[Freesurfer] Re: reg-feat2anat basics

It only uses the example_func, so if that is affected, then the registration will be off. In general, you should not use freesurfer with data you have non-linearly registered with some template. The freesurfer intersubject registration itself is non-linear. doug Georg Homola wrote: Hi Doug!

Re: [Freesurfer] Can fieldsigns be added across sessions?

Jeff Phillips wrote: Hi Doug, Thanks for responding, and I think I need to restate our original question(s). What we are trying to do is to get a metric of the reliability of retinotopic mapping--i.e., across multiple sessions, how often are regional borders replicated? To that end, we ha

[Freesurfer] Re: postdoc position

Dear Freesurfers: There is a research asst job available at UC Berkeley in Bill Jagust's lab coordinating a multi-site study on the analysis of an Alzheimer's treatment using PET-FDG scanning. More information can be found at: http://jobs.berkeley.edu/ Look for position #9731 Thanks! ___

[Freesurfer] reg-feat2anat basics

Hi Doug! May be a very basic question for better understanding, but how much does reg-feat2anat care about the FSL preprocessing e.g. dewarping? And especially important for me, does it make a difference if you FNIRT or FLIRT on first level? Is it a good idea to process non-linearly registered sub

Re: [Freesurfer] Can fieldsigns be added across sessions?

Hi Doug, Thanks for responding, and I think I need to restate our original question(s). What we are trying to do is to get a metric of the reliability of retinotopic mapping--i.e., across multiple sessions, how often are regional borders replicated? To that end, we have been splitting up our dat

Re: [Freesurfer] Can fieldsigns be added across sessions?

Hi Y'all, sorry for not chiming in sooner. Jeff, if you have multiple eccen or polar runs, you should just be able to set them up as runs in the fsfast directory structure (ie, as dirs with 0-padded, 3digit run numbers), and it should find them and combine them properly. And you can include the

Re: [Freesurfer] average 4d volume

You can use mri_concat 4d.nii --mean --o 3d.nii doug j...@nmr.mgh.harvard.edu wrote: Hi! I tried to use mri_xvolavg to average a 4d nii volume, but does it need me to list each 3d volume separately? Is there a command that I can use to produce an average of a 4d volume, in one 3d image? T

RE: [Freesurfer] Can fieldsigns be added across sessions?

I am not familiar with fsfast, so someone with intimate knowledge of the code (Doug?) could help more. But if you can specify the stimulus order in your paradigm files, then you should not have to do any phase reversals yourself. It seems strange (i.e. bug-like) that your fieldsign comes out

[Freesurfer] Unable to Open GUI

Hi, We are operating x86_64 redhat linux on a server, and we recently installed FreeSurfer on the surfer to help with running multiple recon-all's. However, whenever I attempt to run tkmedit or tksurfer, I get the following error: [and...@scan2 Anatomicals]$ tkmedit Focus_reg_009 brainmask.mgz GL

Re: [Freesurfer] Can fieldsigns be added across sessions?

Hi Don, Thanks for writing back again. Let me clarify: in our last session, we had a scanning menu like this: 1 run polar/clockwise 1 run eccen/expanding 1 run polar/counter-clockwise 1 run eccen/contracting The difference in direction was reflected in our paradigm files (*.par), with clockwis

RE: [Freesurfer] Can fieldsigns be added across sessions?

1. Fieldsign is supposed to be -1 or 1, without values in between. It is the sign of the cross product. I don't see why you would want to average the fieldsign. You will get the best estimate of the fieldsign by calculating it from the average of all your available data. 2. Reversing the sti

[Freesurfer] average 4d volume

Hi! I tried to use mri_xvolavg to average a 4d nii volume, but does it need me to list each 3d volume separately? Is there a command that I can use to produce an average of a 4d volume, in one 3d image? Thanks in advance!! Jake ___ Freesurfer mailin

Re: [Freesurfer] Can fieldsigns be added across sessions?

Sorry, one additional question: per your suggestion, I can handle adding/averaging the real and imaginary component masks, but what syntax can I use in paint-sess to convert those composite masks into fieldsign maps? Thanks, Jeff On Mon, May 11, 2009 at 12:40 PM, Jeff Phillips < jeffrey.s.phill

Re: [Freesurfer] Can fieldsigns be added across sessions?

Hi Don, Thanks for your comments. I will try operating on the eccentricity and polar angle maps first--however, if I calculate a fieldsign from average maps, I presume that the fieldsign map will not be similarly graded, but rather binary. I'll have to think about how to adapt that to our purpos

Re: [Freesurfer] tkmedit multiple orientation view

Sorry, I put the -tcl parameter in the wrong place in my script after a tksurfer command. Now it works perfectly! Thanks again, Attila On Mon, May 11, 2009 at 8:50 AM, Bruce Fischl wrote: > what was your cmdline? > > On Mon, 11 May 2009, Krajcsi Attila wrote: > > Thank you, Bruce! >> >> I trie

Re: [Freesurfer] tkmedit multiple orientation view

what was your cmdline? On Mon, 11 May 2009, Krajcsi Attila wrote: Thank you, Bruce! I tried it, but I get the error message: invalid command name "SetViewPreset" I couldn't find this or similar command in the wiki page: http://surfer.nmr.mgh.harvard.edu/fswiki/TkMeditGuide/TkMeditReference/TkMe

Re: [Freesurfer] tkmedit multiple orientation view

Thank you, Bruce! I tried it, but I get the error message: invalid command name "SetViewPreset" I couldn't find this or similar command in the wiki page: http://surfer.nmr.mgh.harvard.edu/fswiki/TkMeditGuide/TkMeditReference/TkMeditScripting I use FS 4.3. Any idea what could go wrong? Thanks agai