Re: [Freesurfer] Segfault errors in tkmedit and tksurfer

Hi Zeki I'm using OSX 10.7.5. And, yes I have installed XQuartz as instructed by the freesurfer installation website. Thanks! Joon -- Joonkoo Park, Ph.D. Postdoctoral Associate Center for Cognitive Neuroscience Duke University http://www.joonkoo.org/ On Thu, Jun 12, 2014 at 11:51 AM, Z K

[Freesurfer] Segfault errors in tkmedit and tksurfer

Hello, I've used FreeSurfer previously on a linux machine (from a previous lab). Now, I have just installed it on a Mac OSX, using the freesurfer-Darwin-lion-stable-pub-v5.3.0.dmg version. I followed all the instructions on the installation page. However, there were segfault errors when running

[Freesurfer] very high/low values in the mri_glmfit results

Hi FreeSurfers, I'm running a group-level analysis of the fMRI data (beta-maps of individual subjects normalized onto fsaverage). One example would be like: mri_glmfit --y grouprfx/lh.con_0001.norm.mgh --surf fsaverage lh \ --glmdir grouprfx/lh.con_0001.osgm --osgm I understand that

[Freesurfer] converting a vertex (or a set of vertices) from one space to another

Dear FreeSurfers, I have a set of vertices in the fsaverage surface space that I want to convert (or remap) to each subject's native surface space. What's the easiest way to do this? I thought of mri_label2label, and this will involve making label files. Are there any easier methods, either using

[Freesurfer] Two images vs. one image for recon-all?

? Will having two images give me substantial improvement in parcellation and segmentation qualities? I am trying to gauge how important it is to have two scans of high-res images. Thank you! Joon -- Joonkoo Park Ph.D. Candidate, Cognition Cognitive Neuroscience Department of Psychology, University

[Freesurfer] Spatial Smoothing in the processing stream for fMRI-freesurfer integration

Dear freesurfers, How is spatial smoothing performed during a conventional fmri processing stream? I used SPM to (1) run the 1st level analysis on each subject, (2) transformed the resulting volumetric statistical parametric map to the surface space, (3) normalized each individual's surface map

[Freesurfer] references to clusterwise correction for multiple comparisons

Dear FreeSurfers Is there a published reference to the clusterwise correction approach implemented in FreeSurfer ( http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis#ClusterwiseCorrectionforMultipleComparisons)? I'd like to cite it for those readers and reviewers who aren't

[Freesurfer] inconsistencies in surface segmentation and aseg.mgz

this mean that aseg.mgz is not used in subsequent processing stream? What shall I do if I (after visually inspecting this) want to correct the surfaces more similar to the results given be aseg.mgz? Thanks for your help in advance. Joon -- Joonkoo Park Ph.D. Candidate, Cognition Cognitive

Re: [Freesurfer] mri_vol2surf resulting in different dimensions for two different images in the same space

the right dimensions, add --noreshape. doug Joonkoo Park wrote: Dear Surfers, I (successfully) resampled a functional data on the surface map using mri_vol2surf: mri_vol2surf --mov func.nii --reg register.dat --projfrac 0.5 --interp nearest --hemi lh --o lh.func.mgh Then, I normalized

[Freesurfer] Error during Fix Topology

Dear FreeSurfers, I got an error during Fix Topology step (seems like from the right hemisphere) in the recon-all process (see below for more information). I searched the ListServ and learned from other email threads that this may be due to incorrect segmentation of WM or Cerebellum, or possibly

[Freesurfer] mri_vol2surf resulting in different dimensions for two different images in the same space

concerned about many options above)? 2. If so, why is the resulting dimension different from the other one? I assume that it's probably a reshape issue, but how I can reshape the dimension to match 163842 x 1 x 1? Thanks in advance. Joon -- Joonkoo Park Ph.D. Candidate, Cognition Cognitive

[Freesurfer] Surface-based inter-subject registration of both anatomical and functional images

searched through the archive and the documentations but wasn't satisfactory. Thanks in advance! Joon -- Joonkoo Park Ph.D. Candidate, Cognition Cognitive Neuroscience Department of Psychology, University of Michigan ___ Freesurfer mailing list Freesurfer