Re: [Freesurfer] regional surface area differences

r to > how --meas thickness is used for calculating cortical thickness) > 3) Which --surfreg file should I use? sphere.reg vs sphere. Or do I not > need the --surfreg? > > > Thanks, > Abid > > > -- Forwarded message -- > From: Anderson M. Winkler > D

Re: [Freesurfer] volume, surface area, and thickness

Hi Woo-Suk Just adding to Bruce's reply: area isn't a "technically more noisy and usually thus less sensitive" as the reviewer suggests. Area isn't noisier on its own right, and it's measured from the very same surfaces from which thickness is measured. However, there is a much larger variability

Re: [Freesurfer] mri_glmfit-sim permutation testing running after 3 days!

Hi all, In the presence of nuisance (orthogonal or not) the permutation test is only approximate, whatever is the method used. Regressing out the nuisance introduces dependencies between the residuals that render them strictly not exchangeable. However, in practice this is not an issue, and the FL

Re: [Freesurfer] 3 fixed factors and matrix design

Hi Shady, Try assembling the design as this: EV1: Group 1 (coded as 0/1) EV2: Group 2 (coded as 0/1) EV3: Group 3 (coded as 0/1) EV4: Sex (coded as +1/-1) EV5: Site (coded as +1/-1) The contrasts to compare the three groups are then: C1: [1 -1 0 0 0] C2: [1 0 -1 0 0] C3: [0 1 -1 0 0] C4: [-1 1 0

Re: [Freesurfer] Cluster Forming Threshold

Hi Tim, There is no established criterion and a recent, useful guideline is perhaps use the threshold that would correspond to a p=0.001, that is, about 3.1 in a z-map (see Woo et al., Neuroimage, 2014 ). All the best, Anderson On 1 September

Re: [Freesurfer] design matrix palm

Hi Maaike, I know palm! :) Please see below: On 7 September 2016 at 09:34, maaike rive wrote: > Hi all, > > I was adviced to use PALM for permutation of non-orthogonal surface data. > However, I have some questions regarding the design matrix en contrast > files to be used in PALM, but someho

Re: [Freesurfer] Display FSL PALM(permutation) stats in freeview

Hi Ajay, To open the .mgz files produced by PALM you would first load the surface in FreeView (at the top of the left panel, click on "Surface" then on the button with a "+" sign), then after the surface has been loaded, in the menu "Overlay" in the left panel, select "Load generic..." and load th

Re: [Freesurfer] area and smoothing

Hi Seung-Gul, Please see below: On 16 September 2016 at 00:52, Seung Gul Kang wrote: > Dear Freesurfer experts, > > 1. I want to compare the area and/or areapial between two groups in qdec > menu. > I think that the eTIV or total surface area should be used as a covariate. > Which is more appro

Re: [Freesurfer] Display FSL PALM(permutation) stats in freeview

Hi Ajay, The mask is a file of the "curvature" type, that is, it contains vertexwise data, and should mask out the "unknown" region (that region in the medial aspect that is not cortex and is there to ensure the topology is the same as that of a sphere). The mask can alternatively be a .mgz file a

Re: [Freesurfer] Display FSL PALM(permutation) stats in freeview

Hi Ajay, Make sure you have to run palm_hemisplit on the outputs first, i.e.: palm_hemisplit bh.thickness_* Note that the "-o bh.thickness" was a somewhat poor choice of outputs as now it's necessary to use the underscore ("_") to avoid overwriting original inputs; for future runs, consider some

[Freesurfer] Download FS not working?

