Re: [Freesurfer] Cortical parcellation

Sorry i meant brain parcellation ( aseg.mgz ) On Tue, Oct 3, 2017 at 5:33 PM Bruce Fischl wrote: > Hi Fereshte > > all cortical parcels are gray matter. Maybe I'm not understanding your > question? > Bruce > > > On Tue, 3 Oct 2017, Fereshte wrote: > > > Dear

Re: [Freesurfer] Trouble building 6.0.0 on centos7

If you cd into BUILD/freesurfer-6.0.0/lta_convert, does the file lta_convert.help.xml.h exist? Also, run ‘make' while in the lta_convert directory to see if the error output provides more details. If not, can you send me the contents of BUILD/freesurfer-6.0.0/lta_convert/Makefile? thanks

Re: [Freesurfer] Brodmann areas - exvivo labels

Thanks for the speedy reply, Matt and Bruce! In that case I'll go with the .thresh for each Brodmann area. Trisanna -- Ph.D. Candidate McGill University Integrated Program in Neuroscience Psychology On Tue, Oct 3, 2017 at 8:32 PM, Bruce Fischl wrote: > yes, I

Re: [Freesurfer] Brodmann areas - exvivo labels

yes, I agree with Matt. You need different thresholds for different areas (e.g. V1 vs. BA44) and picking one that on average gives you the right sized label seems reasonable Bruce On Tue, 3 Oct 2017, Matt Glasser wrote: I would use the versions where the group size approximately matched the

Re: [Freesurfer] Brodmann areas - exvivo labels

I would use the versions where the group size approximately matched the individual size. Peace, Matt. From: on behalf of Trisanna Sprung-Much Reply-To: Freesurfer support list

[Freesurfer] Brodmann areas - exvivo labels

Hi there If I wanted to compare some spatial probability maps of some sulci of interest with the Juelich Data provided by FreeSurfer, would it make more sense to use the unthresholded Brodmann areas or the .thresh ones? Based on my understanding of how the .thresh was created (by creating a

[Freesurfer] PCA and v.gmh

Dear freesurfers, I contact you since I ran a PCA with mri_glmfit. I do not manage to load the output v.mgh as an overlay as suggested in the documentation, which makes me wonder what is wrong. The output file or me loading it? For clarification, I ran the command: mri_glmfit --surf fsaverage lh

Re: [Freesurfer] Trouble building 6.0.0 on centos7

I think so. I am actually attempting to build an RPM. Here is my spec file: Name: freesurfer Version:6.0.0 Release:1%{?dist} Summary:FreeSurfer Software Suite License:Proprietary URL:https://surfer.nmr.mgh.harvard.edu/ Source0:

[Freesurfer] New Post-doc and Research Associate positions on the MIDUS study at The Center for Healthy Minds

Postdoctoral Fellow in Affective, Cognitive, and Aging Neuroscience Degree and area of specialization: Ph.D. in Neuroscience or Psychology Experience in neuroimaging research in emotion, cognition, and/or aging preferred. Minimum number of years and type of relevant work experience: *

Re: [Freesurfer] Trouble building 6.0.0 on centos7

Hi Sol, I don't recognize this error, but will look into it. Have you set up the required system libraries and library dependencies described in https://surfer.nmr.mgh.harvard.edu/fswiki/freesurfer_linux_developers_page ? Andrew On Oct 2, 2017, at 5:55 PM, Sol Jerome

[Freesurfer] convert asc to fsaverage

Hi, I was wondering if there is a way to convert an asc file to fsaverage. I have a list of vertex values and I want to convert them to a thickness format. I know how to use mri_convert to go form thickness to ascii and I was hoping there is a way to go in the other direction. Thanks! Ali

[Freesurfer] R: Re: R: Re: R: Re: R: Re: Map of covariance

Thank you very much. Where I should put 0 0 0 0 .25 .25 .25 .25? Which are the contrast reported below that I should modify? C1) gr1-gr2_intercept 1 -1 0 0 0 0 0 0 C2 )gr1-gr2_slope 0 0 0 0 1 -1 0 0 C3) gr1-gr3_intercept 1 0 -1 0 0 0 0 0 C4) gr1-gr3_slope 0 0 0 0 1 0 -1 0 C5) gr1-gr4_intercept 1

