[Freesurfer] Paired analysis: use of covariates

Dear FreeSurfer experts, I'm trying to implement the steps you indicate in the Paired Analysis' wiki site, but I still don't get something: In this site, you show the next FSGD file: GroupDescriptorFile 1 Class Main Variables Age Input subject1pair Main 30 Input subject2pair Main 40 Input

[Freesurfer] Research Fellow Positions on Imaging Genetics of Infant Brain

Postdoctoral Fellow Position on Imaging Genetics of Infants Job description: Computation functional anatomy laboratory at National University of Singapore (http://www.bioeng.nus.edu.sg/cfa) focuses on brain and cognition studies using neuroimaging techniques. Our group is leading a large-scale

[Freesurfer] Research Fellow Positions on Imaging Genetics of Infant Brain

Postdoctoral Fellow Position on Imaging Genetics of Infants Job description: Computation functional anatomy laboratory at National University of Singapore (http://www.bioeng.nus.edu.sg/cfa) focuses on brain and cognition studies using neuroimaging techniques. Our group is leading a large-scale

[Freesurfer] New features in TRACULA

Hi all - I have just posted a tracula software update. This update adds some new functionality without any changes to any existing functionality, so you can use it with any analyses you have already done in 5.3. What's new: 1. Compute measures of head motion, as in our recent paper:

Re: [Freesurfer] New features in TRACULA

Hi Vincent - That is correct. The average values of FA/MD/RD/AD in pathstats.byvoxel.txt are averaged over all the sampled paths for that subject at equivalent positions along the trajectory of the path. Roughly speaking, if 0=s=1 is the arc length along the path, where s=0 is the starting

Re: [Freesurfer] xhemi correct for multiple comparisons

Run mris_preproc with --paired-diff-norm which will then compute LI = (L-R)/(.5*(L+R)) Note that some people use LI = (L-R)/(L+R) If that is what you want, then divide the mris_preproc result by 2 doug On 12/08/2013 08:45 PM, krista kelly wrote: Hello, I'm analysing interhemispheric

Re: [Freesurfer] Paired analysis: use of covariates

Hi Aldo, this ok to me. doug On 12/09/2013 04:53 AM, Aldo Cordova wrote: Dear FreeSurfer experts, I'm trying to implement the steps you indicate in the Paired Analysis' wiki site, but I still don't get something: In this site, you show the next FSGD file: GroupDescriptorFile 1 Class

Re: [Freesurfer] xhemi correct for multiple comparisons

Thanks Doug! I'll try that instead. Also, do you or anyone else happen to have the answers to my other questions (reposted below): 1) When viewing the results in tksurfer, which color represents left hemisphere is larger and which represents right hemisphere is larger? 2) I have no idea how to

Re: [Freesurfer] xhemi correct for multiple comparisons

On 12/09/2013 11:53 AM, krista kelly wrote: Thanks Doug! I'll try that instead. Also, do you or anyone else happen to have the answers to my other questions (reposted below): 1) When viewing the results in tksurfer, which color represents left hemisphere is larger and which represents

Re: [Freesurfer] qdec analysis with 2 covariates

Hi Jon, QDEC does not currently allow more than one covariates of interest. You will have to use the command-line stream (ie, mris_preproc, mri_surf2surf, mri_glmfit, mri_glmfit-sim) doug On 12/05/2013 02:57 PM, Jon Wieser wrote: HI freesurfer experts I want to do an analysis in qdec with

Re: [Freesurfer] qdec analysis with 2 covariates

thanks doug, We've run a 2x2 analysis for thickness in Qdec and want the get the average thickness value for each cluster, for each subject. How can i get a table of thickness data , for feach subject in the analysis Jon - Original Message - From: Douglas N Greve

Re: [Freesurfer] qdec analysis with 2 covariates

It is in one of the output files. Look for the .dat file in mri_glmfit-sim --help On 12/09/2013 03:01 PM, Jon Wieser wrote: thanks doug, We've run a 2x2 analysis for thickness in Qdec and want the get the average thickness value for each cluster, for each subject. How can i get a table of

