[Freesurfer] Is the cortical thickness calculated using Hausdorff distance in FreeSurfer?

External Email - Use Caution Dear FS experts: I'm doing a project about the changes of cortical thickness after sleep deprivation. I know that cortical thickness is calculated as the closest distance from the gray/white boundary to the gray/CSF boundary at each vertex. Is th

[Freesurfer] How to estimate the Intracranial area?

Dear FS experts: I'am writting to ask for help about intracranial area. I can find the information of intracranial volume in aseg.stats file. But i did not find the information of intracranial area or is there any way to estimate the intracranial area ? Looking forward to any sugges

[Freesurfer] mri_mcsim error

Dear FS experts: I am writting to ask for help about mri_mcsim. I would like to run mri_mcsim with only one FWHM (e.g. --fwhm 13) instead of FWHM=1:fwhm-max (the default is FWHM=1:30). Thus i tried: mri_mcsim --o $FREESURFER_HOME/average/mult-comp-cor/fsaverage/lh/mask --base mc-z

Re: [Freesurfer] Question about global mean cortical thickness

iliang > >the thickness is the average of the min distance from gray-to-white and >white-to-gray at each vertex. The surface area is the average area of the >triangles attached to a vertex (divided by 3 I think). > >cheers >Bruce > > >On Sun, 13 Aug 2017, Zhiliang Lon

[Freesurfer] Question about global mean cortical thickness

Dear FS experts: I am writting to ask for help about the computation of global mean thickness. On the FAQ page, one suggestion is that the global mean thickness is equal to the (lh.thickness*lh.surfarea + rh.thickness.rh.surfarea) / (lh.surfarea+rh.surfarea). I am wondering how the ?h.thick

[Freesurfer] How to calculate the surface area of a vertex ?

Hi FS experts: I am studying the vertex-level group analysis on surface area between groups. I know that the cortical thickness of a vertex is computed as the distance between white matter surface and pial surface. But I have no idea how to calculate the surface area of a vertex. In my under

[Freesurfer] How are Vertex RAS coordinates calculated in TKsurfer

Dear FS experts: I am studying the coordinate system in FS. I met a problem that confused me. I run tksurfer: tksurfer fsaverage lh inflated. Then I chose a point on surface. It showed that the Vertex Index is 80321, and the Vertex RAS is (-38.53 9.05 40.01). I thought that the Vertex

[Freesurfer] Difference between lh.thickness file and lh.thickness.fsaverage.mgh file

Dear FS experts: I conducted recon-all analysis on my own subjects, and found that there are several kinds of thickness files, such as the lh.thickness file and lh.thickness.fsaverage file. By using MATLAB scripts implemented in FS, different numbers of vertex were found between the two fi

[Freesurfer] How to parcellate the whole white matter into different lobules using Freesurfer ?

Dear freesurfer experts: I was wondering if it would be possible to parcellate whole white matter into different lobules (e.g. white matter in frontal lobule, parietal lobule, temporal lobule, and so on) by using Freesurfer ? My goal is to compute the white matter volume, as well as FA w

Re: [Freesurfer] How to convert a surface to volume space after using mris_preproc?

viewing in MRIcron, the image looked rotated. Could you please help with it? Best, Xiangyu On Mon, Apr 23, 2012 at 4:31 PM, Douglas N Greve wrote: > Hi Xiangyu, just add --identity fsaverage to the surf2vol command line > doug > > > On 04/19/2012 05:57 PM, Long wrote: > > Hi

[Freesurfer] How to convert a surface to volume space after using mris_preproc?

Hi all, I had a question when convert a surface to volume space. First, I converted a volume nifti data to fsaverage: mris_preproc --target fsaverage --hemi lh --iv data.nii bb_register.dat --out data.lh.mgh Then, I want to convert the data.lh.mgh to volume space, I tried mri_surf2vol, however,

Re: [Freesurfer] How to only do spatial normalization in FreeSurfer.

Player < astev...@nmr.mgh.harvard.edu> wrote: > Maybe you can apply the transform using mri_convert or mri_vol2vol created > during autorecon1. Is that what you are looking for? > > http://surfer.nmr.mgh.harvard.edu/fswiki/ReconAllDevTable > > > On Feb 22, 201

[Freesurfer] How to only do spatial normalization in FreeSurfer.

Dear all, I had EPI images and T1 image and the EPI images are already co-registered to T1 image in their native space. I also run 'recon' on T1 image. I'd like to try surface-based spatial normalization in FreeSurfer, so how can I only do the spatial normalization of EPI images in FreeSurfer, i.e

[Freesurfer] How to export non spatial normalization fMRI images?

he co-registered fMRI images in volume space? I think it could start at "fmcpr.up.nii.gz"? Thank you in advance! Best, Xiangyu Long ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/f

[Freesurfer] Question after preprocessing in FreeSurfer.

