Re: [Freesurfer] -qcache in recon-all commnd

External Email - Use Caution Hoping to get some clarification. Any further comments on the correct command to run after making manual edits to wm, brainmask, and adding control control points? The studies were originally processed using the following: recon-all -s -i -hippocampal

[Freesurfer] Longitudinal analysis of multiple scanner acquisitions

External Email - Use Caution Good afternoon Freesurfer team, I want to run the longitudinal pipeline on multiple groups of subjects, the problem is we are at the mercy of the scanners available to us at the various time-points. We have two different Siemens 1.5 scanners (same ty

[Freesurfer] mri_gtmpvc

Dear Dr Greeve, Kindly, I'd like t to inquire about the command "mri_gtmpvc" in PET surfer. Can I use this command to apply partial volume correction on non-PET data (e.g. DTI or ASL)? Thanks! Mohamad ___ Freesurfer mailing list Freesurfer@nmr.mgh.harv

Re: [Freesurfer] Fwd: Correcting defect issue

Hi Julian it looks like there is a spurious inter-hemisphereic connection that is not removed, possibly because some extra-cerebral tissue is left around? Check the wm.mgz and the filled.mgz and edit the wm to correct it cheers Bruce On Thu, 7 Jun 2018, Julian Macoveanu wrote: Ex

[Freesurfer] connectivity between two ROIs

Dear all, I would like to use the fsfast functional connectivity pipeline to compute connectivity between two binarized ROIs. One of the ROIs is a surface ROI, the other is a hippocampal subfield. Based on the tutorial on http://surfer.nmr.mgh.harvard.edu/fswiki/FsFastFunctionalConnectivityWal

[Freesurfer] Python Developer Study

External Email - Use Caution Dear Freesurfer community, We are currently interested in recruiting Python developers for a study. Information can be found below. Thank you, Désirée Lussier, MS Graduate Student Department of Psychology University of Florida [1509730522218_gi

Re: [Freesurfer] "WARNING: Image geometries differ across time" upon running base step of longitudinal pipeline

External Email - Use Caution Hi Bruce, Thanks for your answer! Before seeing this warning (rather: error, as no output is produced), I'd not have thought the pre-post images have different geometries, as I'm pretty sure their acquisition parameters were the same. The pre and post

Re: [Freesurfer] E-TIV and Linux version: Some quick questions

yes, I think that is correct On Thu, 7 Jun 2018, Jeff Crawford wrote: External Email - Use Caution Thanks so much for the reply, Bruce. I just had a follow up to question to #1. If E-TIV is calculated early on is the process, what is the minimum amount of recon I would need to run to b

Re: [Freesurfer] E-TIV and Linux version: Some quick questions

External Email - Use Caution Thanks so much for the reply, Bruce. I just had a follow up to question to #1. If E-TIV is calculated early on is the process, what is the minimum amount of recon I would need to run to be able to calculate that value? Say I was only interested in Fr

Re: [Freesurfer] E-TIV and Linux version: Some quick questions

Hi Jeff 1. This should be fine. 2. I would think this is ok as well, but maybe you should run a few subjects on both and see if there are significant differences cheers Bruce On Thu, 7 Jun 2018, Jeff Crawford wrote: External Email - Use Caution Dear Freesurfer Experts, I

[Freesurfer] E-TIV and Linux version: Some quick questions

External Email - Use Caution Dear Freesurfer Experts, I have two questions that I hope are easy to answer. 1. Would the calculation for E-TIV change if I edited the pial and reran recon-all as in this tutorial below? https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Pi