Re: [Freesurfer] Using a2009s.annot as seed masks for tractography

Hi Lee, Thanks for your reply. I have repeated this step in /Applications/freesurfer/subjects/HC001/mri using the following command: mri_label2vol --seg left_thalamus.nii.gz --temp b0_brain.nii.gz --reg registration2b0.dat --o left_thalamus_dwi_seed.nii.gz And got this output: Number of label

Re: [Freesurfer] crossing medial surfaces

I think noaseg is a bit different as it will not use the aseg in downstream processing. From the help: -noaseg Skips subcortical segmentation steps (same as -nosubcortseg), and does not use aseg.presurf.mgz for inorm2, wm segmentation, or filling. Use this flag for brains that do not support us

Re: [Freesurfer] crossing medial surfaces

  For the approach below you need to edit both the aseg.mgz and brainmask.mgz and run -autorecon-pial for each hemishphere individually. Just make sure you keep a copy of the unedited brainmask.mgz and aseg.mgz so you can do both hemispheres.   Also, I think -autorecon2-noaseg and autorecon2-cp

Re: [Freesurfer] crossing medial surfaces

I don't think you want noaseg. Why not try autorecon2-cp so it starts after the aseg but uses it? cheers Bruce On Thu, 23 Apr 2015, Clara Kuehn wrote: Hi Paul, thanks for your reply. I think the problem is that after editing the aseg.mgz and rerunning -autorecon2-noaseg it doesn't update the

[Freesurfer] Viewing gfeat results on inflated brain

Hi, We are working on the analysis step of a project, in which we are interested in the brain activation pattern in response to five different body part movement. We have done a group analysis using FSL (N=10), to see the average activation pattern for each body part. However, we are having pr

Re: [Freesurfer] Generate patch files outside of tksurfer

Perfect. Thanks Bruce! On Thu, Apr 23, 2015 at 6:46 AM, Bruce Fischl wrote: > Hi Michael > > you can use label2patch for this. > > cheers > Bruce > On Wed, 22 Apr 2015, Michael Waskom wrote: > > > Hi Freesurfers, > > Is there a way to generate patch files from surfaces outside of > tksurfer? I'm

Re: [Freesurfer] Using a2009s.annot as seed masks for tractography

Hi André, Could you send the command that you ran to produce this ouput? Also (just to check), do you have permissions to read the b0_brain.nii.gz file, and is it here: /Applications/freesurfer/subjects/HC001/b0_brain.nii.gz Thanks, Lee On Thu, 23 Apr 2015, André Schmidt wrote: Dear Lee,

Re: [Freesurfer] Freesurfer Updates

The version of freesurfer installed in /usr/local/freesurfer/stable5_3_0 is the same as the release and does not change, so it will not have the updates. The version of freesurfer installed in /usr/local/freesurfer/dev is updated nightly and contains the updates to Tracula and the dmri_group s

Re: [Freesurfer] optseq2 source code

Thank you. Much appreciated. Cheers, PB On Wed, Apr 22, 2015 at 6:25 PM Douglas N Greve wrote: > yes, it is available with the FreeSurfer source code, which you can > download > doug > > On 04/22/2015 04:30 PM, Patrick Beukema wrote: > > Hi, > > Is it possible to get the source for optseq2. I wo

[Freesurfer] Freesurfer Updates

Hi FS experts, In order to start FS I am sourcing the following script routinely: #!/bin/tcsh setenv FREESURFER_HOME /usr/local/freesurfer/stable5_3_0 setenv USE_STABLE5_3_0 setenv LD_LIBRARY_PATH /usr/lib64/GLoverride:/usr/lib/GLoverride setenv FSENV_KEEP_PROMPT setenv SUBJECTS_DIR /autofs/cluste

Re: [Freesurfer] crossing medial surfaces

Hi Paul, thanks for your reply. I think the problem is that after editing the aseg.mgz and rerunning -autorecon2-noaseg it doesn't update the aparc+aseg.mgz, so the surfaces still cross. Cheers, Clara - Ursprüngliche Mail - Von: silve...@gmx.com An: freesurfer@nmr.mgh.harvard.edu Gesen

Re: [Freesurfer] Freesurfer and Tracula installation.

Have you tried these steps: http://wiki.centos.org/TipsAndTricks/NTFS From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Fatma Zribi [zribi.fa...@gmail.com] Sent: Thursday, April 23, 2015 9:14 AM To: freesurf

[Freesurfer] Progrmmatically Drawing in Desikin Killiany or Destrieux Atlas

How do you draw the structure names that are present in aseg.stats and aparc.stats files on Desikin Killiany or Destrieux Atlas? For example, I want to draw lh_bankssts, rh_cunueus and lh_fusiform on any suitable atlas with color scale corresponding to some result from my study. Are there any scr

Re: [Freesurfer] low signal/noise

Hi Noa you need to look at the defects and fix the giant ones (e.g. wm connected to skull or cerebellum). This is documented on the wiki - you need to visualize the defects on the lh.inflated.nofix or lh.orig.nofix and either add cps or edit the wm cheers Bruce On Wed, 22 Apr 2015, Golan,

Re: [Freesurfer] tkmedit neuroscience format

no, sorry Bruce On Wed, 22 Apr 2015, Jon Alan Wieser wrote: Dear freesurfer experts. is it possible for  tkmedit to display volumes in neuroscience format (R is R) rather than radiologic format (R is L)?" Thanks Jon ___ Freesurfer mailing list F

Re: [Freesurfer] Generate patch files outside of tksurfer

Hi Michael you can use label2patch for this. cheers Bruce On Wed, 22 Apr 2015, Michael Waskom wrote: > Hi Freesurfers, > Is there a way to generate patch files from surfaces outside of tksurfer? I'm > specifically > hoping that there is some tool that will allow me to use a label file to > def

Re: [Freesurfer] where to start recon-all after edits

I would think autorecon2-cp autorecon3 would be fine, but maybe Martin can comment? On Wed, 22 Apr 2015, prasser wrote: Repost.Thanks. On Mon, 20 Apr 2015 16:35:29 -0700 wrote Thank you again for your reply. For editing aseg.mgz, as mentioned in https://surfer.nmr

[Freesurfer] Freesurfer and Tracula installation.

Hi everybody, I installed CentOS 6.6 in a machine without using internet connexion. Everything is fine. I would like now to install Freesurfer and Tracula mounting a NTFS partition from an external hard disk. also I note that I can not copy Freesurfer in a FAT32 partition. Actually I'm not sure t