Re: [Freesurfer] Replicating qdec analysis with more than 2 continuous variables

Hi Nick, could you please also provide us with a INTEL MAC qdec.bin binary? Many thanks in advance, Martin On Wednesday 17 March 2010 21:18:19 Nick Schmansky wrote: > you have a couple options: > > 1) assuming you are using 64b linux, you can download a new version of > qdec which supports sele

[Freesurfer] Talairach_MNI

Hello, I would like to know if the output coordinates from the "mri_surfcluster" command is on the MNI space or on the Talairach. Thanks in advance. Best, Kelly _

[Freesurfer] Model setup - comparing correlations

Hi, in my group analysis I found a significant difference in correlation of physiological parameter X and cortical thickness Y1 in an ROI. For each subject and each cortical parcel I also have a average of parameter Y2 and its correlation to X (calculated using GLM in SPSS). Y1 ~ X Y2 ~ X My

Re: [Freesurfer] Averaging cortical thickness maps

Hi, Bruce, Thanks a lot for your suggestion. I have another question. To view the thickness map, we first load a surface of the corresponding subject (i.e. ?h.inflated) and then overlap the thickness map on it. So to view the mean thickness map, do I also need to average the volumes/surfaces of t

Re: [Freesurfer] Averaging cortical thickness maps

Hi Xiaojing, mris_average_curvature will paint onto either the last subject specified in your list, or probably better, to a subject you specify with -o . I would use -o fsaverage, then you can simply load the average thickness onto the fsaverage inflated surface. cheers Bruce On Thu, 18 Mar

[Freesurfer] showing all slices in freeview

Hi, is it possible to show all slices (or every N slices) of a volume in freeview in a particular orientation (e.g. axial or coronal)? Thanks, Thomas ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/l

Re: [Freesurfer] showing all slices in freeview

You mean in light box (mosaic) style? No. I will put that on my features-to-consider list. Ruopeng On 3/18/10 10:34 AM, ythomas wrote: > Hi, > > is it possible to show all slices (or every N slices) of a volume in > freeview in a particular orientation (e.g. axial or coronal)? > > Thanks, > Thom

Re: [Freesurfer] showing all slices in freeview

yes. Thanks! --Thomas On Mar 18, 2010, at 10:37 AM, Ruopeng Wang wrote: > You mean in light box (mosaic) style? No. I will put that on my > features-to-consider list. > > Ruopeng > > On 3/18/10 10:34 AM, ythomas wrote: >> Hi, >> >> is it possible to show all slices (or every N slices) of a vol

Re: [Freesurfer] Averaging cortical thickness maps

Hi, Bruce, The mean thickness map has been got. Thanks a lot. Best, Xiaojing 2010/3/18 Bruce Fischl > Hi Xiaojing, > > mris_average_curvature will paint onto either the last subject specified in > your list, or probably better, to a subject you specify with -o name>. I would use -o fsa

Re: [Freesurfer] Segmentation fault during skull-stripping

Hi Mike, Did you check the talairach. And how do nu.mgz and T1.mgz look. Also you could probably try running the following command to see if the skull strip step finishes without errors. recon-all -skullstrip -no-wsgcaatlas -s Sita. On Thu, 18 Mar 2010, Michael Waskom wrote: > Hi Bruce, N

Re: [Freesurfer] Segmentation fault during skull-stripping

Hi Sita, Running it with the -no-wsgcaatlas seems to do the trick as far as avoiding a segmentation fault. The T1 looks like it has a some motion artifact--might that be causing problems? I checked the Talairach transform and it looks generally alright, although I think it could be improved with

Re: [Freesurfer] Segmentation fault during skull-stripping

Hi Mike, I don't think the motion artifact could've been causing this error. It's probably a good idea to fix the talairach if you think it's off because if you are reporting the talairach coordinates, you would want the talairach transform to be reasonably accurate. Sita. On Thu, 18 Mar 201

[Freesurfer] research jobs in San Francisco, CA

Dear Freesurfer users, We are hiring for multiple positions in our San Francisco-based schizophrenia brain-imaging EEG research lab. Please visit the links below for additional details: http://jobs-ncire.icims.com/jobs/1504/job http://jobs-ncire.ici

[Freesurfer] tksurfer and tcl scripting: looping over subjects

Hello all, I've had great success using tcl scripts to loop over surfaces and overlays for a given subject. Are there scripting options for looping over subjects? The problem I see is that the call to tksurfer initializes the subject ("tksurfer subjid lh inflated -tcl myscript.tcl"), and I'm uns

Re: [Freesurfer] tksurfer and tcl scripting: looping over subjects

Hi Carrie, I believe you just need to use the command "exit" at the end of the tcl script to exit from tksurfer. --Thomas On Mar 18, 2010, at 5:43 PM, Carrie Niziolek wrote: > Hello all, > > I've had great success using tcl scripts to loop over surfaces and > overlays for a given subject. Ar

Re: [Freesurfer] Replicating qdec analysis with more than 2 continuous variables

Yuo can't do it in QDEC, but you can do it by calling mri_glmfit directly and creating an FSGD file. Do a search for FSGD on our wiki for more info. doug Laluz, Victor wrote: > > Hello Freesurfer folks, > > > > I hope this question is simple to answer: Is there any way to do a > surface-base

Re: [Freesurfer] drawing adjacent labels with shared boundaries, and labels near the edge of a patch

Lindsay, I think this wiki page might help: https://surfer.nmr.mgh.harvard.edu/fswiki/tksurfer_labeledit Allison -- On Tue, 16 Mar 2010, Lindsay Lewis wrote: > hi, > > I am trying to manually draw a "grid" of many small ROIs/labels on an > occipital flattened surface patch in tksurfer, and am h