Re: [Freesurfer] Susceptibility artifact

no, we don't. Is that affecting the brain? On 04/12/2018 05:26 PM, John Anderson wrote: > Dear Freesurfer experts, > I would like t inquire if there is any tool or method in Freesurfer > that can help to fix susceptibility artifacts in T1 image like attached > > > Any suggestion is highly

Re: [Freesurfer] tksurkfer save error

yes,, there is a command line option (-ss I think) cheers Bruce On Thu, 12 Apr 2018, Douglas N. Greve wrote: We are not really supporting tksurfer anymore. You can use freeview to save a png from the GUI. Ruopeng, is there a way to take a snap shot from the command line? On 04/12/2018

[Freesurfer] Data Analyst & Research Assistant Position(s) - Child Mind Institute (New York)

Child Mind Institute is seeking a Data Analyst to join our team. The Data Analyst’s role is to assist and support the acquisition, manipulation, and analysis of data, as well as the reporting results. In particular, our work includes: 1) support the preprocessing of large fMRI dataset in human and

Re: [Freesurfer] LME univariate data

Dear Kersten, Thanks for reply. I have new question. When I set model use total_i_vol_stats = lme_fit_FS(X,[1 2],Y(:,2),ni) and total_i_vol_stats = lme_fit_FS(X,[1],Y(:,2),ni). But Bhat of two models' year have a lot different, for example, with 2 is 1.2422 without 2 is -0.5737. The direction has

Re: [Freesurfer] Group Analysis Design Matrix

If you want to test for an interaction between Age and Weight, you need to create a new covariate which is Age*Weight, then test the sig of this covariate. I would demean Age and Weight for both the inidvidual covaraite and before computing the product. On 04/12/2018 12:35 PM, David S Lee

Re: [Freesurfer] -qcache in recon-all commnd

Right. And you'd need to redo it after all manual edits On 04/12/2018 11:06 AM, Alexopoulos, Dimitrios wrote: > > Thanks. We are starting an analysis of a pediatric cohort using FS 6.0 > and may/may not use QDEC downstream for surface-based group analysis. > > That said, it sounds like it is

[Freesurfer] tksurkfer save error

Ok, thanks for the reply. It sounds like the ENIGMA folks need to updage their commands to use freeview. I'll try using ImageMajick's import as a workaround. Jen Message: 11 Date: Thu, 12 Apr 2018 10:59:58 -0400 From: "Douglas N. Greve" Subject: Re:

Re: [Freesurfer] RV: "preproc-sess" with intermediate volume

Thank you very much!! De: freesurfer-boun...@nmr.mgh.harvard.edu en nombre de Douglas N. Greve Enviado: jueves, 12 de abril de 2018 16:39 Para: freesurfer@nmr.mgh.harvard.edu Asunto: Re:

[Freesurfer] Group Analysis Design Matrix

Hi FreeSurfer Experts, I have two groups (Male and Female) and two covariates (Age and Weight). I want to test change of cortical thickness with age and weight, after removing effects of Group. In other words, is there an interaction between age and weight, regressing out the effects of groups.

[Freesurfer] Roundness of a surface label

Hi, I was wondering if there was any existing freesurfer script to calculate the roundness and/or the perimeter of a surface label? If anyone has ideas on how to calculate this, I would appreciate it. Thanks, Jonathan ___ Freesurfer mailing list

Re: [Freesurfer] Freesurfer and crypt

Hello Bennet, Maybe someone else can chime in on this, as I have not worked on a system with FIPS, but perhaps there is a way for the FIPS administrator to white list all the Freesurfer binaries (and the license file), as security exempt. I know some Enterprise/business applications like

Re: [Freesurfer] -qcache in recon-all commnd

Thanks. We are starting an analysis of a pediatric cohort using FS 6.0 and may/may not use QDEC downstream for surface-based group analysis. That said, it sounds like it is not a bad idea use -qcache other than more preprocessing time. Basically, same output as without -qcahe but more files

Re: [Freesurfer] tksurkfer save error

We are not really supporting tksurfer anymore. You can use freeview to save a png from the GUI. Ruopeng, is there a way to take a snap shot from the command line? On 04/12/2018 10:29 AM, Evans, Jennifer (NIH/NIMH) [F] wrote: > > Hi, > > This is a repost as I didn’t get a reply to the one I

Re: [Freesurfer] tksurkfer save error

Hi Jen tksurfer is deprecated and this sounds like an error in your graphics environment. Have you tried using freeview instead? Generating snapshots should be pretty easy cheers Bruce On Thu, 12 Apr 2018, Evans, Jennifer (NIH/NIMH) [F] wrote:     Hi,   This is a repost as I didn’t

