Re: [Freesurfer] T2pial correction options

External Email - Use Caution Re-posting to see if anyone has had this problem before and solutions they've implemented. > Hi Freesurfer team, > > We’re having some trouble with the T2pial option. We are currently getting > the Martinos Center ABCD project Tisdall/van der Kouwe

Re: [Freesurfer] Troubles to determine the type of recon editing needed

External Email - Use Caution Ok I will test it on normal subjects. Do I have to put this -bigventricles flag on all recon-all commands following manual editing of brainmask, white matter,...etc or just once at the first recon-all -all command ? Best, Matthieu Le mar. 18 sept.

Re: [Freesurfer] Troubles to determine the type of recon editing needed

I think it should be ok. It will be a bit slower, but shouldn't reduce accuracy I don't think. Try it and see Bruce On Tue, 18 Sep 2018, Matthieu Vanhoutte wrote: External Email - Use Caution Hi Bruce, Thanks, but in this case will recon-all with -bigventricles flag work

Re: [Freesurfer] Troubles to determine the type of recon editing needed

External Email - Use Caution Hi Bruce, Thanks, but in this case will recon-all with -bigventricles flag work well on normal patients without big ventricles ? Best, Matthieu 2018-09-18 15:56 GMT+00:00 Bruce Fischl : > Hi Matthieu > > yes, you will want to run all of your

Re: [Freesurfer] Troubles to determine the type of recon editing needed

Hi Matthieu yes, you will want to run all of your subjects with it cheers Bruce On Tue, 18 Sep 2018, Matthieu Vanhoutte wrote: External Email - Use Caution Dear Bram, It looks like the -bigventricles flag fixed my problem with my specific subject. Not only, this took

Re: [Freesurfer] Troubles to determine the type of recon editing needed

External Email - Use Caution Dear Bram, It looks like the -bigventricles flag fixed my problem with my specific subject. Not only, this took into account large ventricles but also corrected grey matter segmentation from extra Dura tissue that was erroneously segmented in GM. I

Re: [Freesurfer] mris_register problem

how much? Maybe we should expand the default range? I thought it was already pretty broad, but I haven't looked at it in a long time Glad to hear it worked out cheers Bruce On Tue, 18 Sep 2018, Chris Adamson wrote: External Email - Use Caution Thanks Bruce.   I had to

Re: [Freesurfer] How the resolution requirement was determined

Hi Jo the resolution requiirement is determined by cortical geometry. Once you get to about 2mm, you can no longer resolve the cortex in many places, and even worse you start losing the ability to resolve adjacent banks of a sulcus, resulting in topological catastrophes in the resulting

Re: [Freesurfer] Questions on multiple inputs

Most of FS/recon-all will run using the T1 only. The T2 can be used to refine the pial surface (-T2 T2file.mgz -T2pial) On 9/18/18 4:56 AM, limiyu wrote: External Email - Use Caution Dear developers I have a question on how could I segment two registered MRI images and get

[Freesurfer] 1-year position for an engineer to work in Parkinson, in the frontiers of imaging and machine learning (Bilbao, Spain)

External Email - Use Caution We are looking for an Engineer with skills in computer vision, programming and machine learning to collaborate in the research project entitled: "Study of the retina and the visual pathway by neuroimaging in genetic and aggressive idiopathic

[Freesurfer] Questions on multiple inputs

External Email - Use Caution Dear developers I have a question on how could I segment two registered MRI images and get only one segmentation result, by command recon-all ? In details, I have two MRI images which are T1-weighted and T2-weighted. They

Re: [Freesurfer] trac-all using nifti

Hi Heidi - The config file that you sent looked fine to me. What is the trac-all command line that you run, and do you get any other output (like a trac-all.log file)? Best, a.y From: freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Heidi Emmanuel Foo