Dear all, Hi, I am a beginner of FreeSurfer. Recently I have run recon-all and preproc-sess on my MRI and fMRI images. Next I'd like to convert surface images to AFNI-SUMA and convert fMRI images to volume space. I found that the T1 image and its surface maps were not normalized and the fMRI image

Re: [Freesurfer] FDR correction in Qdec

Now it works if I enter the FDR in the text box -> press Enter -> click on Set Using FDR Thank you so much. Best, Xiaojing 2010/7/9 Douglas N Greve > That is strange. Can you change the FDR to something ridiculous like .5 and > see if that changes things? > > X

Re: [Freesurfer] FDR correction in Qdec

I tried that. Still no change. And I tried running Qdec on all of my datasets. The problem occurs on all of them. Xiaojing 2010/7/9 Douglas N Greve > That is strange. Can you change the FDR to something ridiculous like .5 and > see if that changes things? > > Xiaojin

[Freesurfer] FDR correction in Qdec

Hi, all, I have some questions about performing the FDR correction in Qdec. I ran recon-all on all my subjects, then ran the surface group analysis following the Qdec tutorial. There are 3 factors in the qdec.table.dat file: age, gender and diagnosis. In the Design tab of Qdec, I selected the dis

Re: [Freesurfer] How to get deformation maps in surface-based registrations

tween the ?h.sphere.reg and the > ?h.sphere. I guess you would want to represent them as arcs of great > circles. > > cheers, > Bruce > > On Tue, 18 May 2010, Xiaojing Long wrote: > > Hi, all, >> >> I have a question regarding how to get the deformation map in >>

[Freesurfer] How to get deformation maps in surface-based registrations

Hi, all, I have a question regarding how to get the deformation map in surface-based registration. I am wanting to use mris_register to align two surfaces. Can I get the deformation maps describing the vertex-to-vertex correspondence? How can I get it? Thanks a lot. Best, Xiaojing _

[Freesurfer] How to convert a cortical thickness map to a NIFTY file

Hi, I have a question regarding how to convert a cortical thickness map (i.e. lh.thickness) to a NIFTY file. I have a subject called 'subjid' and I run recon-all on it. So I got the ?h.thickness files. Does freesurfer provide a tool to convert the surface file to a nifty file? I tried using the

Re: [Freesurfer] Averaging cortical thickness maps

I would use -o fsaverage, then you can simply load the average > thickness onto the fsaverage inflated surface. > > cheers > Bruce > > > > On Thu, 18 Mar 2010, Xiaojing Long wrote: > > Hi, Bruce, >> >> Thanks a lot for your suggestion. >> >>

Re: [Freesurfer] Averaging cortical thickness maps

the subjects? Thank you. Best, Xiaojing 2010/3/17 Bruce Fischl > Hi Xiaojing, > > mris_average_curvature will do it, and I think Doug has some other tools > that will as well. > > cheers, > Bruce > On Wed, 17 Mar 2010, Xiaojing Long wrote: > > Hi, >> &

[Freesurfer] Averaging cortical thickness maps

Hi, I have a question regarding how to average cortical thickness maps. I have a dataset with 10 MR brain images and I've run recon-all on each of them. So I've got thickness maps ?h.thickness for each subject. I wonder whether freesurfer provides a tool that can average the cortical thickness ma

Re: [Freesurfer] Problem with recon-all on the tutorial data (bert)

. In both cases, I have got the same result as described in the previous mail: segmentation fault. Would you have any suggestion for this problem? Thank you. Bests, Long On Tue, Nov 24, 2009 at 9:05 AM, Bruce Fischl wrote: > Hi Long, > > have you run out of disk space? > Bruce > &

Re: [Freesurfer] How to use mris_register

another, but in our experience using the atlas statistics and the > measures of cross-subject variability stabilizes the whole procedure > > On Tue, 6 Oct 2009, Xiaojing Long wrote: > > Hi, Douglas, >> >> Thank you so much for your help. >> >>

Re: [Freesurfer] How to use mris_register

something different? > > doug > > Xiaojing Long wrote: > >> Hi, all, >> I am new to FreeSurfer world. I am trying to do the surface-based >> registration using FreeSurfer. I found a tool called mris_register, >> which is defined as a command registering a surface t

Re: [Freesurfer] How to use mris_register

arguments? Thank you again. Best, Xiaojing 2009/10/6 Bruce Fischl > Hi Xiaojing, > > the inputs are an individual subject sphere created with mris_sphere, and > statistics in an atlas coordinate system, usually stored in a tif file that > we supply. > > cheers, > B

[Freesurfer] How to use mris_register

Hi, all, I am new to FreeSurfer world. I am trying to do the surface-based registration using FreeSurfer. I found a tool called mris_register, which is defined as a command registering a surface to an average surface template(or another single-subject's surface). But I don't understand how to use