Re: [Freesurfer] PET/MRI registration failed with bbregister or mri_coreg

Hi Douglas, Please find below the mri_coreg terminal output : *$Id: mri_coreg.c,v 1.27 2016/04/30 15:11:49 greve Exp $* *cwd /NAS/tupac/matthieu/FS5.3/207118_M0_2014-01-29/pet* *cmdline mri_coreg --s 207118_M0_2014-01-29 --mov BS7_PET.lps.nii.gz --reg Pet2T1.BS7.register.dof6.mri_coreg.lta --regd

Re: [Freesurfer] problem of using freesurfer

Hi HsinTsung FreeSurfer V6 isn't out yet, but we are moving towards having a beta. I'll leave the registration questions for Doug cheers Bruce On Mon, 3 Oct 2016, Hsin-Tsung Lee wrote: Dear freesurfer community    I have used the freesurfer v5.30 stable on linux, I want to fusion the C

Re: [Freesurfer] Gaussian curvature or Mean curvature

Hi Han I'm not sure I understand you question. The sign of the curvature depends on the arbirary convention you choose for the normal vector field over the surface. We pick and outwards pointing normal, which means that gyral regions in general have negative curvature (since they lie 'below' t

[Freesurfer] Brainhack: Anatomy edition in Paris, 24-26 October 2016

Registration is now open for Brain-anatomy-hack in Paris. Brain-anatomy-hack aims at promoting the interaction between scientists on questions concerning (1) the investigation of brain anatomy based on magnetic resonance imaging or post mortem dissection; (2) the evolution of nervous systems acros

Re: [Freesurfer] PET/MRI registration failed with bbregister or mri_coreg

Can you tar up the FS anat analysis and BS7_PET.lps.nii.gz and send it to me on our filedrop? On 10/3/16 6:55 AM, Matthieu Vanhoutte wrote: Hi Douglas, Please find below the mri_coreg terminal output : / / /$Id: mri_coreg.c,v 1.27 2016/04/30 15:11:49 greve Exp $/ /cwd /NAS/tupac/matthieu/FS5.

Re: [Freesurfer] PET/MRI registration failed with bbregister or mri_coreg

Hi Douglas, I have just sent it to you on Filedrop. Best regards, Matthieu 2016-10-03 17:45 GMT+02:00 Douglas Greve : > Can you tar up the FS anat analysis and BS7_PET.lps.nii.gz and send it to > me on our filedrop? > > On 10/3/16 6:55 AM, Matthieu Vanhoutte wrote: > > Hi Douglas, > > Please fi

[Freesurfer] Input file in subcortical analysis using mri_glmfit

Dear FS users I am trying to compare subcortical volumes of 3 groups (and no co-variates) pre and post an intervention using mri_glmfit in Paired-Analysis. My question pertains to which file I should specify as the input (--y) in the mri_glmfit command. The examples in the Wikis use either a prep

[Freesurfer] Quantifying volumes

Dear Douglas, I have a segmented gyrus curvature file (.curv or .w) and I would like to calculate the volume (and other statistics) of this gyrus. I currently only know mris_anatomical_stats to perform that, but requiring a '.label' file. Can I extract statistics directly from the ".curv" f

Re: [Freesurfer] problem of using freesurfer

Dear Dr. Bruce I have one more question, does the "mri_coreg" available in version 5.30 stable, or it only available in v6.0(or it's beta version)? Best Regard HsinTsung Lee 2016-10-03 21:30 GMT+08:00 Bruce Fischl : > Hi HsinTsung > > FreeSurfer V6 isn't out yet, but we are moving towards

Re: [Freesurfer] Gaussian curvature or Mean curvature

Dear Bruce Fischl ?h.white.H, ?h.curv, and H Mean reflected the vector fields with 'sign(+ or -)', and MeanCurv reflected the integral of the 'absolute' value of mean curvature. Am I understanding this correctly? Best Wishes, Han On Mon, Oct 3, 2016 at 7:49 AM, Bruce Fischl wrote: > Hi Han

Re: [Freesurfer] problem of using freesurfer

you can get it from here https://gate.nmr.mgh.harvard.edu/safelinks/greve/mri_coreg On 10/03/2016 12:46 PM, Hsin-Tsung Lee wrote: > Dear Dr. Bruce > I have one more question, does the "mri_coreg" available in > version 5.30 stable, or it only available in v6.0(or it's beta version)? > > Best

Re: [Freesurfer] Gaussian curvature or Mean curvature

yes, I believe so On Mon, 3 Oct 2016, Hanbyul Cho wrote: Dear Bruce Fischl ?h.white.H,  ?h.curv, and H Mean reflected the vector fields with 'sign(+ or -)', and MeanCurv reflected the integral of the 'absolute' value of mean curvature.  Am I understanding this correctly? Best Wishes, Han On

Re: [Freesurfer] Gaussian curvature or Mean curvature

Dear Bruce Fischl I appreciate your explanation. Thank you. Best Wishes, Han On Mon, Oct 3, 2016 at 11:37 AM, Bruce Fischl wrote: > yes, I believe so > > On Mon, 3 Oct 2016, Hanbyul Cho wrote: > > Dear Bruce Fischl >> >> ?h.white.H, ?h.curv, and H Mean reflected the vector fields with 'sign(

Re: [Freesurfer] Cortical thickness using qdec (between scanners)

