Re: [Freesurfer] recon all with 7T data

hi Xiaomin, 7T data can sometimes cause Talairach failures with the standard registration tools due to the strong bias fields. the Talairach transformation is used for identifying seed points, and the -use-mritotal flag just specifies that the MINC software will be used for the Talairach'ing. se

Re: [Freesurfer] recon-all pipeline for (sub-millimeter) 7T data

yep, i wrote a command a while back that just refines a mesh. the command name is mris_mesh_subdivide and has options for both approximating and interpolating schemes. if it is not distributed i would be happy to post the binaries. -jon On Sat, 17 Oct 2015, Bruce Fischl wrote: > Hi Kendric

Re: [Freesurfer] temporal lobe pial surface problem

hi Xiaomin, it is tough to say what might be causing the problem since a lot can go wrong in the anterior temporal lobes at 7T. you say that your contrast is low there? it is possible to have OK gray-white contrast but low overall signal levels (so poor gray-CSF contrast) due to dielectric effect

Re: [Freesurfer] recon from 7T data

Auftrag von Bruce Fischl > Gesendet: Montag, 25. März 2019 20:27 > An: Freesurfer support list > Cc: freesurfer-boun...@nmr.mgh.harvard.edu; Andre van der Kouwe > ; Jonathan Polimeni > Betreff: Re: [Freesurfer] recon from 7T data > > Hi Valeria > > Jon Polimeni and Andre van

Re: [Freesurfer] retinotopy description

hi michelle, the Sereno et al. 1995 Science paper has details about the phase encoded retinotopic data analysis, especially in the endnotes of the article. also for more details you can look at the MATLAB code embedded in the command 'selfreqavg', which is used for the basic retinotopy analysis a

Re: [Freesurfer] mapping bow-tie retinotopy

hmmm...i think it depends on whether the two ends of the bow-tie are ever in the same hemifield simultaneously, which would lead to ambiguity in the mapping of stimulus phase. scott slotnick had a paper on this a few years back... in principle the bow-tie stimulus for mapping polar angle is more

Re: [Freesurfer] retinotopy starting with blanks

hi dahlia! the 'mkanalysis' script in the retinotopy analysis stream has an optional 'nskip' argument that allows you to ignore N TRs from the beginning of each run. so you can just append '-nskip 2' to your 'mkanalysis' command. -jon On Thu, 18 May 2006, Dahlia Sharon wrote: > Hi, > > I'

Re: [Freesurfer] File Conversion Inquiry

hi gregory, to address your last question: no, tksurfer does not require both eccentricity and polar angle data to display either coordinate map by itself. as bruce wrote, the convention is that the eccentricity and polar angle data are each stored in two separate overlay or ".w" files. the ".w"

[Freesurfer] Re: retinotopic questions in Freesurfer

hi lei, please see below. On Tue, 12 Sep 2006 [EMAIL PROTECTED] wrote: > Hi, Jonathan, > > I'm glad to know you via Nick's email and I want you could give me some > guidances with my retinotopic analysis. > I have scanned the retinotopic runs with eccen and polar, and the > parameters were a

Re: [Freesurfer] FW: field sign and colour lables

hi kristofer, the labels tksurfer uses for the two retinotopic coordinate maps, i.e., the eccentricity and polar angle maps, denote the temporal phase of the activation of each voxel driven by the periodic visual stimulus. depending on your stimulus, these phases computed by the analysis will cor

Re: [Freesurfer] retinotopy question

hi lars, the FSFast retinotopy analysis stream is geared towards temporal phase encoded data analysis, which produces field sign maps that can be used to define area boundaries. if you opt to use stationary wedge stimuli to activate the horizontal and vertical meridian representations in visual

Re: [Freesurfer] retinotopy question

lysis)... > could you explain me (shortly) what to do than with my data > > regards, > Lars. > > -design info: 8hz flickering checkerbords, 20 scans at horizontal meridian, 20 > scans vertical..x10 repetitions... > > > > > Jonathan Polimeni schrieb: > >

Re: [Freesurfer] Retinotopy stimuli

hi anders, the optimal set of stimulus parameters will depend somewhat on what cortical area(s) you are trying to map and on the details of your acquisition. in general, stimulating with both clockwise- and counterclockwise-rotating wedges for polar angle mapping and with both expanding and contr

[Freesurfer] mris_flatten usage

hello all! i have a fast question regarding the usage of mris_flatten: what are the available command line options? the usage message displayed by mris_flatten only lists the "-w" and "-distances" options, but i also know of the "-p" option, and there was an earlier posting that mentioned a "-s"