[Freesurfer] Situation with OASIS

Hi, I was wondaring, what is the situation with OASIS data? Could you please share with us, in which form you will make the results of your great effort available? Thanks in advance for the great job (and reply of course). Martin ___ Freesurfer maili

[Freesurfer] reg -feat2anat error reg -feat2anat error

Hi Doug we tried adding the binaries Doug sent us (MRI_convert, reg2anat and tkregister2, make average subject, make average surface anfd make avergae volume), but now we get a different error:reg-feat2anat --feat ./disc2/Kate/Data_FSL/Pre_AM/AM_preAM_BET.feat/reg/ --subject AMoore 'nknown opt

[Freesurfer] ANCOVA model in Freesurfer

Dear Freesurfer users I am trying to create the GroupDescriptorFile 1 for an ANCOVA in order to analyze local cortical thickness. I intend to compare two groups while controlling for age and mean cortical thickness. Am I right that I can leave out the term "class" and model group as a variable?

Re: [Freesurfer] Situation with OASIS

Hi Martin, it's all processed and checked, and we're now working (with BIRN) on tools to put it online. cheers, Bruce On Mon, 4 Jun 2007, Martin Kavec wrote: Hi, I was wondaring, what is the situation with OASIS data? Could you please share with us, in which form you will make the results

Re: [Freesurfer] reg -feat2anat error reg -feat2anat error

wow, not sure what's going on there. Can you add --debug to the cmd line, caputre the terminal output, and send it to me? Furlong, Carolyn wrote: Hi Doug we tried adding the binaries Doug sent us (MRI_convert, reg2anat and tkregister2, make average subject, make average surface anfd make av

Re: [Freesurfer] ANCOVA model in Freesurfer

Juergen Haenggi wrote: Dear Freesurfer users I am trying to create the GroupDescriptorFile 1 for an ANCOVA in order to analyze local cortical thickness. I intend to compare two groups while controlling for age and mean cortical thickness. Am I right that I can leave out the term "class" and

[Freesurfer] Masking at the individual level

Dear FreeSurfers, Quick question about masking. I routinely make a brainmask for each subject and include the mask flag in the mkanalysis (see below), but I note that when I run contrasts and plot results-either for individual subjects or for group-level stuff-I get statistical results for voxe

RE: [Freesurfer] reg -feat2anat error reg -feat2anat error

Hi Doug This is what happened when I ran it with --debug Kate/Flatmap1> reg-feat2anat --feat /disc2/Kate/Data_FSL/Pre_AM/AM_preAM_BET.feat --subject AMoore --debug 'nknown option: `- Usage: tcsh [ -bcdefilmnqstvVxX ] [ argument ... ]. After I replaced the binaries that you suggested in previous

Re: [Freesurfer] Masking at the individual level

I have never masked out out-of-brain voxels. For visualization purposes, I usually mask out in tkmedit by loading the brain.mgz as aux and then applying aux as a mask from the View menu. It is strange that you are getting out-of-brain activation in the group analysis. How close is it to the e

Re: [Freesurfer] reg -feat2anat error reg -feat2anat error

what platform are you running on? Furlong, Carolyn wrote: Hi Doug This is what happened when I ran it with --debug Kate/Flatmap1> reg-feat2anat --feat /disc2/Kate/Data_FSL/Pre_AM/AM_preAM_BET.feat --subject AMoore --debug 'nknown option: `- Usage: tcsh [ -bcdefilmnqstvVxX ] [ argument ... ]

Re: [Freesurfer] problem with tksurfer (fwd)

Dear Nick, Thanks for the suggestion! I have to admit that I had found it unlikely that the graphics driver could solve the problem but we made the download anyway and it has helped!! Thanks again Claus --- Claus Tempelmann

[Freesurfer] how to import private color scales

dear freesurfers, how do i import my own 'private' colorscales, i.e., colormaps for the overlay data ? something richer in colors than 'heat' ? what's the format and size for such a file? thanks, bye, pisti - [EMAIL PROTECTED] ___ Free

Re: [Freesurfer] how to import private color scales

Sorry, there's no way to do that for overlay data. On Mon, 2007-06-04 at 13:23 -0400, Istvan Akos Morocz wrote: > dear freesurfers, > > how do i import my own 'private' colorscales, i.e., colormaps for the > overlay data ? something richer in colors than 'heat' ? what's the > format and size fo

[Freesurfer] Re: mri_surfcluster problem

hi, sorry to bother the mailinglist again, but i haven't received a response to this question. i just wanted to make sure that it hadn't slipped through the cracks. any help would be very much appreciated, emily On 6/1/07, Emily Cooper <[EMAIL PROTECTED]> wrote: hi, i am having a strange pro

Re: [Freesurfer] fmri conjunction/correlation map

Hi all, I have a few questions on two related topics. Topic 1, conjunction analysis: Thank you Doug for your response pointing out the mergecontrasts tool. I have 2 questions for anyone who may have used this in the past. First, do I specify the two contrasts to merge using the contrast flag twice?

Re: [Freesurfer] Re: mri_surfcluster problem

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 adjusts the threshold for a single-tailed (signed) test, which means that it subtracts log10(2) = 0.3 from th

[Freesurfer] w file to label

Hello, I am trying to convert a w file into a label file, and the best way I came up with seems like it is too complicated to be the actual best way. What I am doing below is reading a list of subjects, and then for each subject, 1.) running mri_surfcluster, 2.) merging its output into a new