Re: [Freesurfer] Re: mri_surfcluster problem

2007-06-06 Thread Emily Cooper
thanks so much! that seems to have done the trick, emily On 6/4/07, Doug Greve <[EMAIL PROTECTED]> wrote: Sorry, it did fall thru the cr cks. Can you try running it with --no-adjust? When you give it a sign (ie, --pos), it assumes that the input values and threshold are -log10(p) and then adj

[Freesurfer] mapping aseg.mgz to group FEAT analyses

2007-06-06 Thread Eric Feczko
Hey, I noticed on the freesurfer wiki a workflow for registering an individual's subcortical segmentation(aseg.mgz) to individual feat sessions using aseg2feat. Are there any scripts for registering an individual's subcortical segmentation to a group feat session (.gfeat directory)? -Eric

[Freesurfer] Cortical ROIs analysis

2007-06-06 Thread jorge luis
Hello all I have a question: How to threshold a thickness statistical parametric map by using FDR just in one specific label of the fsaverage cortical surface parcelation? In advance thank you a lot Jorge __ LLama Gratis a cualquie

Re: [Freesurfer] Turn Off Verbose Output

2007-06-06 Thread James N. Porter
Doug- It's not really a 'problem' per se, I'm just writing analysis scripts and I only want my terminal to display things that I write, like "Registering subject X" instead of flying through the ras-to-vox tables and such. It's just a visual aesthetic display issue for me. The cat advice wor

Re: [Freesurfer] w file to label

2007-06-06 Thread Doug Greve
I've modifed mri_cor2label to (almost) do what you want to do. You can get the new version from here: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_cor2label It will operate on mgh files, not .w files. Convert your .w file into an mgh with mri_surf2surf, then follow the i

Re: [Freesurfer] tkmedit error niiread

2007-06-06 Thread Doug Greve
This is the same problem as before. You'll need to either get a new version of freesurfer or convert the zmap through freesurfer, eg mri_convert zstats1.nii.gz zstats1.nii.gz if you have the new version of mri_convert. doug uzay emir wrote: Hi I am trying to Overlay zmap onto the orig volu

Re: [Freesurfer] reg- feat2anat error-problem

2007-06-06 Thread Doug Greve
How did you check it? Can you check it with reg-feat2anat --feat Akkaya_Zuhre_1_9++.feat/ --subject akkaya --manxfm func2std doug uzay emir wrote: Hi doug the example_func to standard space registration is correct. I do not know what to do. Uzay Doug Greve <[EMAIL PROTECTED]> wro

RE: [Freesurfer] w file to label

2007-06-06 Thread Dahlia Sharon
Hi Doug, I'm starting analysis of a new study after a long FSFAST hiatus, and am noting your remark about moving away from using w files. In the FSwiki page for paint-sess, it seems like its output is still w files. Does the current way to present functional data include a command instead of pa