Re: [Freesurfer] within-subject contrast between runs

Best wishes Chris Von: freesurfer-boun...@nmr.mgh.harvard.edu im Auftrag von Douglas N. Greve Gesendet: Freitag, 6. März 2020 17:54:16 An: freesurfer@nmr.mgh.harvard.edu Betreff: Re: [Freesurfer] within-subject contrast between runs On 3/6/2020 11:15 AM,

[Freesurfer] within-subject contrast between runs

External Email - Use Caution Dear Freesurfer Experts, I have a very basic questions about creating subject-wise contrasts between runs Background Study with two runs per subject where each run corresponds two a different condition (i.e. Stimulation A (on - off) and Stimulati

[Freesurfer] Definition of circular label centered on peak vertex

External Email - Use Caution Dear FS experts I`m interested in extracting beta values from a FSFAST analysis performed in the subject`s native space. The beta values shall be extracted from a circular label around the peak vertex. How can you define a circular label centered

[Freesurfer] epidewarp.fsl radian phase range error

Dear FS experts, I also encountered this problem when trying to apply epidewarp.fsl: ERROR: input phase image exceeds allowable phase range. Allowable range is 6.283 radians. Image range is: 12.5633 radians I read that there is an updated version of epidewarp.fsl which might solve this problem

[Freesurfer] interhemispheric registration in native space

Dear Freesurfer experts, is there a way to perform an interhemispheric registration with rh, lh surfaces in native space? Preferentially, I would perform the registration with smoothwm surfaces. I only found the xhemi command which refers to fsaverage as a target Best wishes, Christ

Re: [Freesurfer] mri_vol2surf nii.gz to .mgh conversion

On 07/02/2015 10:05 AM, Milde, Christopher wrote: > Dear Doug, > > thanks for the immediate response. Actually I checked the > registration with freeview/tkregister2 and print out the quality > values which are perfectly fine > > I did the following fMRI-analysis steps &g

Re: [Freesurfer] mri_vol2surf nii.gz to .mgh conversion

An: freesurfer@nmr.mgh.harvard.edu Betreff: Re: [Freesurfer] mri_vol2surf nii.gz to .mgh conversion How did you create the EX.sm5.lh analysis? It is probably the case that it is already on the surface in which case you don't need to run vol2surf. doug On 07/02/2015 04:54 AM, Milde, Christoph

[Freesurfer] mri_vol2surf nii.gz to .mgh conversion

Dear Freesurfers, I have problems converting .nii.gz files into .mgh files needed e.g. for performing ROI analysis. I used mri_vol2surf and mri_vol2vol to produce .mgh files either to visualize contrast estimates and significance maps on volumes or surfaces I think the problem is due to voxel

[Freesurfer] Vertex Index to Vertex RAS withouth using surface visualizer (tksurfer or tkmedit)

Dear FS experts I extracted the vertex indices of several subjects. But unfortunately I did not extract the corresponding Vertex RAS values. Is there a command to translate the Vertex Index into a Vertex RAS so that I do not have to scroll through all the subjects again? I would like to script

[Freesurfer] computing cluster overlap

Dear Freesurfer-Experts, I'm looking for an elegant way of computing degree of overlap between activated clusters within-subject and between sessions (transversal) on the smoothwm. I thought about running a conjunction analysis between the sessions to detect the extents of common activations, b

[Freesurfer] missing files in fsaverage folder

Dear Freesurfer Experts, is there an easy way to update only folders within the Freesurfer folder? Accidentally, I deleted the fsaverage folder from the Freesurfer version. I copied the fsaverage folder from another Freesurfer installation. But seemingly some essential files (e.g. perirhinal la

Re: [Freesurfer] multiple comparisons correction for individual hemispheres (native space)

1 An: freesurfer@nmr.mgh.harvard.edu Betreff: Re: [Freesurfer] multiple comparisons correction for individual hemispheres (native space) Are you using 1.3 or 1,3 ? On 12/09/2014 03:10 AM, Milde, Christopher wrote: > Dear Doug, > > I tried to run MCC with cluster-sess but unfortuna

Re: [Freesurfer] multiple comparisons correction for individual hemispheres (native space)

isons correction for individual hemispheres (native space) Hi Christopher, sorry for the delay. I had a write a new program. You can download it from here ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/cluster-sess Let me know how it goes doug On 11/14/2014 06:05 AM,

[Freesurfer] multiple comparisons compensation for first-level analysis

Dear Freesurfer experts, I'm not sure how to apply cluster-wise correction for multiple comparisons when one is not interested in doing group statistics. For group analysis you concatenate individuals into one file and use mri_glmfit and mri_glmfit-sim to run general linear model and simulation

[Freesurfer] multiple comparisons correction for individual hemispheres (native space)

Dear Freesurfer experts, I performed fMRI analysis using FSFast resulting in uncorrected significance maps (fsig.nii.gz). For selxavg3-sess I did not use the -fwhm flag (I rerun selxavg3-sess with -fwhm at moment). How can I use simulations for native space hemispheres?. I tried to adapt mri_

