[Freesurfer] Running A Single Time Point Through Longitudinal Processing

on-all.log is attached. Please advise, Thank you, -Eric Cunningham recon-all.log Description: Binary data ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this

[Freesurfer] (no subject)

on-all.log is attached. Please advise, Thank you, -Eric Cunningham recon-all.log Description: Binary data ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this

[Freesurfer] the effects of cortical edits

Hello Freesurfer Experts, Our group is trying to determine the importance of manual edits on our data. After discovering poor white matter segmentation in the supramarginal/inferiorparietal regions, we performed manual edits as described in the FsTutorial. Surprisingly, the areas we edited had r

[Freesurfer] Linear Mixed Effects Models

Hello Freesurfer Experts, I am currently trying to run the Linear Mixed Effects Models described in the wiki here: http://surfer.nmr.mgh.harvard.edu/fswiki/LinearMixedEffectsModels And I am running into difficulties that are fairly well described by the last message in this previous mail thread:

[Freesurfer] comparing models

Hello Freesurfer experts, I have a question about how to determine if a covariate is important in a mixed effects model for example: Y1 = B1 + B2(time) + B3(rand_effect1) + B4(rand_effect*time) + B5(covariate_1) +B6(covariate_2) Y2 = B1 + B2(time) + B3(rand_effect1) + B4(rand_effect*time) + B5(cov

Re: [Freesurfer] comparing models

(covariate_1) The difference between the two that I was trying to highlight is the presence of the second covariate term. Thanks, -E On Tue, Mar 4, 2014 at 11:18 AM, Eric Cunningham wrote: > Hello Freesurfer experts, > I have a question about how to determine if a covariate is important in a &

[Freesurfer] mris_preproc, mri_surf2surf and lme_mass_vw

Hello Freesurfer experts, The lme_mass_vw script runs for a long time and outputs info into the matlab terminal. Most look like this: Location #: Algorithm did not converge. Initial and final likelihoods: ###, ### Running this script, for almost every line, the initial and final likelihood

[Freesurfer] LME advice

Hello Freesurfer experts, I am getting some unusual results with the lme pipeline, and I would appreciate help with identifying the most likely step in which the problem may have originated. Running lme_fit_FS.m on a single vertex, followed by lme_F on the output of that (stats) yields a p-value

[Freesurfer] reproducing sig.mgh

Hello Freesurfer Experts, I am trying to reproduce the values in sig.mgh using matlab, just to confirm that I know what is going on. My numbers do not match exactly, and I am hoping someone can explain my error, or point me in the right direction. With Qdec, I built a model with one discrete fac

[Freesurfer] subjects_dir

Greetings Freesurfer experts, The README file in the $SUBJECTS_DIR says that a different directory can be specified by setting the env var SUBJECTS_DIR prior to the 'source $FREESURFER_HOME/FreeSurferEnv.csh' statement. Do the original contents of SUBJECTS_DIR (such as fsaverage) need to be moved

Re: [Freesurfer] subjects_dir

Other than fsaverage, are there any other files that need to be linked for recon-all to work? Thanks On Mon, Nov 23, 2015 at 4:57 PM, Bruce Fischl wrote: > Hi Eric > No, you can just symlink fsaverage and such > Cheers > Bruce > > > On Nov 23, 2015, at 9:40 PM, E

[Freesurfer] fixing the talairach.xfm

Hi, I have a few very basic clarification questions regarding the recon-all processing pipeline. I am currently following the instructions here: http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Talairach Near the end of the page, it instructs me to rerun the whole process using my new talairach

[Freesurfer] talairach.xfm error frequency

, but most seem like they could be made better by a tweak here or there. At what point would I just be adding randomness by manually editing? About what percent of a given dataset would you expect to manually edit? Much appreciated, -Eric Cunningham

