[Freesurfer] optseq2 for a (sparse) 1-back task

Hi all, I figured I would have some luck tapping expertise on using optseq2 in this mailing list. There are 8 trials times 8 conditions in an event-related design. We are using a 1-back task just to keep participants paying attention. Thus, we are not attempting to match the number of 1-back-y

[Freesurfer] optseq enforcing consecutive trials

Hi all, I posed a question back in November but got no replies, so I'll try to restate it briefly: Is there a means of enforcing at least one set of consecutive trials for a condition in an optseq schedule (or even consecutive trials with an intervening NULL event)? I am trying to produce a s

[Freesurfer] Sphere vertices

Hi, I wanted to confirm whether spherical inflation generates meshes with the same number of vertices across individuals? Or would you have to use something like mri_surf2surf to map everyone's sphere to a template sphere? Thanks, Chris ___ Freesurfer

Re: [Freesurfer] Standard surface tessellation

Hi Justin, This is quite similar to a question I had asked previously: https://www.mail-archive.com/freesurfer%40nmr.mgh.harvard.edu/msg33421.html I believe the solution is to generate a 14000 vertex template, and then appy mri_surf2surf to all 10 subjects, which will map the vertices of all 10

[Freesurfer] Finding adjacent vertices/labels

Hello Freesurfers, I was wondering if there is information embedded in the annotation/label files that could be used to determine whether two labels represent anatomically adjacent regions? For example, I have parcellated a bunch of participants using connectomemapper into 1000 ROIs. I was just

[Freesurfer] fs-fast preprocessing resting state

Hello, I'm getting started with freesurfer. I've played around with some of the tutorial data for fs-fast (http://surfer.nmr.mgh.harvard.edu/fswiki/FsFastTutorialV5.1) and was able to follow along and successfully carry out the preprocessing exercises (which sufficed for my purposes), which a

Re: [Freesurfer] fs-fast preprocessing resting state

Hi Doug, Thanks for your help. To be sure of my preproc-sess line, I just ran preproc-sess on my other participant: preproc-sess -s sub00294 -fsd rest -per-run -surface self lhrh -mni305 -fwhm 0 Here's the error output from where it goes south: Tue Nov 6 16:32:30 CST 2012 mc-sess completed S

[Freesurfer] What provides mri_annot2aparc?

Hello all, I've posted this question on the cmtk-users google group as well. In that forum there was an author who had been working on applying the Lausanne 2008 parcellation scheme to a functional data analysis. After running the connectomemapper toolkit to subdivide the Freesurfer parcellat

[Freesurfer] Extracting resting state time series from surface space using Lausanne 2008 parcellation

Hi all. I have a question regarding the use of freesurfer + fs-fast preprocessing to apply the Lausanne 2008 parcellation scheme to some structural data, and then extract from those ~1000 ROIs the average time series from a 4D resting state functional run. I'm posting what I have carried out s

Re: [Freesurfer] Extracting resting state time series from surface space using Lausanne 2008 parcellation

Thanks, Doug That was quite helpful, and I have just extracted the mean timeseries from one of my parcellations. I just wanted to note a discrepancy between the mri_segstats output and what is indicated in the mri_segstats --help output. According to the program help: --avgwf textfile

[Freesurfer] De-trending resting state data

I'm working with raw timeseries waveform data from a resting state dataset. There's one run per participant, so no between-run normalization is required. With Doug's help, I have mastered extracting the timeseries information from individual ROIs in surface space. The timeseries data is the pro

[Freesurfer] Detrending timeseries with yhat.mgh from mri_glmfit

Hello, I have a question regarding the yhat.mgh file generated from some resting-state functional data after running: mri_glmfit --y fmcpr.siemens.sm0.self.?h.nii.gz --glmdir $dest_dirname --qa --save-yhat I had assumed that the yhat file was the detrended data, but after plotting it in matlab

[Freesurfer] Merging .annot files

Hello all, I posted this question on the cmtk users google group, but no takers, and perhaps this is the more appropriate venue anyways. I've been successfully using cmtk within iPython. After running connectomemapper parcellate() to get the Lausanne parcellation scheme, I get six .annot fil

Re: [Freesurfer] mni152reg error (file permission denied)

This is on FS 5.1.0 stable. The error seems linux box independent. Please let me know if you need further info. Thanks! Bests, Tommi -- Chris McNorgan Postdoctoral Researcher Developmental Cognitive Neuroscience Laboratory Northwestern University, Evanston, IL DCNL Lab: http://t

[Freesurfer] Merging .annot files using mris_label2annot puts labels in the wrong place

Hi all, I posted this back in January, and got a direct email reply from someone on the mailing list, who gave me a helpful tip, but it doesn't seem to be working out quite right. The problem: I have 3 .annot files per hemisphere, each based on the ?h.aparc.

[Freesurfer] Discrete video card: ATI/AMD success stories?

s if I go with the standard configurations, or if I should press to get an nVidia card certified for the system. Thanks -- Chris McNorgan Assistant Professor Department of Psychology University at Buffalo ___ Freesurfer mailing list Freesurfer@nmr.mgh.h