Re: [Freesurfer] threshold method used to obtain *exvivo.thresh.labels

Dear experts, concerning my question regarding thresholding method of entorhinal and perirhinal labels, I looked at Augustinack JC et al, Predicting the location of human perirhinal cortex, Brodmann's area 35, from MRI, Neuroimage 2013 Jan 1;64:32-42. where I found the text: For each label,

Re: [Freesurfer] mri_vol2surf

Hi Douglas, Thank you for your help, So I still can't convert my volumetric file to a surface file and I don't know what I am doing wrong. My nifti volumetric file looks like : 1. screenshot As you said, i have first registered the volumetric file using bbregister. I have used this command

[Freesurfer] preproc-sess - Cannot allocate memory

Hey all, I'm running preproc-sess, and getting the following error: ... Reading in mov rest/tmp.bbregister.28405/template.nii Reading in ref .../mri/brainmask.mgz Reading in and applying refmask .../mri/aparc+aseg.mgz Cannot allocate memory I checked, and the aparc+aseg.mgz file is ok (I can read

[Freesurfer] Resting State group comparison procedure

Hello, I'm currently doing a resting state functional connectivity analysis. I have two groups and my ultimate goal is to compare the resting state network of group 1 to that of group 2. What is the standard procedure for comparing resting state connectivity across groups? I've followed the

Re: [Freesurfer] ACPC alignment before or after running on Freesurfer?

Also, re-slicing already acquired data will introduce blurring into the data you input to FreeSurfer, which may hurt reconstruction. hth d On Wed, Mar 1, 2017 at 10:30 AM, Bruce Fischl wrote: > Hi Kristine > > no, it doesn't. Randy Buckner did a small study on this

[Freesurfer] Reslice image

Dear experts: I have nifti file with 96 slices. I want to re-slice it to form nifti file with 200 slice. Are there any tools in Freesurfer that can help to achieve this? Many thanks for any suggestion John___ Freesurfer mailing list

Re: [Freesurfer] recon-all exited with error.

Thanks. Z K Best, Paul On Fri, Mar 3, 2017 at 12:14 PM, Z K wrote: > Im looking into this now, but I think their might be a bug when using > the -parallel flag on Mac platforms. I should have a fix shortly. I will > let you know. > > On 03/03/2017 12:10 PM, miracle

Re: [Freesurfer] recon-all exited with error.

Im looking into this now, but I think their might be a bug when using the -parallel flag on Mac platforms. I should have a fix shortly. I will let you know. On 03/03/2017 12:10 PM, miracle ozzoude wrote: > Thanks Antonin. I also have different error when running another > subject. Recon fails

[Freesurfer] transform a custom segmentation to native space

Dear all, We've segmented some brain regions on orig.mgz using another program (this custom segmentation is called our_segmentation.mgz). Is it possible to transform this segmentation into the original native anatomical space using the following command? mri_label2vol --seg our_segmentation.mgz

Re: [Freesurfer] recon_all error on MacOS 10.12.13 Sierra: during mris_smooth. dyld: lazy symbol binding

I could be wrong, but I dont think it has anything to do with the installation location. Can you upload your subject folder so I can take a look? https://surfer.nmr.mgh.harvard.edu/fswiki/FtpFileExchange On 03/03/2017 09:11 AM, Daniela wrote: > I second the problem found in this thread: >

Re: [Freesurfer] Hippocampal overestimation 5.3 vs 6.0

Dear Dawn. We have observed that the hippocampal volumes obtained from the subfield module are ~10% smaller than those from the main recon-all stream - but, in any case, very highly correlated. I believe that the discrepancy is due to the smaller voxel size in the analysis, and due to the fact

Re: [Freesurfer] FreeSurfer v6.0 in an AWS cloud configuration (hipposubfield/brainstem failures)

Thanks Antonin,We had suspected as much.  For those who might want to use NITRC-CE (FS v6.0 via their AWS service in the future), please note that our initial (and memory-insufficient) "instance" was "c3.large" .  As you can see in the table below, we should have paid more attention to the

Re: [Freesurfer] panning Freeview on MacBook Pro

Sorry, that appears to only work with 3D view. On 2D view you’ll have to use Cmd + arrow keys to pan. I’ll fix it in future update. > On Mar 3, 2017, at 9:58 AM, Ruopeng Wang wrote: > > If you have middle mouse button defined, use middle button. Otherwise, Shift >

Re: [Freesurfer] panning Freeview on MacBook Pro

If you have middle mouse button defined, use middle button. Otherwise, Shift + Left Button should do it. Best, Ruopeng > On Mar 3, 2017, at 9:51 AM, m...@marychin.org wrote: > > Hi, > > How do I pan on Freeview on a Mac please? Mine is an El Capitan, MacBook > Pro (Early 2011). > > On >

[Freesurfer] panning Freeview on MacBook Pro

Hi, How do I pan on Freeview on a Mac please? Mine is an El Capitan, MacBook Pro (Early 2011). On https://surfer.nmr.mgh.harvard.edu/fswiki/FreeviewGuide/FreeviewGeneralUsage/FreeviewNavigation it reads: You can pan across the data, which is especially useful when zoomed in. To do so while in

Re: [Freesurfer] LME mass univariate model

Hi Bronwyn, I think years-between-scans should be years-from-baseline-scans . You may need to compute that if what you have is really years between neighbouring scans. 1. Usually people use intercept and maybe years-from-baseline as random effects. I would not include too many random effects,

[Freesurfer] Hippocampal overestimation 5.3 vs 6.0

Eugenio and Freesurfer team, Many thanks for responding to these questions. My question relates to hippocampal volume overestimation. I believe that a European team recently evaluated the performance of hippocampus segmentation using different automated segmentation methods including