[Freesurfer] DOSS FS 5.3

Dear Experts, Hi, I have already done my data analysis having group as fixed factor and age as nuisance factor in QDEC FS 5.3. I also need to run it with DOSS. Would you please advise how to run the same analysis with DOSS from terminal and if it is possible to look at the results in QDEC Display

[Freesurfer] gamma.mgh

Dear FreeSurfers, I've been looking at between-group (controls and disease) differences in cortical thickness cross-sectionally and longitudinally (PC1). I've outputted sig.mgh maps and effect size maps (gamma.mgh) but the cross-sectional gamma.mgh maps are coming up blank. Could you explain wh

[Freesurfer] -hippo-subfields error

Hi, I had a subject already run through recon-all. After making recon-all -s ID -hippo-subfields or recon-all -s ID -hippo-subfields -make all it is failing. It is the first subject ever failing with the hippo-subfields. The rest of the subjects are ok. This subject is properly segmented (tkmedit

Re: [Freesurfer] gamma.mgh

what do you mean they are "coming up blank" On 10/16/2013 05:15 AM, Rees, Elin wrote: > Dear FreeSurfers, > > I've been looking at between-group (controls and disease) differences > in cortical thickness cross-sectionally and longitudinally (PC1). I've > outputted sig.mgh maps and effect size ma

Re: [Freesurfer] DOSS FS 5.3

From the command line you will need to run mri_glmfit. The mri_glmfit.log file in the QDEC output folder will have a sample mri_glmfit command line. You will need to modify this by adding "doss" after the FSGD file. You will also need to create new contrast matrices to match the DOSS model.

[Freesurfer] gamma.mgh

Sorry, I mean the gamma.mgh maps for the cross-sectional differences appear to be blank as no overlay is overlaid on the fsaverage when I do the same command as with the longitudinal gamma.mgh. The commands I am running for the cross-sectional group comparison are: mri_glmfit --glmdir lh_groupd

Re: [Freesurfer] gamma.mgh

So by "blank" you mean that there is nothing above threshold? Have you tried changing the threshold? On 10/16/2013 12:54 PM, Rees, Elin wrote: > Sorry, I mean the gamma.mgh maps for the cross-sectional differences appear > to be blank as no overlay is overlaid on the fsaverage when I do the same

[Freesurfer] 2x2 repeated measures ANOVA?

Hi Freesurfer Experts, is it possible to run a 2x2 repeated measures ANOVA for functional data on the surface in Freesurfer (both factors have two levels and are fully within subjects)? If not, is there a way to use mri_glmfit-sim on results calculated in Matlab to correct for multiple comparisons?

Re: [Freesurfer] Freeview Volume & Surface alignment

Would it be possible to send us the command line and the files that produces the screenshot? Thanks, Ruopeng On Oct 16, 2013, at 2:28 PM, Kambiz Tavabi wrote: > I would like to inspect the results of my surface boundary on the volume as > per the approach in tkmedit. However in freeview the s

Re: [Freesurfer] -hippo-subfields error

Gari, can you send us the log of the hippo subfield module (or the screen output; they should be the same) Cheers, /Eugenio On 10/16/2013 10:22 AM, Garikoitz Lerma-Usabiaga wrote: Hi, I had a subject already run through recon-all. After making recon-all -s ID -hippo-subfields or recon-all -s ID

[Freesurfer] Easiest way to resample a volume..?

Hi all -- I have a volume of say 100x100x100 1mm^3 and I'd like to resample it to 300x300x300 0.33mm^3. What's the easiest way to do this? Will 'mri_convert' do the trick? Best -=R -- Rudolph Pienaar, M.Eng, D.Eng / email: rudo...@nmr.mgh.harvard.edu MGH/MIT/HMS Athinoula A. Martinos Center f

Re: [Freesurfer] Freeview Volume & Surface alignment

Hi Ruopeng, Sorry for the confusion in my initial post. The screen capture is actually a grab from one of the viewing windows in FREEVIEW; so I am actually not doing anything on the command line with tkmedit. In freeview, I am loading the original T1 volume and then loading the skin, outer skull, o

Re: [Freesurfer] Easiest way to resample a volume..?

Perfect! That worked :-) Thanks On 10/16/13 16:03 , Juan Eugenio Iglesias wrote: > Hi Rudolph, > yes, you can use mri_convert with the flag -vs 0.33 0.33 0.33 > You might want to play with -rt as well to switch from linear to cubic > resampling. > Cheers, > /Eugenio > > > On 10/16/20

Re: [Freesurfer] Easiest way to resample a volume..?

Thanks, Jon -- although the '-ds' seems depreciated: [paris:x86_64-Linux-chb-fs-stable]...olphpienaar/tmp$>mri_convert -vs 1 1 1 -ds 0.25 0.25 0.25 BM05_recon.nii BM05_recon3.nii mri_convert -vs 1 1 1 -ds 0.25 0.25 0.25 BM05_recon.nii BM05_recon3.nii mri_convert: unknown flag "-ds" type mri_con

Re: [Freesurfer] How do you create labels from binary masks?

I think you need to use mri_cor2label (not very well named:) doug On 10/16/13 4:24 PM, Marcos Martins da Silva wrote: Hi, Freesurfers. I need to create some labels from binary masks. Sometime ago I read a post (https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2013-October/033783.html )

[Freesurfer] tkmedit error message

Hello, I am a new freesurfer user. I tried to view subject data with tkmedit for the first time after the recon-all process finished without errors. Here is what I typed and the message I got: [ariana:~/Desktop/ELISSA_ THESIS/ATO] cmurphy% tkmedit ATO brainmask.mgz -aux T1.mgz -surfs -aseg Wed Oc