Hi guys, I've been trying in the last days to download FS but it doesn't seem to work: winkler@volans:~ $ wget ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/5.3.0/freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0.tar.gz --2014-01-09 20:47:12-- ftp://surfer.nmr.mgh.har

Re: [Freesurfer] Multiple comparisons to confirm atrophy

Hi Clare, This is something that PALM can do. It seems we're in the same Dept. Please send me an email off-list and we can try to have this sorted out. All the best, Anderson On 19 November 2015 at 08:37, Clare Loane wrote: > Dear All, > > I have

Re: [Freesurfer] Usage of --area option in estimating the vertex-wise maps of surface area

Hi Xi-Nian, As Doug said, they don't do the same thing. The method in the paper uses a different kind of interpolation to allows the preservation of the amount of area, whereas mris_preproc achieves the same globally using a Jacobian correction. The results aren't expected to be identical at the v

Re: [Freesurfer] problem with surface area regression

Hi Wen, Brain volume has a good relationship with the overall surface area measured in native space (so, irrespective to any kind of interpolation). We found an R^2 of 0.856, which is higher even than the correlation of brain volume with gray matter volume as measured via VBM-like methods. Howeve

Re: [Freesurfer] winkler surf data with qdec ?

Hi Greg, It's ok to smooth using FS tools, as long as the different sizes of the faces of the ico7 are taken into account. This means that, after running "rpncalc", the "smoothdpx" command can be skipped, and the data can be converted to vertexwise and imported into qdec, which will then smooth it

Re: [Freesurfer] Freesurfer vertex wise area reference

Dear Mahinda, For the mris_preproc, I think Doug posted already explaining how it works - it uses a jacobian correction in a way that makes it mass-conservative. You may want to search the archives. For the ROIs, the standard method is to add up the areas of their constituent vertices, so it shoul

Re: [Freesurfer] Antw: Re: thickness and area in aparc.stats and mri_glmfit

eassuring response, but I am still puzzled about the > lack of association between mean area (rh_medialorbitofrontal_area) and > area in qdec (see area.png). I thought that technically there must be > larger areas for vertices within medialorbitofrontal? > > Best wishes, > Wolff &

Re: [Freesurfer] Surface area computation

Dear Shantanu, An implementation that runs in Matlab or Octave is available here: http://brainder.org/download/areal I was planning to write a compiled version that could be integrated more easily in FS. However, just by the time as the paper was published, I moved to another country and started

Re: [Freesurfer] download freesurfer

Hi Merlin, Have you tried "wget -c" to resume an interrupted download? You can put the command inside an infinite loop that will keep retrying even if the connection is interrupted when you are not watching (say, overnight). The following should work: while (true) ; do wget -c -T 60 ftp://surfer.

Re: [Freesurfer] mean thickness covariate, mean area covariate, & mri_anatomical_stats for multiple subjects

Hi Laura, >1. Is there a paper that I could cite that recommends using mean >cortical thickness rather than ICV? > > If it helps, we used cortical thickness and area as covariate for the respective analysis of regional thickness and area. Brain volume, which is more closely related to ICV

Re: [Freesurfer] mean thickness covariate, mean area covariate, & mri_anatomical_stats for multiple subjects

nceptually it might be that the pial surface > area is more sensitive to atrophy but I don't know if that is born out in > the data... > > Laura. > > > On Sat, Mar 9, 2013 at 11:49 AM, Anderson M. Winkler < > wink...@fmrib.ox.ac.uk> wrote: > >> Hi

Re: [Freesurfer] Multiple comparison question

Hi VM, Please see below: On 1 February 2017 at 02:38, neuroimage analyst < neuroimage.anal...@gmail.com> wrote: > Hi, > > We extracted volume measures from 7 ROIs in 2 groups and compared > a) Mean of each ROI volume between group, and compared independently such > as > i) whether mean of ROI 1

Re: [Freesurfer] Multiple comparison question

e are several other measures such as volume, > thickness, FA, can I then put them in a single csv file and run the > command or I have to create 3 csv files, one each for volume, thickness,and > FA and also invoke -corrmod? > > Thanks > > Regards > VM > > On Feb 2, 2017 1

Re: [Freesurfer] Error viewing corrected results

Hi all, That's exactly as Antonin says -- I have very little to add :-) Only a few suggestions: - With surfaces, both cluster and TFCE statistics tend to be slow. Consider using the tail approximation ("-approx tail -n 500 -nouncorrected") - Include -logp, so that the p-values are in log-10 sca

