[Freesurfer] converting a mask made in MNI space to subject space

2018-07-25 Thread Sims, Sara A
External Email - Use Caution Hello, I am trying to put a mask that I made on the MNI brain (that had been run through recon) into individual subject space. I have already created a registration matrix using the following command: mni152reg --s $patient --o $registration/$patient/

Re: [Freesurfer] ICV as covariate for controls vs. patients

2018-07-25 Thread Martin Juneja
External Email - Use Caution Dr. Greve, I am sorry if my questions were not clear in previous email. Basically, I do not know what to conclude from this gamma comparison i.e. with and without ICV as covariate. Clearly, adding ICV as covariate here, is reducing effect size all ove

Re: [Freesurfer] petsurfer

2018-07-25 Thread John Anderson
External Email - Use Caution Dear Dr Greve, thank you for great responses and detailed explanation! Very highly appreciated!! Thank you for sharing that valuable manuscript! Wish you all the best, John On 7/25/18 8:31 AM, John Anderson wrote: Dear Petsurfer experts, I used par

Re: [Freesurfer] ICV as covariate for controls vs. patients

2018-07-25 Thread Douglas Greve
The gammas do look different, but it is hard to tell whether they are, eg, changing sign. Not sure what you want me to comment on. On 7/24/18 2:17 PM, Martin Juneja wrote: External Email - Use Caution Just to add some more info here: The peak location of regions, X1 and X2, which I

Re: [Freesurfer] Matched analysis with 2 controls 1 case weighting

2018-07-25 Thread Douglas Greve
On 7/24/18 1:56 PM, Dowling, Kevin Francis wrote: Hi Doug, Thank you very much for your reply and my apologies for this belated response. The two approaches you mentioned were the only ones we could think that might work for a DV like cortical thickness. That being said, we were originally th

Re: [Freesurfer] petsurfer

2018-07-25 Thread Douglas Greve
On 7/25/18 8:31 AM, John Anderson wrote: External Email - Use Caution Dear Petsurfer experts, I used partsurfer in FS6 and had applied partial volume correction (PVC) on PET data. I followed the same steps as in wiki which was very well explained! Thank you!. The analyses went fine.

[Freesurfer] longitudinal qdec contrasts

2018-07-25 Thread Courtney Haswell
External Email - Use Caution We are working in Matlab to analyze longitudinal data using the mass-univariate approach to Linear Mixed Effects (LME) Modeling. Step 1: Below is the design matrix (first few rows) we created in an effort to compare subjects with low, moderate, and hi

[Freesurfer] petsurfer

2018-07-25 Thread John Anderson
External Email - Use Caution Dear Petsurfer experts, I used partsurfer in FS6 and had applied partial volume correction (PVC) on PET data. I followed the same steps as in wiki which was very well explained! Thank you!. The analyses went fine... I would like to inquire about some