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> 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? > > 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? > > 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 > > 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? > > 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 > > 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) > > 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)? > > > > On 15 April 2013 23:52, Nick Schmansky <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 >> > 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. >> > >
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