Re: [Freesurfer] R: Re: R: Re: R: Re: Map of covariance

probably you want 0 0 0 0 .25 .25 .25 .25 On 10/3/17 10:10 AM, std...@virgilio.it wrote: > Many thank for your response. > Claryfing my question on point 3, > When I look in group.effect.slope, the map show the group difference removing > the effect of the covariate. > Conversely, I would to

[Freesurfer] R: Re: R: Re: R: Re: Map of covariance

Many thank for your response. Claryfing my question on point 3, When I look in group.effect.slope, the map show the group difference removing the effect of the covariate. Conversely, I would to obtain the map reporting only the effect of covariate on dependent variable (functional

Re: [Freesurfer] Cortical parcellation

Hi Fereshte all cortical parcels are gray matter. Maybe I'm not understanding your question? Bruce On Tue, 3 Oct 2017, Fereshte wrote: Dear Experts,How to figure out if a cortical parcellation is Considered as a part of gray matter or white matter ?  Thank you! 

Re: [Freesurfer] how to separate any sub cortical region in freesurfer ?

yes, you can do that with either of the binaries I mentioned cheers Bruce On Tue, 3 Oct 2017, Vidhu Agrawal wrote: > Respected Sir, > > I meant to ask that if i want to separate for example hippocampus and view as > a separate volume what > code should i implement? > > On Mon, Oct 2, 2017 at

Re: [Freesurfer] Cortical parcellation

cortex is always GM On 10/3/17 2:19 AM, Fereshte wrote: Dear Experts, How to figure out if a cortical parcellation is Considered as a part of gray matter or white matter ? Thank you! ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu

Re: [Freesurfer] how to separate any sub cortical region in freesurfer ?

use, for example, mri_binarize --i aseg.mgz --match 17 --o left-hippo.mgz The 17 is the index for left hippo as found in $FREESURFER_HOME/FreeSurferColorsLUT.txt On 10/3/17 6:48 AM, Vidhu Agrawal wrote: Respected Sir, A segment.dat file is formed and when i am running:  mri_label2vol

Re: [Freesurfer] how to separate any sub cortical region in freesurfer ?

Respected Sir, A segment.dat file is formed and when i am running: mri_label2vol --label lh-avg_central_sulcus.label --temp 1.nii --reg segment.dat --fillthresh .5 --o cent-lh.nii.gz Then error is coming: Error reading betplaneres from segment.dat On Tue, Oct 3, 2017 at 4:13 PM, Vidhu

[Freesurfer] ExploreDTI Workshop in March 2018

ExploreDTI Workshop - A course on processing, analyzing, and visualizing diffusion MRI data When: 12-14 March, 2018 Where: Utrecht, Netherlands Details: http://www.exploredti.com/workshop Cheers, Szabolcs ___ Freesurfer mailing list

Re: [Freesurfer] how to separate any sub cortical region in freesurfer ?

Respected sir, I have run the code: mri_label2vol --label lh-avg_central_sulcus.label --temp 1.nii --reg register.dat --fillthresh .5 --o cent-lh.nii.gz it is giving error: Loading registration from register.dat regio_read_register(): No such file or directory Could not open register.dat

Re: [Freesurfer] how to separate any sub cortical region in freesurfer ?

Hi Vidhu, You could use mri_vol2label or mri_binarize ( check freesurfer site or help in terminal for details ) Cheers On Tue, Oct 3, 2017 at 11:05 AM Vidhu Agrawal wrote: > Respected Sir, > > I meant to ask that if i want to separate for example hippocampus and view >

Re: [Freesurfer] how to separate any sub cortical region in freesurfer ?

Respected Sir, I meant to ask that if i want to separate for example hippocampus and view as a separate volume what code should i implement? On Mon, Oct 2, 2017 at 6:44 PM, Bruce Fischl wrote: > what do you mean by separate? Extract into a separate volume? If so,

[Freesurfer] Cortical parcellation

Dear Experts, How to figure out if a cortical parcellation is Considered as a part of gray matter or white matter ? Thank you! ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The