Re: [Freesurfer] High resolution GM/WM segmentation

2014-01-17 Thread Megha K.
Dear Nick and the Freesurfer team, We are following the pipeline “HiResRecon” to process our 0.7mm isotropic data. The pipeline completed without error but we cannot visualize the Grey/White matter segmentation using "-surfs”. The error messages is shown below: TM:~ Timwang$ tkmedit hires_3 brai

Re: [Freesurfer] Fwd: Control point failure - CA Normalize

2014-01-17 Thread Mark Plantz
I actually just tried to test the talairach.lta with this command: tkregister2 --mov $FREESURFER_HOME/average/RB_all_2008-03-26.gca \ --targ ../brainmask.mgz --lta-inv talairach.lta --reg talairach.lta.reg.dat \ --surfs --s $subject I seem to be getting an error that "--lta-inv is not an opti

Re: [Freesurfer] Fwd: Control point failure - CA Normalize

2014-01-17 Thread Bruce Fischl
see if the talairach.lta looks reasonable On Fri, 17 Jan 2014, Mark Plantz wrote: Hi Bruce,     The nu.mgz file looks OK to me (I also attached a picture). When I opened the talairach with "tkregister2" everything looked ok, except I couldn't get the green lines from the original surface to sho

Re: [Freesurfer] Desikan atlas in MNI space (in a nii file)?

2014-01-17 Thread Douglas N Greve
the aparc+aseg.mgz in fsaverage is in mni305 space. will that work? On 01/17/2014 01:29 PM, Fred Sampedro wrote: > Dear FreeSurfer users, > > I am searching for the Desikan atlas (which I have in the tailarach > space) in the MNI space, as a file (Desikan_mni.nii). I am aware that > transformi

[Freesurfer] Desikan atlas in MNI space (in a nii file)?

2014-01-17 Thread Fred Sampedro
Dear FreeSurfer users, I am searching for the Desikan atlas (which I have in the tailarach space) in the MNI space, as a file (Desikan_mni.nii). I am aware that transforming from one space to the other is not a very good idea but nevertheless I would like to test some computations. Anyone can att

Re: [Freesurfer] Fwd: xhemi correct for multiple comparisons

2014-01-17 Thread Douglas N Greve
There is still no difference between that and doing a regular thickness study with two groups. Were are you getting stuck? doug On 01/17/2014 12:35 PM, krista kelly wrote: > Hi Doug, > > Sorry I should have specified BETWEEN groups analyses. I have two > groups (control, patient) and I wanted

Re: [Freesurfer] Fwd: xhemi correct for multiple comparisons

2014-01-17 Thread krista kelly
Hi Doug, Sorry I should have specified BETWEEN groups analyses. I have two groups (control, patient) and I wanted to see if the hemisphere asymmetries (or laterality indices) differed between groups. Is there a way to do that? Thanks for all you help! Krista On Mon, Jan 13, 2014 at 6:25 PM, Dou

Re: [Freesurfer] V1.thresh

2014-01-17 Thread krista kelly
Thanks so much Louis! This was exactly what I was looking for. The Hinds et al. (2009) paper also has this info. On Thu, Jan 16, 2014 at 5:02 PM, Louis Nicholas Vinke < vi...@nmr.mgh.harvard.edu> wrote: > Hi Krista, > I believe the v?.thresh labels are thresholded at p=0.8. This threshold > is

Re: [Freesurfer] xyztrans error

2014-01-17 Thread Douglas N Greve
Hi Tessa, I don't know what nmrenv5 is. Is this one of your programs or your lab's? I would use stable53. The stable nightly is actually fairly unstable since we are updating "stable" for eventual release as a new stable. stable53 will not change. doug On 01/17/2014 10:47 AM, Tessa Vuper wr

Re: [Freesurfer] xyztrans error

2014-01-17 Thread Tessa Vuper
When I open the terminal, I type nmrenv5 --> setenv USE_STABLE_5_NIGHTLY --> nmrenv5 again. Should I be sourcing /usr/local/freesurfer/nmr-stable53-env instead? On Jan 16, 2014, at 1:14 PM, Douglas N Greve wrote: > > what file do you source to set up the env? > > > On 01/16/2014 01:12 PM, Tessa

Re: [Freesurfer] Standalone Freeview?

2014-01-17 Thread Louis Nicholas Vinke
Hi Jeni, Yes it's possible. You could download the most recent version of FS and then just source that version for when you want to use freeview, or copy the freeview.bin over to your current version. If you tell me the OS version you are running I'll send you the proper freeview.bin file. Ju

Re: [Freesurfer] aseg.stats vs. volumes in native T1 space

2014-01-17 Thread Douglas Greve
Try using mri_label2vol instead of mri_convert. mri_convert just does a mapping whereas mri_label2vol knows that this is a segmentation doug On 1/17/14 8:23 AM, Bruce Fischl wrote: > Hi Gabor > > the volumes must change with reslicing. As to why they get consistently > bigger in the hippocampus

Re: [Freesurfer] aseg.stats vs. volumes in native T1 space

2014-01-17 Thread Bruce Fischl
Hi Gabor the volumes must change with reslicing. As to why they get consistently bigger in the hippocampus I'm not sure, probably something to do with its geometry cheers Bruce On Fri, 17 Jan 2014, Gabor Perlaki wrote: > Dear all, > > I've run the freesurfer on 3 subjects and converted the as

[Freesurfer] aseg.stats vs. volumes in native T1 space

2014-01-17 Thread Gabor Perlaki
Dear all, I've run the freesurfer on 3 subjects and converted the aseg.mgz into *.nii.gz in the native space: "mri_convert -rl rawavg.mgz -rt nearest aseg.mgz aseg2raw.nii.gz" I've did a stats on left and right hippocampal volumes in the native space using fslstats: "fslstats aseg2raw.nii.gz -