selxavg3-sess checks to see whether preproc has been run and runs it if it is needed, so all that stuff can go on in the background. It does look like the differences you are seeing come from the whitening. This attempts to account for temporal correlation in the noise. Whether you need it or not depends on what you actually report. If you report the volume of activation for each subject, then you'll probably want some sort of whitening. In general, people don't report this. If you are going to just hand the 1st level results up to the next higher level (eg, group analysis), then I don't think it makes a difference. A reviewer may balk if there has not been whitening performed at the first level, but this is usually just a misunderstanding on their part.
doug
Katie Bettencourt wrote:
When I registered the 4.5 version, I did it fully manually, using tkregister2, but with the version5 one I initially didn't do anything outside of the commands I listed below (though the register.dat was present from the 4.5 version), but then to check that I went through and ran register-sess on the version 5, and then double checked it in tkregister2 (as the output to register-sess suggested I do) and at least at a coarse look it looked fairly well aligned, and rerunning selxavg3-sess after running register-sess didn't change the output (in fact, the picture I attached before was from the register-sess version). Does selxavg3-sess automatically run this registration in version 5 or do you need to do the registration separately everytime? Similarly, I didn't run preproc-sess separately for version5, did I need to?
rerunning it with the -no-whiten flag seems to have pushed it in the other direction. I now get more activation in v5 than v4.5 (see attached pictures) which honestly I guess I like better... Do I need to run it with the -no-whiten flag each time? Exactly what is this flag doing?
Katie
On Tue, Dec 7, 2010 at 2:20 PM, Douglas N Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:
Hmmm, not sure what's going on with that. Can you verify that the registration is correct in the v5 results? The only other thing that I can think of is that the whitening may be a bit different between 4.5 and 5.0. Try turning off the whitening in v5 (-no-whiten when running mkanalysis-sess). doug Katie Bettencourt wrote: I was attempting to run an analysis that was previously done in freesurfer 4.5 in version 5 to see if I cuold switch over to the new version. However, I am getting very different results for the two versions. Below are the commands I ran in both and attached are pictures of the differences. I get much much less activation (and much less than expected) when using version 5. I assume this is because I've done something wrong with the way I set up my version 5 analysis, but I don't knwo what it is. Any help would be appreciated. version 5: mkanalysis-sess -analysis supIPS-gamma-5rh -TR 1.5 -paradigm supIPS.dat -event-related -runlistfile supIPSruns.txt -nskip 2 -nconditions 6 -gammafit 2.25 1.25 -surface self rh -fwhm 0 -refeventdur 6 mkcontrast-sess -analysis supIPS-gamma-5rh -contrast act_vs_fix -a 1 -a 2 -a 3 -a 4 -a 5 -c 0 selxavg3-sess -s 101103TM_supIPS -df supIPS.dir -analysis supIPS-gamma-5rh tksurfer-sess -s 101103TM_supIPS -a supIPS-gamma-5rh-c act_vs_fix -df supIPS.dir version 4.5 mkanalysis-sess -analysis supIPS-gamma -TR 1.5 -paradigm supIPS.dat -designtype event-related -funcstem fmc -motioncor -runlistfile supIPSruns.txt -inorm -tpexclude tpexclude.dat -nconditions 6 -gammafit 2.25 1.25 -noautostimdur mkcontrast-sess -analysis supIPS-gamma -contrast act_vs_fix -a 1 -a 2 -a 3 -a 4 -a 5 -c 0 tksurfer-sess -s 101103TM_supIPS -df supIPS.dir -a supIPS-gamma -c act_vs_fix -hemi rh Katie ------------------------------------------------------------------------ ------------------------------------------------------------------------ ------------------------------------------------------------------------ _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto: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 <mailto:greve@nmr.mgh.harvard.edu> Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
So we won't actually be doing group analysis on this except ROI analysis. We are using this data to look at overlap in activations on individual subject levels. Since the v5 whiten seems much more extreme than v4.5, I'm not really sure how to interprete this in terms of what I need to do for accurate represenations of the data for my experiments, if that makes sense.
