Re: [Freesurfer] Error loading a constructed annotation file

It does look like the problem is the rh.orig. Do you have read permissions for that file? It may be that the file is corrupt. Can you load just that file in freeview or tksurfer? If not, you can try to regenerate it by running mris_fix_topology (look in the subject/scripts/recon-all.log file fo

Re: [Freesurfer] Error loading a constructed annotation file

Thanks for your quick answer. Yes, I have read permissions for that file. I can also load the rh.orig into freeview without any error message appearing in the terminal. Looks quite nice. I tried using mris_fix_topology by taking the exact command from the recon-all.log of the particular subject.

[Freesurfer] smoothing T1 images

Hi FS experts, I have T1 images with low quality (noise and artifacts). I am wondering if smoothing these images, before runing the command "Recon-all", can help to improve the segmentation and parcellation process for these images. Thanks for any advice! Bests, John ___

Re: [Freesurfer] smoothing T1 images

Hi John you can try mri_nlfilter if you like. It implement a nonlocal means/medians algorithm that I wrote in 1995 or so: Bruce Fischl and Eric L. Schwartz. 1999. Adaptive Nonlocal Filtering: A Fast Alternative to Anisotropic Diffusion for Image Enhancement. IEEE Trans. Pattern Anal. Mach. I

Re: [Freesurfer] FSFAST- Cerebellum

Hi Yeo- Thanks very much for your answer. Yes the data is in mni305 space. I process my fmri data with preproc-sess -s rest210 -fsd bold -surface fsaverage lhrh -mni305 -fwhm 6 -per-run -stc odd and then to extract ROI time series values I did mri_segstats --annot fsaverage rh aparc --i rest210/b

Re: [Freesurfer] XQuartz 2.7.9 update results in errors

Hello Kate, Thanks for the information. We have seen similar behavior with previous XQuartz releases in the past as well. This tends to "freeze" certain vesion of OSX with certain versions of XQuartz. I will take a closer look but this is usually something that we have to deal with. -Zeke On

Re: [Freesurfer] cortical surface pattern matching

Hi Greg you could threshold then look at Hausdorff distance of the blobs. Or you could smooth before computing correlation as that will take spatial stuff into account. Or if you have a patch that you want to cross-correlate against the rest of the surface you could do it on the sphere, althou

[Freesurfer] matrix is ill-conditioned or badly scaled, condno = 1e+08

Hello, Hello, I am getting the following error: ERROR: matrix is ill-conditioned or badly scaled, condno = 1e+08 Command line: mri_glmfit --y lh.BD_SD.thickness.10B.mgh --fsgd FSGD_Collapsed_Across_Smokers_demeaned.fsgd dods --C BDvsSD1.mtx --surf fsaverage l

[Freesurfer] Yeo 2011 Functional Cortical Parcellations

Hi Mailing List, I am attempting to apply the Yeo 2011 7-network fucntional parcellations to a set of fs MRIs processed with v5.1.0. Below are listed the first three steps I plan to take and I am seeking advice as to: A) Whether this approach is valid. B) Steps to take next. * Steps 1-3: *

[Freesurfer] aseg mask error

FREESURFER_HOME: /home/rcf-proj/kap/shared/freesurfer Build stamp: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 RedHat release: CentOS release 6.7 (Final) Kernel info: Linux 2.6.32-573.22.1.el6.x86_64 x86_64 Hello Freesurfer, For some strange reason, a participant's entire aseg is being

[Freesurfer] LGI

*Hello,* *I’m trying to run recon-all -lgi - s Subjectname on my data but i am getting this error!* *** Error in dsearchn (line 79) [d(i),t(i)] = min(sum((x-yi).^2,2)); Error in mesh_vertex_nearest (line 29) nearestIndex = dsearchn(ve

[Freesurfer] Quality control with different pipelines

Hi everyone, I processed and edited 300 participants for our study using Freesurfer 5.3 and I'd like to move to using the dev version that's currently available because we have a bunch more data that's been collected and I think it does a better job. (This question also applies to moving to v 6 wh