[Freesurfer] NU_evaluate crash while running Longitudinal Analysis with FS 5.3

Hi, I have been trying to run the FS longitudinal analysis on a subject with 3 time points. I ran each time point thourgh FS, made the template, but when I run the last step I do not get mri/norm files and the output files state nu_evaluate: crashed while running mincmath (termination status = 768

[Freesurfer] Available post doc position

Available post doc/ PhD position At the Research group for lifespan changes in brain and cognition (LCBC) at the University of Oslo (Norway), we have an available post doc position on the project "Patterns and mechanisms of brain atrophy in healthy aging and dementia: Why is the aging brain sus

Re: [Freesurfer] Volume ROI statistics

On 07/03/2013 02:09 PM, Garikoitz Lerma-Usabiaga wrote: > Thanks Doug and Bruce! > this is the process I followed (just in case is of help for somebody > else). Questions below. > > One subject to fsaverage > > mri_vol2vol --mov $SUBJECTS_DIR/fsaverage/label/myROI.nii --o > $SUBJECTS_DIR/fsaver

Re: [Freesurfer] Volume ROI statistics

Thanks Doug and Bruce! this is the process I followed (just in case is of help for somebody else). Questions below. One subject to fsaverage mri_vol2vol --mov $SUBJECTS_DIR/fsaverage/label/myROI.nii --o $SUBJECTS_DIR/fsaverage/label/myROI.mgh --reg from_mySubject_to_fsaverage.dat --targ fsavera

Re: [Freesurfer] [tracula] running into trouble with nifti data

Hi Satra - There are 2 ways to put things "in proper orientation for fsl tools": 1. L-R flip the gradient vectors: This is a hack, in the sense that it anticipates that FSL will treat your volume as L-R flipped when it has a certain type of orientation, but now you've broken your bvecs for t

Re: [Freesurfer] How to change the color of the boundary surface?

Dear Bruce, Thank you very much! Sincerely, Ye On Wed, Jul 3, 2013 at 10:41 AM, Bruce Fischl wrote: > in tkmedit? View->configure->surface > > > cheers > Bruce > > On Wed, 3 Jul 2013, ye tian wrote: > > Dear freesurfers, >> Does anyone know how to change the color (default yellow) of the surf

Re: [Freesurfer] How to change the color of the boundary surface?

in tkmedit? View->configure->surface cheers Bruce On Wed, 3 Jul 2013, ye tian wrote: > Dear freesurfers, > Does anyone know how to change the color (default yellow) of the surface > between the grey matter and the white matter? I see green and blue in the > tutorial. > > Thank you very much! >

Re: [Freesurfer] Xhemi files can not be downloaded

Hi Hamza, try mri_convert.mac doug On 07/03/2013 07:27 AM, Hamza Alshuft wrote: > Thanks for the help > Unfortunately after your reply I could only > downloadftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mris_preproc > the rest of the files are still un-downloadable! > > I have

[Freesurfer] How to change the color of the boundary surface?

Dear freesurfers, Does anyone know how to change the color (default yellow) of the surface between the grey matter and the white matter? I see green and blue in the tutorial. Thank you very much! Sincerely, Ye ___ Freesurfer mailing list Freesurfer@nmr

Re: [Freesurfer] longitudinal analyses for one group

Sandra, what was your final command line? doug On 07/03/2013 06:28 AM, Sandra Preissler wrote: > Dear Doug, > > Thanks a lot for your advice. > > We followed the examples on the wiki > (http://ftp.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis#AssembletheData.28mrispreproc.29) > > and trie

Re: [Freesurfer] error in downloading tutorial dataset

Hello Claudia, Nearly everytime someone tells us they are having trouble downloading freesurfer (or the datasets) it is because they are trying to access the files via an employers or guest wifi network with restrictions. Please try downloading the files using a network which your are sure has

Re: [Freesurfer] error in downloading tutorial dataset

Hi Claudia, I downloaded the tutorial data set two weeks ago to Mac OX Snow Lion with curl. I didn't have your problem. Ye On Wed, Jul 3, 2013 at 3:02 AM, Claudia Dacquino wrote: > Hi freesurfers, > > I'm trying downloading the tutorial dataset but after several attempts I > still couldn't co

[Freesurfer] Fwd: Qdec error

Begin forwarded message: > From: Anupa AV > Date: July 3, 2013, 2:03:26 AM EDT > To: "zkauf...@nmr.mgh.harvard.edu" > Subject: Re: [Freesurfer] Qdec error > Reply-To: Anupa AV > > Thank you so much.. > It worked.. :) > > > From: "zkauf...@nmr.mgh.harvard.edu" > To: Anupa AV > Cc: Frees

Re: [Freesurfer] Xhemi files can not be downloaded

Thanks for the help Unfortunately after your reply I could only download ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mris_preproc the rest of the files are still un-downloadable! I have Mac freesurfer v5.1 and use "curl –O ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/f

Re: [Freesurfer] longitudinal analyses for one group

Dear Doug, Thanks a lot for your advice. We followed the examples on the wiki (http://ftp.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis#AssembletheData.28mrispreproc.29) and tried to analyze our data as described. We have a single group with two continuous covariates. Therefore we cr

[Freesurfer] Postdoctoral position: the brain connectome in twins populations

Dear brain imaging fellows, One post-doc position is available in our group, the deadline is 30-08-2013. Please find the details below: *** Department Center of Neurodevelopmental Disorders at Karolinska Institutet (KIND) (www.ki.se/kind) KIND is a competence center for research, development a

[Freesurfer] error in downloading tutorial dataset

Hi freesurfers, I'm trying downloading the tutorial dataset but after several attempts I still couldn't connect to the server and I recived this message repeately, even with the -c flag: "server response error, closing connection". I'm working on Linux Centos System and using the wget command.