Re: [Freesurfer] Comparing lists of activated regions between task>ctrl contrasts

>From your original mail: I agree with Dr. Kanwisher. When you ask if it is >appropriate to "(visually) compare" list of regions, I would answer that it is >absolutely not. A direct comparison is necessary. See e.g. Nieuwenhuis et al., >2011, Nature Neuroscience. For your second, I would say t

[Freesurfer] rtview

Hi Freesurfers Sorry for my previous email today (see below), I found a bug in my SPM code. Now, the fsig.nii image works fine and does the job. However, I have some additional questions: 1. Is there a way I can change the colour specification for rtview e.g. swapping red and green c

Re: [Freesurfer] Hippocampus in WM region, Unknown voxels still persist

can you upload a dataset with this problem and tell us exactly (what voxel coords) you see them at? On Thu, 27 Aug 2015, fmri wrote: > processing attempt on latest dev 8/15 did not resolve the subcortical > annotation within WM tracks, the unknown voxels continue to persist. > > > On Aug 26, 201

Re: [Freesurfer] Hippocampus in WM region, Unknown voxels still persist

processing attempt on latest dev 8/15 did not resolve the subcortical annotation within WM tracks, the unknown voxels continue to persist. On Aug 26, 2015, at 7:06 AM, Bruce Fischl wrote: > it would fix the hippocampal problems and maybe the cortical ones as well > > cheers > Bruce > On > Tue

Re: [Freesurfer] Hippocampus in WM region, Unknown voxels still persist

the Problem is that they were labeled as cortex in the aseg but as "unknown" in the aparc, so they get labeled as "unkown" in the aparc+aseg the Resolution is still not clear. I was directed to follow instructions https://surfer.nmr.mgh.harvard.edu/fswiki/tksurfer_labeledit, but the 'unkonwn'

Re: [Freesurfer] Computing SA from an older FS version

1. Yes, I would expect that 2. Because the pial surface is bigger. (Unless I'm misunderstanding the question?) From: freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Gerrits, Niels Sent: Thursday, August 27, 2015 10:36 AM To: Freesurfer support list Subje

Re: [Freesurfer] Comparing lists of activated regions between task>ctrl contrasts

Sorry, forgot to add one additional (related) question: is it ever correct to say "for region Y, the activations found for taskA were smaller than for taskB" just based on the two contrasts *taskA>baseline *and *taskB>baseline*? Or is it necessary that taskA and taskB be contrasted directly to be

[Freesurfer] Comparing lists of activated regions between task>ctrl contrasts

Hello all, I have seen several (older) papers that draw conclusions about the implication of a brain region in a given task by using the following logic: region X was activated in the contrast *taskA>baseline*, but not in the contrast *taskB>baseline*; therefore, region X is implicated in/essentia

[Freesurfer] Doss/Dods

Dear Freesufers, I am currently running mri_glmfit using a relatively simple design: Two groups and one covariate. Design is: 1 -1 0 0 .. to control for the co-variate (age). It is the example with two groups and one covariate in your web-page http://freesurfer.net/fswiki/Fsgdf2G1V I was under t

Re: [Freesurfer] hello freesurfer developer~

Specify something for --seg. It just needs to be a surface overlay of the same size as the input. On 08/27/2015 01:49 AM, A-reum Min wrote: > Hello doug > > i enter the ' mri_segstats --i y.mgh --vox 33 0 0 --avgwf out.dat' > then, error occured --> ERROR: must specify a segmentation volume > > H

[Freesurfer] Postdoc opening in visual neuroscience

Postdoctoral Associate in Visual Neuroscience University of Minnesota, Minneapolis, MN, USA The University of Minnesota's Center for Magnetic Resonance Research is searching for a Postdoctoral Associate in Visual Neuroscience. This will be in the newly created laboratory of Dr. Kendrick Kay (htt

Re: [Freesurfer] Computing SA from an older FS version

Dear Experts, With your help, I recalculated the surface area, now using the pial surface instead of the wm/gm boundary. I am, however, somewhat surprised by the discrepancy between my previous and current results, because the cortical surface area that is calculated using the pial is surface i

[Freesurfer] Missing clusters in Qdec

Dear all, After my analysis for pial_lgi using fsaverage as common space subject, I started a Monte Carlo correction in Qdec. The terminal lists the significant clusters after Monte Carlo correction. Is it normal that the clusters listed in the Terminal are not all highlighted in the Qdec di

[Freesurfer] Monte Carlo correction

Dear all, During my analysis for pial_lgi instead of using fsaverage I prepared my own average surface using make_average and recon-all qcache. Now, I want to correct the results for multiple comparisons using Monte Carlo Null-Z simulation in Qdec. However, when I use my own average as common-

Re: [Freesurfer] IBSR dataset

Hi Michael IBSR is not part of the FreeSurfer training set, but does use the same manual labeling protocol. cheers Bruce On Thu, 27 Aug 2015, Michaël Sdika wrote: Hi, Does anyone known if (and how) the 43 structures IBSR dataset and FreeSurfer are related ? The subcortical segmentation of f

Re: [Freesurfer] Automatic Subcortical Segmentation Editing?

Hi Jen I guess you would just use freeview to do the manual editing and then rerun the autorecon2/3 stages that come later. cheers Bruce On Thu, 27 Aug 2015, Jennifer Eastman wrote: > Hello All, > > I am hoping to make some edits to subcortical segmentations, and while I have > found instruct

[Freesurfer] Two Post-Doctoral positions in brain imaging – University of Geneva

Applications are invited for two Post-Doctoral positions in the Brain and Language Lab (www.brainandlanguagelab.org) at the University of Geneva. The positions are both are for 2.5 years, and will be at the new Biotech Campus (http://www.campusbiotech.ch/en/

[Freesurfer] IBSR dataset

Hi, Does anyone known if (and how) the 43 structures IBSR dataset and FreeSurfer are related ? The subcortical segmentation of freesurfer give results very similar to the IBSR segmentation maps (same structure, same index set). I suspect the IBSR data are part of the training dataset of FreeSur

[Freesurfer] fsig.nii with rtview

Dear Freesurfers I started using rtview to be able to delineate regions in my retinotopy data, however, I ran into problem with the fsig.nii file. I do my analysis in SPM, so I create the sine, cosine and significance images there as follows: The sine and cosine images are regressors (parametri