Tudor, To follow-up on the repeated analysis question: each 'Design' can be named by changing the 'Design Name' text box on the 'Design' tab from something other than 'Untitled', which has the effect of saving all results to a directory of that name, so that you can revisit them later (by loading results in freeview for instance).
Nick On Thu, 2013-04-18 at 20:12 -0400, Douglas N Greve wrote: > Here's part 1. I'll write until I have to catch my shuttle, answer the > rest tomorrow ... > > On 04/18/2013 05:27 PM, Tudor Popescu wrote: > > Apologies for my previous long email; if anyone gets a chance to look > > over the questions I'd be really grateful! > > Many thanks indeed, > > Tudor > > > > On 16 April 2013 19:40, Tudor Popescu <tud...@gmail.com > > <mailto:tud...@gmail.com>> wrote: > > > > Thanks Nick, (and thanks Doug too for the answer to question 2.) > > > > It must indeed have been a disk-space issue, as running the > > -qcache again, after clearing up some space, produced all the > > expected .mgh files > > > > If I can follow up on two of my previous questions: > > > > 3) Not sure I understand your answer. So it seems discrete > > variables, such as gender, cannot be taken as covariates or > > nuisance variables, only as factors. But users might want to take > > some discrete variables as covariates, rather than as factors, as > > I might not be interested in their direct effect on the brain > > measure but simply want to parcel out the variance that they > > contribute. Are you suggesting that they should be taken as > > factors even if they aren't of interest? > > > Yes. There is no real distinction between between something that is of > interest and something that is not. The way the software is set up, the > continuous factors can be listed as nuisance and get around the > limitation of only have two covariates. > > > > > > 4) Does the ideal value of FWHM depend on the blob size in the > > sense that if one expects small blobs in the results (how small?), > > then one should use small FWHMs in QDEC, and large FWHMs if > > expecting large blobs? > > > Yes. > > > > > > I apologise for the amount of questions I keep asking, but I have > > a few more: > > > > A) When trying repeated analyses (designs) in QDEC, do I need to > > delete the output files of previous analyses, and/or restart QDEC > > every time? Or are the results of each analysis displayed > > correctly independently of previously-made analyses in the same > > QDEC session? I'm asking because I see that, once the "Set using > > FDR" button is pressed, the corrected t threshold remains in use > > for subsequent analyses, but after restarting QDEC and redoing the > > last analysis, the t threshold is no longer the same > > > Not sure, have to check. I think you can name the output folders > differently for each analysis. If you do not change the name, then the > output is totally deleted and recreated. > > > > > > B) Must all QDEC analyses always be done for the two hemispheres > > separately? Is there no analysis that can be done on the whole > > brain, such that the t-value thresholds are FDR-corrected at the > > whole-brain level? > > > There is none. > > > > > > C) I would like to extract the cortical thickness of several > > cortical ROIs including the IPS, IFG and SPL; I didn’t know > > whether the Desikan-Killiany or the Destrieux atlas would be more > > appropriate, but I tried the command given here > > > > <http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/AnatomicalROI#TableoftheaveragethicknessofeachcorticalparcellationintheDestrieuxatlas>, > > hoping to obtain a table with the thickness of all ROIs from the > > parcelation corresponding to the Destrieux atlas. However, > > although the command results in the message " > > lh.aparc.a2009.thickness.table", I found no such file anywhere in > > my $SUBJECTS_DIR > > > Did it go into the directory that you ran the command from? > > > > > > D) How should a regression-type analysis be made in QDEC, i.e. one > > where I have a continuous predictor such as behavioural score, > > whose correlation with the brain measure (cortical thickness) I > > want to compare between my two groups? Because of QDEC's > > preference for discrete variables as factors, it seems that only > > ANOVA-type analyses can be done (i.e. effect of discrete factor(s) > > on brain measure), rather than regression-type (i.e. correlation > > between continuous factor and brain measure) > > > Enter it in as a covariate (continuous factor). QDEC will automatically > produce a contrast testing the difference in thickness/score slopes (ie, > an interaction between group factor and continuous factor). > > > > > > E) The average brain with inflated cortex that results are > > projected on – is this the same average that is normally used in > > most papers, or does the inflating algorithm differ? And is the > > colour-coding the same (dark gray = sulci, light gray = gyri)? > > > It is mostly the same. Some papers may display on the pial or the white > or do a custom inflation to keep some of the gyral shape instead of > having it so smooth. The colors I assume are the same. > > whew! made it through all of them before my shuttle. > doug > > > > > > > > > On 15 April 2013 23:52, Nick Schmansky <ni...@nmr.mgh.harvard.edu > > <mailto:ni...@nmr.mgh.harvard.edu>> wrote: > > > > Tudor, > > > > In the recon-all.log, it has this line: > > ERROR: writing lh.jacobian_white.fwhm15.fsaverage.mgh > > > > but earlier in the log it saved > > lh.jacobian_white.fwhm10.fsaverage.mgh > > correctly, so this indicates to me that it might have run out > > of disk > > space. is that the case? > > > > to answer the others: > > 2. not sure > > 3. you can select discrete can a regular variate along with > > your main > > variate. 'nuisance' variates are like any other. > > 4. depends on the expected 'blob' size > > 5. the selection of fwhm in qdec corresponds directly with the > > values > > selected by qcache (they are one-to-one related, ie the 10mm > > fwhm values > > created by qcache are used by the 10mm fwhm selection in qdec). > > > > Nick > > > > > > > > On Mon, 2013-04-15 at 18:38 +0200, Tudor Popescu wrote: > > > Dear experts, > > > > > > Upgrading to 5.2.0 stopped QDEC (specifically, mri_concat) from > > > misbehaving, and so after running a first whole-brain group > > cortical > > > thickness analysis on my structural data, I have some questions: > > > > > > 1. After running recon-all with the –qcache flag (i.e. > > presmoothing), > > > files of the type lh.thickness.*.mgh were created for all 38 > > subjects > > > (19 in each group), however files of the type > > rh.thickness.*.mgh were > > > not created for 5 out of the 19 subjects of the first group. > > Log files > > > recon-all-status.log and recon-all.log (attached, for one of > > those 5 > > > subjects) both mention that the process ran on Mar22nd ended > > with > > > errors, although I can't quite see what that was > > > > > > > > > > > > 2. When I take age as a continuous factor (covariate), the > > list of > > > clusters in my results look dramatically different from the > > clusters > > > that I get for the same contrast ran without the covariate. > > Why is > > > that, given that normally adding a covariate very rarely > > changes the > > > results by a great deal? Also in my case, I had quite a > > narrow (and > > > well-balanced between the groups) age range! > > > > > > > > > > > > 3. I know that discrete factors cannot be taken as nuisance > > factors, > > > but it seems they also can't be taken as covariates. How > > does one, > > > then, control for the effects of e.g. gender in a group > > comparison? > > > > > > > > > 4. When should values other than 10 be used for the FWHM > > parameter of > > > the smoothing? > > > > > > > > > 5. How come QDEC allows you to set the FWHM parameter, when > > in fact it > > > is also set in the qcache stage of recon-all, which precedes > > QDEC? > > > > > > > > > Many thanks in advance!! > > > > > > Tudor > > > _______________________________________________ > > > Freesurfer mailing list > > > Freesurfer@nmr.mgh.harvard.edu > > <mailto:Freesurfer@nmr.mgh.harvard.edu> > > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > > > > > > 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 mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
