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Hi Matthieu, I think PALM will include --demean automatically if needed and issue a warning, but you may as well include it if an intercept isn't already present in the model. All the best, Anderson On Mon, 29 Oct 2018 at 08:37, Matthieu Vanhoutte < [log in to unmask]> wrote: > Hi Anderson, > > Thank you for this detailed answer. > > One further question concerning design matrix of this correlation study > between imaging modalities including a voxel-wise regressor: > 1) do I have to include a column of 1s with no demeaning > *OR* > 2) No column of 1s and demeaning of variables + design (with --demean > option) ? > > Best, > Matthieu > > Le lun. 29 oct. 2018 à 11:59, Anderson M. Winkler <[log in to unmask]> > a écrit : > >> Hi Matthieu, >> >> Please see below: >> >> On Sun, 28 Oct 2018 at 18:12, Matthieu Vanhoutte < >> [log in to unmask]> wrote: >> >>> Hi Anderson, >>> >>> 1) Thank you for this explanation. So, in order to test correlation >>> between voxel-wise variables PALM will compute t-maps and corrected p-maps >>> associated showing significant t-values, right ? >>> >> >> Yes. >> >> >>> >>> 2) Once I got t-maps, I will use fslmaths with the link to the formulae >>> you gave to me in order to compute partial correlation coefficients maps. >>> But once I got these should I only to consider partial correlation >>> coefficients where p is significant ? >>> >> >> The formula gives a direct mapping t -> r, and vice-versa. The p-value >> for r is the same as for t. It's up to you to do the conversion only for >> significant voxels, or for all of them, and then perhaps mask the >> non-significant out. >> >> >>> >>> 3) What's the difference between Pearson correlation coefficients and >>> partial correlation coefficients ? >>> >> >> I don't think Pearson considered nuisance variables in 1895 but the >> partial correlations are a direct extension of it. There is no conceptual >> difference, only the partial takes into account the effect of nuisance, >> whereas the original Pearson's method doesn't. The core idea is still his, >> though (or Galton's...). >> >> All the best, >> >> Anderson >> >> >>> Thanks for your lights ! >>> >>> Best, >>> Matthieu >>> >>> >>> Le lun. 10 sept. 2018 à 18:17, Anderson M. Winkler < >>> [log in to unmask]> a écrit : >>> >>>> Hi Matthieu, >>>> >>>> Only if you want to. You can: >>>> >>>> a) Test either positive or negative. >>>> b) Test either positive or negative, and include the option -twotail. >>>> c) Test both positive and negative, and correct for the fact that you >>>> are looking into two contrasts with the option -corrcon. >>>> >>>> For just 2 contrasts that are one the reverse of the other, the (a) and >>>> (b) take half of the time compared to (c), but (c) is better in general >>>> that it works for any arbitrary set of contrasts, not just one the negative >>>> of the other, and don't require much manipulation to find out whether >>>> significant results are positive or negative. >>>> >>>> From the description of the experiment it seems there is no reason to >>>> suspect that results would be necessarily directional so I think I'd use >>>> (b) or (c), with a preference towards (c) as it will allow less work for >>>> you later to make figures (but more work for the computer, which is what it >>>> is for anyway...) >>>> >>>> Hope this helps! >>>> >>>> All the best, >>>> >>>> Anderson >>>> >>>> >>>> On Mon, 10 Sep 2018 at 10:23, Matthieu Vanhoutte < >>>> [log in to unmask]> wrote: >>>> >>>>> Hi Anderson, >>>>> >>>>> Thank you this helps ! >>>>> >>>>> To test the correlation should I to define two contrasts for positive >>>>> and negative correlation ? >>>>> >>>>> Best, >>>>> Matthieu >>>>> >>>>> 2018-09-10 12:56 GMT+00:00 Anderson M. Winkler <[log in to unmask] >>>>> >: >>>>> >>>>>> Hi Matthieu, >>>>>> >>>>>> In the -evperdat you need to specify which positions in the design X >>>>>> and Z occupy. Something as: >>>>>> >>>>>> palm -i Y.nii -evperdat X.nii 2 -evperdat 3 -d ttest.csv -t >>>>>> tcontrasts.csv [...other options...] >>>>>> >>>>>> The ttest.csv would contain various EVs, and EV2 and EV3 would be >>>>>> "dummy" regressors that would be replaced by the voxelwise EVs specified by >>>>>> the -evperdat options. EV1 could be an intercept for example, and there >>>>>> could be