[Freesurfer] Cuda 8, Centos 7, FreeSurfer 6

Hello. We recently installed Centos 7 with cuda 8 and tried to build the FreeSurfer 6.0 using the wiki instructions but were unsuccessful to do so. Has anyone successfully built FreeSurfer 6 on Cuda 8 (Centos 7) and willing to share the binaries with us or share their steps with us? We will

[Freesurfer] 3D conversion of Desikan-Killiany Atlas

Hi, all. Is there a 3D MNeI space version of Desikan-Killiany Atlas? (e.g. a sample 3D parcellation using MNI152 brain) Please let me know where I can find it or how I can get it in using Freesurfer. Thank you very much! Sincerely, Kwangyeol Baek

[Freesurfer] Grey matter misclassified as white matter

Dear experts, I am using freesurfer V5.3. I am trying to fix some error in freesurfer outputs. The issue is that grey matter misclassified as white matter in temporal lobe (lh). I tried to edit Wm.mgz and re-run with -autorecon2-wm, but it did not work. Looking at the brainmask.mgz, white matter

[Freesurfer] help

> On May 18, 2017, at 11:29 AM, freesurfer-requ...@nmr.mgh.harvard.edu wrote: > > Send Freesurfer mailing list submissions to >freesurfer@nmr.mgh.harvard.edu > > To subscribe or unsubscribe via the World Wide Web, visit >https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >

[Freesurfer] Questions about FreeSurfer

Dear FreeSurfers, I received FreeSurfer structural MRI brain data to analyze, but there are some questions about specific FreeSurfer variables that I could not find answered on your wiki or in the mail archive: 1.- "Non-White Matter hypointensities": 1.a - Are these the same thing as "gray

Re: [Freesurfer] Improving the brainmask.mgz using aseg.mgz for getting rid of dura

Hi Karteek the aseg isn't surface based, sorry, but the watershed that we use to do the skull stripping is and does use smoothness constraints. If it is leaving dura around try using mri_gcut. cheers Bruce On Thu, 18 May 2017, Karteek Popuri wrote: > Hi, > My goal is to use the best

Re: [Freesurfer] Improving the brainmask.mgz using aseg.mgz for getting rid of dura

You can use the aseg.mgz (in v6) or aparc+aseg.mgz in any version. On 05/18/2017 10:42 AM, Karteek Popuri wrote: > Hi, > My goal is to use the best possible skull-stripped version of the input MRI. > Is brainmask.mgz the one? or I was wondering if anyone has tried improving > the brainmask.mgz

[Freesurfer] Improving the brainmask.mgz using aseg.mgz for getting rid of dura

Hi, My goal is to use the best possible skull-stripped version of the input MRI. Is brainmask.mgz the one? or I was wondering if anyone has tried improving the brainmask.mgz further by masking it out using the aseg.mgz. Will that help with regards to getting rid of the dura in the

Re: [Freesurfer] mri_mcsim for individual subjects and references {Disarmed}

I don't know of a tool that would do it. I could imagine measuring the spatial autocorrelation function, then running the MC simulation using that instead of a gaussian (AFNI added this, but it only runs in the volume). Getting a particular ACF on the surface would be hard. On 05/16/2017

Re: [Freesurfer] Freesurfer white matter outer edge to volume

how were you examining the registration? When I run the command, the rh.white.mgz aligns perfectly with the T1.mgz On 05/16/2017 05:38 PM, Gamaliz wrote: > Douglas, > > The previous message had an images attached that seemed to be too big. > it was "bounced" automatically. I guess too many

Re: [Freesurfer] manuel edits

1. No, we usually do wm edits/control points first as this can fix the pial problems. 2. You can put control points in any voxel that is clearly WM with no other tissue class partial-volumed into it. The intensity threshold depends on the MR sequence, where you are in the brain and

Re: [Freesurfer] Mean gray-white contrast for each ROI

You will want the "Mean" column. The value is 100*(W-G) GWC = - 0.5*(W+G) The area is the surface area of the label. The "SNR" is the spatial mean gwc divided by the spatial stddev gwc, probably not very useful On 05/17/2017 01:43 PM, Yaakub, Siti

Re: [Freesurfer] Question of longitudinal processing

Hi Martin, Thanks a lot. So it is uncorrected. Can one use the following cmd to do multiple comparison correction? mri_glmfit-sim \ --glmdir lh.testretest.thickness-pc1.fwhm15 \ --cache 4 neg \ --cwp 0.05\ --2spaces I tried to run above cmd, it shows ERROR: thresh = 4,0, must be 1.3,

[Freesurfer] manuel edits

Dear FS team, I have two questions regarding manuel editing. We were looking at inter-rater reliability, but noticed it was not too high... However, during editing we used different criteria. Therefore I would like to ask: 1. Does the order of pial correction, topological deficit, wm

[Freesurfer] Postdoctoral position in psychosis studies - Oslo, Norway

Dear All, At the NORMENT – K.G. Jebsen Research Centre for Psychosis Research, a Centre of Excellence, Institute of Clinical Medicine, University of Oslo, Oslo University Hospital and Diakonhjemmet Hospital, Norway, there is a position available as a postdoctoral student with employment at

Re: [Freesurfer] LME : longitudinal correlations between imaging and cognition scores

Hi Martin, Thank you this helps ! Please find last question below inline. Best, Matthieu Le 18 mai 2017 10:33 AM, "Martin Reuter" a écrit : Hi Matthieu, 1) you would put a column of score and a column of score X time. The first allows you to test if the

Re: [Freesurfer] LME : longitudinal correlations between imaging and cognition scores

Hi Matthieu, 1) you would put a column of score and a column of score X time. The first allows you to test if the intercept changes based on scores (e.g. if hippocampal volume is affected by the score, controlling for whatever else you included, e.g. age and gender etc) and the second

Re: [Freesurfer] Question of longitudinal processing

Hi Jahanvi, there should be a way to display the bar, but I don’t know how (others will know)! sig is not FDR corrected. Best, Martin > On 18 May 2017, at 08:56, jahanvi patel wrote: > > Hi Martin, > > Thanks a lot for the reply. Is there a way to display the

Re: [Freesurfer] Question of longitudinal processing

Hi Martin, Thanks a lot for the reply. Is there a way to display the bar in effect size? And is this sig.mgh already statistically corrected? (FDR?) Best, Jahanvi On Thu, May 18, 2017 at 1:55 AM, Martin Reuter wrote: > Hi Jahanvi, > > I think red is positive (some