Hi all, we're using 5.1 to analyze some single subject, event-related functional data, and are getting some strangely high values for % signal change when using func2roi-sess and roisummary-sess.
Here are the commands we're running:
func2roi-sess -s LMV2012_N01_heading -roidef rhmed_singlevsdouble_1 -analysis glheadgen_analysis -labelfile /home/vmrao17/freesurfer/subjects/LMV2012_N01/label/rhmed_singlevsdouble_1.label -maskcontrast allvsoff -maskthresh 1.50 -masktail pos -maskmap sig
roisummary-sess -sumfile /home/vmrao17/tmp/summary.txt -roidef rhmed_singlevsdouble_1 -analysis glheadgen_analysis -s LMV2012_N01_heading
And this is the output of summary.txt:
LMV2012_N01_heading 51 12 123.737160 1.535988 1572.000000 0.050000 -0.000000 21 1 0.734151 3.595402 4.435675 5.482294 0.544176 -0.166144 2.951724 2.114511 3.178010 2.814232 0.944738 0.466052 8.508595 7.646451 6.767788 9.197896 8.802674 11.339759 7.822568 4.040024 8.018742
The problem is that the effect size values seem very high and/or the baseline seems very low (e.g., 100*11.33/123.7=9%!).
In 4.5 we were computing a scaling factor for these values, but my understanding was that in 5.1 that was no longer needed, correct? Is there anything else we should be doing differently when computing % signal change from this output now? The only other strange thing I notice is that the TER value is 0.05, but documentation describes TR/20 and our TR=2sec, which would seem to suggest it should be 0.1 instead of 0.05?
I'm attaching the full output log for the two commands above as well. Anything that we're obviously doing wrong? Thanks!
Hi Finnegan, there's nothing there that looks wrong with your commands, but I agree that those values look too high. It is possible that some of the 12 voxels in the ROI is causing the problem. If you go into the subject's analysis dir, you'll see a mask there that corresponds to your ROI. You can load that in matlab, find the voxels in the mask, then load the beta.nii.gz and extract out the values from those voxels to see if something looks funny. Also, check to see whether any of the mask falls into ventricle. doug
Finnegan Calabro wrote:
Hi all, we're using 5.1 to analyze some single subject, event-related functional data, and are getting some strangely high values for % signal change when using func2roi-sess and roisummary-sess.
Here are the commands we're running:
func2roi-sess -s LMV2012_N01_heading -roidef rhmed_singlevsdouble_1 -analysis glheadgen_analysis -labelfile /home/vmrao17/freesurfer/subjects/LMV2012_N01/label/rhmed_singlevsdouble_1.label -maskcontrast allvsoff -maskthresh 1.50 -masktail pos -maskmap sig
roisummary-sess -sumfile /home/vmrao17/tmp/summary.txt -roidef rhmed_singlevsdouble_1 -analysis glheadgen_analysis -s LMV2012_N01_heading
And this is the output of summary.txt:
LMV2012_N01_heading 51 12 123.737160 1.535988 1572.000000 0.050000 -0.000000 21 1 0.734151 3.595402 4.435675 5.482294 0.544176 -0.166144 2.951724 2.114511 3.178010 2.814232 0.944738 0.466052 8.508595 7.646451 6.767788 9.197896 8.802674 11.339759 7.822568 4.040024 8.018742
The problem is that the effect size values seem very high and/or the baseline seems very low (e.g., 100*11.33/123.7=9%!).
In 4.5 we were computing a scaling factor for these values, but my understanding was that in 5.1 that was no longer needed, correct? Is there anything else we should be doing differently when computing % signal change from this output now? The only other strange thing I notice is that the TER value is 0.05, but documentation describes TR/20 and our TR=2sec, which would seem to suggest it should be 0.1 instead of 0.05?
I'm attaching the full output log for the two commands above as well. Anything that we're obviously doing wrong? Thanks!
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Thanks Doug. Looking at the beta.nii.gz values in the mask (assuming the first N entries in beta correspond to the N events, with nuisance variables after that), the values for event 18 (which had a particularly high % signal change) look like:
4.3453 21.4786 16.6500 8.1440 31.4507 5.0272 15.9165 36.8251 7.9907 20.7835 14.6263 18.0771 19.3031 9.8763 5.2008 9.1234 21.6566 22.7819 27.9337 22.8663 22.2126
So it doesn't seem to be one (or a small number) of voxels skewing the data. I don't think we're landing in the ventricles either, in part because this is happening to all of the 7 ROIs we've defined all over the cortex. We also looked at cespct.nii.gz and see lots of pretty high values in there as well (though that's for a contrast, not an event, and I'm not sure whether those values should necessarily match).
Can you think of anything else we should check that could be causing this? (it was a pretty standard analysis design i think, but could something wrong at that stage have produced results like this?).
Thanks very much!
