[Freesurfer] Changing primary slice direction

Hi Freesurfer Community, I am using matlab to do a histogram segmentation on a FLAIR volume. The algorithm I am using best works with axial direction. Is there any way to change the primary slice direction from sagittal to axial? I have tried mri_convert with --out_orientation set to LIA but tha

[Freesurfer] Outputting all tracula statistics to table

Hi, What is the proper way to generate a single table containing all tracula generated statistics for all subjects in a study? I tought tractstats2table was the way to do this, I am confused as to how trac-all -stat factors into this process in the latest (12-09-13 version)? Thank you. -Sal

[Freesurfer] Problem with the Monte Carlo simulation

Dear FreeSurfer experts, We are running group analyses in 430 young healthy volunteers using Qdec interface and FreeSurfer 5.3. FDR correction seems to be not enough restrictive and on the contrary use a Bonferroni correction with the total number of vertices would be too much restrictive. In th

[Freesurfer] Applying two registration matrices

Hi Freesurfer Experts, I was wondering what the best way to apply two registration matrices to the same data set would be, ideally without re-slicing after the first registration? Thanks, Caspar ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu h

[Freesurfer] Fwd: Tracula Error: bvecs and bvals don't have the same number of entries

Hi, Sorry Anastasia, I'm seeing that my question was not so clear. The files I sent you in the first mail are the bvecs and bvals saved by trac-all -prep in the dmri directory. The original files are in attachment in this mail, Francesco Baldacchini 2014/1/13 Anastasia Yendiki > > Hi Francesc