Re: [Freesurfer] local gyrificaton index

Hi all, I found answers to ponts 1 and 2 in the webpage. Sorry for my question Angela > Hi all, > > I would need some information about the local gyrification index. > I run the analyses and found which are the average indices for subject and > hemisphere. > > 1. Is there a method to perform

Re: [Freesurfer] What provides mri_annot2aparc?

Hi Chris, I think you must want mri_aparc2annot doug On 11/28/2012 03:42 PM, Chris McNorgan wrote: > Hello all, > > I've posted this question on the cmtk-users google group as well. In > that forum there was an author who had been working on applying the > Lausanne 2008 parcellation scheme to a

[Freesurfer] What provides mri_annot2aparc?

Hello all, I've posted this question on the cmtk-users google group as well. In that forum there was an author who had been working on applying the Lausanne 2008 parcellation scheme to a functional data analysis. After running the connectomemapper toolkit to subdivide the Freesurfer parcellat

Re: [Freesurfer] FW: TRACULA some fiber volumes being too small

Hi Fernando - I looked at your data and changing the sign of the z coordinate in your gradient table gave me eigenvectors that looked fine in both fslview and freeview. Why you would get eigenvectors that look different in freeview and fslview before flipping z but not after is still a myster

Re: [Freesurfer] (no subject)

Hugh, That fix is described in the Known Issues section of 5.1 on the Release Notes page: https://surfer.nmr.mgh.harvard.edu/fswiki/ReleaseNotes look for the section where you need to edit your recon-all script to comment-out the line where the control point is used by ca_norm. Nick On Tue, 2

Re: [Freesurfer] Subgroup analysis

Hi, I think (hope) i am finally getting to grips with how to analyse things but wanted to check one last thing. Say I have 1 factor with 3 levels (3 groups of subjects) and 2 covariates (age and icv). My design matrix would include: Regressor 1 - ones for subject in Gp 1, 0 otherwise, codes

Re: [Freesurfer] preproc-sess and option -mni305-1mm results in an error

Just subcortical. BTW, going to 1mm will probably create very large files. doug On 11/28/2012 03:52 AM, Jörg Pfannmöller wrote: > A last question to this topic. Does the resolution of the MNI305 brain > affected the surface based analysis or is it exclusively affecting the > subcortical analysis

Re: [Freesurfer] optseq2 using dependent trials

Hi Danielle, there is not a way to do this directly. You can use the --focb argument (first-order counterbalancing) to optimize the likelihood that you get an equal number of cong following incong, etc. Maybe use --focb 1000 doug On 11/28/2012 09:49 AM, Danielle Miller wrote: > > Hi Freesurfe

[Freesurfer] local gyrificaton index

Hi all, I would need some information about the local gyrification index. I run the analyses and found which are the average indices for subject and hemisphere. 1. Is there a method to perform vertex-wise group statistics? that is may I compare maps of gyrification across groups? 2. Is there a m

Re: [Freesurfer] Info extraction hippocampus

Hi Andre no, sorry, that's how long it takes Bruce On Wed, 28 Nov 2012, Andrea Tateo wrote: Hello FS experts, I would like to extract from head's MRI a bunary image showing  only hippocampus. I used command: ### mri_convert FILE_NAME.nii path/directory/NAME_OUTPUT.mgz recon-

Re: [Freesurfer] TRACULA tract path failure

Hi Arman - Have you ruled out any issues with the gradient directions? In situations where the problem is wide-spread, this seems to be the usual suspect. If you've checked the eigenvectors and they're ok, can you send an example case where the problem persists? You can use this page to uploa

[Freesurfer] Info extraction hippocampus

Hello FS experts, I would like to extract from head's MRI a bunary image showing only hippocampus. I used command: ### mri_convert FILE_NAME.nii path/directory/NAME_OUTPUT.mgz recon-all -s SUBJECT_name -autorecon-all mri_extract_label aseg.mgz 17 53 hippocampi.mgz #

[Freesurfer] optseq2 using dependent trials

Hi Freesurfer, I have a paradigm in which the conditions are dependent on each other. That is, trials (e.g., congruent or incongruent) are linked to each other in that I want an equal number of trials to follow each other (e.g., congruent- congruent, congruent- incongruent, incongruent-congruent,

Re: [Freesurfer] bad reconstructions

Hi Cathy, yes, specify -clean on the recon-all comomand line and it should remove previous edits cheers Bruce On Wed, 28 Nov 2012, Catherine Bois wrote: > Hi, sorry I have an additional question; when reconstructed 9with edits), if > the scan seemingly is worse off than before the > edits were

[Freesurfer] hippocampal segmentation converting mgz to nii

Dear freesurfer users, I have used freesurfer to segment hippocampal subfields. Then I used freeview to convert the derived .mgz files in .nii files for further analysis. I estimated the hippocampal subfields volumes with the command: kvlQuantifyPosteriorProbabilityImages $ FREESURFER_HOME/ dat

[Freesurfer] bad reconstructions

Hi, sorry I have an additional question; when reconstructed 9with edits), if the scan seemingly is worse off than before the edits were made; is there a "recon clean" command; that one can use that takes away all the edits and "starts from scratch? Thank you, Cathy _

Re: [Freesurfer] preproc-sess and option -mni305-1mm results in an error

A last question to this topic. Does the resolution of the MNI305 brain affected the surface based analysis or is it exclusively affecting the subcortical analysis? On Tue, 27 Nov 2012 13:30:04 -0500 Douglas N Greve wrote: > Note that each of those set commands should be a single line. The file