Re: [Freesurfer] vertex-wise ROI analysis

You can do a vertex-wise analysis in any region you like (e.g. cortex, superior temporal cortex, etc.) check the "--label" option of mri_glmfit. see also: https://surfer.nmr.mgh.harvard.edu/fswiki/BuildYourOwnMonteCarlo -joost

[Freesurfer] BuildYourOwnMonteCarlo

Hi, A question about building your own Monte Carlo. here: https://surfer.nmr.mgh.harvard.edu/fswiki/BuildYourOwnMonteCarlo it says: "If you want to restrict the correction to a smaller area to reduce the severity of the correction, you can specify a mask or a label and change the output folder".

[Freesurfer] Fwd: hardware question

Hi, We're thinking of buying a computer with the main goal simultaneous processing of 'recon-all's'. the computer cannot be a 'cluster' and must be linux. These specs looked good to us: - Intel Core i7-5820K 3.3Ghz - Asus X99-A - Arctic Cooling Freezer A30 CPU Cooler - G.Skill Aegis DDR4 2400

[Freesurfer] mri_glmfit-sim

Hi, Linux jjanssen 3.8.0-25-generic #37-Ubuntu SMP Thu Jun 6 20:47:07 UTC 2013 x86_64 x86_64 x86_64 GNU/Linux command: mri_glmfit-sim --glmdir lh.thickness.20 --cache 2.0 pos error: ERROR: thresh = 1,3, must be 1.3, 2.0, 2.3, 3.0, 3.3, 4.0 i saw 1 prior email about this error message but no so

Re: [Freesurfer] mri_glmfit-sim

Hi, for those experiencing the same issue: we solved it by commenting out line 608 from mri_glmfit-sim -joost On Mon, Aug 12, 2013 at 4:56 PM, Douglas N Greve wrote: > use 1.3 not 1,3 > > > On 08/12/2013 10:44 AM, joost janssen wrote: > > Hi, > > > > Linux jjanss

Re: [Freesurfer] hippocampal subfields downsampling question

Great question! El 26/10/2017 17:09, "NIELS JANSSEN ." escribió: > In the mri output folder, I noticed that both the 0.33 mm and 1 mm > (voxelspace) maps have subfields that do not overlap in space, meaning that > each subfield occupies a unique location in space that does not overlap > with oth

Re: [Freesurfer] Longitudinal processing with different FS versions

Susanna carino!! On Fri, Apr 13, 2018 at 10:21 AM, Susanna Carmona Cañabate < susannacarm...@gmail.com> wrote: > Dear Freesurfers, > > We are running a longitudinal study with 4 time points. The first two time > points

[Freesurfer] ?h.area

External Email - Use Caution Hi, Short: Is it possible to generate v6.-style ?h.area based on v5.1-recon output? If so, how? Long: I have 5.1 processed data and would like to re-generate ?h.area v6-style (Winkler et al. 2018). I would like to avoid complete rerunning through v6.

Re: [Freesurfer] ?h.area

think you can do it with mris_make_surfaces by setting the number of > iterations to 0 (-n 0) so it doesn't do any deformation, and starting with > the surface you want to end with (e.g. -orig_white white) > > cheers > Bruce > > On Fri, 27 Apr 2018, Joost Janssen wrote:

[Freesurfer] inherent smoothing

External Email - Use Caution Dear Doug, I'd like to determine the inherent smoothing of ?h.thickness in my sample. What is the best way to do this? Thanks, -joost ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.n

Re: [Freesurfer] inherent smoothing

is, there will be a fwhm.dat file with the > estimate of the Gaussian full width half max. The smoothess is not > Gaussian, but it gives a measure. Does that work? > > > On 05/08/2018 04:20 AM, Joost Janssen wrote: > > > > > > Dear Doug, > > > > I'd lik

Re: [Freesurfer] Adjusting/accounting for between scanner variance

External Email - Use Caution https://github.com/Jfortin1/ComBatHarmonization -joost Op di 26 jun. 2018 18:50 schreef Heidi Lindroth : > External Email - Use Caution > > Hi there, > > Is there a standard method to use for adjusting for between scanner > variance? In the

[Freesurfer] xhemi

External Email - Use Caution Dear Doug, The objective is to have _regional_ laterality index for thickness for aparc mapped to the left hemisphere. The following commands work without error but are they correct for meeting my objective? Thanks. surfreg --s $subject --t fsaverage_

Re: [Freesurfer] xhemi

thickness to > mgh format > > On 11/27/2023 10:01 AM, Joost Janssen wrote: > > External Email - Use Caution > Dear Doug, > > The objective is to have _regional_ laterality index for thickness for > aparc mapped to the left hemisphere. The following commands work