[Freesurfer] Using an ROI and not correcting/"fixing" the rest of the image

Hi, I am planning on looking at a specific region of interest, and I am wondering it is possible to only "quality check" this region and leave the rest of the brain as is. Meaning, can I save the time of going through every slice and re-assigning voxels for the entire brain and just focus on m

Re: [Freesurfer] Using an ROI and not correcting/"fixing" the rest of the image

: Kairys, Anson Cc: 'freesurfer@nmr.mgh.harvard.edu' Subject: Re: [Freesurfer] Using an ROI and not correcting/"fixing" the rest of the image Hi Anson yes, that's ok as long as you make sure that the registration (sphere.reg) is ok for group results. cheers Bruce On Thu,

[Freesurfer] Creating ROI and only looking at this ROI in analysis

Hi everyone, I am attempting to create and ROI and look at cortical thickness only within this region (ignoring results outside this region in hopes of saving some time going through and re-assiging voxels with poor segmentation). Question: How should I create the ROI (typically I would use MA

[Freesurfer] Building ROI from SPM5 MNI results

Hi Everyone, I would like to "import" an ROI into a FS analysis and extract thickness measures form within this region. Is this at all possible? Thanks Anson K, ** Electronic Mail is not secure, may not be read every day, and should not be

[Freesurfer] Qdec error

I got an error beginning with this. Thanks for any help Error in analyze: command failed: mri_glmfit --y //qdec/LH_insula_thick/y.mgh --fsgd ** Electronic Mail is not secure, may not be read every day, and should not be used for urgent or

[Freesurfer] Qdec Error (more/better info)

Hi everyone, I got the error I just mentioned. Terminal window says "no contrasts specified". I am trying to use "timepoint" (1-4) as a discrete factor to look at thickness across time. I guess I will have to resort to longitudinal processing? Thanks for the help -Anson ***

[Freesurfer] Question on longitudinal statistics

Hi, In the longitudinal tutorial it states that: "In order to analyze your longitudinal data, you have different options. You could, e.g., open the stats text files in each tpN.long.templateID/stats/ dir, containing statistics such as volume of subcortical structures or thickness averages for c

[Freesurfer] Longitudinal analysis question

Hello FS experts, I am running a group up subjects pre/post treatment. When trying to do group analysis, after converting data with the mri_slope command, when I made the long table into a cross table, I noticed in qdec it averaged my "time" variable and only supplies a mean and there is no lon

Re: [Freesurfer] Longitudinal analysis question

treatment. Best Anson K. -Original Message- From: Martin Reuter [mailto:mreu...@nmr.mgh.harvard.edu] Sent: Thursday, July 19, 2012 5:51 PM To: Kairys, Anson Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Longitudinal analysis question Hi Anson, Qdec can only do cross sectional

Re: [Freesurfer] Longitudinal analysis question

ssage- From: Martin Reuter [mailto:mreu...@nmr.mgh.harvard.edu] Sent: Friday, July 20, 2012 9:39 AM To: Kairys, Anson; 'Martin Reuter' Cc: freesurfer@nmr.mgh.harvard.edu Subject: RE: [Freesurfer] Longitudinal analysis question Hi Anson Yes, mixed effects models is the better option. I&#x