[Freesurfer] Weighted Average of Cortical Thickness

Hi, I had 2 questions relating to measuring global mean cortical thickness with the weighting factor of surface area bh.thickness = ( (lh.thickness * lh.surfarea) + (rh.thickness * rh.surfarea) ) / (lh.surfarea + rh.surfarea) 1.) If this weighting is recommended, then shouldn't it be performed f

[Freesurfer] Ascii file of thickness overlay with vertex index and coordinates

misunderstanding something Could this info be extracted with converting a surface (e.g., inflated) with mris_convert? If so, where can I find info on how to read the ascii surface files. In other words, what I'm trying to do is for each vertex: Best, Mike -- Michael Kranz Graduate Res

Re: [Freesurfer] fslmaths like utility for surface overlays?

Thanks!! These options do the trick On Wed, Mar 29, 2017 at 2:03 AM, Michael Kranz wrote: > Hi, > > Is there a way to create a subject specific overlay with an intensity > value of 1 (or another constant value across the entire cortical mantle)? > (I'm thinking a command

[Freesurfer] fslmaths like utility for surface overlays?

Hi, Is there a way to create a subject specific overlay with an intensity value of 1 (or another constant value across the entire cortical mantle)? (I'm thinking a command like fslmaths in FSL but on the surface for each vertex). Best, Mike -- Michael Kranz Graduate Research Assi

[Freesurfer] Whole brain mediation analysis

given the outputs from mri_glmfit, it seems like it would be possible with Freesurfer. Best, Mike -- Michael Kranz Graduate Research Assistant | Beckman Institute University of Illinois 314-323-1329 ___ Freesurfer mailing list Freesurfer

[Freesurfer] Comparing aparc labels with volume ROIs in MNI152 2mm space

Hi guys, I want to overlay an ROI mask created in FSL in the MNI152 2mm volume space (from a metaanalysis) with the aparc labels in Freesurfer to compare the two ROI schemes (so I can have justification for picking some of the Freesurfer ROIs for analyses). I'm thinking of running the MNI152 2mm

[Freesurfer] Longitudinal fMRI analysis

Hi, I have two groups and two time points (pre and post). I want to investigate group*time interactions in an fMRI task taken at both time points. I have run all the subjects through first level FEAT analyses in FSL as well as the longitudinal Freesurfer pipeline. I'm thinking of registering the

[Freesurfer] mris__label__calc intersect error in longitudinal qcache

Hi, I'm having trouble figuring out following problem: For one subject (out of 200), I get the following error (this error only persists for the right hemisphere-- left hemisphere works fine for this subject). mris_label_calc intersect /SUBJECTS_DIR/sub2.long.subt/label/rh.cortex.label /SUBJECTS

[Freesurfer] Longitudinal data for cross sectional individual differences study

better to use longitudinally processed stats (as opposed to the cross sectional stats)? I ask because I'm not aware of any publications that do this... Thanks much, Mike Kranz Michael Kranz Graduate Research Assistant | Beckman Institute University of Illinois 314-323

[Freesurfer] Striatum and cerebellum parcellation stats from Choi2012 and Buckner 2011

Hi all, I was wondering how I could go about getting anatomical stats for the different regions from the Choi2012 and Buckner 2011 parcellations. The Yeo 2011 cortical parcellation files were available in the fsaverage folders and I could get stats and labels for those, but I couldn't figure out

[Freesurfer] Curvature/folding stats

Hi all, What's the difference between the curvature and folding measures outputted in the aparc stats files (i.e. mean, gaussian, folding index, and curvature index)? Additionally, which measures are the most reliable for individual differences? Thanks, Mike Michael Kranz Graduate Res

Re: [Freesurfer] Brodmann Area Atlas

Nvm just read an old thread. Sorry about that. https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2011-August/019825.html On Fri, Aug 16, 2013 at 11:24 AM, Michael Kranz wrote: > Hi all, > > Is there a place where I could find an atlas with all of the Brodmann > areas? O

[Freesurfer] Brodmann Area Atlas

Hi all, Is there a place where I could find an atlas with all of the Brodmann areas? Or is the one available with a portion of the areas the only existing atlas? Thanks, Mike ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mg

Re: [Freesurfer] Cerebellum Subcortical edits

istinguish. It depends on what you are after in your > analysis if you need to take care or not. > > Regards, > > Martin > > Sent from my iPad > > On 31.7.2013, at 23:23, Michael Kranz wrote: > > > Hi guys, > > > > I was just wondering approximately how

[Freesurfer] Processing Multiple Subjects

Hi all, If I process more subjects than the recommended amount given my number of cores and memory, will this affect the stats/surfaces or just slow the process down? I'm asking due to the sensitivity of workstations and also I seem to be getting slightly different stats sometimes when I re-sub

[Freesurfer] Using the T2 pial flag for pial refinement

Hi all, I'm having trouble determining whether or not to use our T2 images for the new pial refinement feature. *Most importantly, I'm wondering if our T2 image parameters are sufficient for the T2 pial refinement. The parameters of our T2 images are as follows:* T2 TSE overlay with a voxel size