[Freesurfer] Proposed addition for Freesurfer - automated control points

External Email - Use Caution Freesurfer devs, I presented an automated control point adding tool at HBM and a few freesurfer lab people came over and had a look. I was wondering if someone would like to review it for either inclusion or to perhaps reference from the wiki as a

[Freesurfer] Freeview not showing images

External Email - Use Caution Hi. I'm a newbie to Freeview, hoping that this is a simple problem. When I open it (specifying the lh.pial surface), I get this view: [cid:image001.jpg@01D40F16.EC48FB10] Anyone have an idea what's going on here, is it an issue with the screen

[Freesurfer] mri_glmfit question

External Email - Use Caution Hello FreeSurfer Users, I want to run an ROI-based analysis on mri_glmfit as opposed to vertex-based. I know that if I run mri_glmfit with the --table flag and give it the output of asegstats2table or aparcstats2table, it will run the analysis on

[Freesurfer] recon.all strange run time

External Email - Use Caution Hi!I have a macbook pro MY 2014 with a Intel Core i7(quad core,2.7 ghz) and 16 gb of ram with El Capitan.This Macbook to run recon-all it takes 47 hours with -openmp 8 flag. A Dell with Intel Core i7 3632Q,8 GB RAM DDR3 1600mhz with Linux takes 8

Re: [Freesurfer] Poor occipital signal and low contrast

Hi Megha looking at the scan you sent I can tell gray from white over most of the occipital lobe, so I think control points could recover reasonable surfaces. I would try leaving a "trail" of them going from the inferior-most, very dark places heading up. cheers Bruce On Thu, 28 Jun 2018,

Re: [Freesurfer] Poor occipital signal and low contrast

External Email - Use Caution Hi, I'm just resending this email in case you missed it. Thanks! Megha From: freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Chawla, Megha Sent: Wednesday, June 20, 2018 11:11 AM To:

Re: [Freesurfer] Errors in scans

Hi Doug Thanks for your reply. I have not unpacked the error ones! I will go for it and let you know if there was a problem. Zahra (Mona) Nasiriavanaki Postdoctoral Research Fellow Martinos Center for Biomedical Imaging Massachusetts General Hospital 149 13th Street, 149-2615

Re: [Freesurfer] Errors in scans

Are the output volumes being created? Do they look ok? Sometimes unpacksdcmdir will print out an error when there is not actually an error there (eg, if it does not see the expected number of files, but some times its expectation is wrong). In dcmunpack (the replacement for unpacksdcmdir), I

[Freesurfer] Errors in scans

Hi Freesufer developers We are getting some errors in our resting state and ASL scans. Everything goes fine while we are scaning the subjects, but when we look at the data in BORGET, some of them come out with errors. I copied one of the scaninfo files, so you can see the errors. Is there

Re: [Freesurfer] Moderation analysis in Freesurfer

I don't think it is possible to do as a mixed effect. You can do this with the standard GLM by using a per vertex regressor (--pvr thickness.mgh to mri_glmfit) On 06/27/2018 12:12 PM, Mark Wagshul wrote: > > External Email - Use Caution > > Dear Freesurfer experts, > > We are

Re: [Freesurfer] error when running eddy_correct

Can you replicate the error outside of dt_recon? If so, then you should make a  posting to the FSL group. On 06/28/2018 02:03 AM, Куликова Софья Петровна wrote: > > External Email - Use Caution > > Hello FreeSurfer Developers, > > I was trying to run dt_recon (on centos7 system) but have

[Freesurfer] error when running eddy_correct

External Email - Use Caution Hello FreeSurfer Developers, I was trying to run dt_recon (on centos7 system) but have got an error at the eddy_correct stage, saying there is no $FSLDIR/bin/imglob file. Indeed, it is not there. However, I gave installed FSL according to their