Re: [Freesurfer] Amazon EC2 Version of FreeSurfer 5.1 Available

Ok. I'll label as private this AMI that has .license file. Maybe we can make a tutorial on how to create an AMI instead. - Pedro Paulo de Magalhães Oliveira Junior Netfilter & SpeedComm Telecom -- www.netfilter.com.br -- For mobil

Re: [Freesurfer] Amazon EC2 Version of FreeSurfer 5.1 Available

Glad to hear it works well. To revisit the issue of the license (in the form of the .license file which needs to be in the $FREESURFER_HOME directory and the request of which is used for usage tracking), I think the convention to follow for any publicly available AMI freesurfer instances should be

Re: [Freesurfer] Freesurfer on Windows!

I'd try reinstalling virtualbox. Then I'd make sure that you adjust the vm with enough ram, videocard memory, etc. It should work fine. I run the same setup all the time, and I don't believe that this is a 'known issue'. Joshua On Mon, Nov 14, 2011 at 8:25 AM, wrote: > Hello Friends, > > I am

Re: [Freesurfer] Amazon EC2 Version of FreeSurfer 5.1 Available

Thanks again Pedro. I just ran 220 brains through in day or two using the cloud. Fantastic. The script people have been talking about would have been useful. One thing I didn't realize was that I should have moved the freesurfer subject directory from /usr/local/freesurfer/subjects to the larger di

Re: [Freesurfer] dt_recon registration

Hi Antonella, 1) I will be very grateful if you can confirm if my coding is write. First can you please let me know if by default dt_recon is re-sample FA to talairch space? In this case because I want to register   on CVS should I add the  --no-tal flag? I am asking this question because af

Re: [Freesurfer] flipping surface data

Try these instructions. You won't actually need to do the download and install in you're local, but you will need to use the dev env. doug Download these files ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing

[Freesurfer] CVS template for registration

Dear all: Based on the DTI Basic Tutorial I understood that MRI data can be resampled & registered in CVS space (by running  mri_cvs_register), but alternatively can be normalized  in any other (for example, MNI or Talairach). Can you please let me know how this can be done in MNI152 spac

Re: [Freesurfer] CVS template for registration

Hi Antonella we have had good results with surface-based registration that is the heart of CVS down to below age 5. See: Evaluating the validity of volume-based and surface-based brain image registration for developmental cognitive neuroscience studies in children 4 to 11 years of age., Satr

[Freesurfer] DTI Group Analysis Study

Dear Anastasia, Thank you very much for your help. I have done a TBSS group analysis in FSL and I would like to do a similar study using Freesurfer. I understood I can use TRACULA for a similar TBSS study. Is this right? Or I should better use the dt_recon? I would like to compare my res

[Freesurfer] CVS template for registration

Dear all: Based on the DTI Basic Tutorial I understood that MRI data can be resampled & registered in CVS space (by running  mri_cvs_register), but alternatively can be normalized  in any other (for example, MNI or Talairach). Can you please let me know how this can be done in MNI152 space? Sho

Re: [Freesurfer] DTI Group Analysis Study

Dear Anastasia, Thank you very much for your help. I have done a TBSS group analysis in FSL and I would like to do a similar study using Freesurfer. I understood I can use TRACULA for a similar TBSS study. Is this right? Or I should better use the dt_recon? I would like to compare my results

[Freesurfer] error with mri_glmfit and question about registering rh to lh

Hi all, I receive the error: ERROR: MRISread: cannot read surface data from file ./long/surf/lh.thickness.fsaverage.S1-S3.mgh! when I run mri_glmfit with the command: mri_glmfit --glmdir long/g1v0 --surf long lh thickness.fsaverage.S1-S3.mgh --fsgd long/S1-S3.fsgd --osgm I am working on mri_glmf

Re: [Freesurfer] reconstruction stop

what was your command line? On Mon, 14 Nov 2011, LAOUCHEDI MAKHLOUF wrote: hi    i am new in freesurfer (even if i used it many times doing reonstructions using the script reconn-all in the past and on another machine), i launched  a reconstruction of one patient using the reconn-all script and

[Freesurfer] Freesurfer on Windows!

Hello Friends, I am a newcomer to freesurfer and wanted to use it in windows. I downloaded as instructed the freesurfer-Virtualbox-linux-x86-stable-pub-v5.1.0-full.vdi-for windows the virtual box version is 4.1.6 and installed with the required settings as mentioned in your website. I tried it

[Freesurfer] reconstruction stop

hi    i am new in freesurfer (even if i used it many times doing reonstructions using the script reconn-all in the past and on another machine), i launched  a reconstruction of one patient using the reconn-all script and i gave before this the path to the SUBJECTS_dir.  and one or two minutes la