additional EVs (EV4, EV5, etc). >>>>>> >>>>>> The tcontrasts.csv would have size compatible with the number of EVs >>>>>> then. >>>>>> >>>>>> Hope this helps! >>>>>> >>>>>> All the best, >>>>>> >>>>>> Anderson >>>>>> >>>>>> >>>>>> On Mon, 10 Sep 2018 at 08:37, Matthieu Vanhoutte < >>>>>> [log in to unmask]> wrote: >>>>>> >>>>>>> Hi Anderson, >>>>>>> >>>>>>> Thank you for your answer. So, in my case where I want to test >>>>>>> correlation between Y and X regressing out Z should I use basically: >>>>>>> palm >>>>>>> -i Y >>>>>>> -evperdat X >>>>>>> -evperdat Z >>>>>>> -d ttest.csv >>>>>>> -t tcontrasts.csv >>>>>>> >>>>>>> where ttest.csv is a file with only one column of 1 as intercept and >>>>>>> tcontrasts.csv is a file with both 1 and -1 contrasts ? >>>>>>> >>>>>>> Best, >>>>>>> Matthieu >>>>>>> >>>>>>> 2018-09-10 12:21 GMT+00:00 Anderson M. Winkler < >>>>>>> [log in to unmask]>: >>>>>>> >>>>>>>> Hi Matthieu, >>>>>>>> >>>>>>>> The option "-pearson" isn't compatible with "-evperdat", which >>>>>>>> means you need to drop "-pearson" and compute the usual t-stat. Then, once >>>>>>>> you have it, it can be converted to a Pearson correlation coefficient using >>>>>>>> fslmaths. The formula is under the heading "Partial correlation >>>>>>>> coefficient", at this link: >>>>>>>> https://brainder.org/2015/03/04/all-glm-formulas/ >>>>>>>> >>>>>>>> The option "-person" will likely be removed from future versions as >>>>>>>> it creates a whole lot of confusion. In fact, the most accurate p-values >>>>>>>> are produced with the t and F-statistics. Remember that PALM was created as >>>>>>>> the testbed for many things I was working on during my DPhil. The -pearson >>>>>>>> wasn't really intended to be used in practice. It is not wrong but it lacks >>>>>>>> some nice properties that t and F have, and it can be used only in more >>>>>>>> restricted situations. Consider not using it (but it's ok to convert t to r >>>>>>>> using the formula from the link). >>>>>>>> >>>>>>>> All the best, >>>>>>>> >>>>>>>> Anderson >>>>>>>> >>>>>>>> >>>>>>>> On Mon, 10 Sep 2018 at 05:17, Matthieu Vanhoutte < >>>>>>>> [log in to unmask]> wrote: >>>>>>>> >>>>>>>>> Dear Anderson, >>>>>>>>> >>>>>>>>> I am stucked in how defining PALM design/contrasts and command >>>>>>>>> line options in order to compute Pearson's correlation maps between >>>>>>>>> modality Y and modality X when regressing out a modality Z. >>>>>>>>> >>>>>>>>> Could you provide me help ? >>>>>>>>> >>>>>>>>> Best regards, >>>>>>>>> Matthieu >>>>>>>>> >>>>>>>>> ------------------------------ >>>>>>>>> >>>>>>>>> To unsubscribe from the FSL list, click the following link: >>>>>>>>> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=FSL&A=1 >>>>>>>>> >>>>>>>> >>>>>>>> ------------------------------ >>>>>>>> >>>>>>>> To unsubscribe from the FSL list, click the following link: >>>>>>>> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=FSL&A=1 >>>>>>>> >>>>>>> >>>>>>> >>>>>>> ------------------------------ >>>>>>> >>>>>>> To unsubscribe from the FSL list, click the following link: >>>>>>> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=FSL&A=1 >>>>>>> >>>>>> >>>>>> ------------------------------ >>>>>> >>>>>> To unsubscribe from the FSL list, click the following link: >>>>>> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=FSL&A=1 >>>>>> >>>>> >>>>> >>>>> ------------------------------ >>>>> >>>>> To unsubscribe from the FSL list, click the following link: >>>>> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=FSL&A=1 >>>>> >>>> >>>> ------------------------------ >>>> >>>> To unsubscribe from the FSL list, click the following link: >>>> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=FSL&A=1 >>>> >>> >>> ------------------------------ >>> >>> To unsubscribe from the FSL list, click the following link: >>> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=FSL&A=1 >>> >> >> ------------------------------ >> >> To unsubscribe from the FSL list, click the following link: >> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=FSL&A=1 >> > > ------------------------------ > > To unsubscribe from the FSL list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=FSL&A=1 > ######################################################################## To unsubscribe from the FSL list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=FSL&A=1