[Freesurfer] make movies of non eeg/meg temporal data ?

2014-09-30 Thread Gregory Kirk
I would like to make a movie of the temporal evolution of data on the cortical surface from something im doing. similar to what mne_make_movie does, but it's not eeg/meg data. is there a way to make and display movies of data in tksurfer or freeview ? or i guess i could `trick` mne and display m

[Freesurfer] Can't set values in tksurfer "Phase encoded data display" window

2014-09-30 Thread Andre Salles Cunha Peres
Hello, I'm working with retinotopic maps, and how my experiments was with polar stimulus I want to change the angle cycles to 2 in tksurfer, however it is impossible to change the values in the "Phase encoded data display" window (View>Configure>Phase encoded data display). I can select the t

[Freesurfer] Two questions: 1. Regarding ASEG and reduced FOV; 2. Regarding ventral diencephalon contents

2014-09-30 Thread Matthew Sacchet
Hi all, I was hoping to gain insight regarding two questions associated with the use of FreeSurfer's aseg (Fischl, Neuron 2002): 1. I have been using aseg to assess volumetric differences across populations. For one of our individuals a portion of the right hemisphere was not fully collected. The

[Freesurfer] Problems with manual grey matter editing

2014-09-30 Thread Zamroziewicz, Marta Karolina
Hello, We have some reconstructions with a significant amount of grey matter excluded in the temporal cortex and are having problems using manual voxel editing to fix this. Our correction process for brain tissue that wasn’t included in the pial/white matter outlines has been as follows: 1. Whe

Re: [Freesurfer] bbregister for MRA

2014-09-30 Thread Douglas N Greve
Did you stick with the pial surface or change it to white? On 09/30/2014 02:05 PM, SHAHIN NASR wrote: > For the record, I applied two changes: > > 1) I used my AAScout scan as --int and it worked. > 2) As you suggested I also used --t2 rather than --t1 this time and it > also helped. > > Combinati

Re: [Freesurfer] pial surface crossing white

2014-09-30 Thread Harms, Michael
Yeah, the time stamps look fine, and the euler numbers are correct. I've uploaded the pre-edited (L408_base_orig.tgz) and edited (L408_base.tgz) directories. This was related to the creation of a 'base' template, so the commands are a little bit involved.  For the "L408_base_orig" set of

Re: [Freesurfer] bbregister for MRA

2014-09-30 Thread SHAHIN NASR
For the record, I applied two changes: 1) I used my AAScout scan as --int and it worked. 2) As you suggested I also used --t2 rather than --t1 this time and it also helped. Combination of these two changes worked very well. Thanks On Tue, Sep 30, 2014 at 1:11 PM, Douglas N Greve wrote: > > A

Re: [Freesurfer] Righty and left hemispheric white matter volume

2014-09-30 Thread Douglas N Greve
Yes! On 09/30/2014 01:13 PM, Alshikho, Mohamad J. wrote: > > Dear FS Experts, > > I am beginner in FS and I need you precious advice… > > In order to compare the volume of the right and left hemispheric white > matter in my dataset (29 controls 23 patients). I did recon_all for my > T1 data then

[Freesurfer] Righty and left hemispheric white matter volume

2014-09-30 Thread Alshikho, Mohamad J.
Dear FS Experts, I am beginner in FS and I need you precious advice... In order to compare the volume of the right and left hemispheric white matter in my dataset (29 controls 23 patients). I did recon_all for my T1 data then I used the volume of the Left and right cerebral white matter which a

Re: [Freesurfer] bbregister for MRA

2014-09-30 Thread Douglas N Greve
A couple of suggestions ... It looks like the new sequence is T2 weighted, so you can try using --t2 with the white surface It may be that the fsl is not initializing the BBR registration properly. Try using spm (which may still fail because it is partial brain coverage). Do you have a whole-

Re: [Freesurfer] Out of memory error on mri_cvs_register

2014-09-30 Thread Lilla Zollei
Hi Mohammadi-Nejad, The creation of the non-linear deformation field will require more memory than what you currently have and that is causing the problem. Is there any way you can assign twice (or at least 1.5x) as much memory to this process as you are currently using? Lilla On Mon, 29 S

Re: [Freesurfer] bbregister for MRA

2014-09-30 Thread SHAHIN NASR
Hi Doug, Sorry for interrupting you again with this topic but recently we changed couple of parameters in our MRA to increase our chance or detecting veins. The problem is that, bbregister can not register the MRA volume to T1 scans anymore. As an example, here you can see the old version

Re: [Freesurfer] Overclocking CPU for Freesurfer

2014-09-30 Thread Jonca, Jacek
As Matt pointed out for as long as you achieve a stable overclock and have ample cooling for the CPU and memory freesurfer (and any other programs) will run just fine. I used to run subjects on Intel Q6600 overclocked from 2.8ghz to 3.4ghz with a push-pull cooling solution and had no problems.

Re: [Freesurfer] LME Models

2014-09-30 Thread jorge luis
Hi Karishma The Matlab LME toolbox is only intended for univariate and mass-univariate analyses and not for multivariate analysis. However the recently developed spatiotemporal model can be modified to work with multivariate data (instead of regions of voxels there will be multiple variables a