Re: [Freesurfer] talairach.xfm error frequency

Hi Bruce, I am running version 5.10 Thanks, -Eric On Wed, Oct 10, 2012 at 3:13 PM, Bruce Fischl wrote: > Hi Eric > > what version are you running? > Bruce > > On Wed, 10 Oct 2012, Eric Cunningham wrote: > > Greetings, >> >> I am trying to determine how bad a

Re: [Freesurfer] talairach.xfm error frequency

fically has a problem with Talairach accuracy (is that > right Nick?). Should be much better with the next release > > On Wed, 10 Oct 2012, Eric Cunningham wrote: > > Hi Bruce, >> I am running version 5.10 >> Thanks, >> -Eric >> >> On Wed, Oct 10, 20

Re: [Freesurfer] talairach.xfm error frequency

Would you recommend subjects through autorecon1 in freesurfer 5.0 and then through autorecon2 and autorecon3 in 5.1? Thanks, -Eric On Wed, Oct 10, 2012 at 4:35 PM, Eric Cunningham wrote: > Hi all, > Ah, good to know that there is a Talairach accuracy problem. What have > other gr

[Freesurfer] checking talairach.lta

Hi folks, In previous threads, the command provided to check the talairach.lta is... tkregister2 --mov $FREESURFER_HOME/average/RB_all_2008-03-26.gca \ --targ ../brainmask.mgz --lta-inv talairach.lta --reg talairach.lta.reg.dat \ --surfs --s $subject When I try to run this command, I run into t

Re: [Freesurfer] checking talairach.lta

0/tktools/ (after making a copy of the one there). > doug > > > > > On 11/5/12 5:00 PM, Eric Cunningham wrote: > > [e4fs@cluster bin]$ ls -l `which tkregister2.bin` > -rwxr-xr-- 1 jsadinol fs 21663433 May 22 2011 /apps/fs510/tktools/ > tkregister2.bin > &g

[Freesurfer] regarding use-mritotal

Hi, this link: http://surfer.nmr.mgh.harvard.edu/fswiki/TalFailV5.1 discusses a solution to bad talairach.xfm transforms, the -use-mritotal flag. this link: http://surfer.nmr.mgh.harvard.edu/fswiki/eTIV mentions that the talairach.xfm is used to calculate the total intracranial volume. is using

Re: [Freesurfer] gray matter surface

intensities look like gray matter, but it could be damaged white matter > instead. > > cheers > Bruce > > > > > On Tue, 19 Feb 2013, Eric Cunningham wrote: > > hello freesurfer experts, >> >> attached is an image drawn from the tutorial page. &

[Freesurfer] skullstripping outside freesurfer

External Email - Use Caution Dear Freesurfer Experts, I have recently processed some data with the following 2 steps: 1) Perform skullstripping outside freesurfer to generate a nifti file (mostly using AFNI). 2) Run that through freesurfer using the -noskullstrip flag. Comparing

[Freesurfer] mri_glmfit and R

External Email - Use Caution Hello Freesurfer Experts, I am trying to plot the ${meas} values at the maximum vertex in a significant cluster found by the group analysis pipeline (mri_glmfit). I created an .mgh file with mris_preproc, rh.cbd7.area.10.mgh. I read this file into ma

Re: [Freesurfer] mri_glmfit and R

, -Eric On Thu, Aug 13, 2020 at 9:42 AM Douglas N. Greve wrote: > Do you have a 1-off error? Ie, FS starts counting at 0 and matlab starts > counting at 1. So vertex 53263 is vertex 53264 in matlab. > > On 8/12/2020 5:31 PM, Eric Cunningham wrote: > > External Email - U

Re: [Freesurfer] mri_glmfit and R

gender), would I be able to define that as a numeric variable with > values 0 and 1, rather than splitting up my other categories? > > Thank you for your help, > -Eric > > On Thu, Aug 13, 2020 at 9:42 AM Douglas N. Greve > wrote: > >> Do you have a 1-off erro