Re: [Freesurfer] extracting mean thickness values across subjects from qdec clusters

Thanks Doug, I've FileDropped you the zip. Running FS 5.3.0 on Virtualbox 4.2.12 (Ubuntu guest, Windows host) T On 4 April 2014 22:09, Douglas N Greve wrote: > > Can you upload the y.mgh file and fsgd file so that I can try to replicate > it? What platform are you running on and what version of

Re: [Freesurfer] extracting mean thickness values across subjects from qdec clusters

Can you upload the y.mgh file and fsgd file so that I can try to replicate it? What platform are you running on and what version of FS? doug On 04/02/2014 06:34 PM, Tudor Popescu wrote: > Hi Doug > Sorry, again I wasn't sure whether you'd noticed my reply amonst the > latest list messages. Hope

Re: [Freesurfer] extracting mean thickness values across subjects from qdec clusters

> >> Your mri_glmfit-sim command line is not correct and does not match >> examples in the help. Basically you need to spec "--cache 1.3 abs" >> not "--cache 1.3 --sim-sign abs" >> >> Thanks Doug, now it worked, however I'm getting this error, which several >> other people seem to get:

Re: [Freesurfer] extracting mean thickness values across subjects from qdec clusters

Did you look at the mri_glmfit-sim --help yet? On 04/01/2014 04:42 PM, Tudor Popescu wrote: > Sorry I know that our questions often have an answer in the > documentation, but this case does not seem straightforward. I ran the > following command > mri_glmfit-sim --glmdir > /media/math/all

Re: [Freesurfer] extracting mean thickness values across subjects from qdec clusters

That is weird. the easiest thing is to just run mri_glmfit-sim using the same parameters as qdec is using. You can probably even get the command-line from the terminal window doug On 03/31/2014 02:39 PM, Tudor Popescu wrote: > Yes, in qdec I selected .05 for Monte-Carlo Null-Z and ran the > co

Re: [Freesurfer] extracting mean thickness values across subjects from qdec clusters

Yes, in qdec I selected .05 for Monte-Carlo Null-Z and ran the correction, which created the mc-z.abs.th13.* files (but no y.ocn). I repeated the analysis just now - same result. On 31 March 2014 20:13, Douglas N Greve wrote: > > And did you run the clusterwise correction for multiple compariso

Re: [Freesurfer] extracting mean thickness values across subjects from qdec clusters

And did you run the clusterwise correction for multiple comparisons? Either from qdec or with mri_glmfit-sim? That y.ocn file should be there On 03/31/2014 02:02 PM, Tudor Popescu wrote: > 5.3.0 > > > On 31 March 2014 19:07, Douglas N Greve > wrote: > > > w

Re: [Freesurfer] extracting mean thickness values across subjects from qdec clusters

5.3.0 On 31 March 2014 19:07, Douglas N Greve wrote: > > what version of FS are you running > > > On 03/31/2014 12:48 PM, Tudor Popescu wrote: > > Hi Doug > > > > The only OCN files I have in my qdec correlation contrast folder > > (after having run the MC-Z correction) are mc-z.abs.th13.sig.oc

Re: [Freesurfer] extracting mean thickness values across subjects from qdec clusters

what version of FS are you running On 03/31/2014 12:48 PM, Tudor Popescu wrote: > Hi Doug > > The only OCN files I have in my qdec correlation contrast folder > (after having run the MC-Z correction) are mc-z.abs.th13.sig.ocn.annot > and mc-z.abs.th13.sig.ocn.mgh. > > How should I obtain mc-z.

Re: [Freesurfer] extracting mean thickness values across subjects from qdec clusters

Hi Doug The only OCN files I have in my qdec correlation contrast folder (after having run the MC-Z correction) are mc-z.abs.th13.sig.ocn.annot and mc-z.abs.th13.sig.ocn.mgh. How should I obtain mc-z.abs.th13.y.ocn.dat, and what command (if not mri_glmfit-sim) should I use on it in order to extra

Re: [Freesurfer] extracting mean thickness values across subjects from qdec clusters

The file you are looking for should be something like mc-z.abs.th13.y.ocn.dat you dont need to run mri_glmfit-sim again On 03/31/2014 12:25 PM, Tudor Popescu wrote: > Thanks Doug, > Presumably that file is mc-z.abs.th13.pdf.dat, which gets created > after running the null-z correction. > Based

Re: [Freesurfer] extracting mean thickness values across subjects from qdec clusters

Thanks Doug, Presumably that file is mc-z.abs.th13.pdf.dat, which gets created after running the null-z correction. Based on the --help and on a previous thread, I gathered it's this command that I need: mri_glmfit-sim

Re: [Freesurfer] extracting mean thickness values across subjects from qdec clusters

If you ran the clusterwise correction, then there will be an output file with the data you want already there. Run mri_glmfit-sim --help to get more info doug On 03/31/2014 11:28 AM, Tudor Popescu wrote: > Dear Freesurfer experts, > > After a qdec contrast that asked where does thickness correl

[Freesurfer] extracting mean thickness values across subjects from qdec clusters

Dear Freesurfer experts, After a qdec contrast that asked where does thickness correlate with behavioural score, I got 2 significant clusters, and I would like, for each of these clusters, to have a list of extracted average thickness values (across the entire cluster), for each subject that I can