Katie
On Tue, Dec 7, 2010 at 2:46 PM, Douglas N Greve greve@nmr.mgh.harvard.eduwrote:
selxavg3-sess checks to see whether preproc has been run and runs it if it is needed, so all that stuff can go on in the background. It does look like the differences you are seeing come from the whitening. This attempts to account for temporal correlation in the noise. Whether you need it or not depends on what you actually report. If you report the volume of activation for each subject, then you'll probably want some sort of whitening. In general, people don't report this. If you are going to just hand the 1st level results up to the next higher level (eg, group analysis), then I don't think it makes a difference. A reviewer may balk if there has not been whitening performed at the first level, but this is usually just a misunderstanding on their part.
doug
Katie Bettencourt wrote:
When I registered the 4.5 version, I did it fully manually, using tkregister2, but with the version5 one I initially didn't do anything outside of the commands I listed below (though the register.dat was present from the 4.5 version), but then to check that I went through and ran register-sess on the version 5, and then double checked it in tkregister2 (as the output to register-sess suggested I do) and at least at a coarse look it looked fairly well aligned, and rerunning selxavg3-sess after running register-sess didn't change the output (in fact, the picture I attached before was from the register-sess version). Does selxavg3-sess automatically run this registration in version 5 or do you need to do the registration separately everytime? Similarly, I didn't run preproc-sess separately for version5, did I need to?
rerunning it with the -no-whiten flag seems to have pushed it in the other direction. I now get more activation in v5 than v4.5 (see attached pictures) which honestly I guess I like better... Do I need to run it with the -no-whiten flag each time? Exactly what is this flag doing?
Katie
On Tue, Dec 7, 2010 at 2:20 PM, Douglas N Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:
Hmmm, not sure what's going on with that. Can you verify that the registration is correct in the v5 results? The only other thing that I can think of is that the whitening may be a bit different between 4.5 and 5.0. Try turning off the whitening in v5 (-no-whiten when running mkanalysis-sess). doug Katie Bettencourt wrote: I was attempting to run an analysis that was previously done in freesurfer 4.5 in version 5 to see if I cuold switch over to the new version. However, I am getting very different results for the two versions. Below are the commands I ran in both and attached are pictures of the differences. I get much much less activation (and much less than expected) when using version 5. I assume this is because I've done something wrong with the way I set up my version 5 analysis, but I don't knwo what it is. Any help would be appreciated. version 5: mkanalysis-sess -analysis supIPS-gamma-5rh -TR 1.5 -paradigm supIPS.dat -event-related -runlistfile supIPSruns.txt -nskip 2 -nconditions 6 -gammafit 2.25 1.25 -surface self rh -fwhm 0 -refeventdur 6 mkcontrast-sess -analysis supIPS-gamma-5rh -contrast act_vs_fix -a 1 -a 2 -a 3 -a 4 -a 5 -c 0 selxavg3-sess -s 101103TM_supIPS -df supIPS.dir -analysis supIPS-gamma-5rh tksurfer-sess -s 101103TM_supIPS -a supIPS-gamma-5rh-c act_vs_fix -df supIPS.dir version 4.5 mkanalysis-sess -analysis supIPS-gamma -TR 1.5 -paradigm supIPS.dat -designtype event-related -funcstem fmc -motioncor -runlistfile supIPSruns.txt -inorm -tpexclude tpexclude.dat -nconditions 6 -gammafit 2.25 1.25 -noautostimdur mkcontrast-sess -analysis supIPS-gamma -contrast act_vs_fix -a 1 -a 2 -a 3 -a 4 -a 5 -c 0 tksurfer-sess -s 101103TM_supIPS -df supIPS.dir -a supIPS-gamma -c act_vs_fix -hemi rh Katie
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto: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 <mailto:greve@nmr.mgh.harvard.edu> Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
-- 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
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
It's hard to say what the right thing to do is. In principle, the larger activation you are seeing in 4.5 could be false negatives, and you probably don't want something that is going to include those. You can get to something closer to the 4.5 whitening by adding the following to your mkanalysis-sess line:
... -acf-bins 10 -acf-fwhm 0 ...
see if that helps
doug
Katie Bettencourt wrote:
So we won't actually be doing group analysis on this except ROI analysis. We are using this data to look at overlap in activations on individual subject levels. Since the v5 whiten seems much more extreme than v4.5, I'm not really sure how to interprete this in terms of what I need to do for accurate represenations of the data for my experiments, if that makes sense.
