[Freesurfer] FreeSurfer algorithms

Surfers,Can someone please point me towards some detailed description of the algorithms that freesurfer uses to process the data...maybe there are some papers that talk about  this??  Anthony ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu

[Freesurfer] inflated images

Hello all, Can some one edify me regarding how FreeSurfer is able to maintain the same basic brain geometry (hemisphere shape) when it creates an inflated file image.  I would figure that some areas (because of deeper sulci) would blow up (produce more inflated surface) much differently than others

[Freesurfer] Ventricular Volume in FreeSurfer?

Hello All, I am wondering. Does FreeSurfer log ventricular volume? -Anthony ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

[Freesurfer] autorecon2 on rh only

Can you please tell me the command line for running recon-all autorecon2 on only the right hemisphere?  It isn't entirely clear to me from the wiki. I appreciate it, Anthony ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.h

[Freesurfer] Noncompletion of autorecon2

Hello,   I am having some trouble.  I have all of the left hemisphere data that autorecon2 makes but not all from the right hemisphere.  I have 2 questions:1.  If freesurfer encountered a problem and ended with an "error" would that error appear at the end of the recon-all log? 2.  If the computer

[Freesurfer] autorecon2

I was running autorecon2 and it did not finish.  The status.log file tells me that it is finished but the data does not appear in the surf folder (some of the lh data is there but no rh).  Here is the end of the log file..does that help?  I tried to run autorecon3 and that was the "new invocati

[Freesurfer] tksurfer overlay display

Hello,How can the color scale bar of the overlay display be changed so that it only shows positive values?I know if you use the truncate function in "Configure Overlay Display" that takes the color for the negative values off the display but the scale itself still shows negative values.  If further

[Freesurfer] color scale bar

if you are using the overlay color display how can you configure the scale?  In the paper "Measuring the thickness of the human cerebral cortex from magnetic resonance images" the images show the overlay color bar in many different scales.  Thanks ___ Fre

[Freesurfer] Curvature

How should one interpret the curvature function...what is the essence of it's being...what does it mean? ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

[Freesurfer] tksurfer - view - information - distance

tksurfer -> view -> information - >  distancewhat is the reference point for this command, ie when the cursor is on point x with a value of, say 0.02 what is that the distance of?Thanks. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://

[Freesurfer] recon-all -subjid < > -autorecon2

I have tried to run this command 2 times and it does not seem to finish the command.  The log file just says:Em registration (date/time)CA Normalization (date/time)CA Reg (date/time)The log file ends each time with Left_Thalamus_Proper (10): linear fit = 1.00 x + 0.0 (4319 voxels, overlap=0.599)al

[Freesurfer] tksurfer - cuvature - thickness

I loaded the curvature -> thickness file...I don't understand how this gives you thickness measurments.  On the surfer interface what are the distance and curvature numbers measured in.what are the units?  What is taken as center for those measurements as well?  Thanks very much for your h

[Freesurfer] cortical thickness in freesurfer

Hello, I am wondering how to view cortical thickness data in freesurfer.  thanks ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer