[Freesurfer] Extraction of T2 map statistics-per-segment

Hello — I’m trying to extract quantitative T2 values for different brain segments. I’ve converted my T2 set of DICOMs to .mgz format using mri_convert and loaded them into freeview. >> mri_convert -it siemens_dicom -ot mgz T2_maps_Dir/slice_1_T2_map.dcm >> T2_in_mgz.mgz After loading T2_in_mgz.

[Freesurfer] longitudinal pipeline

Hi Freesurfer Experts, Is the longitudinal pipeline still recommended for the DTI data analysis if structural changes occur at different time points (e.g., pre and post-treatment)? Or is it better to use the standard pipeline? Are other options available? Thanks so much! Song _

Re: [Freesurfer] Extract mean time series from parcellated region

what do you mean you can't get them? The program fails? It produces 0s? On 1/26/15 3:48 PM, sabin khadka wrote: Hi FS user, I am trying to extract time series of fmri rest data of certain parcellated regions (both cortical and subcortical). for that I am doing following # bbregister --s -

Re: [Freesurfer] extracting pvalues

what do you mean? Just a list of values? the column, row, slice as well? On 1/26/15 4:02 PM, Hirsch, Gabriella wrote: Hi FreeSurfer experts, Is there a way to extract significant pvalues from sig.mgh files (Obtained from the GroupAnalysisDng tutorial)? I've looked online but having troubl

Re: [Freesurfer] vertex-wise covariate for gyrification index

That's fine. mri_glmfit-sim has a little anxiety when it finds mri_glmfit options it does not recognize. doug On 1/26/15 5:00 PM, angela.fav...@unipd.it wrote: > Hi Doug, > thank you for this hint. > I have included --pvr in my mri_glmfit command using a stack of cortical > thickness maps of the

Re: [Freesurfer] vertex-wise covariate for gyrification index

Hi Doug, thank you for this hint. I have included --pvr in my mri_glmfit command using a stack of cortical thickness maps of the same hemisphere (and same subjects in the same order). I also added a column in my design matrix. It seems to work. Only when I use the mri_glmfit-sim command, this messa

[Freesurfer] extracting pvalues

Hi FreeSurfer experts, Is there a way to extract significant pvalues from sig.mgh files (Obtained from the GroupAnalysisDng tutorial)? I've looked online but having trouble. Somehow mris_covert isn't working. Thanks! Gabriella ___ Freesurfer mailing

[Freesurfer] Extract mean time series from parcellated region

Hi FS user, I am trying to extract time series of fmri rest data of certain parcellated regions (both cortical and subcortical). for that I am doing following # bbregister --s --mov --init-fsl --reg register.dat --bold# mri_label2vol --aparc+aseg --subject --temp --fillthresh 0.5 --reg regs

Re: [Freesurfer] FREESURFER] ERROR: matrix is ill-conditioned or badly scaled, condno = 164365

Try demeaning your covariates. Do so on a sample-wise basis (ie, compute the mean age across all subjects, then subtract that mean from all ages) doug On 01/14/2015 07:30 PM, i_geschwind2013 wrote: > /Hello/ > /I’m trying to do an group analysis using mir_glmfit but I met this error./ > ERROR: m

Re: [Freesurfer] vertex-wise covariate for gyrification index

QDEC does not allow it, but you can do it with mri_glmfit with the --pvr option. Run mri_glmfit with --help to get more info. doug On 01/25/2015 11:16 AM, angela.fav...@unipd.it wrote: > Hi all, > I wrote a paper about gyrification in a sample of malnourished patients. I > found only little overl

Re: [Freesurfer] cortical thickness analysis

what is your mri_glmfit-sim command line? Try running it with --cwp 1 to get all clusters regardless of their p-value doug On 01/23/2015 04:01 PM, Hirsch, Gabriella wrote: > > Hi freesurfer experts, > > I have a question I was hoping someone could help me with; > > I am currently analysing the co

Re: [Freesurfer] Some questions about fsaverage

You'll need to get a copy of mri_surf2surf.{linux,mac}. It was there all the time I just did not put it on the installation page. I've updated the page with this link ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/5.1.0/xhemi/mri_surf2surf.{linux,mac} When you re-run delete the xhemi fo

Re: [Freesurfer] mri_cnr and bash

Dear all, I have come up with a pretty good preliminary solution namely: I run the first loop that returns me CNR and some other stuff from the command mri_cnr. It creates one txt. file for each subject. for i in *3T; do mri_cnr $i/surf $i/mri/norm.mgz > $i/"$i"_cnr.txt; done (All of my subje

Re: [Freesurfer] average values per cluster

We get these kind of reports occasionally. When I ask people to confirm that they use exactly the same design matrix in SPSS, I never hear back, so I assume that it gets resolved. So please check. The other thing you can do is to run in matlab, something like cd glmdir/contrast X = load('Xg.da

[Freesurfer] average values per cluster

Dear Freesurfer experts, Sorry to bother you again, but I have two more questions about extracting (thickness/surface/GI) values from a certain cluster. As I understood, the abs.y.ocn.dat file gives the average values for a given significant cluster (e.g. a cluster where there is a significant Ax