Re: [Freesurfer] 001 vs brainmask views in freeview

External Email - Use Caution Thanks for info. If I open only the brainmsk.mgz only from a new terminal it is rotated and not in its native orientation (which is 001's orientation). Why does it not appear to be in native space in freeview? Jim From:

[Freesurfer] 001 vs brainmask views in freeview

External Email - Use Caution Hi all, I ran a 2yo subject through FS6.0 using 'recon-all -i /firstdicom.dcm -all' and the output segmentations and surfaces looks good. Can someone explain why I see different alignments when I view the 001.mgz and brainmask.mgz files in

Re: [Freesurfer] 001 vs brainmask views in freeview

Hi, When you load brainmask.mgz as the second volume, it will be realigned to 001.mgz. The default resample method is nearest-neighbor. Thus you get the blocky look. You can try loading it with trilinear or cubic resampling like this from the command-line: freeview -v 001.mgz brainmask.mgz

Re: [Freesurfer] mkcontrast-sess question

Hi Freesurferers I appreciate if anyone could give me their thoughts on this question. Thanks Mona Zahra (Mona) Nasiriavanaki Postdoctoral Research Fellow Martinos Center for Biomedical Imaging Massachusetts General Hospital 149 13th Street, 149-2615 Charlestown, MA, USA, 02129

[Freesurfer] Freeview error

External Email - Use Caution Dear Freesurfer devs, I tried to open the brainmask.mgz file in freeview but I obtained this error: mghRead(/usr/local/freesurfer/subjects/4227/mri/brainmask.mgz, -1): could not open file MRIread failed: Unable to read from

Re: [Freesurfer] Longitudinal stream finalsurfs misalignment?

External Email - Use Caution Hey Martin, Sounds like a logical approach. I'll give it a try and let you know how it ends up. I am using version 6.0 by the way. Thanks, Doug -Original Message- From: Martin Reuter Sent: Monday, September 16, 2019 2:39 AM To:

Re: [Freesurfer] Freeview error

External Email - Use Caution Dear Ruopeng, I put that command in the freeview command console and this is the output [FreeView] ls /usr/local/freesurfer/subjects/4227/mri/brainmask.mgz This is not a shell. Only freeview commands are supported. Type '-h' for all the available

Re: [Freesurfer] 001 vs brainmask views in freeview

Yes, these two volume are aligned. But they are sliced differently. When you display a single volume alone in freeview, it is by default displayed in its native slice orientation. Ruopeng On 9/16/19 3:39 PM, Alexopoulos, Dimitrios wrote: External Email - Use Caution I’m still a

[Freesurfer] Hippocampal and Amygdala Segmentation Error - Incorrect Path and Missing Files

External Email - Use Caution To whom it may concern, I am attempting to run the hippocampal and amygdala segmentation (https://surfer.nmr.mgh.harvard.edu/fswiki/HippocampalSubfieldsAndNucleiOfAmygdala) on the development version of FreeSurfer. However, I am running into a

Re: [Freesurfer] 001 vs brainmask views in freeview

The first volume is always displayed in its original orientation where pixel data are stored. So that the pixel data don't get resampled (unless you force it with '-r' flag to resample it in standard RAS). Ruopeng On 9/16/19 1:06 PM, Alexopoulos, Dimitrios wrote: External Email -

Re: [Freesurfer] 001 vs brainmask views in freeview

External Email - Use Caution I'm still a little confused. When I open up the brainmask.mgz in freeview I see the following. It is rotated compared to the native 001.mgz below. [cid:image002.jpg@01D56C9C.9A38CF50] I then open the 001.mgz with freeview in a NEW terminal

Re: [Freesurfer] Questions about labels and tkmedit

Not that I know of, it is pretty limited. On 9/13/19 11:13 AM, Zeng,Victor (BIDMC - Psychiatry) wrote: Hi all, ​ I know tkmedit has been deprecated, but we're thinking about using it just for quality check purposes since we found that it is less resource intensive. We're trying to load

Re: [Freesurfer] mkcontrast-sess question

Are you trying to do a parametric analysis? See https://surfer.nmr.mgh.harvard.edu/fswiki/FsFastParametricModulation On 9/13/19 11:08 AM, Nasiriavanaki, Zahra wrote: Dear Freesurfer experts Hi I have a question about weighting different contrasts using mkcontrast-sess commmand. I have single

Re: [Freesurfer] Freeview error

Can you run the command in the command window that you start freeview? Ruopeng > On Sep 16, 2019, at 5:11 PM, Miguel Ángel Rivas Fernández > wrote: > > External Email - Use Caution > > > Dear Ruopeng, > > I put that command in the freeview command console and this is the

Re: [Freesurfer] Extract ThickAvg ThickStd from rh/lh.aparc.stats of a specific structure for group of subjects

You can use a PARCSFILE. Run aparcstats2table with --help to get more info On 9/14/19 3:30 PM, vin rasa wrote: External Email - Use Caution Dear Freesurfer experts, Is there a shortcut to extract mean thickness(ThickAvg) and std (ThickStd) from rh/lh.aparc.stats for let's say 4

Re: [Freesurfer] Longitudinal stream finalsurfs misalignment?

Hi Doug, probably something went wrong during the editing. E.g maybe you edited files in the cross sectional or base directories and copied/saved these to the longitudinals or vice-verca. There should be no mis-alignments. I would recommend this: 1. run one such subjects without edits through