Katie
On Tue, Dec 7, 2010 at 2:46 PM, Douglas N Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:
selxavg3-sess checks to see whether preproc has been run and runs it if it is needed, so all that stuff can go on in the background. It does look like the differences you are seeing come from the whitening. This attempts to account for temporal correlation in the noise. Whether you need it or not depends on what you actually report. If you report the volume of activation for each subject, then you'll probably want some sort of whitening. In general, people don't report this. If you are going to just hand the 1st level results up to the next higher level (eg, group analysis), then I don't think it makes a difference. A reviewer may balk if there has not been whitening performed at the first level, but this is usually just a misunderstanding on their part. doug Katie Bettencourt wrote: > When I registered the 4.5 version, I did it fully manually, using > tkregister2, but with the version5 one I initially didn't do anything > outside of the commands I listed below (though the register.dat was > present from the 4.5 version), but then to check that I went through > and ran register-sess on the version 5, and then double checked it in > tkregister2 (as the output to register-sess suggested I do) and at > least at a coarse look it looked fairly well aligned, and rerunning > selxavg3-sess after running register-sess didn't change the output (in > fact, the picture I attached before was from the register-sess > version). Does selxavg3-sess automatically run this registration in > version 5 or do you need to do the registration separately everytime? > Similarly, I didn't run preproc-sess separately for version5, did I > need to? > > rerunning it with the -no-whiten flag seems to have pushed it in the > other direction. I now get more activation in v5 than v4.5 (see > attached pictures) which honestly I guess I like better... Do I need > to run it with the -no-whiten flag each time? Exactly what is this > flag doing? > > Katie > > On Tue, Dec 7, 2010 at 2:20 PM, Douglas N Greve > <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>> wrote: > > Hmmm, not sure what's going on with that. Can you verify that the > registration is correct in the v5 results? The only other thing > that I can think of is that the whitening may be a bit different > between 4.5 and 5.0. Try turning off the whitening in v5 > (-no-whiten when running mkanalysis-sess). > > doug > > Katie Bettencourt wrote: > > I was attempting to run an analysis that was previously done > in freesurfer 4.5 in version 5 to see if I cuold switch over > to the new version. However, I am getting very different > results for the two versions. Below are the commands I ran in > both and attached are pictures of the differences. I get much > much less activation (and much less than expected) when using > version 5. I assume this is because I've done something wrong > with the way I set up my version 5 analysis, but I don't knwo > what it is. Any help would be appreciated. > > version 5: > mkanalysis-sess -analysis supIPS-gamma-5rh -TR 1.5 -paradigm > supIPS.dat -event-related -runlistfile supIPSruns.txt -nskip 2 > -nconditions 6 -gammafit 2.25 1.25 -surface self rh -fwhm 0 > -refeventdur 6 > mkcontrast-sess -analysis supIPS-gamma-5rh -contrast > act_vs_fix -a 1 -a 2 -a 3 -a 4 -a 5 -c 0 > selxavg3-sess -s 101103TM_supIPS -df supIPS.dir -analysis > supIPS-gamma-5rh > tksurfer-sess -s 101103TM_supIPS -a supIPS-gamma-5rh-c > act_vs_fix -df supIPS.dir > > version 4.5 > mkanalysis-sess -analysis supIPS-gamma -TR 1.5 -paradigm > supIPS.dat -designtype event-related -funcstem fmc -motioncor > -runlistfile supIPSruns.txt -inorm -tpexclude tpexclude.dat > -nconditions 6 -gammafit 2.25 1.25 -noautostimdur > mkcontrast-sess -analysis supIPS-gamma -contrast act_vs_fix -a > 1 -a 2 -a 3 -a 4 -a 5 -c 0 > tksurfer-sess -s 101103TM_supIPS -df supIPS.dir -a > supIPS-gamma -c act_vs_fix -hemi rh > > > Katie > > ------------------------------------------------------------------------ > > > ------------------------------------------------------------------------ > > ------------------------------------------------------------------------ > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto: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 <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> > Phone Number: 617-724-2358 Fax: 617-726-7422 > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > > > > The information in this e-mail is intended only for the person to > whom it is > addressed. If you believe this e-mail was sent to you in error and > the e-mail > contains patient information, please contact the Partners > Compliance HelpLine at > http://www.partners.org/complianceline . If the e-mail was sent to > you in error > but does not contain patient information, please contact the > sender and properly > dispose of the e-mail. > > > > ------------------------------------------------------------------------ > > > ------------------------------------------------------------------------ > -- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
freesurfer@nmr.mgh.harvard.edu
-
Douglas N Greve -
Katie Bettencourt