[Freesurfer] Transformation between individual subject and FsAverage

Dear Experts, if functional volume data are mapped to cortical surfaces, using mri_vol2surf and FsAverage as the target surface, a surface registration is carried out. As far as I can see the program surfreg does the surface registration. In this registration the cortical maps of the individual

[Freesurfer] missing files in fsaverage folder

Dear Freesurfer Experts, is there an easy way to update only folders within the Freesurfer folder? Accidentally, I deleted the fsaverage folder from the Freesurfer version. I copied the fsaverage folder from another Freesurfer installation. But seemingly some essential files (e.g. perirhinal la

[Freesurfer] Fully funded PhD studentship at Durham University

Dear colleagues, Applications are invited for a fully funded PhD position (3 years) in the Department of Psychology at Durham University. The successful applicant will work with Paige Scalf in the Centre for Vision and Visual Cognition (CVVC) on the neural processes underlying vision, attention an

Re: [Freesurfer] recon2 processing appears to be stuck

Hi Noreen look at the orig.nofix or the inflated.nofix and see if there is a giant defect caused by something like a spurious attachment between wm and the skull or cerebellum. If so, you'll need to correct this manually either by editing the wm.mgz or adding control points cheers Bruce On

Re: [Freesurfer] Transformation between individual subject and FsAverage

It is done by a nonlinear morph (encoded by ?h.sphere.reg). Not a simple matrix. doug On 04/22/2015 03:01 AM, pfannmo...@uni-greifswald.de wrote: > Dear Experts, > > if functional volume data are mapped to cortical surfaces, using mri_vol2surf > and FsAverage as the target surface, a surface reg

Re: [Freesurfer] missing files in fsaverage folder

On 04/22/2015 04:27 AM, Milde, Christopher wrote: > > Dear Freesurfer Experts, > > is there an easy way to update only folders within the Freesurfer > folder? Accidentally, I deleted the fsaverage folder from the > Freesurfer version. I copied the fsaverage folder from another > Freesurfer ins

Re: [Freesurfer] QDEC failed due to missing files

You need to run recon-all -s subject -qcache doug On 04/21/2015 06:34 PM, Manish Dalwani wrote: > Hello Freesurfers, > > In the past I have been able to run QDEC v 4.5 on images without any > problem. Recently I ran recon-all on some new set of images. I was > able to run the regression analyses

[Freesurfer] Generate patch files outside of tksurfer

Hi Freesurfers, Is there a way to generate patch files from surfaces outside of tksurfer? I'm specifically hoping that there is some tool that will allow me to use a label file to define the part of the surface I want to keep as a patch. Thanks! Michael ___

Re: [Freesurfer] Optseq2: efficiency and vrf

On 04/21/2015 03:26 PM, Dan Goldman wrote: > Thanks for this. I should be more clear. The reasoning and figures > tasks are completely separate and are not being compared to each > other. Each task has two conditions. For example, in the reasoning > task, I have two conditions: Spatial and

[Freesurfer] tkmedit neuroscience format

Dear freesurfer experts. is it possible for tkmedit to display volumes in neuroscience format (R is R) rather than radiologic format (R is L)?" Thanks Jon ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mai

Re: [Freesurfer] tkmedit neuroscience format

no, sorry On 04/22/2015 12:25 PM, Jon Alan Wieser wrote: > > Dear freesurfer experts. > > is it possible for tkmedit to display volumes in neuroscience format > (R is R) rather than radiologic format (R is L)?" > > Thanks > > Jon > > > > ___ > Freesurf

Re: [Freesurfer] QDEC failed due to missing files

Thank you Doug! Manish From: Douglas N Greve To: freesurfer@nmr.mgh.harvard.edu Sent: Wednesday, April 22, 2015 8:58 AM Subject: Re: [Freesurfer] QDEC failed due to missing files You need to run recon-all -s subject -qcache doug On 04/21/2015 06:34 PM, Manish Dalwani wrote: > Hel

[Freesurfer] Kurtosis and Skewness

Hi FS experts, I was wondering whether there is a tool to measure the kurtosis and skewness of an ROI. (For instance would the mri_kurtosis.m script under the FS home directory be the best option for the measurement of kurtosis?) Thanks in advance, Panos __

