Hi Doug,
I divided everything by 10, but the problem remains. I have been searching a bit more. Could it be that the problem is that the range in cognitive scores in the control group is very small? When I run the groups separately, the patients are not a problem (the range in cognition is very large), but the controls are still the problem.
Thanks! Heidi ================================================ Dr. Heidi Jacobs Postdoc researcher Faculty of Health, Medicine and Life Sciences School for Mental Health and Neurosciences Division Cognitive Neuropsychiatry and Clinical Neurosciences Alzheimer Center Limburg h.jacobs@maastrichtuniversity.nl www.maastrichtuniversity.nl www.heidijacobs.nl
Dr. Tanslaan 12, 6229 ET Maastricht P.O. Box 616, 6200 MD Maastricht, The Netherlands T +31 43 38 84 090 F +31 43 38 84 092 ================================================ ________________________________________ Van: Douglas N Greve [greve@nmr.mgh.harvard.edu] Verzonden: vrijdag 23 augustus 2013 17:31 Aan: Jacobs H (NP) CC: freesurfer@nmr.mgh.harvard.edu Onderwerp: Re: [Freesurfer] FW: FW: Contrast and F-test
The values in the interaction column are probably much larger than the values in the other columns (thus they are "badly scaled"). You can divide them by a number to bring their scale down to that of the other columns without changing the p-values. Version 5.x does this automatically.
On 08/23/2013 11:25 AM, Jacobs H (NP) wrote:
I am using version 4.5, as all the old analyses were also done with this version. What do you mean with rescale? THanks Heidi ________________________________________ Van: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] namens Douglas N Greve [greve@nmr.mgh.harvard.edu] Verzonden: vrijdag 23 augustus 2013 17:23 Aan: freesurfer@nmr.mgh.harvard.edu Onderwerp: Re: [Freesurfer] FW: FW: Contrast and F-test
what version of FS are you using? It may be that you just need to rescale that column (if the scale is much more than the other columns)
On 08/23/2013 11:12 AM, Jacobs H (NP) wrote:
Hi again!
I am trying to run these contrasts but FreeSurfer tells me that "ERROR: matrix is ill-conditioned or badly scaled, condno = 101380 Possible problem with experimental design: Check for duplicate entries and/or lack of range of continuous variables within a class."
Could this be due to the fact that there is a high correlation between cognition, education and cognition x education? (the product is correlated with the factors of that product) Or is something else going on? How can I solve this?
Thanks Heidi
Van: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] namens Douglas N Greve [greve@nmr.mgh.harvard.edu] Verzonden: donderdag 22 augustus 2013 17:52 Aan: freesurfer@nmr.mgh.harvard.edu Onderwerp: Re: [Freesurfer] FW: FW: Contrast and F-test
both of those contrasts are correct doug
On 08/22/2013 10:51 AM, Jacobs H (NP) wrote:
Arrghh, again wrong email, sorry....
Thanks. I think I understand the rational behind it. Just to be sure, would this be correct:
For each group separately 0 0 0 1 0 0 (group - cognition - education - cognition x education - age - ICV)
For the F-test (same order) 0 0 0 0 0 0 0 0 0 1 -1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 -1 0 0 0 0 0 0
Heidi
Van: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] namens Douglas N Greve [greve@nmr.mgh.harvard.edu] Verzonden: donderdag 22 augustus 2013 16:46 Aan: freesurfer@nmr.mgh.harvard.edu Onderwerp: Re: [Freesurfer] FW: Contrast and F-test
you need to have all 3. If you want to examine the interaction, then you need a new contrast to test the interaction. Set all to 0 except for the interaction term doug
On 08/22/2013 10:42 AM, Jacobs H (NP) wrote:
Dear Doug, Thank you for the information. Sorry for not sending this to the list. Do you mean that I then have to include the three variables (covariate 1, covariate 2, product of these two) or only the product in the fsgd file? If I need to include all three of them, can you advise me on the contrasts? If it is only the product, I think I can use the same contrasts as before, right?
Thanks Heidi ================================================ Dr. Heidi Jacobs Postdoc researcher Faculty of Health, Medicine and Life Sciences School for Mental Health and Neurosciences Division Cognitive Neuropsychiatry and Clinical Neurosciences Alzheimer Center Limburg h.jacobs@maastrichtuniversity.nl www.maastrichtuniversity.nl www.heidijacobs.nl
Dr. Tanslaan 12, 6229 ET Maastricht P.O. Box 616, 6200 MD Maastricht, The Netherlands T +31 43 38 84 090 F +31 43 38 84 092 ================================================ ________________________________________ Van: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] namens Douglas N Greve [greve@nmr.mgh.harvard.edu] Verzonden: donderdag 22 augustus 2013 16:34 Aan: freesurfer@nmr.mgh.harvard.edu Onderwerp: Re: [Freesurfer] Contrast and F-test
If you want to test for an interaction between continuous variables, then you should create a new regressor by multiplying them together then test that regressor doug
On 08/22/2013 08:09 AM, Jacobs H (NP) wrote:
Hi all,
I my manuscript, I examined the association between cognition and cortical thickness. I first did this in three groups separately and then ran a F-test. One of the reviewers, now wants me to examine the interaction between cognition and education (all continuous).
Would this be the correct contrast for each group separately (last two zeros are for covariates, also continuous)
0 1 -1 0 0
Would this be the correct way for the F-test:
0 0 0 0 0 1 -1 0 -1 1 0 0 0 0 0 0 0 0 0 0 1 0 -1 -1 0 1 0 0 0 0 0 0
Thanks!
Heidi
================================================ Dr. Heidi Jacobs Postdoc researcher Faculty of Health, Medicine and Life Sciences School for Mental Health and Neurosciences Division Cognitive Neuropsychiatry and Clinical Neurosciences Alzheimer Center Limburg h.jacobs@maastrichtuniversity.nl www.maastrichtuniversity.nl www.heidijacobs.nl
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Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
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-- 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: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
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