[Freesurfer] using custom templates

Greetings, I have generated custom surface templates from pediatric data sets. To apply it to the larger data set, is it sufficient to simply run the autorecon3 steps (perhaps skipping the mris_sphere step)? If so, is there a handy flag for running this with recon-all and/or a way to run autorecon3

Re: [Freesurfer] using custom templates

obably have to edit the recon-all script. And > by template do you just mean the folding pattern .tif files, or do you > meant the parcellation atlases (*.gcs)? > > cheers > Bruce > On Thu, 5 Mar 2015, Jason Tourville > wrote: > > > Greetings, > > I have generate

Re: [Freesurfer] using custom templates

t; > > On 03/05/2015 03:18 PM, Bruce Fischl wrote: > > Hi Jason > > > > I don't think so - you'll probably have to edit the recon-all script. And > > by template do you just mean the folding pattern .tif files, or do you > > meant the parcellation atlas

Re: [Freesurfer] using custom templates

On Thu, Mar 5, 2015 at 3:58 PM, Douglas N Greve wrote: > The mris_register command is what does the registration and creates a > new sphere.reg file. surfreg just implements that command mris_register > command. > > I'm not sure what you mean by the labeling steps. > >

[Freesurfer] latest freeview

Hi there, Looking over the freeview development page, it looks like there are some (relatively) new features that would come in handy. Could I get a link to download the latest freeview beta? Thanks, Jason -- Jason A. Tourville, Ph.D. Research Assistant Professor Department of Speech, Language,

[Freesurfer] local intensity inhomogeneity

Hello freesurfers, We've seen some poor surface reconstructions due to local inhomogeneities that remain in the brainmask volume. We see omission of significant portions of brain tissue due to signal fall off (both gray and white voxels are darker than in surrounding area) that we are unable to cur

[Freesurfer] restoring wm.mgz

Hi there, I'm working on a project in which I manually "erased" voxels (changed to '1') in the optic chiasm region in the wm.mgz and brainmask.mgz. This was done to eliminate those voxels from the surface reconstructions. We've since realized that this isn't necessary...our results are largely unaf

[Freesurfer] tksurfer command for saving multiple view tiff

Is there a command for the "saving multiple views as TIFFs" function in tksurfer that can be used in a TCL script? Thanks, Jason -- Jason A. Tourville, Ph.D. Research Assistant Professor Department of Speech, Language, and Hearing Sciences Boston University 677 Beacon St. Boston, MA 02215 Phone:

[Freesurfer] surface repositioning tool documentation

Hi, Is there documentation for the use of freeview's surface repositioning tool? Including the recon-all steps that should be rerun to ensure that the surface edits are reflected in the surface stats? Are edits made with this tool applied to future runs through the recon-all process (like pial and

[Freesurfer] norm2b, norm2n

Greetings, I am working with pediatric data and have some early evidence that running recon-all with the flag -norm2-b 20 -norm2-n 5 improves the anterior temporal lobe segmention as suggested in the v5.2 release notes (I am running this with v5.3). I'd like to experiment more with this parameters

[Freesurfer] -3T and -mprage flags

Hi there, I am working on a project that involves pediatric data, ages 3-12. We are using Freesurfer to generate cortical surfaces. Information regarding the T1 acquisition is listed below. Is it appropriate to use the -3T and mprage flags for such data? Is there an alternative, pediatric atlas, t

[Freesurfer] optimal T1 protocol

Hello freesurfer experts, Do you have a recommended "optimal" T1 protocol on Bay 1 for cortical reconstruction? For the past couple years, we've been using the 'tf1_mgh_multiecho_1mm_iso" protocol which has PAT = 2 and a TA = 6:02. 􀀈􀀎 I'm wondering if a faster option at the same resolution is no

[Freesurfer] pial surface midline fix

Hi, I've encountered a recon-all'ed scan in which the pial surface along the posterior midline "jumps" on cortex in the opposite hemisphere. Is there a simple fix for this, perhaps using a hemisphere mask? Thanks, Jason -- Jason A. Tourville, Ph.D. Research Assistant Professor Department of Spee

[Freesurfer] freeview surface vertex point save?

Hi there, The tksurfer/tkmedit combo allowed one to select and save a point on the inflated surface and then go to that point in the volume. Does freeview have a similar capability? Thanks, Jason -- Jason A. Tourville, Ph.D. Research Assistant Professor Department of Speech, Language, and Hearin

[Freesurfer] freeview save error

Hi there, Occassionally when using the "save volume" function from the gui to save edits made to the wm.mgz, freeview crashes (see command line error report below) and the wm.mgz being deleted from subject's 'mri' directory (the temp wm.mgz~ is still present...but all edits are lost). I am running

[Freesurfer] recon-all after manual edits

Hi there, I am doing manual edits on the brainmask.mgz, wm.mgz, and brain.finalsurfs.manedit.mgz volumes and adding control points. What autorecon flag or from which stage of processing should I rerun recon-all such that all of these manual edits are respected? Thanks, Jason -- Jason A. Tourvill

[Freesurfer] preserve manual edits?

