[Freesurfer] credits for talk

Hi Folks, I remember somewhere there was a page describing how we should put the credits for a publication. How do you want the credit to read for a clinical conference talk reporting freesurfer cortical thickness group study results G. ___ Freesurfer

[Freesurfer] viewing group analysis results

Hello users, I am doing the group analysis stats results...using FDR correction 0.01 and checking the pial surface with curvature and overlay. I see this line come up whenever i change the FDR..is this some kind of error which I need to be concerned about? surfer: Error sending tcl command

[Freesurfer] cortical mask for group analysis

I would like to make a mask for group analysis that excludes the unknown parcellation area. Since I would like to apply the same mask to all subjects (I have already brought them into alignment with mri_preproc), I was wondering how I can convert the average template label/?h.aparc.annot to a

Re: [Freesurfer] cortical mask for group analysis

Hi Morgan, no thickness should not be used in the cc. Bruce On Fri, 6 Apr 2007, Morgan Hough wrote: I would like to make a mask for group analysis that excludes the unknown parcellation area. Since I would like to apply the same mask to all subjects (I have already brought them into

Re: [Freesurfer] cortical mask for group analysis

Thanks Bruce, Are there any other parcellation units that should be excluded? That seems to be the only white matter PU. Cheers, -Morgan Bruce Fischl wrote: Hi Morgan, no thickness should not be used in the cc. Bruce On Fri, 6 Apr 2007, Morgan Hough wrote: I would like to make a mask

Re: [Freesurfer] cortical mask for group analysis

which parcellation are you using? On Fri, 6 Apr 2007, Morgan Hough wrote: Thanks Bruce, Are there any other parcellation units that should be excluded? That seems to be the only white matter PU. Cheers, -Morgan Bruce Fischl wrote: Hi Morgan, no thickness should not be used in the cc.

Re: [Freesurfer] Recommended Linux flavour

freesurfer works fine on Slackware too, v11.0 and v10.1, using Xeon chips. bye, pisti Date: Thu, 05 Apr 2007 13:08:46 -0400 From: Nick Schmansky [EMAIL PROTECTED] Subject: Re: [Freesurfer] Recommended Linux flavour To: [EMAIL PROTECTED] Cc: Freesurfer Mailing List

Re: [Freesurfer] cortical mask for group analysis

I am using ICA on what would be input to mri_glmfit but since ICA is multivariate I need to exclude regions that don't have interpretable thickness or distortion measures. It seems like unknown and corpus callosum are the two to exclude. Are there any others I should exclude? I would like to

Re: [Freesurfer] cortical mask for group analysis

Morgan, If you do this: mri_annotation2label --subject subjid --hemi rh \ --outdir ./labels you will get label files in the ./labels directory. Those label files are text files listing the vertices and x,y.z of each label, including 'unknown' and 'corpuscallosum' (which are the only

[Freesurfer] patches from labels

To all, I'm interested in creating some flattened patches from a region of auditory cortex. I have done the full recon-all processing on the datasets with version 3.0.4. Is there some way to create patch files without manually tracing the region you want to flatten in tksurfer? Is there a

Re: [Freesurfer] cortical mask for group analysis

Hi Nick, I see. I am just not sure how to put this back together again to match the registered thickness files in the .mgh file. Do the vertices have unique ids? Can I cat and sort them? Can I dump matching information from my particular thickness group file and then sort? Is there someway

Re: [Freesurfer] cortical mask for group analysis

If you're using glmfit, you can --label $SUBJECTS_DIR/fsaverage/lh.Medial_wall.label --mask-inv Morgan Hough wrote: Hi Nick, I see. I am just not sure how to put this back together again to match the registered thickness files in the .mgh file. Do the vertices have unique ids? Can I

Re: [Freesurfer] cortical mask for group analysis

Thanks Doug, Does a mask.mgh file get written out to the glmdir? Cheers, -Morgan Doug Greve wrote: If you're using glmfit, you can --label $SUBJECTS_DIR/fsaverage/lh.Medial_wall.label --mask-inv Morgan Hough wrote: Hi Nick, I see. I am just not sure how to put this back together

Re: [Freesurfer] cortical mask for group analysis

I see this does output a mask.mgh which is just what I need. I can convert this and have my nifti mask. Thanks again. Doug Greve wrote: If you're using glmfit, you can --label $SUBJECTS_DIR/fsaverage/lh.Medial_wall.label --mask-inv Morgan Hough wrote: Hi Nick, I see. I am just not

Re: [Freesurfer] cortical mask for group analysis

Yep, that's an inclusive mask. Morgan Hough wrote: Thanks Doug, Does a mask.mgh file get written out to the glmdir? Cheers, -Morgan Doug Greve wrote: If you're using glmfit, you can --label $SUBJECTS_DIR/fsaverage/lh.Medial_wall.label --mask-inv Morgan Hough wrote: Hi Nick, I

Re: [Freesurfer] credits for talk

Hi Greg, you can put in references to some of our papers, or you can just say FreeSurfer, developed, maintained and distributed by the Athinoula A Martinos Center, MGH/Harvard Medical School. thanks for asking. Bruce On Fri, 6 Apr 2007, Kirk, Gregory wrote: Hi Folks, I remember somewhere

Re: [Freesurfer] cortical mask for group analysis

Well, I don't really know what you need. You can convert it to nifti (assuming that there's not a problem with the number of vertices being having it's largest prime factor greater than 32k -- ask Steve why:). Morgan Hough wrote: I see this does output a mask.mgh which is just what I need. I