Re: [Freesurfer] Xhemi questions

Thanks you for your quick answer Doug,Just one clarification, in the correction for multiple comparisons, which is the main difference between the mc-z and the permutation test? rather than making simultaions or working on original data. And Why is 5000 runs recommended to mc-z and 1 for

[Freesurfer] longitudinal processing with -FLAIRpial

Dear Freesurfer Ninjas, I have been playing around with the new beta version, and am very interested in the -FLAIRpial option. I have been using this successfully on cross-sectional runs, but would like to extend it to cross sectional runs. I have played around with trying to get this to work,

Re: [Freesurfer] mrisReadTriangleFile failed

Hi Jon I'm not sure what this means, but -make all is the thing to do in this case. cheers Bruce On Wed, 6 Feb 2013, Jonathan Holt wrote: Just had a cluster of computers lock up, unfortunately resulting in several freesurfer jobs terminating prior to completion. It's possible I may have a

[Freesurfer] Trying to email out on the FreeSurfer mailing list

Hi, I've been trying to email out for help to the FreeSurfer community, using the below addresses. However, I am not receiving my own email back, though I am a member of the mailing list via this email address. Can you tell me what I'm doing wrong? Thank you! Susan Kuo -- Forwarded

Re: [Freesurfer] longitudinal processing with -FLAIRpial

Hi Charles, the FLAIRpial is a recent addition and has only been added to the cross sectional stream so far. I can take a look at porting this to the longitudinal stream but probably not for 5.2. Best, Martin On Feb 7, 2013, at 7:23 AM, Charles Malpas c.mal...@student.unimelb.edu.au wrote:

[Freesurfer] white matter hyperintensities

Dear freesurfer experts, I have a question regarding white matter hyperintensities (ie values above 110)..if these are included in the brainmask accurately, ie as white matter when it is indeed white matter, does hyperintensities still cause problems, and if so why? Regards Linn

Re: [Freesurfer] white matter hyperintensities

Hi Linn no, they shouldn't I don't think cheers Bruce On Thu, 7 Feb 2013, Linn Mittlestein wrote: Dear freesurfer experts, I have a question regarding white matter hyperintensities (ie values above 110)..if these are included in the brainmask accurately, ie as white matter when it is

[Freesurfer] BEDPOSTX - seychelles option

Hi FreeSurfer community, I would like to run '-bedp' with TRACULA, to run the bedpostx option. I see from the *./subjID/scripts/trac-all.cmd* file that the actual command issued was *bedpostx_seychelles*, which allows for the PBS queueing system running on seychelles and is used by the Martinos

Re: [Freesurfer] DOSS and FDR in QDec

On 02/04/2013 02:10 AM, Sean Hatton wrote: Hi FreeSurfers, These should be a simple questions but they have been bugging me. 1. I have two diagnostic groups that I want to compare controlling for gender and age. I am entering them in Qdec with diagnosis and gender as discrete

Re: [Freesurfer] mean cortical thickness of significant clusters in qdec

it does not look like you changed the command line. Also, please cut and paste the info into the email instead of taking a snapshot. thanks doug On 02/04/2013 07:26 AM, Richter, Julia wrote: This doesn't work either (see attachment) :( -Ursprüngliche Nachricht- Von: Douglas N Greve

Re: [Freesurfer] qdec and file -qcache

Hi Sophie, can you cut and paste the actual command line that you are using? I don't know what all the symbols mean. doug On 02/04/2013 08:15 AM, Sophie Maingault wrote: Hello everyone ! I want to use qdec so I tried to smooth the subjects with the following command: recon-all -s t0001 …

Re: [Freesurfer] annotating only certain regions

No, sorry, the labeling of all structures is done simultaneously. doug On 02/04/2013 08:20 AM, Hemant Bokil wrote: Hi all, Is there a way to get freesurfer to annotate only certain selected structures (e.g. basal ganglia). I suspect not, since the underlying model involves spatial

Re: [Freesurfer] qdec and file -qcache

Hi Sophie, you can only run one subject at a time. What is your command for one subject? doug On 02/07/2013 11:41 AM, Sophie Maingault wrote: Actually, I have more than 450 subjects but I will give an example with less subjects (here 3 subjects). So the command line that I run is : recon-all

[Freesurfer] Download v. 5.0 on Mac Lion 10.7.5

Hello, I need to download an older version of freesurfer (Version 5.0) on a Mac Lion 10.7.5. In the archives I don't see a file for Lion, just Leopard and Tiger. Is it possible that either of these will work for Lion? Also, are there any step by step instructions on how to install? Thanks!

Re: [Freesurfer] patched version of mris_preproc for 5.1 user?

that link should work now doug On 02/07/2013 12:53 PM, Uri Hasson wrote: Dear Doug, We're still using version 5.1 for a pipeline, and need to send surface-based measures (volume, area, thickness) to a standard space for whole-brain analysis. I read you had a patched version of

Re: [Freesurfer] Download v. 5.0 on Mac Lion 10.7.5

Hello Krista, freesurfer v5.0 does not have a Lion build. Im fairly certain Lion did not even exist when 5.0 was released. I suggest you give the Leopard build a try, I *think* it will work, but I haven't tested it. If you download the the .dmg file the install should be fairly self explanatory.

Re: [Freesurfer] Download v. 5.0 on Mac Lion 10.7.5

I just noticed their are two Leopards builds... go with the leopard-i686 version. -Zeke Hello Krista, freesurfer v5.0 does not have a Lion build. Im fairly certain Lion did not even exist when 5.0 was released. I suggest you give the Leopard build a try, I *think* it will work, but I

[Freesurfer] Postdoctoral Fellow position: UNSW SYDNEY AUSTRALIA

Postdoctoral Fellow UNSW Faculty of Medicine School of Psychiatry REF. 9160NET FIXED TERM: - Salary: (Level A Step 6-8) A$78K – A$84K per year (plus up to 17% employer superannuation plus leave loading.) The School of Psychiatry, Faculty of Medicine, The University of New South Wales, invites