[Freesurfer] Does 'color scale bar' show the cortical thickness or [-log10(p)]?

Dear All, I am puzzled by the meaning of 'color scale bar', which appears in the first figure of the FsTutorial/Visualization (https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Visualization) Could you please let me know the meaning of colorbar? Does the 'color scale bar' show the cortical

[Freesurfer] Make_average_subject error

Hi all I have run the script make_average_subject and the error message at the end is: ln: creating symbolic link `rh.sphere' to `rh.sphere.reg': Operation not permitted only rh* files have been created. Can you help? Best wishes Carolyn ___

[Freesurfer] Make_average_subject error

Hi all, I tried running it again with --no-symlink but this error came up ERROR: Flag --no-symlink unrecognized. any advice? Best wishes Carolyn ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu

RE: [Freesurfer] Does 'color scale bar' show the cortical thickness or[-log10(p)]?

Hi Rhuang, On that particular page the color bar is showing the sigificance (-log10(p)) for the group difference in that example. However, if you were displaying a cortical thickness map for an individual subject the color bar would then be showing the cortical thickness values (in mm). It is

Re: [Freesurfer] Make_average_subject error

I have been able to run it with --no-symlink (the flag has to go last), but I get errors like this: mris_make_average_surface: could not read surface file /Volumes/data/NL-GCS/subjects/freesurfer_3.0.1/GCS_adults/--no-symlink/surf/rh.sphere.reg Thanks. Anthony Furlong, Carolyn wrote: Hi

Re: [Freesurfer] Does 'color scale bar' show the cortical thicknessor[-log10(p)]?

Hi Jenni Thanks a lot for your reply. Following the descriptions on FsTutorial/Visualization (https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Visualization) the 'color scale bar' indicates area coded in blue == cortical thickness of Female that of Male (eg. 1mm 2mm), area

Re: [Freesurfer] fMRI stats on the surface

Thank you very much! I assume that when doing the first-level analysis with Feat and then project onto the surface, one shouldn't smooth so much in 3D volume space, right? How much smoothing should be used? Thanks a lot, Christine Bruce Fischl [EMAIL PROTECTED] wrote: Hi Christine, we have

Re: [Freesurfer] fMRI stats on the surface

Hi Christine, I'm not certain you'd want to smooth on the volume at all. See this paper for illustrations Desai R, Liebenthal E, Possing ET, Waldron E, Binder JR. (2005) Volumetric vs. surface-based alignment for localization of auditory cortex activation. *Neuroimage* *26:*4

Re: [Freesurfer] Does 'color scale bar' show the cortical thicknessor[-log10(p)]?

Hi, I'm not sure where you are getting the descriptions below. This statistical map on the surface is actually looking at the correlations of thickness and age, not gender. Can you be more specific as to what you are refering to with the following descriptions: the 'color scale bar'

Re: [Freesurfer] Make_average_subject error

you may be using a version that does not have this option. Try using these doug ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/make_average_subject ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/make_average_surface Furlong, Carolyn wrote: Hi all, I tried

Re: [Freesurfer] Does 'color scale bar' show the cortical thicknessor[-log10(p)]?

Hi Jenni, Many thanks for message. I tried to go through the Freesurfer Tutorial (https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial) There are three sessions in Day-2, including Session_1a and Session_1b. In Session_1a (FreeSurfer Tutorial: Group Analysis), the FSGD file was presented as

Re: [Freesurfer] fMRI stats on the surface

In general, it is better not so smooth in the volume. However, we often smooth some ( 5mm) as the epi-anatomical registration is sometimes inaccurate due to epi distortion. doug [EMAIL PROTECTED] wrote: Hi Christine, I'm not certain you'd want to smooth on the volume at all. See this

Re: [Freesurfer] Does 'color scale bar' show the cortical thicknessor[-log10(p)]?

Hi, So the contrast used to perform this statistical test kept the two groups (male and female) constant and only looked for an interaction between thickness and age. So in this case the blue is where thickness and age are negatively correlated (as the age goes up the cortex gets thinner)

Re: [Freesurfer] Does 'color scale bar' show the cortical thicknessor[-log10(p)]?

Rhuang, The inflated surface figure shows the -log10(p) significance map of thickness vs. age, for both groups (male and female). When you click on a vertex to bring-up a plot, it is showing you the actual thickness data (in mm) for that vertex for each of the subjects. This is intended to

Re: [Freesurfer] Re: mris_thickness_diff computation method?

Dave, Here is some more information on mris_thickness_diff: mris_thickness_diff uses closest Euclidean distance to define correspondence across the two surfaces. It does not assume that the correspondence is given by the vertex IDs. But if one has two surfaces that are the 'same' but not