Re: [Freesurfer] xhemi correct for multiple comparisons

Great Thanks! On Mon, Dec 9, 2013 at 11:57 AM, Douglas N Greve gr...@nmr.mgh.harvard.eduwrote: On 12/09/2013 11:53 AM, krista kelly wrote: Thanks Doug! I'll try that instead. Also, do you or anyone else happen to have the answers to my other questions (reposted below): 1) When

[Freesurfer] mris_anatomical_stats error

Hi, I'm trying to run mris_anatomical_stats to get cortical thickness from labels for each participant but I keep getting the following error: MRISread: file '/Applications/freesurfer/subjects/MB19/surf/lh.thickness' has many more faces than vertices! Probably trying to use a scalar data file as

Re: [Freesurfer] mris_anatomical_stats error

Hi Krista the optional last argument for mris_anatomical_stats is a surface name (not a scalar field over the surface, like the thickness file) cheers Bruce On Mon, 9 Dec 2013, krista kelly wrote: Hi, I'm trying to run mris_anatomical_stats to get cortical thickness from labels for each

Re: [Freesurfer] qdec analysis with 2 covariates

I found data for the average thickness all subjects for each cluster, but I haven't found the individual subject's thickness for each cluster. can you direct me to that data? Jon - Original Message - From: Douglas N Greve gr...@nmr.mgh.harvard.edu To: Jon Wieser wie...@uwm.edu Cc:

[Freesurfer] viewing the atlas?

Hello, I'm looking for a way to view the Desikan-Killiany atlas. I'd like to open the file $FREESURFER_HOME/average/?h.curvature.buckner40.filled.desikan_killiany.gcs in Freeview (or Tkmedit, or similar) and be able to see the segmentations and segmentation names, as well as pan through all

Re: [Freesurfer] qdec analysis with 2 covariates

which file did you look in? It should have a name like cache.th20.abs.y.ocn.dat On 12/09/2013 05:09 PM, Jon Wieser wrote: I found data for the average thickness all subjects for each cluster, but I haven't found the individual subject's thickness for each cluster. can you direct me to that

[Freesurfer] Cortical thickness values of significant clusters

Dear Freesurfer users, I have just ran mri-glmfit on cortical thickness data and corrected for multiple comparisons using Monte Carlo Simulation. I have significant clusters (cwp .05), however, when I analyse the average thickness measures from the xxx.y.ocn.dat file in SPSS, there are no

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:

Re: [Freesurfer] viewing the atlas?

Do you mean you want to view it in the volume or the surface? If you want to load it as a volume, you can try using the aparc+aseg.mgz in the fsaverage folder doug On 12/9/13 5:26 PM, Gregg, Brian E. wrote: Hello, I'm looking for a way to view the Desikan-Killiany atlas. I'd like to

[Freesurfer] after PialEdit_tktools

Dear all, I run recon-all -autorecon-pial -s subjects after editing the pial by PialEdit_tktools. However I only find -autorecon2-pial option in recon-all manual. So I donot know whether I should run the recon-all -s subjects -autorecon3 to complete all the 31 stages? Thanks. All the best.

Re: [Freesurfer] Occipital cortex segmentation

Higher than 1mm resolution helps a lot. We use 0.7mm isotropic in the HCP. Peace, Matt. From: Megha K. megha...@gmail.com Date: Monday, December 9, 2013 10:23 PM To: freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] Occipital cortex segmentation Dear Sir/Madam, I am using freesurfer

Re: [Freesurfer] Cortical thickness values of significant clusters

Hi Doug, thank you for your reply. It is unusual as I also get a significant result in SPSS for a non-significant cluster in mri-glmfit. Just to make sure I am doing things correctly - I am interpreting each column in the xxx.y.ocn.dat file as a cluster in the xxx.sig.cluster.summary file (in