[Freesurfer] Fsaverage for ROI analysis of children

Hello all, I have been conducting an ROI analysis and following the cortical thickness ROI tutorial found here: https://surfer.nmr.mgh.harvard.edu/fswiki/VolumeRoiCorticalThickness. After going through this tutorial with a few of my subjects I’ve noticed the ROI when registered to the fsavera

Re: [Freesurfer] Fsaverage for ROI analysis of children

Can you back up and tell us what it is you are trying to do? Where did the ROI come from and how did you create it? doug On 11/3/14 8:56 AM, Smith, Michael wrote: Hello all, I have been conducting an ROI analysis and following the cortical thickness ROI tutorial found here: https://surfer.nm

Re: [Freesurfer] Fsaverage for ROI analysis of children

Hi Doug, We are trying to look at the cortical thickness of a few different ROIs (primary auditory cortex) and see how these areas relate to the EEG ERPs we collected on these subjects as a function of age and development. I created the ROIs using the mri_annotation2label command per hemisph

Re: [Freesurfer] Fsaverage for ROI analysis of children

Did you make the from the ?h.aparc.annot of fsaverage? If so, why not make the label from the ?h.aparc.annot from the individual subject and then calculate the thickness from that? doug On 11/3/14 9:44 AM, Smith, Michael wrote: Hi Doug, We are trying to look at the cortical thickness of a

Re: [Freesurfer] Fsaverage for ROI analysis of children

I made the ROI on an individual subject basis, not from fsaverage. Not sure if the labels I made came from the .aparc.annot files, what is the default of mri_annotation2label? I used the -outdir flag. From: Douglas Greve mailto:gr...@nmr.mgh.harvard.edu>> Reply-To: Freesurfer support list mai

[Freesurfer] I got ERROR during recon-all

I'm new on FREESURFER and have tried to run recon-all refer to https://surfer.nmr.mgh.harvard.edu/fswiki/QuickInstall#Practicedata.26commands However, I got an ERROR .. could you tell me how to run it. Last login: Mon Nov 3 23:53:19 on ttys000 freesurfer-Darwin-lion-stable-pub-v5.3.

Re: [Freesurfer] Question

Hi, I just took the FreeSurfer course. I am using the command reconall -s -i -all. Frequently, because I log on remotely to the server and because of the time that it takes, the terminal disconnects and therefore the process is not complete entirely. Can you point me to a way to redo just the

Re: [Freesurfer] Question

You can run it with recon-all -s subject -make all In the future, you can run recon-all with nohup, ie, nohup recon-all -s subject ... & ie, put "nohup" as the first item and "&" as the last item. This will cause it to run in the background and it should continue to run even if you log out

[Freesurfer] registering coronal images

Dear all, I have some T1 images which are originally in coronal view and the in-plane resolution is 0.5x0.5mm and slice thickness is 2mm. The matrix size is 512x512. I need to segment the left and right hemisphers. As the head is tilted I also need to register the images. Which atlas you recommend

Re: [Freesurfer] registering coronal images

is this the only T1-weighted image you have, or do you also have something more isotropic? On Mon, 3 Nov 2014, Mahmoud wrote: Dear all, I have some T1 images which are originally in coronal view and the in-plane resolution is 0.5x0.5mm and slice thickness is 2mm. The matrix size is 512x512. I

Re: [Freesurfer] registering coronal images

Dear Bruce, Unfortunately, this is the only thing I have. Mahmoud On Mon, Nov 3, 2014 at 2:44 PM, Bruce Fischl wrote: > is this the only T1-weighted image you have, or do you also have something > more isotropic? > > > On Mon, 3 Nov 2014, Mahmoud wrote: > > Dear all, >> >> I have some T1 imag

Re: [Freesurfer] registering coronal images

I see. You can try running it through recon-all, but the 2mm is at the edge of what will work On Mon, 3 Nov 2014, Mahmoud wrote: Dear Bruce, Unfortunately, this is the only thing I have. Mahmoud On Mon, Nov 3, 2014 at 2:44 PM, Bruce Fischl wrote: is this the only T1-weighted image you

Re: [Freesurfer] Fwd: Underinclusion of Gray Matter

Hi Christina it's tough to tell from just a single image, but it looks to me like you are missing a bunch of white matter. Can you tell us more about the scan? The typical way you would fix this is by setting some thresholds in mris_make_surfaces using the expert options. Probably max_csf sho

[Freesurfer] mri_watershed -brain_atlas undocumented?

Hi all, I noticed that during skull stripping the standard recon-all pipeline uses option "-brain_atlas" in the routine "mri_watershed". However documentation of this argument cannot be found in the help section or on the website. mri_watershed --help | less -p atlas https://surfer.nmr.mgh.harvar

Re: [Freesurfer] Fwd: Underinclusion of Gray Matter

dear all, i am new on Mac and freeSusrfer. I have installed freesurfer through the tutorial. Is there any tutorial how to run on Mac. Is there any method to extract stats on excel or spps? The .mgz file shows the brain radiologically (r/l) or vice versa John Papatriantafyllou On Mon, Nov 3, 2014 a