On Mar 8, 2012, at 11:58 AM, Douglas N Greve wrote:
Hi Finnegan, there's nothing there that looks wrong with your commands, but I agree that those values look too high. It is possible that some of the 12 voxels in the ROI is causing the problem. If you go into the subject's analysis dir, you'll see a mask there that corresponds to your ROI. You can load that in matlab, find the voxels in the mask, then load the beta.nii.gz and extract out the values from those voxels to see if something looks funny. Also, check to see whether any of the mask falls into ventricle. doug
Finnegan Calabro wrote:
Hi all, we're using 5.1 to analyze some single subject, event-related functional data, and are getting some strangely high values for % signal change when using func2roi-sess and roisummary-sess. Here are the commands we're running:
func2roi-sess -s LMV2012_N01_heading -roidef rhmed_singlevsdouble_1 -analysis glheadgen_analysis -labelfile /home/vmrao17/freesurfer/subjects/LMV2012_N01/label/rhmed_singlevsdouble_1.label -maskcontrast allvsoff -maskthresh 1.50 -masktail pos -maskmap sig
roisummary-sess -sumfile /home/vmrao17/tmp/summary.txt -roidef rhmed_singlevsdouble_1 -analysis glheadgen_analysis -s LMV2012_N01_heading
And this is the output of summary.txt:
LMV2012_N01_heading 51 12 123.737160 1.535988 1572.000000 0.050000 -0.000000 21 1 0.734151 3.595402 4.435675 5.482294 0.544176 -0.166144 2.951724 2.114511 3.178010 2.814232 0.944738 0.466052 8.508595 7.646451 6.767788 9.197896 8.802674 11.339759 7.822568 4.040024 8.018742
The problem is that the effect size values seem very high and/or the baseline seems very low (e.g., 100*11.33/123.7=9%!).
In 4.5 we were computing a scaling factor for these values, but my understanding was that in 5.1 that was no longer needed, correct? Is there anything else we should be doing differently when computing % signal change from this output now? The only other strange thing I notice is that the TER value is 0.05, but documentation describes TR/20 and our TR=2sec, which would seem to suggest it should be 0.1 instead of 0.05?
I'm attaching the full output log for the two commands above as well. Anything that we're obviously doing wrong? Thanks!
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
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.
Nothing comes to mind. Can you send me the X.mat file in the analysis dir?
Finnegan Calabro wrote:
Thanks Doug. Looking at the beta.nii.gz values in the mask (assuming the first N entries in beta correspond to the N events, with nuisance variables after that), the values for event 18 (which had a particularly high % signal change) look like:
4.3453 21.4786 16.6500 8.1440 31.4507 5.0272 15.9165 36.8251 7.9907 20.7835 14.6263 18.0771 19.3031 9.8763 5.2008 9.1234 21.6566 22.7819 27.9337 22.8663 22.2126
So it doesn't seem to be one (or a small number) of voxels skewing the data. I don't think we're landing in the ventricles either, in part because this is happening to all of the 7 ROIs we've defined all over the cortex. We also looked at cespct.nii.gz and see lots of pretty high values in there as well (though that's for a contrast, not an event, and I'm not sure whether those values should necessarily match).
Can you think of anything else we should check that could be causing this? (it was a pretty standard analysis design i think, but could something wrong at that stage have produced results like this?).
Thanks very much!
On Mar 8, 2012, at 11:58 AM, Douglas N Greve wrote:
Hi Finnegan, there's nothing there that looks wrong with your commands, but I agree that those values look too high. It is possible that some of the 12 voxels in the ROI is causing the problem. If you go into the subject's analysis dir, you'll see a mask there that corresponds to your ROI. You can load that in matlab, find the voxels in the mask, then load the beta.nii.gz and extract out the values from those voxels to see if something looks funny. Also, check to see whether any of the mask falls into ventricle. doug
Finnegan Calabro wrote:
Hi all, we're using 5.1 to analyze some single subject, event-related functional data, and are getting some strangely high values for % signal change when using func2roi-sess and roisummary-sess. Here are the commands we're running:
func2roi-sess -s LMV2012_N01_heading -roidef rhmed_singlevsdouble_1 -analysis glheadgen_analysis -labelfile /home/vmrao17/freesurfer/subjects/LMV2012_N01/label/rhmed_singlevsdouble_1.label -maskcontrast allvsoff -maskthresh 1.50 -masktail pos -maskmap sig
roisummary-sess -sumfile /home/vmrao17/tmp/summary.txt -roidef rhmed_singlevsdouble_1 -analysis glheadgen_analysis -s LMV2012_N01_heading
And this is the output of summary.txt:
LMV2012_N01_heading 51 12 123.737160 1.535988 1572.000000 0.050000 -0.000000 21 1 0.734151 3.595402 4.435675 5.482294 0.544176 -0.166144 2.951724 2.114511 3.178010 2.814232 0.944738 0.466052 8.508595 7.646451 6.767788 9.197896 8.802674 11.339759 7.822568 4.040024 8.018742
The problem is that the effect size values seem very high and/or the baseline seems very low (e.g., 100*11.33/123.7=9%!).
In 4.5 we were computing a scaling factor for these values, but my understanding was that in 5.1 that was no longer needed, correct? Is there anything else we should be doing differently when computing % signal change from this output now? The only other strange thing I notice is that the TER value is 0.05, but documentation describes TR/20 and our TR=2sec, which would seem to suggest it should be 0.1 instead of 0.05?
I'm attaching the full output log for the two commands above as well. Anything that we're obviously doing wrong? Thanks!
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
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.
freesurfer@nmr.mgh.harvard.edu
-
Douglas N Greve -
Finnegan Calabro