Re: [Freesurfer] Data interest of the CorticalParcellation_Yeo2011

2015-05-14 Thread Thomas Yeo
Hi Annie, I have previously extracted individual regions from the 7 and 17 networks. You can download them here (https://www.dropbox.com/s/u23nn3ov18tlhfs/Yeo_JNeurophysiol11_SplitLabels.zip?dl=0). Please see the README in the folder for more explanations. There should be a precuneus DMN region.

[Freesurfer] Freeview mountain lion

2015-05-14 Thread Isabelle Deschamps
Hi there,I recently tried to update the Freeview version so I can have the recon edit button. I managed to copy the file over but now I get the following error:dyld: Library not loaded: @executable_path/../Frameworks/QtScriptTools.framework/Versions/4/QtScriptTools  Referenced from: /Applications/f

Re: [Freesurfer] Fwd: Problem with Freesurfer 5.3

2015-05-14 Thread Bruce Fischl
Hi Cecilio all our measures are in native space and not corrected for head size. The estimated total intracranial volume (etiv) is what we typically use for correction, and it should be in the aseg.stats file. In general I think it is preferable to use it as a regressor rather than divide, but

[Freesurfer] Help FreeSurfer

2015-05-14 Thread Marta Favali
Dear FreeSurfer Users, I have tried to download FreeSurfer but I am not sure I’ve done it correctly. Could you send me a guide to download it properly? Inside freesurfer there is only “Freeview” as a program. Is that correct? I notice that there is a folder “matlab”, isn’t there a description of

Re: [Freesurfer] Freeview mountain lion

2015-05-14 Thread zkaufman
Hello Isabelle, Freeview has been undergoing many changes and you simply got unlucky and downloaded an unstable version of the program. I will be posting an updated version within the day and I will email you directly when it becomes available. -Zeke > Hi > there,I recently tried to update the F

Re: [Freesurfer] problem with mris_label2annot

2015-05-14 Thread Douglas N Greve
does it work if you don't use --maxstatwinner ? On 05/13/2015 05:31 PM, Aaron Goldman wrote: > Hello, > > >From the standard "fsaverage" subject, I'm trying to map a series of > labels (?h.oasis.chubs.*) to a group of my own subjects. My end goal > is to create summary files equivalent to ?h.apa

[Freesurfer] isxconcat-sess

2015-05-14 Thread SHAHIN NASR
Hi, Does anyone know what has changed in isxconcat-sess command in nmr-dev-env? Previously I could use it to average different sessions of the same subject. But now I am getting this error: INFO: trgsubject is self, this will fail unless all sessions are the same subject ERROR: cannot find /cl

[Freesurfer] ROI Analysis

2015-05-14 Thread Chris Wertz
Hello Freesurfer experts, I ran an analysis using mri_glmfit and a manually drawn label of the parietal lobe that was mapped to every subject and a tablefile was used as the dependent measure. The output is a negative log 10 p-value. I was curious if I could possibly view that in freeview on an fs

Re: [Freesurfer] xhemi final iteration

2015-05-14 Thread Derek James Dean
Hi Doug, Thanks for your help. When I run the following command: images$ make_average_subject --out myatlas.i3 --surf-reg myatlas.i2.sphere.reg --fsgd laterality.fsgd --xhemi --lh ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr

Re: [Freesurfer] isxconcat-sess

2015-05-14 Thread Douglas N Greve
I just made a fix. Can you try it out and let me know if it works? On 05/14/2015 11:38 AM, SHAHIN NASR wrote: > Hi, >Does anyone know what has changed in isxconcat-sess command in > nmr-dev-env? Previously I could use it to average different sessions > of the same subject. But now I am getti

Re: [Freesurfer] xhemi final iteration

2015-05-14 Thread Douglas N Greve
can you run it with --debug as the first option and send the terminal output? On 05/14/2015 05:35 PM, Derek James Dean wrote: > > Hi Doug, > > Thanks for your help. > > When I run the following command: > images$ make_average_subject --out myatlas.i3 --surf-reg > myatlas.i2.sphere.reg --fsgd lat

Re: [Freesurfer] xhemi final iteration

2015-05-14 Thread Derek James Dean
Here is the debug output.  ~$ cd $SUBJECTS_DIR ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addresse

Re: [Freesurfer] xhemi final iteration

2015-05-14 Thread Douglas N Greve
there's nothing there (?) On 05/14/2015 06:13 PM, Derek James Dean wrote: > Here is the debug output. > > > > ~$ cd $SUBJECTS_DIR > > > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/fr

Re: [Freesurfer] xhemi final iteration

2015-05-14 Thread Derek James Dean
Sorry about that, Outlook seems to be preventing me from sending the code in email. I have attached a text document of the output.  output Description: output ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/ma

Re: [Freesurfer] isxconcat-sess

2015-05-14 Thread SHAHIN NASR
Hi Doug, It works without any error. Thanks a lot On Thu, May 14, 2015 at 5:47 PM, Douglas N Greve wrote: > I just made a fix. Can you try it out and let me know if it works? > > On 05/14/2015 11:38 AM, SHAHIN NASR wrote: > > Hi, > >Does anyone know what has changed in isxconcat-sess co