Re: [Freesurfer] Checking optseq efficiency of a custom par file.

You need to build a wrapper that creates all possible combinations of the three sets of par files. Then use this to build a design matrix for each one. Then estimate the efficiency (eff) and VRF (vrf) for the contrasts of interest. M = C*inv(X'*X)*C'; eff = 1/trace(M); vrf =

Re: [Freesurfer] White matter and cp edits don't produce new results after reconall

Dear Bruce, Thank you. I transferred via ftp, the entire Freesurfer subject folder (Sub5.zip). The most pronounced "miss" segmentation is around coordinate 169 158 91, but it extends from about 168 155 85 up until 168 164 106. Thank you very much for taking a look at it. Best, Annelinde

[Freesurfer] Error - extracting percent signal

Hello freesurfer experts, I am trying to extract an average percent signal change from a functional roi label I created in tkmedit using fsaverage. I followed previously discussed methods: 1) mri_label2vol --label --temp fsaverage/mri.2mm/orig.mgz --regheader fsaverage/mri/orig.mgz --o 2) I

[Freesurfer] Cluster coordinates in QDEC

Dear FreeSurfer Experts,   while I'm doing my first FreeSurfer analysis with QDEC (cortical thickness in controls vs. patients) I'm having a problem with the coordinates QDEC puts out in the Terminal. I read some rather old posts about that but wondered if there has been some development since.

Re: [Freesurfer] QA tools

Thank you Bruce and MIke! I was not really looking for something INSTEAD of manual inspection, but for a measure of the quality of my dataset similarly to what is reccomended for functional MRI (in that case a SNR below 100 can be considered a criterion of exclusion). What are the meaning of these

Re: [Freesurfer] Edit the number of segments in the segmentation of the corpus callosum

Hi Bruce, DELL R910 Intel(R) Xeon(R) CPU E7520 @ 1.87GHz (16 cores) 32 Go RAM CentOS release 5.10 (Final) kernel 2.6.18-371.3.1.el5 On Mon, Nov 23, 2015 at 7:32 PM, Bruce Fischl wrote: > Hi Genevieve > > I just tracked this down and it is a bug in mri_cc. If you

Re: [Freesurfer] subjects_dir

Hi Eric I think if FREESURFER_HOME is set properly recon-all will create the symlinks it needs so you won't have to do it yourself (including the fsaverage one - I just checked). cheers Bruce On Mon, 23 Nov 2015, Eric Cunningham wrote: > Other than fsaverage, are there any other files that