Hi Doug and Freesurfers,
I am currently analyzing data acquired from the Sternberg memory task, which involves memorizing sets of 1, 3, 5, and 7 letters. I have created an analysis (see attached analysis.info and paradigm example) which allows me to create maps of the load-based activation when going from 1 to 3 to 5 to 7 letters, which accounts for the analysis' single "contrast". My PI was hoping that, for some subjects, we could look at the regression from JUST 1 to 3 to 5, since they have poor 7-letter data.
From looking at the analysis setup, it looks like I would have to
make this change at the paradigm level since subjects have already been run with the current analysis with just the 1,3,5,7 regression contrast. I would probably have to change the "2"s in the paradigm file to "1"s for the 7-letter sets (since the contrast is 2vFix, and this alteration would essentially "ignore" the 7-letter condition), but a change at the paradigm file level, I believe, would essentially necessitate the formation of a new analysis entirely, which would then have to be run again individually on subjects, which can be a time consuming process. I was wondering if there was a way I could bypass this step and modify the analysis to suit these newer needs, or will I have to essentially make a new analysis based on my current one for this to work?
Thanks,
Adam Nitenson, B.S. Brain Genomics Lab Massachusetts General Hospital nitenson@nmr.mgh.harvard.edu Phone: 617-643-3215
Hi Adam, why not just make a new contrast with 1, 3, and 5? You can then run selxavg3-sess -- it will recognized that you only added a contrast and just re-run the contrast (should be pretty quick).
doug
Adam Nitenson wrote:
Hi Doug and Freesurfers,
I am currently analyzing data acquired from the Sternberg memorytask, which involves memorizing sets of 1, 3, 5, and 7 letters. I have created an analysis (see attached analysis.info and paradigm example) which allows me to create maps of the load-based activation when going from 1 to 3 to 5 to 7 letters, which accounts for the analysis' single "contrast". My PI was hoping that, for some subjects, we could look at the regression from JUST 1 to 3 to 5, since they have poor 7-letter data.
From looking at the analysis setup, it looks like I would have to
make this change at the paradigm level since subjects have already been run with the current analysis with just the 1,3,5,7 regression contrast. I would probably have to change the "2"s in the paradigm file to "1"s for the 7-letter sets (since the contrast is 2vFix, and this alteration would essentially "ignore" the 7-letter condition), but a change at the paradigm file level, I believe, would essentially necessitate the formation of a new analysis entirely, which would then have to be run again individually on subjects, which can be a time consuming process. I was wondering if there was a way I could bypass this step and modify the analysis to suit these newer needs, or will I have to essentially make a new analysis based on my current one for this to work?
Thanks,
Adam Nitenson, B.S. Brain Genomics Lab Massachusetts General Hospital nitenson@nmr.mgh.harvard.edu Phone: 617-643-3215
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
I'm not sure how I could do that considering that, in the paradigm file, the 1, 3, 5, and 7 loads are all designated with the same condition number (2), while the weight is what varies. My current contrast (2vFix) encompassed all four loads so I'm not sure how I could just make a new contrast without altering the condition number for the 7-load, and thus requiring a new analysis.
-Adam
Hi Adam, why not just make a new contrast with 1, 3, and 5? You can then run selxavg3-sess -- it will recognized that you only added a contrast and just re-run the contrast (should be pretty quick).
doug
Adam Nitenson wrote:
Hi Doug and Freesurfers,
I am currently analyzing data acquired from the Sternberg memorytask, which involves memorizing sets of 1, 3, 5, and 7 letters. I have created an analysis (see attached analysis.info and paradigm example) which allows me to create maps of the load-based activation when going from 1 to 3 to 5 to 7 letters, which accounts for the analysis' single "contrast". My PI was hoping that, for some subjects, we could look at the regression from JUST 1 to 3 to 5, since they have poor 7-letter data.
From looking at the analysis setup, it looks like I would have to
make this change at the paradigm level since subjects have already been run with the current analysis with just the 1,3,5,7 regression contrast. I would probably have to change the "2"s in the paradigm file to "1"s for the 7-letter sets (since the contrast is 2vFix, and this alteration would essentially "ignore" the 7-letter condition), but a change at the paradigm file level, I believe, would essentially necessitate the formation of a new analysis entirely, which would then have to be run again individually on subjects, which can be a time consuming process. I was wondering if there was a way I could bypass this step and modify the analysis to suit these newer needs, or will I have to essentially make a new analysis based on my current one for this to work?
Thanks,
Adam Nitenson, B.S. Brain Genomics Lab Massachusetts General Hospital nitenson@nmr.mgh.harvard.edu Phone: 617-643-3215
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html
Adam Nitenson, B.S. Brain Genomics Lab Massachusetts General Hospital nitenson@nmr.mgh.harvard.edu Phone: 617-643-3215
Oh, sorry, I had misunderstood your question. Yes, you will need to create a new paradigm file and a new analysis to go with it. The actual analysis should not take that much time because all the preprocessing is already done. It will probably take 15-20 min per subject. doug
Adam Nitenson wrote:
I'm not sure how I could do that considering that, in the paradigm file, the 1, 3, 5, and 7 loads are all designated with the same condition number (2), while the weight is what varies. My current contrast (2vFix) encompassed all four loads so I'm not sure how I could just make a new contrast without altering the condition number for the 7-load, and thus requiring a new analysis.
-Adam
Hi Adam, why not just make a new contrast with 1, 3, and 5? You can then run selxavg3-sess -- it will recognized that you only added a contrast and just re-run the contrast (should be pretty quick).
doug
Adam Nitenson wrote:
Hi Doug and Freesurfers,
I am currently analyzing data acquired from the Sternberg memorytask, which involves memorizing sets of 1, 3, 5, and 7 letters. I have created an analysis (see attached analysis.info and paradigm example) which allows me to create maps of the load-based activation when going from 1 to 3 to 5 to 7 letters, which accounts for the analysis' single "contrast". My PI was hoping that, for some subjects, we could look at the regression from JUST 1 to 3 to 5, since they have poor 7-letter data.
From looking at the analysis setup, it looks like I would have to
make this change at the paradigm level since subjects have already been run with the current analysis with just the 1,3,5,7 regression contrast. I would probably have to change the "2"s in the paradigm file to "1"s for the 7-letter sets (since the contrast is 2vFix, and this alteration would essentially "ignore" the 7-letter condition), but a change at the paradigm file level, I believe, would essentially necessitate the formation of a new analysis entirely, which would then have to be run again individually on subjects, which can be a time consuming process. I was wondering if there was a way I could bypass this step and modify the analysis to suit these newer needs, or will I have to essentially make a new analysis based on my current one for this to work?
Thanks,
Adam Nitenson, B.S. Brain Genomics Lab Massachusetts General Hospital nitenson@nmr.mgh.harvard.edu Phone: 617-643-3215
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html
Adam Nitenson, B.S. Brain Genomics Lab Massachusetts General Hospital nitenson@nmr.mgh.harvard.edu Phone: 617-643-3215
freesurfer@nmr.mgh.harvard.edu
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Adam Nitenson -
Douglas N Greve