Thanks Dr. Harms and Dr. Greve. So can I do the cortical thickness comparison if we have healthy controls data from the same scanner but acquired using different protocol e.g. if we get access of age-matched healthy controls data from another lab who used the same scanner? Thanks. On Fri, Sep 30,

Re: [Freesurfer] Cortical thickness using qdec (between scanners)

I would still say no -- the differences could still be due to differences in acquisition parameters On 10/03/2016 02:30 PM, Martin Juneja wrote: > Thanks Dr. Harms and Dr. Greve. > So can I do the cortical thickness comparison if we have healthy > controls data from the same scanner but acquire

Re: [Freesurfer] Output uncorrected p-values using mri_surfcluster

Hi all, just following up on my previous question. For the purposes of showing uncorrected p-values <0.005 as well as the corrected results (via mri_glmfit-sim) I would like to get the table of uncorrected p-values. I have tried using mri_glmfit-sim --glmdir results.glmdir --cache 2.3 abs --cwp 1 -

Re: [Freesurfer] Output uncorrected p-values using mri_surfcluster

In the table produced by glmfit-sim, the maximum vertex-wise uncorrected -log10(p) is given. Is that enough? On 10/03/2016 02:55 PM, Corinna Bauer wrote: > Hi all, just following up on my previous question. For the purposes of > showing uncorrected p-values <0.005 as well as the corrected resul

[Freesurfer] Best way to run GLM on a single subject across multiple sessions?

Hello, I am looking to run a GLM on a single subject, where data was collected across several different sessions. What is the best way to go about doing this in the FSFAST pipeline? I was thinking that I should just 1) drop the data for all the runs into a single BOLD directory as though they were

Re: [Freesurfer] mri_glmfit: Hierarchical Regression?

Sorry for the delay ... 1. FS cannot do hierarchical regression. Can you elaborate on the sum of squares types? Or point me to a web page/ 2. DODS will account for all 2 way interactions between discrete and continuous variables. If you want other interactions, you'll have to add them. For exa

Re: [Freesurfer] Best way to run GLM on a single subject across multiple sessions?

You can do it that way. If you use the -per-run option, it will motion correct and coregister each run separately and only combine them in the common space (eg, surface space). The alternative is to analyze each separately, then combine the results using a fixed effect model using mri_glmfit.

Re: [Freesurfer] Warping an ROI from one subject to another

Doug- I'm really sorry to keep pestering you about this but I just can't seem to get this to work. See my replies below: On 09/30/2016 02:00 PM, Douglas N Greve wrote: > First, bring up the ROI on the volume along with the surface in the > volume. You can do this with FreeView. Make sure that t

Re: [Freesurfer] problem of using freesurfer

you can get a copy of mri_coreg here https://gate.nmr.mgh.harvard.edu/safelinks/greve/mri_coreg On 10/03/2016 09:30 AM, Bruce Fischl wrote: > Hi HsinTsung > > FreeSurfer V6 isn't out yet, but we are moving towards having a beta. > I'll leave the registration questions for Doug > cheers > Bruce

Re: [Freesurfer] Warping an ROI from one subject to another

Sorry, it sent before I finished. I'll try this again. On 09/30/2016 02:00 PM, Douglas N Greve wrote: > First, bring up the ROI on the volume along with the surface in the > volume. You can do this with FreeView. Make sure that the ROI intersects > the surface. Yes, this looks fine > Then run mr

[Freesurfer] QCACHE always produces zeros for some vertices in the left hemisphere

Dear list, I'm trying to extract vertex-level measures of thickness, area, etc, for all of my subjects. I ran recon-all -all on all subjects as normal, then ran: recon-all -s {subject} -qcache where {subject} is the subject ID. This was followed by `mris_convert` to make the values human-readabl

Re: [Freesurfer] Warping an ROI from one subject to another

I think it might have to do with the format of your output file - perhaps try .mgz? This is what I used. Then open the surface and use the "overlay" option to overlay your ROI as a surface overlay. Trisanna -- Ph.D. Candidate McGill University Integrated Program in Neuroscience Psychology On M

Re: [Freesurfer] Output uncorrected p-values using mri_surfcluster

Should be, so long as it is the uncorrected value. Is that the CWPmax? On Mon, Oct 3, 2016 at 2:57 PM, Douglas N Greve wrote: > In the table produced by glmfit-sim, the maximum vertex-wise uncorrected > -log10(p) is given. Is that enough? > > > On 10/03/2016 02:55 PM, Corinna Bauer wrote: > > Hi

Re: [Freesurfer] Output uncorrected p-values using mri_surfcluster

No, it is labeled as "Max", the 2nd column of the table. The next column is the VtxMax, the vertex where the max uncorrected appeared On 10/03/2016 05:43 PM, Corinna Bauer wrote: > Should be, so long as it is the uncorrected value. Is that the CWPmax? > > On Mon, Oct 3, 2016 at 2:57 PM, Douglas

Re: [Freesurfer] Error using LGI script despite making suggested chages to Matlab script.

Thanks for your help. Yes. It looks like it is crashing during make_roi_paths.m Any ideas? Thanks. On Fri, 30 Sep 2016 06:32:06 -0700 Alan Francis wrote Hi Prasser: Did you set the environment for MATLAB e.g., setenv MATLABPATH /Applications/MATLA