Re: [Freesurfer] MCR

Matlab is not needed for basic FS analysis. I think the only things it is used for in FS is hippocampal subfields, FSFAST, and lGI. I don't think there are any limitations, but I'm not sure. I don't know about spm12 On 04/10/2018 01:35 PM, John Absher wrote: > > Hi, > > I was pleased to learn

Re: [Freesurfer] Freesurfer and crypt

It appears that FreeSurfer is not compatible with systems for which FIPS level security is mandated. In our case, I am told this is part of our data use agreement with the VA. We tried to run it, and I get the following stack trace showing what appears to be license validation using the crypt()

Re: [Freesurfer] mri_vol2surf: unable to compare volume maps

Hi Srishti, you will need to be much more specific to allow me to help you. mni152_subject is not a file that can be input to recon-all (it should be a dicom or nifti or mgz). If you use the same input to recon-all that you used to view it in spm, then the FS output should align with your map.

Re: [Freesurfer] RV: "preproc-sess" with intermediate volume

Hi David, move your intermediate volume to session_1/ifsd/001/orig.mgz then try -bbr-int ifsd orig On 04/12/2018 04:10 AM, David Sánchez Bestué wrote: > Dear all, > > I have a problem with the command: > "preproc-sess" > > I wanted to use the Registration option to add an intermediate

[Freesurfer] tksurkfer save error

Hi, This is a repost as I didn’t get a reply to the one I sent a few weeks ago. This error basically means I can’t automatically generate a webpage of all of the segmentation results. I getting an error when trying to save a tiff file using tksurfer on a linux machine via NoMachine

Re: [Freesurfer] mri_vol2surf: unable to compare volume maps

What is the "MNI template" that you are using. I mean an exact file used. Did you use this file when you ran recon-all? On 04/12/2018 10:23 AM, srishti goel wrote: > Yeah, I am unsure where to go from here as well. So the results can be > viewed in SPM and on the MNI template space itself,

Re: [Freesurfer] mri_vol2surf: unable to compare volume maps

Yeah, I am unsure where to go from here as well. So the results can be viewed in SPM and on the MNI template space itself, since SPM typically does not have a problem showing multiple images in different sizes. Best, Srishti Social/Clinical Research Specialist Child Imaging Research and Life

Re: [Freesurfer] mri_vol2surf: unable to compare volume maps

When you use bbregister, it is expecting the input nii file to represent the actual anatomy of the subject, so it does not surprise me that it does not work that well. I'm not sure what to do about this because a meta analysis image will never have decent anatomy. In theory, it should be

[Freesurfer] Abstract submission deadline extended - 1st International Workshop on Predictive Processing

We would like to inform you that the abstract submission deadline to PREDICTIVE PROCESSING has been extended. The new deadline is April 16th. The conference dates are June 20-22, 2018 Dear Researcher, We are happy to announce the new discussion arena fully centred on predictive processing. The

[Freesurfer] 3T flag recon-all

Hi all, Would you recommend using the 3t flag for recon-all when analyzing data from a 3t scanner? I read about it in some papers but not everybody seems to use it. Also, do you know whether the flag can be used in the longitudinal stream as well or does it only apply to the crosssectional

Re: [Freesurfer] newbie trac-all -bedp question

Thanks for all the help and explanation, Anastasia. Best - Don From: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Yendiki, Anastasia Sent: Wednesday, April 11, 2018 9:18 PM To: Freesurfer support list

[Freesurfer] CFP: The first International Workshop on Machine Learning in Clinical Neuroimaging (MLCN 2018)

Apologize for multiple posting ***Dear Colleagues,We are delighted to invite you to join us for the MLCN 2018 workshop as a satellite event of MICCAI 2018 conference, Granada, Spain.

[Freesurfer] Postdoctoral Position

*Postdoctoral position in the Team “Multimodal Neuroimaging and Lifestyle in Aging and Alzheimer’s disease” (Dr. Gaël Chételat , UMR-S U1237-PhIND, Caen, France) ** Duration: 2 years (1 year renewable 1 year). * Starting date: June 2018 * Research team: Multimodal Neuroimaging and Lifestyle in

[Freesurfer] RV: "preproc-sess" with intermediate volume

Dear all, I have a problem with the command: "preproc-sess" I wanted to use the Registration option to add an intermediate volume. The only documentation I could find about it was the one that appears with the command: "preproc-sess --help" Registration options -init-fsl : use fsl to