Re: [Freesurfer] Fsgd file format

I understand, I think! So our matrix should be something like this, which includes each of the 4 components we are using as variables, all possible interactions, and the covariate of mean cortical thickness? group - Var1 - Var2 - Var3 - Var4 - 1x2 - 1x3 - 1x4 - 2x3 - 2x4 - 3x4 - 1x2x3 - 1x2x4 - 1x

[Freesurfer] CWP values

Hello, I see that after having qdec apply MonteCarlo correction to a certain contrast, the CWP cluster-wise probability is displayed. Those values, however, are not displayed when the "Find clusters and go to max" button is used, either before or after correction. WHy is that, when it seems that t

Re: [Freesurfer] CWP values

ONe more question about this - when reporting significant clusters, should one refer to the cluster by 1) its annotation label, e.g. "sig differences were found in the precentral gyrus", 2) its max vertex as displayed after using the "Find clusters and go to max" button, e.g. "significant differenc

[Freesurfer] The FreeSurfer lab is seeking Research Technicians

Please see the job descriptions at the following links: https://surfer.nmr.mgh.harvard.edu/fswiki/ResearchAssistant https://surfer.nmr.mgh.harvard.edu/fswiki/ResearchTechnologist Allison ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://

[Freesurfer] FWHM in mri_glmfit-sim

Hi Doug, I have a few queries regarding FWHM used in multiple comparisons correction program mri_glmfit-sim My data at present is analysed in FSL & Freesurfer following the procedure in the link http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/FslFeatFreeSurfer. No volume based smoothing at

Re: [Freesurfer] Fsgd file format

That all looks right. Your final contrast matrix that you have a question about tests whether Var1+Var2=0 doug On 03/31/2014 08:33 AM, Clint Johns wrote: > I understand, I think! So our matrix should be something like this, > which includes each of the 4 components we are using as variables, all

[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

Re: [Freesurfer] FWHM in mri_glmfit-sim

On 03/31/2014 10:05 AM, Mariam Sood wrote: > Hi Doug, > > I have a few queries regarding FWHM used in multiple comparisons correction > program mri_glmfit-sim > > My data at present is analysed in FSL & Freesurfer following the procedure in > the link > http://surfer.nmr.mgh.harvard.edu/fswiki/

Re: [Freesurfer] CWP values

This is just the way that the interface was programmed. It was fairly easy to add a button to run the correction, more difficult to pull that information back into the interface in a reasonable way. I agree that it makes using the interface less intuitive: once you get a button to press, you c

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

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

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

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

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] CWP values

I see, makes sense! I had a second question, which I repeat below. When reporting significant clusters, should one refer to the cluster by 1) its annotation label, e.g. "sig differences were found in the precentral gyrus", 2) its max vertex as displayed after using the "Find clusters and go to max"

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

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

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

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

[Freesurfer] What coordinate space is freesurfer output in?

Hi, I was wondering what the default freesurfer coordinate space is called? (MNI, something else)? Thanks, Sal ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in

Re: [Freesurfer] SEEDING in Tracula

Hi Durai - Tracula is not for exploratory tractography, i.e., to answer questions like "what is this region connected to"? It uses prior anatomical information on known pathways to reconstruct those specific pathways. The anatomical information comes from the FreeSurfer anatomical segmentatio

Re: [Freesurfer] Monte Carlo simulation - Longitudinal Pipeline

Thanks, Doug! Should I run the mri_preproc and and smooth the output using mri_surf2surf with, let’s say, 10mm, and than run the LME normally in MatLab? Would this be problematic with a different smoothing procedure in mri_glmfit? How will mri_glmfit deal with the longitudinal design? Does this

Re: [Freesurfer] What coordinate space is freesurfer output in?

Native anatomical space of the individual subject. doug On 3/31/14 7:16 PM, Salil Soman wrote: Hi, I was wondering what the default freesurfer coordinate space is called? (MNI, something else)? Thanks, Sal ___ Freesurfer mailing list Freesurfer@

Re: [Freesurfer] SEEDING in Tracula

Hi Anastasia, On a related note, with tracula, you can't let's say track the amygdala to the vmpfc (there is a study already demostrating that there is a white matter tract that connects these two structures). Can I do something like that...take the amygdala as the seed and the vmpfc as the

Re: [Freesurfer] SEEDING in Tracula

Hi Anastasia, Although the website says: In addition to the tract-based analysis that can be performed on the tract-based averages of anisotropy and diffusivity, the same maps could also be used for other voxel-based and ROI-based group analyses. So this makes me think that this type of group