Re: [Freesurfer] mkanalysis-sess blocked design

I solved the problem. I figured out that the event-related flag also refers to blocked-designs Best wishes Chris Von: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] Im Auftrag von Milde, Christopher Gesendet: Mittwoch, 3. September 2014 14:12 An

[Freesurfer] mkanalysis-sess blocked design

Dear Freesurfer Experts, I want to run mkanalysis-sess for a blocked design, but unfortunately only the flags -abblocked, -event-related, -retinotopy and -notask do exist. How can I specify the designtype for a blocked design with one condition and on fixation with different block lengths for co

Re: [Freesurfer] 3dvolreg.afni error during mc-sess

d.edu Betreff: Re: [Freesurfer] 3dvolreg.afni error during mc-sess Hmm, that means that 3dvolreg.afni that comes with FS does not run properly on your system. Do you already have a full version of AFNI installed on your system? doug On 08/22/2014 05:00 AM, Milde, Christopher wrote: > Dear Fr

[Freesurfer] 3dvolreg.afni error during mc-sess

Dear Freesurfer Experts, I'm struggling with running only motion correction. After running mktemplate-sess which ran well, the mc-sess terminates with the following error. The terminal otput is attached: "3dvolreg.afni: symbol lookup error: 3dvolreg.afni: undefined symbol: afni_ncerr ERROR: 3dv

Re: [Freesurfer] mri_surfcluster for FEAT cluster maxima

Dear Doug, thanks for your helpful comments according to the reading out fMRI cluster peak vertices! Actually, I'm able now to read out cluster peak vertices (see bottom). I applied the mri_surfcluster command for resampled and surface smoothed Feat stats on smoothwm surface with projfrac 0.5

[Freesurfer] mri_surfcluster for FEAT cluster maxima

Dear Freesurfers, I’m struggling with finding a way of getting a table of the cluster maxima of FEAT functional data registered to (reg-feat2anat) and resampled to (feat2surf) reconstructed surfaces. I want to extract cluster maxima for single subjects but preferentially NOT in fsaverage group

Re: [Freesurfer] smoothing functional data on smoothwm surface

Auftrag von Douglas Greve Gesendet: Montag, 16. Juni 2014 17:30 An: freesurfer@nmr.mgh.harvard.edu Betreff: Re: [Freesurfer] smoothing functional data on smoothwm surface Use mri_surf2surf with the --fwhm option doug On 6/16/14 3:13 PM, Milde, Christopher wrote: Dear Freesurfers, I'm interes

[Freesurfer] smoothing functional data on smoothwm surface

Dear Freesurfers, I'm interested in smoothing preprocessed (but unsmoothed) functional FEAT data, which was coregistered and resampled to the anatomical surface (using: reg-feat2anat/feat2surf). I want to apply smoothing on the functional data preferentially on a surface which doesn't suffer f

[Freesurfer] Extract peak voxel (vertex) coordinates from surfaces

Dear Freesurfers, I would be interested in figuring out the peak vertex of clusters based on coregistered functional FEAT data with the reconstructed anatomical surfaces. The FEAT preprocessing was run without smoothing and smoothing was applied after the feat2surf Does anyone know how to obta

[Freesurfer] finding cluster peak vertices

Dear Freesurfers, Is there a way to smooth already preprocessed functional images* (FEAT, FSL), which I coregistered to the reconstructed surfaces (reg feat2anat), on the cortical surface? Furthermore, I would be interested in finding the cluster peak vertex after smoothing the EPI on the reco

Re: [Freesurfer] distance comparisons across subjects in fsaverage group sphere

d by the registration cheers Bruce On Mon, 12 May 2014, Milde, Christopher wrote: > > Dear Freesurfers, > > > > In Fischl et al. 1999 it is highlighted, that the topological structure of > the original > surface is preserved in the spherical space and due to the na

[Freesurfer] distance comparisons across subjects in fsaverage group sphere

Dear Freesurfers, In Fischl et al. 1999 it is highlighted, that the topological structure of the original surface is preserved in the spherical space and due to the nature of a sphere, computations (distance, area) measures are easy to make. My question now, concerns the comparability of distan

[Freesurfer] native or fsaverage spherical space for distance measures?

Dear Freesurfers, according to my research and 'playing-around' with Freesurfer tools on measuring distances between vertices or peak voxels, I'm still unsure about the most adequate way of comparing distances between peak voxels corrected for folding patterns. To my current knowledge, I figur

Re: [Freesurfer] combine FEAT data with inflated ANATOMY to measure distances

doug On 03/20/2014 10:43 AM, Milde, Christopher wrote: > > Dear Surfers, > > At moment I'm dealing with a huge dataset, preprocessed (with and > without smoothing) and statistically analyzed in FSL FEAT. > > I used the reg-feat2anat to project functional EPI on inflate

[Freesurfer] combine FEAT data with inflated ANATOMY to measure distances

Dear Surfers, At moment I'm dealing with a huge dataset, preprocessed (with and without smoothing) and statistically analyzed in FSL FEAT. I used the reg-feat2anat to project functional EPI on inflated MPRAGE (recon-all). Because I'm interested in measuring Euclidian distances between peak vox