Re: [Freesurfer] create label from cluster obtained with mri_glm-fit-sim

External Email - Use Caution Dear Dr. Douglas, Thank you so much for your response. With your instruction, it works. This is how I did. First, copy the significant cluster annot file from the simulation fold to one of subject label folder. Secondly, use the

Re: [Freesurfer] mri_watershed Error

Hi Boris the input to that watershed call is the T1.mgz, but it is already problematic as you can see from the log. You should take a look at the nu.mgz and make sure it is correct. You can also email me the nu.mgz and the talairach.xfm (in the mri/transforms dir) if you want and I'll take a

[Freesurfer] Postdoctoral position open to work on brain MRI function & microstructure (Italy)

External Email - Use Caution [Apologies for cross-posting] The MRI Group of the Center for Mind/Brain Sciences, University of Trento, Italy  (https://r.unitn.it/en/cimec/mri/) has an open postdoctoral position to develop/apply MRI acquisition and analyses methods to

Re: [Freesurfer] mri_watershed Error

External Email - Use Caution Hi again, sorry. Please find attached the recon-all.log. I´m not sure how to check the input to watershed. recon-all.log Description: Binary data Thanks, Boris > Am 11.10.2018 um 18:55 schrieb Bruce Fischl : > > Hi Boris > > can you check to

[Freesurfer] FreeSurfer Errors

External Email - Use Caution Hey! I have recently started using FreeSurfer. I have encountered multiple errors over the past few days, and I would like to mention them all. 1. While testing the installation, the code ran for roughly 4-6 hours and generated the T1 and wm output

Re: [Freesurfer] Correction Needed for the Midline

Hi Maxime, I'll take a look at your data and the issue you're having and get back to you after the weekend. Best, Bram From: freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Maxime Perron Sent: Tuesday, September 25, 2018 1:14:08 PM To: Freesurfer

Re: [Freesurfer] Ynt: Ynt: Desikan Atlas in MNI Space

External Email - Use Caution I tried to confirm VBM analysis lots of platform i study in CAT, these days. Thanks for your reply. Greve, Douglas N.,Ph.D. şunları yazdı (11 Eki 2018 18:47): > Which template surface? fsaverage? Are you using the 2mm MNI template > for VBM?

Re: [Freesurfer] denoising and recon-all {Disarmed}

External Email - Use Caution The ONLM denoising algorithm in the following package:

Re: [Freesurfer] mri_watershed Error

Hi Boris can you check to make sure that the input to the watershed looks ok? Also, in general it is a lot easier for us to help if you send us the full command line and screeen output and attach the recon-all.log cheers Bruce On Thu, 11 Oct 2018, Boris Rauchmann wrote:

Re: [Freesurfer] denoising and recon-all

External Email - Use Caution What are you using for denoising? Matt. From: mailto:freesurfer-boun...@nmr.mgh.harvard.edu>> on behalf of Lisa Crystal Krishnamurthy mailto:lkrishnamur...@gsu.edu>> Reply-To: Freesurfer support list mailto:freesurfer@nmr.mgh.harvard.edu>> Date:

Re: [Freesurfer] Ynt: Ynt: Desikan Atlas in MNI Space

Which template surface? fsaverage? Are you using the 2mm MNI template for VBM?  If so, then you can use mri_label2vol specifying the desikan annotation as the --annot and using $FREESURFER_HOME/average/mni152.register.dat as the registration file. On 10/11/2018 11:42 AM, ece ulug wrote: > >    

[Freesurfer] Ynt: Ynt: Desikan Atlas in MNI Space

External Email - Use Caution Thanks for your response; I had already mapped normalized volume to template surface, so now I want to map the desikan atlas into the vbm volume. Gönderen: Greve, Douglas N.,Ph.D. adına

Re: [Freesurfer] mri_watershed Error

can you send the recon-all log file? On 10/11/2018 11:22 AM, Boris Rauchmann wrote: > > External Email - Use Caution > > When I run recon-all i get the follwing error message: > >  mri_watershed Error: >  GLOBAL region of the brain empty ! > Linux 02f92500bcfb 4.15.0-36-generic

Re: [Freesurfer] Ynt: Desikan Atlas in MNI Space

I'm not sure what you are trying to do. Do you want to map the vbm results to the surface and visualize the aparc (desikan atlas) or do you want to map the aparc into the vbm volume? On 10/11/2018 09:59 AM, ece ulug wrote: > > External Email - Use Caution > > Hi, > > May be i cannot

[Freesurfer] mri_watershed Error

External Email - Use Caution When I run recon-all i get the follwing error message: mri_watershed Error: GLOBAL region of the brain empty ! Linux 02f92500bcfb 4.15.0-36-generic #39~16.04.1-Ubuntu SMP Tue Sep 25 08:59:23 UTC 2018 x86_64 x86_64 x86_64 GNU/Linux recon-all -s

[Freesurfer] Ynt: Desikan Atlas in MNI Space

External Email - Use Caution Hi, May be i cannot tell well, I would like to use the Desikan atlas, which is a surface-based atlas normally, as a volume template. Generally Desikan_surface.gii file is accesible. Can I visualize VBM results correctly in for instances SPMglass

Re: [Freesurfer] Recon-all with/without T2 give the same stats

External Email - Use Caution The aparc stats with T2 changed using this script. Now the stats with/without T2 are different, thanks! It seems that in 5.3 the aparc stats are computed before refining the pial. Greve, Douglas N.,Ph.D. 于2018年10月11日周四 上午2:24写道： > I think this was a

Re: [Freesurfer] Difference between 2 mgh files in surf dir (or: effects of 'mri_surf2surf --prune' without smoothing)

External Email - Use Caution Looks like, it the output of that command is `diffcount 0`. If you binary-diff them you see some differences near the start, but that's most likely just header info like creation time or something. Ok, that answers my question. Thanks for your help!

Re: [Freesurfer] masking cortical thickness

External Email - Use Caution Hi, Thank you so much , it works. BRG, Nazanin On Wed, Oct 10, 2018 at 9:41 PM Greve, Douglas N.,Ph.D. < dgr...@mgh.harvard.edu> wrote: > if you want to mask the thickness, then use mri_mask > > On 10/10/2018 10:30 AM, N Saf wrote: > > > >