Re: [Freesurfer] using tkregister2 to check registration to custom atlas

--targ $SUBJECTS_DIR/subject/mri/orig.mgz --ixfm $SUBJECTS_DIR/subject/mri/transforms/talairach.xfm -outxfm $SUBJECTS_DIR/subject/mri/transforms/talairach.xfm --reg deleteme.reg --s subject --surfs Best, Lindsay On Wed, Jan 16, 2019 at 10:04 AM lindsay hanford wrote: > Hi, > I just wan

Re: [Freesurfer] using tkregister2 to check registration to custom atlas

the same space. Thanks, Lindsay On Wed, Dec 19, 2018 at 10:36 AM lindsay hanford wrote: > Hello Freesurfer Community, > > I am interested in seeing how well my subject scan registered to a custom > atlas after being run through recon-all. From Freesurfer Wiki, although it > is

Re: [Freesurfer] recalculate mean cortical thickness and/or regional thickness using a SD threshold or exclusion mask

anted to exclude. matlab code: datafile_lh=MRIread('data_lh.mgh') maskfile_lh=MRIread('mask_lh.mgh') newmatrix=datafile.vol.*mask.vol). Thanks again! Lindsay On Fri, Jan 4, 2019 at 10:05 AM lindsay hanford wrote: > Hi Bruce, > Sorry for the late reply. I have b

Re: [Freesurfer] recalculate mean cortical thickness and/or regional thickness using a SD threshold or exclusion mask

External Email - Use Caution Hi Bruce, Sorry for the late reply. I have been searching the forum and the freesurfer wiki. Are there instructions somewhere on how to do this in matlab? Thanks, Lindsay On Thu, Dec 20, 2018 at 2:41 PM lindsay hanford wrote: > Hello Freesur

[Freesurfer] recalculate mean cortical thickness and/or regional thickness using a SD threshold or exclusion mask

External Email - Use Caution Hello Freesurfer Community, I am wondering if it is possible to recalculate cortical thickness metrics (perhaps using mri_segstats or aparcstats2table) while including either a SD threshold or an exclusion mask. Using mri_surf2surf to register scans t

[Freesurfer] using tkregister2 to check registration to custom atlas

External Email - Use Caution Hello Freesurfer Community, I am interested in seeing how well my subject scan registered to a custom atlas after being run through recon-all. From Freesurfer Wiki, although it is possible to see this in freeview, tkregister2 seems to be the best metho

[Freesurfer] Extract individual vertex thickness values from cortical parcellations

parcellated regions. https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2012-January/022097.html Thank you in advance, Lindsay -- *Lindsay Hanford, PhD* *The Buckner Laboratory* *|* *Harvard University* ___ Freesurfer mailing list Freesurfer

[Freesurfer] create mask from cluster number?

Hello Freesurfer Developers, The main point of my post is to determine whether its possible to create a mask from a cluster ID run using a subset of the sample, and then use that mask to extract cortical thickness values from a model run with the full sample. I am running a pretty basic cortical

Re: [Freesurfer] Contrast files for a complex ANCOVA (involving multiple categorical covariates) model

0.25 0.25 -0.25 -0.25 -0.25 -0.25 0.25 0.25 0 0 0 0 0 0 0 0 or perhaps? 0.5 0.5 0 0 -0.5 -0.5 0 0 0 0 0 0 0 0 0 0 0 0 0.5 0.5 0 0 -0.5 -0.5 0 0 0 0 0 0 0 0 Once again, thank you in advance!! Lindsay -- Lindsay Hanford, BSc, PhD Candidate McMaster Integrative Neuroscience Discovery &

Re: [Freesurfer] Contrast files for a complex ANCOVA (involving multiple categorical covariates) model

w should I proceed? Thanks again, Lindsay -- Lindsay Hanford, BSc, PhD Candidate McMaster Integrative Neuroscience Discovery & Study | *Department of Psychology, Neuroscience & Behaviour * McMaster University *|* 1280 Main Street West, PC329 Psychology Building *|* Hamilton, ON, L8S 4L8 9

[Freesurfer] Contrast files for a complex ANCOVA (involving multiple categorical covariates) model

ndsay -- Lindsay Hanford, BSc, PhD Candidate McMaster Integrative Neuroscience Discovery & Study | *Department of Psychology, Neuroscience & Behaviour * McMaster University *|* 1280 Main Street West, PC329 Psychology Building *|* Hamilton, ON, L8S 4L8 905 525 9140 x24784 *|* lindsay.hanf

Re: [Freesurfer] mri_glmfit error: matrix is ill-conditioned or badly scaled, condno = 1e+08

Thank you Doug! I replaced all my spaces with new spaces and it worked! Much appreciated! Lindsay On Fri, Dec 12, 2014 at 12:09 PM, lindsay hanford wrote: > > Hi Doug! > > Thank you very much for your reply. I made the fsgd file in a plain-text > file using the textedit progr

Re: [Freesurfer] mri_glmfit error: matrix is ill-conditioned or badly scaled, condno = 1e+08

. Lindsay On Thu, Dec 11, 2014 at 9:09 AM, lindsay hanford wrote: > > Hello, > > Has anyone had a chance to look at this? I still haven't been able to > solve the problem. > Thanks! > > Lindsay > > On Mon, Dec 1, 2014 at 2:41 PM, lindsay hanford >

Re: [Freesurfer] mri_glmfit error: matrix is ill-conditioned or badly scaled, condno = 1e+08

Hello, Has anyone had a chance to look at this? I still haven't been able to solve the problem. Thanks! Lindsay On Mon, Dec 1, 2014 at 2:41 PM, lindsay hanford wrote: > Hello Freesurfer Experts! > > I am encountering the dreaded mri_glmfit error: matrix is ill-conditioned >

[Freesurfer] mri_glmfit error: matrix is ill-conditioned or badly scaled, condno = 1e+08

group analysis (diagnosis) not controlling for sex or age, however, as soon as I try to run four groups, I encounter this error. I have no idea how to proceed. I am looking forward to your response! Thanks, Lindsay -- Lindsay Hanford, BSc, PhD Candidate McMaster Integrative Neuroscience Discovery