Re: [Freesurfer] [FreeSurfer] Axis of Alignment

> On 08/11/2015 02:59 PM, Bruce Fischl wrote: >> Ruopeng should be able to help you out >> >> cheers >> Bruce >> On Tue, 11 Aug 2015, fmri wrote: >> >>> Is there a wiki instruction block on how to reorient all volumes? >>> >>> Thanks >>

Re: [Freesurfer] Hippocampus in WM region, Unknown voxels still persist

I have tried the ftp transfer method, with a file as small as 4KB and one as large ass 295MB error out put; ftp> put /Users/fmri/Studies/FreeSurferMRIs/5235/5235bem.zip local: /Users/fmri/Studies/FreeSurferMRIs/5235/5235bem.zip remote: /Users/fmri/Studies/FreeSurferMRIs/5235/5235bem.zip

Re: [Freesurfer] [FreeSurfer] Aseg.mgz not reflected on aparc+aseg.mgz

> On 9/1/15 8:11 PM, fmri wrote: >> Thank You Much Buddy >> >> That did it :) , Manual edits to aseg.mgz reflected onto aparc+aseg.mgz. >> >> Just to clarify; >> >> Is this the correct order? >> >> 1. manual edit aseg.mgz >> >

Re: [Freesurfer] [FreeSurfer] Aseg.mgz not reflected on aparc+aseg.mgz

:45 AM, Douglas Greve wrote: > > Try running > > mri_aparc2aseg --s subject --volmask > > > On 8/31/15 10:51 PM, fmri wrote: >> after several attempts with multiple subjects >> >> command -autorecon2-noaseg -subjid mysubject >> >> follow

Re: [Freesurfer] [FreeSurfer] Aseg.mgz not reflected on aparc+aseg.mgz

after several attempts with multiple subjects command -autorecon2-noaseg -subjid mysubject followed by command recon-all -aparc2aseg aseg.mgz edits, are Not reflected onto the aparc+aseg.mgz On Aug 25, 2015, at 2:05 PM, Douglas N Greve wrote: > yes > > On 08/25/2015 01:11 PM, f

Re: [Freesurfer] Hippocampus in WM region, Unknown voxels still persist

; Bruce > On > Tue, 25 Aug 2015, fmri wrote: > >> I have already processed 88 subjects in this version, >> >> would it matter if I process or re-process subjects with another version? >> >> >> On Aug 25, 2015, at 3:44 PM, Bruce Fischl wrote: >> &

Re: [Freesurfer] Hippocampus in WM region, Unknown voxels still persist

5, at 3:45 PM, Douglas N Greve wrote: > The non-labeled voxels in the aparc+aseg near hippocampus. I think the > resolution was that they were labeled as cortex in the aseg but as > "unknown" in the aparc, so they get labeled as "unkown" in the > aparc+aseg (since

Re: [Freesurfer] Hippocampus in WM region, Unknown voxels still persist

what version should I try? On Aug 26, 2015, at 7:06 AM, Bruce Fischl wrote: > it would fix the hippocampal problems and maybe the cortical ones as well > > cheers > Bruce > On > Tue, 25 Aug 2015, fmri wrote: > >> I have already processed 88 subjects in this version

Re: [Freesurfer] Hippocampus in WM region, Unknown voxels still persist

abbing a new dev version and see if it improves. > Doug: has the new atlas been put into the dev recon-all? I think it has, > hasn't it? > > On Tue, 25 Aug 2015, fmri wrote: > >> Version >> >> freesurfer-Darwin-lion-dev-20150701 >> >>

Re: [Freesurfer] Hippocampus in WM region, Unknown voxels still persist

sorry, what was ? On Aug 25, 2015, at 3:18 PM, Douglas N Greve wrote: > wasn't this brought up on the list a few weeks back? > > On 08/25/2015 06:08 PM, fmri wrote: >> Dear Freesurfer experts, >> >> on aparc+aseg.mgz there is Hippocampus labeled over WM

Re: [Freesurfer] Hippocampus in WM region, Unknown voxels still persist

ght be dura > cheers > Bruce > > > On Tue, 25 Aug 2015, fmri wrote: > >> Dear Freesurfer experts, >> >> on aparc+aseg.mgz there is Hippocampus labeled over WM regions. >> >> There are cortex "Unknown" voxels that persist through out

Re: [Freesurfer] [FreeSurfer] Aseg.mgz not reflected on aparc+aseg.mgz

Should we run this after recon-all autorecon2-noaseg -subjid ? On Aug 25, 2015, at 7:43 AM, Douglas Greve wrote: > Run recon-all -aparc2aseg > > On 8/24/15 7:00 PM, fmri wrote: >> Hello FreeSurfer, >> >> How do I get edits made on aseg.mgz to reflect onto the ap

[Freesurfer] [FreeSurfer] Aseg.mgz not reflected on aparc+aseg.mgz

Hello FreeSurfer, How do I get edits made on aseg.mgz to reflect onto the aparc+aseg.mgz? I have tried the recon-all -autorecon2-noaseg -subjid mysubject but the aparc+aseg.mgz is not created. Afterward I ran recon-all -autorecon3 -subjid mysubject this erased my edits to aseg and gave me the

Re: [Freesurfer] [FreeSurfer] Axis of Alignment

umes in > freeview if you wanted, but I don't think it's necessary > > cheers > Bruce > > > On Mon, 10 Aug 2015, fmri wrote: > >> Hello FreeSurfer experts, >> >> When MRI slices are not aligned to a more perfect plane of axis as shown

[Freesurfer] Optseq optimizing event design

Dear Prof Douglas, I asked this before but I would like to understand what I am doing and also need your recommendation. I have three conditions : squeezes at three different levels. My aim is that I want to use spm to enter them as a one condition and then enter the parametric response as a c

[Freesurfer] Installing optseq2!!

Hi all, I am trying to install optseq2 in my own laptop. I have linux installed as a virtual window. I am sorry but I really do not have any idea how I should install it after downloading the file. I am new to linux! Any guide please, Thanks AS ___

[Freesurfer] OptSeq first time

Hello all, This is my first question in this list and it is about OptSeq2. I am nee to this command. In brief, I wish to insert the following but Some of them I could not handle it: My experiment has three conditions although I will later specify them as one condition: Moving hand at three d