Hi there, We have performed manual volume edits on a number of scans. Recently, we ran those scans through recon-all with a new Tal volume target. The seg and surfaces are improved using the new target but most of the manual edits performed on the earlier version would improve the surfaces. Is ther

Re: [Freesurfer] preserve manual edits?

Hi Bruce, I used Freeview to edit the brainmask.mgz, wm.mgz, and brain.finalsurfs.manedit.mgz volumes. Cheers, Jason On Fri, Jul 25, 2014 at 9:23 PM, Bruce Fischl wrote: > Hi Jason. > How were the edits done? > Cheers > Bruce > > > On Jul 25, 2014, at 10:40 AM, J

Re: [Freesurfer] preserve manual edits?

ed to use 1 for "off" > and 255 for "on", otherwise we can't track them. > > cheers > Bruce > On Mon, 28 Jul 2014, Jason Tourville wrote: > > Hi Bruce,I used Freeview to edit the brainmask.mgz, wm.mgz, and >> >> brain.finalsurfs.manedit.mgz vo

Re: [Freesurfer] preserve manual edits?

h? Or you > could just copy the whole directory, and rerun recon-all -all on the new > directory and it should recreate everything while preserving edits > > > cheers > Bruce > > On Mon, 28 Jul 2014, Jason Tourville wrote: > > Hi Bruce,Used v5.3 for original edits u

[Freesurfer] surface template construction

We are planning to generate a surface template from edited reconstructions of pediatric cortical surfaces (ages 3-11). We plan use this template for surface coregistration of a large pediatric dataset that we're accruing of roughly the same age range. I.e., we aren't simply trying to generate a tem

[Freesurfer] surface template N

We are planning to generate a surface template from edited reconstructions of pediatric cortical surfaces (ages 3-11). Any thoughts on the minimum number of subjects should be used to generate the template? Thanks, Jason -- Jason A. Tourville, Ph.D. Research Assistant Professor Department of Sp

Re: [Freesurfer] surface template N

t; cheers > Bruce > > > > > On Thu, 18 Dec 2014, Jason Tourville wrote: > > > We are planning to generate a surface template from edited > reconstructions > > of pediatric cortical surfaces (ages 3-11). Any thoughts on the minimum > > number of

Re: [Freesurfer] surface template N

ates a bunch of other useful things (average > volumes and asegs and such), so I would use it > > cheers > Bruce > > On Fri, 19 Dec 2014, Jason Tourville wrote: > > > Thanks for the feedback. We may have sufficient numbers for binning. > > > > Regarding t

[Freesurfer] using custom surface template

External Email - Use Caution Hello FreeSurfers, We use a custom surface template, generated according to the instructions in the SurfaceRegAndTemplates instructions for inter-subject co-registration. We then do cort

Re: [Freesurfer] using custom surface template

an just run your own posthoc? > > cheers > Bruce > > > On Wed, 19 Dec 2018, Jason Tourville wrote: > > > > > External Email - Use Caution > > > > Hello FreeSurfers,We use a custom surface template, generated according > to the instructions

Re: [Freesurfer] DKT vs. DK Freesurfer atlases

curvature. The boundary definitions were also made less ambiguous, making it easier to apply them in the training dataset more consistently. Jason Tourville On Thu, Jun 15, 2017 at 5:15 AM Gabor Perlaki wrote: > Dear all, > > > I've found an article comparing DK and DKT atla

[Freesurfer] Custom templates and longitudinal processing

External Email - Use Caution Hi Freesurfers, We are collaborating with a group at Michigan that planss to use Freesurfer's longitudinal pipeline to process T1 data collected from children (see brief project summary below) at multiple time points. Our role is to oversee recon QA an

[Freesurfer] VGL error

Hello FreeSurferers, I run tksurfer remotely from a linux machine running CentOS (Boston University) using Virtual GL/TurboVNC. I have been able to do this successfully for years but have recently encountered the following error when calling tksurfer: surfer: tkoInitWindow(RMAUT015) [VGL] ERROR:

[Freesurfer] FreeSurfer ROI masks for DTI tractograpy

Hi FreeSurfers, I would like to use cortical surface ROIs generated in FreeSurfer to perform inter-regional WM tractography using FSL's probtrackx tool. My understanding is that start seeds and targest are typically defined by mapping the labeled gray-white surface to the DTI volume. I.e., voxels

[Freesurfer] FreeSurfer ROI masks for DTI tractograpy

Hi FreeSurfers, I would like to use cortical surface ROIs generated in FreeSurfer to perform inter-regional WM tractography using FSL's probtrackx tool. My understanding is that start seeds and targest are typically defined by mapping the labeled gray-white surface to the DTI volume. I.e., voxels

[Freesurfer] surface label generation from vertex?

External Email - Use Caution Hi Freesurfers, I would like to generate a label that extends some distance from a chosen vertex on the surface. Is this possible in the freeview gui? Otherwise? Many thanks for you feedback. Best, Jason ___