Re: [Freesurfer] Data interest of the CorticalParcellation_Yeo2011

Hi Yu-Chieh, I am cc-ing the freesurfer list who may help you with your issues. Can you explain what exactly you are trying do? The parcellation is released in different resolutions including fsaverage5. Why can't you just use the fsaverage5 parcellation? Cheers, Thomas On Fri, May 1, 2015 at 6

Re: [Freesurfer] problem with left/right parallelization

Yup this is a known issue with the mri_segstats binary. Please go to the following page and download the mri_segstats file that corresponds to your version of freesurfer (see contents of $FREESURFER_HOME/build-stampt.txt file to determine your version). Replace the version of mri_segstats in yo

Re: [Freesurfer] Kurtosis and Skewness

Thanks a lot Doug! Additionally, I've been trying to calculate the curvature of an ROI extracted from a CT scan. Is there a way to do that in Freesurfer even though this ROI is not part of an MRI? (I was playing with mris_anatomical_stats and mris_curvature_stats but have been unsuccessful so far s

[Freesurfer] Still time to register for the 2015 HCP Course!

A reminder that it’s not too late to register for the 2015 HCP Course: “Exploring the Human Connectome” , to be held June 8-12, 2015 at the Marriott Resort Waikiki Beach, in Honolulu, Hawaii, USA. Also, a remin

[Freesurfer] Tksurfer_Visualization issue

Hi Doug, I finished running FSFAST on fmri data set. I corrected the data for multiple comparison.In order to visualize the results I ran the following command line: tksurfer fsaverage lh inflated -overlay cache.th30.pos.sig.cluster.nii.gz -annot cache.th30.pos.sig.ocn.annot -fminmax 1.3 3 I a

Re: [Freesurfer] binary noise regressor

I don't necessarily think the exclude file is a better approach. What you are doing is probably fine. doug On 5/1/15 12:12 PM, sha...@nmr.mgh.harvard.edu wrote: > Hi Doug, > The reason that we did not use that 'exclusion method' was that, we > were not sure if the effect of shock is limited t

Re: [Freesurfer] binary noise regressor

That will do what you want if you expect the shock to have the same response to each application. Alternatively, you can set up a time point exclude file to exclude those time points. If you use this, then create the file by putting the time in seconds of the time points you want to exclude. do

[Freesurfer] binary noise regressor

Hi Surfers I want to remove the possible effects of a binary noise (electric shock) from the evoked fMRI. To do so, I have generated a regressor file in which all TRs in which electric shock has been applied are marked as 1 and the rest of TRs are 0. I just want to be sure that, this is all I

Re: [Freesurfer] glmfit-sim question

On 5/1/15 10:13 AM, Hirsch, Gabriella wrote: Hi FS experts, I had a quick question about glmfit-sim in monte carlo. I have followed the FS wiki by using the following command to correct for multiple comparisons separately on both hemispheres: mri_glmfit-sim \ --glmdir_?h.xxx.glmdir \ --

[Freesurfer] problem with left/right parallelization

I have successful runs of recon-all -autorecon1 and recon-all -autorecon2-volonly per your suggested sequence: recon-all -s subj -autorecon1 recon-all -s subj -autorecon2-volonly recon-all -s subj -autorecon2-perhemi -hemi rh -log recon-all-hemi rh.log -notify rh-done.log -openmp 4 & recon-all -s

[Freesurfer] glmfit-sim question

Hi FS experts, I had a quick question about glmfit-sim in monte carlo. I have followed the FS wiki by using the following command to correct for multiple comparisons separately on both hemispheres: mri_glmfit-sim \ --glmdir_?h.xxx.glmdir \ --sim mc-z 1 1.3 mc-z.absolute \ --sim-sign abs --c

Re: [Freesurfer] 2 factor design. error: matrix is ill-conditioned or badly scaled

Try demeaning your covariates, ie, compute the mean of all ses values, then subtract that from each value. doug On 5/1/15 7:25 AM, Sanne Oostermeijer wrote: > Dear Sir/Madam, > > For our longitudinal analyses in freesurfer (5.1) we have a design similar to > http://freesurfer.net/fswiki/Fsgdf6G0

Re: [Freesurfer] Incomplete Cerebellum Segmentation

Hi Jessica, If you want to regenerate the aseg and surfaces you will need to run the subject through the rest of the recon-all pipeline (autorecon2 and autorecon3). The -skullstrip is only going to redo that specific step. Thank you, Ani Varjabedian On 04/30/2015 02:00 PM, Jessica Lynn Hans

Re: [Freesurfer] -openmp 8 and -use-gpu questions

perhaps Nick can comment, but I think the issue is with the memory controller not being efficient with N>4 threads running cheers Bruce On Fri, 1 May 2015, Krieger, Donald N. wrote: Thanks very much for getting back so quickly. The processing times were 5-6 hours for all instances. There is

[Freesurfer] 2 factor design. error: matrix is ill-conditioned or badly scaled

Dear Sir/Madam, For our longitudinal analyses in freesurfer (5.1) we have a design similar to http://freesurfer.net/fswiki/Fsgdf6G0V However we have 2 factor: one is 3 levels (G1/G2/G3); one is 2 level (Male/Female), and a (continues) covariate, and we cant run the analysis due to the error: ma

Re: [Freesurfer] -openmp 8 and -use-gpu questions

Thanks very much for getting back so quickly. The processing times were 5-6 hours for all instances. There is an incremental but only modest improvement for 4/6 vs 8/12 processors. I'll put up more information on the list when I've finished thinking this through. Regards,   Don   Don Krieger, Ph