[Freesurfer] Cortical thickness values of significant clusters

, there are no significant differences between my groups. I'm not sure if I am using the correct approach to extract thickness values for the significant clusters. Thank you for your help, Sinead -- Sinead Kelly Neuropsychiatric Genetics Group Trinity Centre St. James's Hospital Dublin 8

Re: [Freesurfer] Cortical thickness values of significant clusters

: That is the right file to use, and one would expect to see significant results. Are you sure you are using exactly the same model? If you have matlab, I can give you some code to do the analysis using the exact model that mri_glmfit uses. doug On 12/9/13 10:43 PM, Sinead Kelly wrote

[Freesurfer] Recon checker - actual file order disagrees with common file order

, Sinead -- Sinead Kelly Neuropsychiatric Genetics Group Trinity Centre St. James's Hospital Dublin 8 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail

Re: [Freesurfer] Validation of results

in order to see how different they are. doug On 08/07/2013 12:33 PM, Sinead Kelly wrote: Hi Doug, I can't visualize the maps on the linux server I'm using but I have the cluster summary files below for DODS and DOSS. As you can see they are quite different. What do you think might

Re: [Freesurfer] Validation of results

-based Analysis of Language Lateralization and Cortical Asymmetry.http://www.researchgate.net/publication/236906359_A_Surface-based_Analysis_of_Language_Lateralization_and_Cortical_AsymmetryJournal of Cog Neurosci. 2013. doug On 7/30/13 7:53 AM, Sinead Kelly wrote: Dear freesurfer users

Re: [Freesurfer] Validation of results

Analysis of Language Lateralization and Cortical Asymmetry.http://www.researchgate.net/publication/236906359_A_Surface-based_Analysis_of_Language_Lateralization_and_Cortical_AsymmetryJournal of Cog Neurosci. 2013. doug On 7/30/13 7:53 AM, Sinead Kelly wrote: Dear freesurfer users, I

[Freesurfer] Fwd: Validation of results

-- Forwarded message -- From: Sinead Kelly kelly...@tcd.ie Date: 30 July 2013 12:53 Subject: Help required with cortical surface area results To: freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu Dear freesurfer users, I would really appreciate if anybody could

[Freesurfer] tksurfer problem - annotation of vertices

/5.2.0/tktools/tkUtils.tcl Successfully parsed tksurfer.tcl reading white matter vertex locations... % -- Sinead Kelly Neuropsychiatric Genetics Group Trinity Centre St. James's Hospital Dublin 8 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu

[Freesurfer] Validation of results

appreciate if anyone can validate this for me as I have very little experience with freesurfer. Thank you for your help! Sinead Sinead Kelly Neuropsychiatric Genetics Group Trinity Centre St. James's Hospital Dublin 8 ___ Freesurfer mailing list Freesurfer

[Freesurfer] mri_glmfit error with design matix

0.000 0.000 0.000 50.000 0.000; 0.000 0.000 0.000 1.000 0.000 0.000 0.000 27.000; 0.000 0.000 0.000 1.000 0.000 0.000 0.000 54.000; -- Sinead Kelly Neuropsychiatric Genetics Group Trinity Centre St. James's Hospital Dublin 8

[Freesurfer] Qdec error and design problem

. Thank you for your help. Sinead -- Sinead Kelly Neuropsychiatric Genetics Group Trinity Centre St. James's Hospital Dublin 8 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Re: [Freesurfer] nu_correct: Command not found error

? Nick On Fri, 2013-03-08 at 09:50 +, Sinead Kelly wrote: Dear all, I am currently running cortical thickness analysis using Freesurfer v5.2 on a high performance computing cluster however, when I run the 'recon_all' command I get the following error Subject Stamp: freesurfer

[Freesurfer] nu_correct: Command not found error

would be appreciated. Kind regards, Sinead -- Sinead Kelly Neuropsychiatric Genetics Group Trinity Centre St. James's Hospital Dublin 8 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo

Re: [Freesurfer] recon_all exited with errors

that I am running my scripts on a high performance computing cluster and not locally on my linux. Thank you for your help! Sinead -- Sinead Kelly Neuropsychiatric Genetics Group Trinity Centre St. James's Hospital Dublin 8

[Freesurfer] recon_all exited with errors

files have been created, should I be too concerned about this? Also, I should mention that I am running my scripts on a high performance computing cluster and not locally on my linux. Thank you for your help! Sinead -- Sinead Kelly Neuropsychiatric Genetics Group Trinity Centre St. James's

Re: [Freesurfer] recon_all exited with errors

, as the relevant files have been created, should I be too concerned about this? Also, I should mention that I am running my scripts on a high performance computing cluster and not locally on my linux. Thank you for your help! Sinead -- Sinead Kelly Neuropsychiatric Genetics Group Trinity

[Freesurfer] Cortical thickness analysis on data acquired from multiple sites

reading the literature it seems that this is not a major problem but I just wanted to get some more thoughts on this. Thank you for your help, Sinead -- Sinead Kelly Neuropsychiatric Genetics Group Trinity Centre St. James's Hospital Dublin 8

Re: [Freesurfer] Cortical thickness analysis on data acquired from multiple sites

...@nmr.mgh.harvard.edu[ freesurfer-boun...@nmr.mgh.**harvard.edufreesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Bruce Fischl [fis...@nmr.mgh.harvard.edu] Sent: Monday, February 18, 2013 10:59 AM To: Jorge Jovicich Cc: Sinead Kelly; freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Cortical

[Freesurfer] Cortical thickness analysis using *.nii files

Dear members, I am new to Freesurfer and to cortical thickness analysis so I would like to ask a very basic question that I cannot find the answer to online - is it possible to conduct cortical thickness analysis using T1 files in *.nii format? -- Sinead Kelly Neuropsychiatric Genetics Group