Re: [Freesurfer] Kurtosis and Skewness

Yes. I've attached mri_skew.m as well. There are several ways to estimate kurtosis, make sure mri_kurtosis is doing what you want. On 04/22/2015 01:48 PM, pfot...@nmr.mgh.harvard.edu wrote: Hi FS experts, I was wondering whether there is a tool to measure the kurtosis and skewness of an ROI. (

Re: [Freesurfer] TRACULA: drmirc parameteres with already processed and registered data

Hello, I am interested in using TRACULA for my data, but I have a few questions about modifying the dmrirc configuration file. I have already conducted eddycorrect, bet, and dtifit in FSL, registration of T1 and dti using ANTs, and I have also registered individual subject data to a templat

[Freesurfer] low signal/noise

Hi all, I am attempting to process some 4T images that have a pretty bad signal/noise ratio. When running autorecon 1, Freesurfer has gotten stuck on this step: mris_fix_topology -mgz -sphere qsphere.nofix -ga -seed 1234 silvj001a rh I am seeing that "125 defects to be corrected” and freesurf

[Freesurfer] optseq2 source code

Hi, Is it possible to get the source for optseq2. I would like to translate it into python to integrate it into my existing scripts, and also modify the output files to include csv output options, instead of writing post hoc scripts to change the output. Thank you, Patrick _

[Freesurfer] TRACULA -stat flag

Hi Anastasia, I am trying to run the command trac-all with the flag -stat as mentioned in wiki (https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/TraculaStatistics) but I am receiving and ERROR message that this flag unrecognized. Any suggestions please. Mohamad

Re: [Freesurfer] TRACULA -stat flag

Hi Mohamad, Did you download the Tracula update from May 2014? It is available here: https://surfer.nmr.mgh.harvard.edu/fswiki/Tracula Untar this, and move the files to your $FREESURFER_HOME/bin directory (this will overwrite the old versions). This should provide the -stat flaf. Best, Lee O

Re: [Freesurfer] TRACULA -stat flag

Hi Lee, Thank you. But I don't have permissions to overwrite files on the cluster. I am already using Freesurfer 5.3 -Original Message- From: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Lee Tirrell Sent: Wednesday, April 22, 2015 5

Re: [Freesurfer] optseq2 source code

yes, it is available with the FreeSurfer source code, which you can download doug On 04/22/2015 04:30 PM, Patrick Beukema wrote: > Hi, > Is it possible to get the source for optseq2. I would like to > translate it into python to integrate it into my existing scripts, and > also modify the output

Re: [Freesurfer] where to start recon-all after edits

Repost.Thanks. On Mon, 20 Apr 2015 16:35:29 -0700 wrote Thank you again for your reply. For editing aseg.mgz, as mentioned in https://surfer.nmr.mgh.harvard.edu/fswiki/TkMeditGuide/TkMeditWorkingWithData/FreeviewSegmentations it does suggest using -autorecon2-no

Re: [Freesurfer] Edits to longitudinal pial surface and aseg

Repost.Thanks. On Mon, 20 Apr 2015 16:21:38 -0700 wrote Thank you for your reply. Yes, I'm finding that it is only small edits that are required in the Long for the case of pial surface errors. It is usually in areas where no editing was required in the cross and

Re: [Freesurfer] crossing medial surfaces

Hi Clara,   The method for dealing with the crossing medial surfaces that works for me is decribed in the email below. Though, I'm not sure if there are any issues or concerns with this approach particularly in regard to thickness or the segmentations.   Paul     Sent: Tuesday, October 22,

[Freesurfer] Research Assistant II (Non-Clinical) Position - Reposted

Please repost this position for us. Thank you. *Research Assistant II (Non-Clinical) Position* *Primary responsibilities include: * - Conducts research data activities, under general direction of a Principal Investigator and/or Senior Research staff. - Ability to assist in analyzing research d

[Freesurfer] Dialogs go behind freeview

Dear all, Hi, When i open freeview the images at the center of the screen dont let me see an opne dialog, for example when i want to add surface, the opening dialog go behind them and i cant access the dialog. Kind Regards ___ Freesurfer mailing list Fr