Re: [Freesurfer] Longitudinal edits on norm.mgz instead of brainmask

External Email - Use Caution Hi Douglas, Thank you very much for your answer. I tried the command you suggested and it did not seem to transfer the edits, so I added the flag -keep_mask_deletion_edits and that seems to work. Would you mind confirming that the final command

Re: [Freesurfer] Robust Regression with Univariate LME

External Email - Use Caution Hi FreeSurfer Experts, Just bumping this item up. There are a couple of outliers in my data. I had winsorized the variable, but now I am trying to use robust regression to weight these outliers in my longitudinal analyses. In Matlab there is a

Re: [Freesurfer] qdec and mris_anatomical_stats help

External Email - Use Caution Hello Freesurfer experts, Just wanted to follow-up from my last email. If any clarification is needed regarding what I'm trying to understand from mris_anatomical_stats, please let me know! Kind regards, Alex On Fri, May 15, 2020 at 8:17 PM Lab of

Re: [Freesurfer] Group Analysis Covariates

External Email - Use Caution Attached are the fsgd and Xg.dat files. --- Jessica Hua, M.A. Cognitive and Emotional Control Lab Doctoral Candidate Clinical Psychology University of Missouri GroupComparison_AllMRI.AgeSexICV.fsgd Description: GroupComparison_AllMRI.AgeSexICV.fsgd

Re: [Freesurfer] Group Analysis Covariates

External Email - Use Caution I was not sure how to modify the last line in your code in order to calculate adjusted values accounting for age, sex, and ICV for each participant (this is a three group design). Your code: There is not an easy way to do it, but you can do it in

Re: [Freesurfer] vol2subfield single time course from multiple regions

External Email - Use Caution thanks! > Il 18 maggio 2020 alle 16.23 Bruce Fischl < fis...@nmr.mgh.harvard.edu > mailto:fis...@nmr.mgh.harvard.edu > ha scritto: > > > --replaceonly \ > --replaceonly \ > . > . > . > > On Mon, 18 May 2020,

Re: [Freesurfer] Volume timeseries to native and fsaverage

oh, if you want them in conformed space, they are already there On 5/18/2020 11:34 AM, özenç taşkın wrote: External Email - Use Caution Awesome, thanks Doug. That's pretty helpful. I should also use the orig.mgz with tkregister2 instead of rawavg.mgz if the aim is to get surface

Re: [Freesurfer] Longitudinal edits on norm.mgz instead of brainmask

If all you did was to remove voxels from the mask, then you should be able to run mri_mask brainmask.mgz norm.mgz   brainmask.mgz (make backups of brainmask.mgz before you run that as it will be overwritten). On 5/17/2020 7:55 PM, Elena Pozzi wrote: > External Email - Use Caution >

Re: [Freesurfer] Volume timeseries to native and fsaverage

External Email - Use Caution Awesome, thanks Doug. That's pretty helpful. I should also use the orig.mgz with tkregister2 instead of rawavg.mgz if the aim is to get surface maps in native space, am I right ? And by native space I mean the subjects' native brain structure and

Re: [Freesurfer] Get Freesurfer versions 4 and 5

External Email - Use Caution Sorry, found them, never mind! On 18/05/2020 12:26, Ian wrote: External Email - Use Caution Hi freesurfers, Is it possible to download freesurfer versions 4 and 5? Thanks, Ian -- *Ian Hardingham*

[Freesurfer] Get Freesurfer versions 4 and 5

External Email - Use Caution Hi freesurfers, Is it possible to download freesurfer versions 4 and 5? Thanks, Ian -- *Ian Hardingham* ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu

Re: [Freesurfer] vol2subfield single time course from multiple regions

--replaceonly \ --replaceonly \ . . . On Mon, 18 May 2020, std...@virgilio.it wrote: External Email - Use Caution As reported in previous mails I have do it but with some problems. Moreover, how can I do with multiple arguments (more than 2)? Il 17 maggio 2020

Re: [Freesurfer] rh postcentral gyrus segmentation error

Hi Ken have you identified why it is missing cortex? Is the wm dark-ish (<<110) there? Did the skull stripping remove something? Was the wm.mgz/?h.orig correct? cheers Bruce On Mon, 18 May 2020, KennethSPrice wrote: External Email - Use Caution Hello Freesurfer

[Freesurfer] QDEC error Two Groups three covariates

External Email - Use Caution Dear FreeSurfer Developers, I’m attempting to run a cortical thickness correlation analysis regressing out the effect of brain size, age and gender. However, when attempting to run this analysis in qdec (or trying to use mri_glmfit separately) I get

Re: [Freesurfer] vol2subfield single time course from multiple regions

External Email - Use Caution As reported in previous mails I have do it but with some problems. Moreover, how can I do with multiple arguments (more than 2)? > Il 17 maggio 2020 alle 21.30 Bruce Fischl < fis...@nmr.mgh.harvard.edu > mailto:fis...@nmr.mgh.harvard.edu > ha

[Freesurfer] rh postcentral gyrus segmentation error

External Email - Use Caution Hello Freesurfer Experts! I am looking for some guidance on improving the pial surface estimation at the right post-central gyrus. Looking at the aparc+aseg file, it is clear that the pial surface estimation missed some cortex. I have already