[Freesurfer] the difinition about VentralDC

Dear Pedro, Dear Bruce, Dear all, In the previous discussion about VentralDC in the aseg stats file, I learned that it's the the acronym stands for ventral diencephalon. And Dr. Fischl said that It's a mismash of a bunch of different stuff and the CMA pubs have more details on it. However, anyone

[Freesurfer] smoothed data stats

Dear all I would like to look at the change in the average values of thickness after smoothing. But mris_anatomical_stats does not work on the smoothed files as the no of vertices of the annot files and the smoothed files are very different. I tried recreating annot files using the flag -surf p

[Freesurfer] hippocampus volume

hi, expert,   In a paper named "MRI of hippocampal volume loss in early Alzheimer's disease", I can see the average volume of hippocampus is 2133mm^3 for 279 normal controls with std=25 as well as 1631mm^3 for 330 AD subjects with std=34. However, in the aseg.stats, the volume of a normal subject

Re: [Freesurfer] hippocampus volume

In the aging process there's overall cortical atrophy. Other papers like ours shows that too: https://surfer.nmr.mgh.harvard.edu/pub/articles/Oliveira_JAD2010.pdf Cheers - Pedro Paulo de Magalhães Oliveira Junior Diretor de Operaç

Re: [Freesurfer] the difinition about VentralDC

I believe the segmentation definitions can be found here: http://www.cma.mgh.harvard.edu/manuals/segmentation/ --Thomas On Aug 9, 2010, at 4:28 AM, leemon albert wrote: > Dear Pedro, Dear Bruce, > Dear all, > > In the previous discussion about VentralDC in the aseg stats file, I > learned tha

Re: [Freesurfer] the difinition about VentralDC

Hi Meng, you can look for people such as Nikos Makris, David Kennedy and Verne Caviness. cheers Bruce On Mon, 9 Aug 2010, leemon albert wrote: > Dear Pedro, Dear Bruce, > Dear all, > > In the previous discussion about VentralDC in the aseg stats file, I learned > that it's the the acronym stands

Re: [Freesurfer] smoothed data stats

It should work. How are you smoothing the thickness file? You need to smooth it in the native surface space. doug raka maitra wrote: > Dear all > > I would like to look at the change in the average values of thickness > after smoothing. > But mris_anatomical_stats does not work on the smoothed

Re: [Freesurfer] smoothed data stats

Dear Doug Thanks for the clarification. I was using files in the standard fsaverage surface space. Thanks again! Raka From: Douglas N Greve To: raka maitra Cc: freesurfer_mailing_list Sent: Mon, August 9, 2010 4:02:11 PM Subject: Re: [Freesurfer] smoothed d

[Freesurfer] Make_average failure

Following a bug-fix to enable processing large number of scans in make_average_surface ( see http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg14122.html ) Something odd has happpened and I am not able to run the make_average as before. I am trying to make an average map of a single s

Re: [Freesurfer] question abt Destrieux atlas

Hi Rito The answer for the second question is yes : the stable 4.5.0 version includes the 2009 parcellation atlas (see http://surfer.nmr.mgh.harvard.edu/fswiki/ReleaseNotes) For the first one I'm not quite sure if running recon-all with the -cortparc2

Re: [Freesurfer] Make_average failure

You need to make it executable with chmod a+x /Applications/freesurfer/bin/mris_make_average_surface Lena Palaniyappan wrote: > Following a bug-fix to enable processing large number of scans in > make_average_surface > ( see > http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg14122

[Freesurfer] Red Hat vs. CentOs

Hi, I'd like to make sure that a Dell desktop with pre-installed RHEL would work seamlessly with Freesurfer, equivalent to CentOS. Is this correct? Thanks, Dahlia. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.e

Re: [Freesurfer] Red Hat vs. CentOs

Yes, it should be almost no different. On Mon, 9 Aug 2010 dah...@nmr.mgh.harvard.edu wrote: > Hi, > > I'd like to make sure that a Dell desktop with pre-installed RHEL would > work seamlessly with Freesurfer, equivalent to CentOS. Is this correct? > > Thanks, > Dahlia. >

[Freesurfer] Exec format error. Wrong Architecture.

Hello all, I finished running autorecon1 pbsubmit -m kfanucci -l nodes=1:opteron -c "recon-all -i /autofs/cluster/mscat/users/kristina/MS-freesurfer/ms-dicom/MS_pt20_dicom/MEMPRAGE_4e/008/255000-08-49.dcm -subjid MS_pt20_recon -autorecon1" and then tried to look at the skull strip tkme

Re: [Freesurfer] Red Hat vs. CentOs

In my recent experience, no. There were problems with entering text in tksurfer/tkmedit when running on the pre-installed RHEL that went away when CentOS was installed later. > Date: Mon, 9 Aug 2010 15:42:57 -0400 > From: rai...@nmr.mgh.harvard.edu > To: dah...@nmr.mgh.harvard.edu > CC: free

[Freesurfer] [freesurfer] a puzzling installation error

Dear freesurfer experts, I'm running into installation failure and can't quite figure this out (I'm a novice Linux user too). It complains there is no such file or directory although I've downloaded the file and move that to the usr/local directory, so there clearly is the file. Would anybody h

[Freesurfer] region seeding and growing

I have looked at the web site and gone through much of the available documentation (without downloading the installer yet) and cannot find if FreeSurfer offers low-level region seeding and growing capabilities. Anyone able to confirm or deny such a feature? Thanks, Jeff Eriksen, PhD Senior Resear

Re: [Freesurfer] region seeding and growing

can you give us an idea as to what you are trying to achieve. We certainly do different kinds of region growing, but they may not meet your needs. cheers Bruce On Mon, 9 Aug 2010, Eriksen, Jeffrey (Portland) wrote: > I have looked at the web site and gone through much of the available > docume