[Freesurfer] Postdoc positions available at University of Sydney, Australia

Postdoctoral Scientist - Neurocardiovascular Disease and Depression *THE POSITION:* Interested postdoctoral applicants will be joining a dynamic and highly successful collaborative research program aimed at applying cutting edge neuroimaging technology. Our focus is on translating cutting edge

Re: [Freesurfer] Tracula Set: No Match

Hi Katherine - Can you please use the attached version and tell me if it works? You'll have to copy it into $FREESURFER_HOME/bin, to overwrite the version of xfmrot that you have now. If it works, we'll include it in the next version. Thanks! a.y From:

[Freesurfer] minor edits to aseg lead to exist with errors in about 25% of my scans

Dear FS Wiki I run my scan in FS without any problem example: #@#%# recon-all-run-time-hours 8.342 recon-all -s 877 finished without error then I do some edits to the aseg in freeview edits include: relabelling correctly lateral ventricles voxels mostly in the posterior horn of the

Re: [Freesurfer] Demeaning variables

1) Don't use DOSS in QDEC as it sometimes generates the wrong results. 2) Yes On 12/7/16 11:50 PM, Rodrigo Gonzalez Huerta wrote: Hey Doug, First, thanks for your previous answer, it helped me to clarify some issues. Lately, I’ve been doing what you suggested. But something just caught

Re: [Freesurfer] project 3D ROI onto flatmap

You will need a registration between the space where the ROIs are and the anatomical. We usually do this with bbregister, but you will need to identify a volume that is in the ROI space that has anatomical contrast so that the registration can be done (ie, dont use the ROI mask for

Re: [Freesurfer] correlation in mri glmfit controlling for 2 categorical variables and 1 continuous variable

Does this cover your situation? https://surfer.nmr.mgh.harvard.edu/fswiki/Fsgdf4G1V On 12/9/16 9:54 AM, Emmanuel Nwosu wrote: Hi All Am not sure if I can do this in mri glmfit I want to investigate the relationship between cortical thickness and a continuous variable (A) while accounting

Re: [Freesurfer] recon-all -s -localGI

Is matlab in your linux path? On my mac, I had to add this path to my linux path: /Applications/MATLAB_R2011b.app/bin/matlab On 12/13/16 11:16 AM, André Schmidt wrote: Many thanks for your help. According to your suggestion, I modified the start.up file in Users/andre/matlab/startup.m (see

Re: [Freesurfer] Label creation

Not that easy. I would do it by selecting a vertex that is close to the coordinate you want, then 1. Create a surface overlay with all vertices = 0 except your chosen vertex mri_volsynth --template $FREESURFER_HOME/fsaverage/surf/lh.thickness --delta vertexno 0 0 0 --o delta.mgh 2. Smooth

[Freesurfer] Label creation

Hi Freesurfer's experts Is there an easy way to create automatically a circular label with a radius centered on a vertex with predifined RAS/Tailarach coordinates on the fsaverage surface? Thanks Cris ___ Freesurfer mailing list

Re: [Freesurfer] question white matter

I believe they are mean and Gaussian curvature respectively. Cheers, Kevin Aquino > On 13 Dec 2016, at 17:23, tom parker wrote: > > Dear Freesurfers, > > Could anyone tell me what the white.H and white.K measures in Qdec are? > > Thank you so much! >

Re: [Freesurfer] question white matter

white.H is the mean curvature of the ?h.white surface and white.K is the Gaussian curvature cheers Bruce On Tue, 13 Dec 2016, tom parker wrote: > Dear Freesurfers, > > Could anyone tell me what the white.H and white.K measures in Qdec are? > > Thank you so much! > >

[Freesurfer] question white matter

Dear Freesurfers, Could anyone tell me what the white.H and white.K measures in Qdec are? Thank you so much! ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in

Re: [Freesurfer] recon-all -s -localGI

Many thanks for your help. According to your suggestion, I modified the start.up file in Users/andre/matlab/startup.m (see attached). However, I got the following error: Andres-MacBook-Pro:~ andre$ export FREESURFER_HOME=/Applications/freesurfer Andres-MacBook-Pro:~ andre$ source

Re: [Freesurfer] recon-all -s -localGI

The LGI routines run matlab (even though you never actually run any matlab commands yourself). But you have to make sure that matlab knows where the LGI matlab routines are. To do this you must modify your matlab ~/matlab/startup.m file to add the path to the LGI routines to your path. To do

[Freesurfer] recon-all -s -localGI

Dear experts I am trying to compute the local gyrification index but I am not sure how I have to do the following: "You will also need $FREESURFER_HOME/matlab in your matlab path set up in your ~/matlab/starup.m script." Can you please quickly help me what I need to type in the terminal to do

Re: [Freesurfer] Tracula Set: No Match

On Tue, Dec 13, 2016 at 8:34 AM, Yendiki, Anastasia < ayend...@mgh.harvard.edu> wrote: > Ok, if you also send me the first file, /media/Data/Temple/Temple_ > Tracula/31313422_10128/dmri/dwi.ecclog, I'll see if I can replicate the > error. > > -- > *From:*

Re: [Freesurfer] Tracula Set: No Match

Ok, if you also send me the first file, /media/Data/Temple/Temple_Tracula/31313422_10128/dmri/dwi.ecclog, I'll see if I can replicate the error. From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Katherine Damme

Re: [Freesurfer] Tracula Set: No Match

Yes. I immediately tried to enter the command in manually, checked the paths, and looked at the command manual for any format errors. [ksd770@katelinux Temple_Tracula]$ xfmrot /media/Data/Temple/Temple_Tracula/31313422_10128/dmri/dwi.ecclog

[Freesurfer] hard time with mris_pmake

Hi Freesurfer experts, I am new to freesurfer. I installed the last freesurfer version (freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0) and I am trying to compute the shortest cortical path between two sets of vertices. 1- Using the command mris_pmake updated If I understand correctly

Re: [Freesurfer] mris_apply_reg

here you go ... https://gate.nmr.mgh.harvard.edu/safelinks/greve/mris_apply_reg On 12/9/16 4:01 PM, Matthew Defenderfer wrote: Hi All, I am trying to mirror labels across hemispheres and found various threads using mris_apply_reg. Unfortunately the version of that command I have does not

Re: [Freesurfer] (no subject)

To get the t-score, compute the square root of the F, like fscalc F.mgh sqrt -o t.mgh You can then get the clusters with mri_surfcluster --in t.mgh --thmin t-threshold --sign sign --no-adjust --sum sumfile --ocn ocn.mgh ocn (output cluster number) will be a map with the custer number as the

Re: [Freesurfer] Odd Extremely High/Low Banding of Functional Values in Volume

sorry, I don't remember this case. please repost with our previous correspondence included On 12/12/16 5:40 PM, Dowling, Kevin Francis wrote: Hi Doug, Thank you for your note and my apologies for a delayed response. To create the sig.mgh file we used a volume specific mri_glmfit analysis,

Re: [Freesurfer] Freesurfer longitudinal analysis accuracy

Hello Gabor, a few quick comments: i) Although we typically aim for maximizing both, accuracy and reproducibility are different things. In a longitudinal study you are often particularly interested in the reproducibility of the findings, in the sense of their repeatability across different

Re: [Freesurfer] Freesurfer longitudinal analysis accuracy

I've found the article "Within-subject template estimation for unbiased longitudinal image analysis" by Reuter et al. It only examines a limited number of structures for the reproducibility of longitudinal Freesurfer. Are there any other paper that examines the cerebellum as well? Any suggestion