[Freesurfer] Postdoctoral position at the NIH/NIMH

We are seeking enthusiastic applicants for a Post-Doctoral Fellowship position to help with the collection and analysis of large brain-imaging datasets. The successful candidate will use state-of-the-art artificial intelligence methods, with the aim of better understanding psychiatric disorders in

Re: [Freesurfer] problems with cortical surface area maps

Hi Lars, This pattern is because the faces in a geodesic sphere don't have all identical sizes, even if the original icosahedron was perfectly regular, i.e., a Platonic polyhedron. We describe this phenomenon here , and give a simple formula that

Re: [Freesurfer] problems with cortical surface area maps

Hi Lars, I guess you are working with vertexwise rather than facewise data, is this right? You'd need to compute then the area-per-vertex of the same sphere used as the target for the interpolation, i.e., the ico7 (surf/?h.sphere.reg in fsaverage I think). Attached is a Matlab function that calcul

Re: [Freesurfer] meshes/surfaces for sub-cortical structures

Hi Tanya, I think the attached script should do the trick. It calls various FS functions behind the scenes, including mri_tessellate that Bruce was explaining. The outputs will be in a subdirectory called 'ascii' inside each subject directory. All the best, Anderson On 1 June 2014 18:22, Tanya w

Re: [Freesurfer] problems with cortical surface area maps

oops! I forgot to attach the files needed by these two functions... see them attached now. I hope I'm not forgetting any others... On 1 June 2014 19:21, Anderson M. Winkler wrote: > Hi Lars, > > I guess you are working with vertexwise rather than facewise data, is this > rig

Re: [Freesurfer] cortical surface area measurement and vertex-wise analysis

Hi Emma, Could you clarify what would be the disadvantages that you've heard about? I ask because we've studied and tried to clarify many aspects of the analysis of surface area in this paper . Maybe if there's something not cover

Re: [Freesurfer] cortical surface area measurement and vertex-wise analysis

Hi Donna, In that same paper we also comment on the differences between expansion/contraction and absolute areal measurements assessed at each face of the surface (i.e., facewise), which can, after interpolation, be converted to vertexwise to facilitate analysis using current tools (e.g., mri_glmf

Re: [Freesurfer] cortical surface area measurement and vertex-wise analysis

all that is said above about area applies also to cortical volumes. Hope this helps! All the best, Anderson On Sun, Oct 12, 2014 at 3:00 PM, Anderson M. Winkler wrote: > Hi Donna, > > In that same paper we also comment on the differences between > expansion/contraction and abso

Re: [Freesurfer] Running FSL randomise on FS cortical thickness data {Disarmed}

External Email - Use Caution Hi, It's possible to analyse longitudinal designs with PALM. Some mild assumptions must hold, and those assumptions are different than those of an LME model. PALM doesn't assume normality, doesn't require a specified form for the dependence structure,

[Freesurfer] Sources Sought: Octave/MATLAB programmer {Disarmed}

External Email - Use Caution Dear all, The NIMH/NIH is looking for a skilled Octave/MATLAB programmer, with knowledge of multivariate statistics, to implement inference for canonical correlation analysis (CCA) using permutations, as described in the recent paper (https://secure-w

[Freesurfer] Orthographic camera in FreeView

External Email - Use Caution Hi all, Is there a way to configure the camera in the 3D viewport in FreeView to use an orthographic projection instead of perspective (which currently is the default)? Orthographic used to be the default in tksurfer. A nice feature about it is that w

Re: [Freesurfer] Orthographic camera in FreeView

HnNUO4X89Epb7M4agLwMtb3A/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FUpdateFreeview > > Best, > Ruopeng > > On Apr 15, 2022, at 10:23 AM, Anderson M. Winkler > wrote: > > External Email - Use Caution > > Hi all, > > Is there a way to configure the camera in