also tried running session 2 separately (and did not select both conditions), and the first session is still the only session present. (However, for other analyses such as voxel-to-voxel and seed-to-voxel, the second session is present/working fine.)
One thing I just noticed is that when I look in the first level results folder, there appear to be folders called "Dynamic factor _01" with folders for 01 through 10. Inside the first folder (01) there are files called BETA_Subject#_Condition#_Source# where both conditions 001 and 002 are present for each subject (additional files in this folder include corr, p_corr, pFDR_corr, and se). The rest of the Dynamic factor folders (02-10) have different contents with files named resultsROI_Subject#_Condition#.mat where condition # is 001 and 002. I wonder if the first folder contains ROI-to-ROI information, rather than Dynamic FC information.
One last thing of note is that the first level folder (that contains the analysis folders and the Dynamic factor folders 01-10) also contains files (not in any folder) called BETA_Subject#_Condition#_Measure#_Componenet#.nii with conditions 001 and 002, and additional files named PCAcov_Measure#_Component#.nii, and finally a mat file called TEMPORAL1_Measure001. Is it possible that the information is all there but that the folders / files somehow got in the wrong place, or should these folders be arranged in this way?
Thank you again so much for your help on this!
Ruth
Threaded View
| Title | Author | Date |
|---|---|---|
| Ruth Shaffer | Nov 11, 2015 | |
| Alfonso Nieto-Castanon | Nov 12, 2015 | |
| Ruth Shaffer | Nov 12, 2015 | |
| Alfonso Nieto-Castanon | Nov 16, 2015 | |
| Ruth Shaffer | Nov 17, 2015 | |