Re: [Freesurfer] FSGD file problems

You should use "Variables" Note the "s". doug Theodor R?ber wrote: > Dear Freesurfers, > > I recently tried to correlate age in a group of subjects > with their cortical thickness. After having set up an FSDG > file and my contrasts, I ran mris_preproc and > mri_surf2surf, and finally mri_glmf

[Freesurfer] FSGD file problems

Dear Freesurfers, I recently tried to correlate age in a group of subjects with their cortical thickness. After having set up an FSDG file and my contrasts, I ran mris_preproc and mri_surf2surf, and finally mri_glmfit. This, however, did not work and I got this errormessage: gdfReadHeader: re

Re: [Freesurfer] references to clusterwise correction for multiple comparisons

It's just a simulation method. You site Hagler, et al, NI 2006, #33, 1093. Smoothing and cluster threshholding for cortical surface-based group analysis of fMRI data. doug Joonkoo Park wrote: > Dear FreeSurfers > > Is there a published reference to the clusterwise correction approach > impleme

[Freesurfer] references to clusterwise correction for multiple comparisons

Dear FreeSurfers Is there a published reference to the clusterwise correction approach implemented in FreeSurfer ( http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis#ClusterwiseCorrectionforMultipleComparisons)? I'd like to cite it for those readers and reviewers who aren't familiar

Re: [Freesurfer] heterotopias

Hi Jenifer Although this paper (Cortical thickness reduction of normal appearing cortex in patients with polymicrogyria) is about Polymicrogyria we had plenty of cases of heterotopias and other malformations of cortical develo

Re: [Freesurfer] heterotopias

Excellent. Many Thanks! Jenifer -Original Message- From: Bruce Fischl [mailto:fis...@nmr.mgh.harvard.edu] Sent: Monday, June 28, 2010 3:16 PM To: Juranek, Jenifer Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] heterotopias Hi Jenifer, what does "handle" mean? You could la

Re: [Freesurfer] heterotopias

Hi Jenifer, what does "handle" mean? You could label them WM-hypointensities, and I think the new version should handle them in terms of not doing something strange in the surface deformation. cheers Bruce On Mon, 28 Jun 2010, Juranek, Jenifer wrote: > Any suggestions from anyone wrt handli

[Freesurfer] heterotopias

Any suggestions from anyone wrt handling heterotopias? Is it best to use a custom labelname to label them as such? Current labelname="WM-hypointensities". Cheers, Jenifer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.ha

Re: [Freesurfer] recon for pial and wm edits

autorecon2-cp is a superset of autorecon2-pial, so you should be all set just running it and autorecon3 On Mon, 28 Jun 2010, York, Philip wrote: > Hi all, > > I am currently finishing a number of wm and pial edits. Is there a command to string both autorecon2-cp and autorecon2-pial together? >

[Freesurfer] recon for pial and wm edits

Hi all, I am currently finishing a number of wm and pial edits. Is there a command to string both autorecon2-cp and autorecon2-pial together? Thanks, Philip ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mai

Re: [Freesurfer] (no subject)

How do they look in the volume? Can you send pics? Elvira Fischer wrote: > > Dear freesurfer users, > > Maybe somebody could help me with the following problem: > > On my retinotopic map I observe extensive blobs with max. values > (turquoise and yellow, heat color map), that rather look like no

[Freesurfer] (no subject)

Dear freesurfer users, Maybe somebody could help me with the following problem:  On my retinotopic map I observe extensive blobs with max. values (turquoise and yellow, heat color map), that rather look like noise. However these blobs always appear in the same region, around the anterior portion

Re: [Freesurfer] Serious failure of surface reconstruction

Hi Cindy, can you send us the orig.mgz, nu.mgz brain.mgz, wm.mgz and T1.mgz and we'll take a look? cheers Bruce On Mon, 28 Jun 2010, Cindy Eckart wrote: ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mai

Re: [Freesurfer] mne_analyze unable to read inflated surface

usually that means you ran out of disk space. Did you check? cheers Bruce On Mon, 28 Jun 2010, Onerva Korhonen wrote: > Hi all, > > I have problems with mne_analyze - I need to do the coordinate > alignment, but when I try to load the inflated surface (or in fact any > surface), I get error mess

[Freesurfer] how to set the tkmedit window size

Hi, there, When I load a subject volume via Tkmedit, is it possible that we can set the Tkmedit main window to a fixed size by tkmedit commandlines? I am kind of tired of dragging the window and resizing it after viewing 100 subejcts. Thanks a lot! Guang

[Freesurfer] mne_analyze unable to read inflated surface

Hi all, I have problems with mne_analyze - I need to do the coordinate alignment, but when I try to load the inflated surface (or in fact any surface), I get error message: mne_read_float could not read data Inflated surface doesn't work with tksurfer either. Instead I get a message: freadFloat

Re: [Freesurfer] Serious failure of surface reconstruction

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