Re: [Freesurfer] surfstat maps using freesurfer outputs on skull-stripped data

You can map it onto fsaverage, which is made only from 40 subjects, so there is a little more folding On 01/09/2018 06:27 PM, Duran, Tugce wrote: > Total N is 159. I have min # of 52 subjects for certain analyses. I used > avgsubj. lh/rh.pial and lh/rh.thickness.10.mgh for reading surface and

Re: [Freesurfer] How to output particular area from stats subdir

You can pass it the segmentation number, eg, --segno 17 will give you the left hippo. You can have multiple --segno flags to give you multiple ROIs On 02/23/2017 11:55 AM, Jing Gu wrote: > Dear FreeSurfer Developers, > By using the following code, we can get volume data of different areas >

Re: [Freesurfer] surfstat maps using freesurfer outputs on skull-stripped data

Total N is 159. I have min # of 52 subjects for certain analyses. I used avgsubj. lh/rh.pial and lh/rh.thickness.10.mgh for reading surface and thickness data. Can the visualization issue be fixed? Thanks! Tugce dur...@iupui.edu On 1/9/18, 6:19 PM, "freesurfer-boun...@nmr.mgh.harvard.edu on

Re: [Freesurfer] Acquiring Exact p Values

You need to compute p = 10^-5.68 = 2.0893e-06, which is significant :) On 01/08/2018 02:04 PM, Hannah Claussenius-Kalman wrote: > Hello, > > I am conducting surface group analyses and would like to acquire exact > p values. > > The FreeSurfer manual notes that the number listed after the peak

Re: [Freesurfer] surfstat maps using freesurfer outputs on skull-stripped data

This is not entirely unexpected as the volume-based average of pial surfaces will lose folds as you add subjects. How many subjects do you have? Note that this is only a visualization issue if all your underlying analysis is done on the surface. On 01/08/2018 01:14 PM, Duran, Tugce wrote: > >

Re: [Freesurfer] mri_glmfit ERROR: loading gamma0

does this file exist and do you have read permissions? /home/gsalvado/Projects/Amyloid_Staging/Data/FreeSurfer/Stage0-stage1NoSex.intercept.mtx On 01/09/2018 09:34 AM, Gemma Salvadó Blasco wrote: > Hello Freesurfer developers, > I'm make a statistical analysis between two groups. To do this,

Re: [Freesurfer] Using MRS voxel mask in freesurfer surface space

You probably set up the FSFAST analysis to sample onto the fsaverage surface (in your mkanalysis-sess command). There are a couple of things you can do: 1. redo the FSFAST analysis using "self" instead of fsaverage. 2. map the beta.nii to the subject's native anatomy using mri_surf2surf, or 3.

Re: [Freesurfer] LME

Hi Kersten. Thank you very much . I am not planning a new design for sample size calculation. Can you please help me how to find those values? Thank you Getaneh From: freesurfer-boun...@nmr.mgh.harvard.edu

Re: [Freesurfer] Using MRS voxel mask in freesurfer surface space

Hello Freesurfer experts, We are obtaining MRS data and functional MRI data on two separate days for each subject. We use structural scan obtained during both these sessions for the freesurfer segmentation. MRS scan gives us a binary mask (nii format) in the same space as the structural image

Re: [Freesurfer] Surfaces along midline

Hi Romella usually the left/right split is defined by the aseg, so try fixing it and rerunning the surface generation and see if it resolves your problem cheers Bruce On Fri, 22 Dec 2017, Romella Durrani wrote: > Hi, > I'm having problems with the surfaces along the midline for one scan. I

[Freesurfer] TRACULA path segmentation fault error because of bedpostx?

Hello all, I've been running trac-all from the command line without the configuration file since I'm not changing any defaults. I've successfully run several subjects through the trac-all -prep stage, and the -bedp stage. **Although I never got the "trac-all -bedp finished without error"

Re: [Freesurfer] freesurfer segmentation: perirhinal Roi

Hi Mohamed, You can download a new, free license for v6.0 directly from here: http://surfer.nmr.mgh.harvard.edu/registration.html best, Andrew On Jan 9, 2018, at 9:11 AM, m.ba...@uliege.be wrote: Dear Bruce, Many thanks for you answer! I am trying to rerun the

[Freesurfer] mri_glmfit ERROR: loading gamma0

Hello Freesurfer developers, I'm make a statistical analysis between two groups. To do this, I followed the instructions of the Fs tutorial ( https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis) but I'm having a problem at the last step of the process (mri_glmfit). I've checked that

Re: [Freesurfer] freesurfer segmentation: perirhinal Roi

Dear Bruce, Many thanks for you answer! I am trying to rerun the cortical reconstruction with the version 6.0 but I got the following error. May I have a license for this Freesurfer version 6.0? Thanks a lot for your kind help! Best regards, Mohamed

Re: [Freesurfer] freesurfer segmentation: perirhinal Roi

Hi Mohamed I'm pretty sure this was an issue with the ribbon-filling in V5 that is better in V6. Try using it and see if it is fixed. cheers Bruce On Tue, 9 Jan 2018, m.ba...@uliege.be wrote: > Dear Freesurfer experts, > > We would like to use volume and cortical thickness measures obtained

Re: [Freesurfer] Segmentation of hippocampal subfields and nuclei of the amygdala

Great! Thanks! 2018-01-08 16:44 GMT+01:00 Hoopes, Andrew : > Hi Carme, > > segmentHA_T1.sh is available in the fs dev version: ftp://surfer.nmr.mgh. > harvard.edu/pub/dist/freesurfer/dev > > best, > Andrew > > > On Jan 4, 2018, at 9:17 AM, Carme Uribe Codesal

Re: [Freesurfer] LME

Hi Getaneh, please find my responses below. -Original Message- From: "Tefera, Getaneh B" Reply-to: Freesurfer support list To: freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] LME Date:

Re: [Freesurfer] Fail to retrievive data file from https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/repo/annex.git

Update: At first, I did `git clone --depth=1 https://github.com/freesurfer/freesurfer.git` to clone the repo, and it has aforementioned issues.Then, I did git clone again without --depth=1 option. Now, `git fetch datasrc` works as expected. Best, Foucault On Tue, Jan 9, 2018 at 5:01 PM

[Freesurfer] Fail to retrievive data file from https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/repo/annex.git

Hi FreeSurfers, I am trying to build freesurfer from source on ubuntu 16.04 in order to run `recon-all -use-gpu` that is compatible with the latest cuda 9.1. I followed the instruction here to build freesurfer http://surfer.nmr.mgh.harvard.edu/fswiki/freesurfer_linux_developers_page. However, in