Re: [Freesurfer] Transformation between spaces

The latest version of melodic is compatible with CIFTI data (e.g. From the HCP). Peace, Matt. From: on behalf of Florence Campana Reply-To: Freesurfer support list Date: Monday, October 9,

[Freesurfer] Transformation between spaces

Hi Matt, Thank you for your quick input ; I did not try yet to use melodic, it seems indeed to be the most straightforward solution, I will try it, thank you again! Florence Le lundi 9 octobre 2017, Matt Glasser > a écrit : >

Re: [Freesurfer] Transformation between spaces

I¹d note that you can run the group ICA on surface data in surface space pretty easily using melodic, which would avoid the issue that Doug mentions. Peace, Matt. From: on behalf of Douglas Greve Reply-To: Freesurfer support

Re: [Freesurfer] Transformation between spaces

How did you get your ICA analysis into MNI305 (or MNI152) space? You're ICA intergroup comparisons will only be as good as that space -- how you get it onto the surface from there is not so important. You can run recon-all on the MNI152, sample the ICA maps onto the surface, then use the

[Freesurfer] Transformation between spaces

Dear freesurfer experts, I ran a spatial ICA in volume and would like to visualize the components in surface in order to assess the overlap between the independent components and my ROI (defined on surface). However after reading this paper, https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2862732/,

Re: [Freesurfer] Fornix included with hippocampus

no, it isn't On Mon, 9 Oct 2017, Alexopoulos, Dimitrios wrote: A quick question re: the hippocampus segmenation using FS 53.    Is the Fornix included as as part of the hippocampus segmentation/volume.   Looking at the aseg for “bert”, it appears not to be included.   Jim    

Re: [Freesurfer] Qdec image considering multiple variables

You can't run it with missing variables On 10/9/17 12:40 AM, 박경일 wrote: Dear FS developer, I am a FS beginner and trying to make QDEC images  of cortical thickness difference (color-coded inflated brain) between groups. No problem when fsid, diagnosis, age, and sex were only included in

Re: [Freesurfer] volumetric atlas to volumetric subject space

On 10/8/17 10:06 AM, Jonathan Bain wrote: Dear FreeSurfer community, For a template subject (Colin27), I have a volumetric atlas (nifti file, where each brain region is numbered 1, 2, 3...). I am trying to use FreeSurfer to get the volumetric atlas into volumetric subject space (moving

Re: [Freesurfer] Original dimension

what is the dimension of the rawavg.mgz? what is the dimension of the output? What is the terminal output? On 10/8/17 1:51 AM, Fereshte wrote: Dear Experts, I've run " mri_label2vol --seg aseg.mgz --temp rawavg.mgz --o aseg-in-rawavg.mgz --regheader aseg.mgz" as explained, however i can't

Re: [Freesurfer] Hole in fsaverage Pial?

I have noticed it before. I don't think it is a problem, but it is on my list of things to fix. On 10/6/17 4:50 PM, Funk, Quentin wrote: FS Experts, There seems to be a hole in the lh.pial for fsaverage--see the attached screenshot. It doesn't show up when checking the Euler number, but

Re: [Freesurfer] occiptal flattening

What is your command line and what is your terminal output? On 10/6/17 9:57 AM, Patricia Stefancin wrote: Hello, I have been trying to flatten patches (the occipital cortex) in order to create retinotopic maps. However, when I run mris_flatten, the command window says it cannot read the

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

I don't know what you are asking On 10/6/17 9:24 AM, std...@virgilio.it wrote: > 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)

Re: [Freesurfer] Fixed effects fMRI {Disarmed}

Not an easy way to do it. I guess you could create an FSFAST session for it, eg, allconcat/bold/001/all.nii.gz, then run mkanalysis-sess with -funcstem all Alternatively, you have run the individual analyses, then isxconcat-sess, then the FFX analysis in mri_glmfit with the --yffxvar and

Re: [Freesurfer] Problem with New Hippocampus/Amygdala Segmentation

Hi Eugenio, I just wanted to follow up and see if you could tell anything about what was going on from the response I got to running "mri_robust_register" as you suggested. -- Forwarded message -- From: Max Owens Date: Wed, Sep 27, 2017 at 3:51 PM Subject:

Re: [Freesurfer] preproc-sess

Technically, it does not use an anatomical volume but rather the surfaces derived from the conformed volume (so the registration will be good for any conformed volume). No need to reorient the functionals as long as the header info about the head orientation is correct. On 10/6/17 5:29 PM,

Re: [Freesurfer] License files with FreeSurfer 5.2.0

This issue is likely the newness of the OS you are running and the version of glibc libs it has. The license code in the old versions of freesurfer simply will not work with any license file with the newest glibc libs. There may be a workaround by preloading an older libcrypt.so library.

[Freesurfer] Fixed effects fMRI {Disarmed}

Hi all, I would like to perform a fixed effects analysis on a small sample of subjects with FS-fast -- where the time series from all subjects are concatenated together and analysed in a large design matrix. Is there an easy way to do this? I don't know if I'm looking in the wrong place but I

[Freesurfer] [freesurfer] Qdec image considering multiple variables

Dear FS developer, I am a FS beginner and trying to make QDEC images of cortical thickness difference (color-coded inflated brain) between groups. No problem when fsid, diagnosis, age, and sex were only included in qdec.table.dat file. However, adding any other factors such as hypertension,

Re: [Freesurfer] qdec.table_ref

Hi Amy, please send your questions to the freesurfer email list . Try replacing ID with fsid , also you may need to fix the white spaces (replace multiple spaces with a single space or tab). Best, Martin > On 9. Oct 2017, at 03:09, 田阿敏 <237416...@qq.com> wrote: > > > Hi~ > > I am Amy from

Re: [Freesurfer] Original dimension

I found out the problem, thank you. Cheers On Sun, Oct 8, 2017 at 9:21 AM Fereshte wrote: > Dear Experts, > I've run " mri_label2vol --seg aseg.mgz --temp rawavg.mgz --o > aseg-in-rawavg.mgz --regheader aseg.mgz" as explained, however i can't see > any changes in

[Freesurfer] Errors on compiling FreeSurfer

Hi Experts, I tried to compile FreeSurfer on Ubuntu 16. When I ran a command 'make check', I got these error messages: */usr/bin/ld: warning: libtk8.4.so , needed by /home/aziz/centos6-x86_64-packages/KWWidgets/current/lib/KWWidgets/libKWWidgets.so, not found (try using