[Freesurfer] Problem with Longitudinal QDEC file and mris_preproc

--out outpufile Thank you for taking the time to read this email, I sincerely appreciate it. Best, Jennifer Legault Ph.D candidate, Neuroscience Brain, Language, and Computation Lab The Pennsylvania State University -- Jennifer Legault Ph.D candidate, Neuroscience Brain, Language, and Computation

Re: [Freesurfer] Problem with Longitudinal QDEC file and mris_preproc

Hi Martin, Thank you for your help and clarifications. I did run the *_to_table commands and now my LME analyses are running smoothly. Best, Jennifer Legault On Mon, Mar 9, 2015 at 11:35 AM, Martin Reuter wrote: > Hi Jennifer, > > if you are interested in volumes from the stats

[Freesurfer] mri_glmfit error: Matrix is ill-conditioned or badly scaled

/Contrast_math_monly_EnglishParityRT_a_g_TIV.txt --surf fsaverage rh --cortex --glmdir rh.mono_EnglishParityRT_age_gender_TIV_100.glmdir 2. The FSGD file (if using one) 3. And the design matrix above I am also attaching the FSGD file. Best, Jennifer Legault

Re: [Freesurfer] mri_glmfit error: Matrix is ill-conditioned or badly scaled

should take the demeaned x 100 covariates and divide them by the standard deviation? Or would it be better to take regular demeaned values and divide them by the standard deviation? Best, Jennifer Legault On Mon, Jul 18, 2016 at 12:43 PM, Douglas N Greve wrote: > This is almost surel

[Freesurfer] Permission denied error with mri_surfcluster command

x27;t create file /gpfs/home/jtl190/work/structurals/fsaverage/surf/rh.rh_time_cluster.w Permission denied Thank you for taking the time to read this email. Sincerely, Jennifer Legault -- Jennifer Legault Ph.D candidate, Neuroscience Brain, Language, and Computation Lab The Pennsylvania

Re: [Freesurfer] Permission denied error with mri_surfcluster command

On Wed, Feb 10, 2016 at 1:41 PM, Douglas N Greve wrote: > Try specifying the full path to the output > > On 02/10/2016 12:59 PM, Jennifer Legault wrote: > > Dear experts, > > > > I am trying to use the cluster thresholding command for my freesurfer > > LME

Re: [Freesurfer] Permission denied error with mri_surfcluster command

I see the clusterwise P value, like it is shown here <https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysisClusterSummary> ? Best, Jen On Wed, Feb 10, 2016 at 1:50 PM, Douglas N Greve wrote: > I meant for the output files, so the --o in particular > > On 02/10/2016 01:47 P

Re: [Freesurfer] Permission denied error with mri_surfcluster command

the sign of the contrast (or abs). Then the relevant output > will be the --sum. You can run it with --help to get more info. > > > On 2/10/16 5:11 PM, Jennifer Legault wrote: > > Thank you very much for your help! I still received a "cannot read file > type" error

Re: [Freesurfer] Permission denied error with mri_surfcluster command

rected map (a sig.cluster.mgh file) as they do for the Clusterwise Correction for Multiple Comparisons tutorial here <https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis>? Best, Jen On Thu, Feb 11, 2016 at 11:39 AM, Douglas N Greve wrote: > > > On 02/11/2016 11:19 A

Re: [Freesurfer] Permission denied error with mri_surfcluster command

ing it in mri_glmfit with --osgm just to get the FWHM out > of it. > > You should be able to output a .mgh file instead of a .w file > > > On 02/11/2016 01:07 PM, Jennifer Legault wrote: > > That's very useful, thank you. In terms of FWHM, I am examining gray > > m

[Freesurfer] How to view entire brain results in Freeview for LME data

rc and aseg. * Currently I can only view the aparc results for each of the hemispheres separately (and I haven't found a way to visualize the aseg data). Thank you for taking the time to read this email. Best, Jennifer Legault Ph.D candidate, Neuroscience Brain, Language, and Computation Lab The Pe

Re: [Freesurfer] How to view entire brain results in Freeview for LME data

; aseg data? > > On 04/01/2016 10:46 AM, Jennifer Legault wrote: > > Dear Freesurfer Experts, > > > > I have run my participants' longitudinal sMRI data through the > > preprocessing longitudinal pipeline, ran the LME multivariate > > analysis, cluster-th

Re: [Freesurfer] How to view entire brain results in Freeview for LME data

N Greve wrote: > > > On 04/01/2016 04:44 PM, Jennifer Legault wrote: >> Hi Doug, >> >> Thanks for your quick response! When running the LME mass univariate >> analysis, I am assuming this also includes subcortical structures, >> correct? > Which proces

Re: [Freesurfer] How to view entire brain results in Freeview for LME data

t;done the cluster-thresholding for the aparc > data" > > The aparc data is an ROI and so you should not have (could not have) > done clusterwise thresholding (?) > > On 04/08/2016 12:57 PM, Jennifer Legault wrote: >> Hi Doug, >> >> I'm currently runnin

[Freesurfer] Is it possible to run a conjunction analysis on longitudinal sMRI data in Freesurfer?

the .sig files from the LME analyses, given that these are structural MRI data? I've only ever seen these analyses being done with fMRI data. Thank you for taking the time to read this email. Best, Jennifer Legault -- Jennifer Legault Ph.D candidate, Neuroscience Brain, Language, and Computa

[Freesurfer] Error with FSGD format

extra spaces at the end of lines, I still get this error. I am attaching one such file here. Any feedback would be greatly appreciated. Best, Jen -- Jennifer Legault PhD, Neuroscience Postdoctoral Scholar Language Acquisition and Brain Lab University of Delaware GroupDescriptorFile 1 Title

[Freesurfer] How to convert a functional FSL mask to an anatomical Freesurfer mask

x Nsubjects)? Thanks for all your help! Best, Jen -- Jennifer Legault PhD, Neuroscience Postdoctoral Scholar Language Acquisition and Brain Lab University of Delaware ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https

[Freesurfer] mri_glmfit will not use mask or label

ask). Are there any recommendations for steps I should take to make sure I'm only searching for regions inside the mask? Best, Jen -- Jennifer Legault PhD, Neuroscience Postdoctoral Scholar Language Acquisition and Brain Lab University of Delaware ___ Freesurfe

Re: [Freesurfer] mri_glmfit will not use mask or label

External Email - Use Caution Thank you, that worked perfectly! Best, Jen On Wed, Jun 26, 2019 at 5:27 PM Greve, Douglas N.,Ph.D. < dgr...@mgh.harvard.edu> wrote: > Try running it without --cortex > > On 6/26/19 4:57 PM, Jennifer Legault wrote: > > >