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help > RE: saving thresholded mask image (second level)
Mar 31, 2016 05:03 PM | Alfonso Nieto-Castanon - Boston University
RE: saving thresholded mask image (second level)
Hi Matt,
Yes, you may use something like the following:
h = conn_display('SPM.mat',1); % loads second-level results
conn_display(h,'vox-thr',{.005,1}); % sets voxel-level threshold (p-uncorrected < .005)
conn_display(h,'clu-thr',{.05,3}); % sets cluster-level threshold (p-FDR<.05)
conn_display(h,'switch',1); % sets one-sided positive stats
conn_display(h,'export_mask','masfilenamePos.nii'); % exports mask file
conn_display(h,'switch',2); % sets one-sided negative stats
conn_display(h,'export_mask','masfilenameNeg.nii'); % exports mask file
Let me know if this is what you had in mind and/or if you run into any issues
Best
Alfonso
Originally posted by matt dixon:
Yes, you may use something like the following:
h = conn_display('SPM.mat',1); % loads second-level results
conn_display(h,'vox-thr',{.005,1}); % sets voxel-level threshold (p-uncorrected < .005)
conn_display(h,'clu-thr',{.05,3}); % sets cluster-level threshold (p-FDR<.05)
conn_display(h,'switch',1); % sets one-sided positive stats
conn_display(h,'export_mask','masfilenamePos.nii'); % exports mask file
conn_display(h,'switch',2); % sets one-sided negative stats
conn_display(h,'export_mask','masfilenameNeg.nii'); % exports mask file
Let me know if this is what you had in mind and/or if you run into any issues
Best
Alfonso
Originally posted by matt dixon:
Hi Alfonso,
Thank you for the CONN toolbox - it is amazing!
I was wondering if it is possible to do a Batch script that loads second level results and then saves/exports a mask image with specific p and cluster thresholds.
For example, I have seed-to-voxel results for many different seeds, and I would like to save/export a mask image with the results thresholded at p = .005, and cluster FDR corrected for each seed, for positive and negative contrasts separately. I was hoping there is a way of scripting this so I don't have to do each manually.
Please let me know if this is possible.
Thanks so much for your time!
Matt
Thank you for the CONN toolbox - it is amazing!
I was wondering if it is possible to do a Batch script that loads second level results and then saves/exports a mask image with specific p and cluster thresholds.
For example, I have seed-to-voxel results for many different seeds, and I would like to save/export a mask image with the results thresholded at p = .005, and cluster FDR corrected for each seed, for positive and negative contrasts separately. I was hoping there is a way of scripting this so I don't have to do each manually.
Please let me know if this is possible.
Thanks so much for your time!
Matt
Threaded View
| Title | Author | Date |
|---|---|---|
| matt dixon | Mar 25, 2016 | |
| Alfonso Nieto-Castanon | Mar 31, 2016 | |
| matt dixon | Apr 1, 2016 | |