[Freesurfer] ASEG Extraction Inquiry

ck to see what each of the measures mean (i.e. atlas)? Thank you for your time! -- David S. Lee Associate Research Specialist Center for Healthy Minds University of Wisconsin - Madison (608) 890-1115 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harv

[Freesurfer] FreeSurfer Manual Edit Sequence

ggests that "autorecon2-pial is used after editing brain volume *after running -autorecon2". In other words, is it okay to perform "autorecon2-pial" before "autorecon2-wm"? Thank you for your time, -- David S. Lee Associate Research Specialist Center for Healthy Min

[Freesurfer] (Follow-Up) Interaction Contrast

need to put in age, weight, AND age*weight. If you have two classes and use DODS, then the contrast would be 0 0 0 0 0 0 0.5 0.5 On 4/13/18 8:02 PM, David S Lee wrote: Hi Douglas, Thank you for your reply. To follow up, I am setting up GLM analysis with 1 categorical variable and 1 continuous

[Freesurfer] FreeSurfer Error Edit Sequence

ad: Brain Mask --> Control Points --> GM --> WM? The justification here is to minimize the time spent to perform hand edits. Thank you for your time, -- David S. Lee Associate Research Specialist Center for Healthy Minds University of Wisconsin - Madi

[Freesurfer] FreeSurfer Edit Sequence Inquiry

Hello FreeSurfer Group, I am writing to inquire about Editing Sequence. The "Troubleshooting your output" page (https://surfer.nmr.mgh. harvard.edu/fswiki/FsTutorial/TroubleshootingData) explains the edits sequence as brain mask --> wm volume --> white surface --> control points. Do you suggest

[Freesurfer] Group Analysis Design Matrix

. How can I set up my Design Matrix to test this? Thank you, -- David S. Lee Associate Research Specialist Center for Healthy Minds University of Wisconsin - Madison (608) 890-1115 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https

[Freesurfer] Group Analysis Contrast (Follow-up)

you tell me if following contrast vector will correctly test for this? *0 0 0.5 0.5* Thank you for your time, -- David S. Lee Associate Research Specialist Center for Healthy Minds University of Wisconsin - Madison (608) 890-1115 ___ Freesurfer mailing

[Freesurfer] QDEC Interaction of Two Covariates

that is a dot product (covariate1*covariate2) of the two to represent interaction. After analyzing, when I look at the data points at a single voxel, there is no visual indication of interaction. There also is no fitted line. Am I utilizing QDEC correctly? Thank you for your help! -- David S. Lee

[Freesurfer] 3T Intensity Normalization (Re-Submission)

lag option as it produces slightly better output for me. Would you be able to guide me to a documentation on this -3T flag? Thank you! -- David S. Lee Associate Research Specialist Center for Healthy Minds University of Wisconsin - Madison (608) 890-1115 ___

[Freesurfer] GM and WM intensity thresholds (Manual Edits)

s to perform more accurate manual editing. 3. If these GM and WM intensity parameters can be changed from default, do you recommend doing so? If there is a documentation I can refer to find answers (I've failed to find one so far), please let me know. Thank you for your time as always, -- David

[Freesurfer] Gray Matter Manual Edit Reverting

this tool seems to be not working in 6.0. Would you be able to help me troubleshoot this? If there is a better alternative to revert GM removal, please let me know! Thank you for your help. -- David S. Lee Research Specialist Center for Healthy Minds University of Wisconsin - Madison (608

Re: [Freesurfer] Gray Matter Manual Edit Reverting

> However, this tool seems to be not working in 6.0. Would you be able to > help me troubleshoot this? If there is a better alternative to revert GM > removal, please let me know! > > Thank you for your help. > > -- > David S. Lee > Research Specialist > Ce

[Freesurfer] Hippocampal/Amygdala subfield segmentation - Anterior Amygdala Area / Medial Nucleus Errors

course of action to resolve these issues? Is there a way to see volumetric measures in the freeview GUI (when clicking a region) to possibly manually trace the missing regions? Thank you for your time, -- David S. Lee Research Specialist Center for Healthy Minds University of Wisconsin - Madiso

[Freesurfer] Reposting a Question RE: Hippocampal/Amygdala subfield segmentation - Anterior Amygdala Area / Medial Nucleus Errors

posted on April 30, 2019, but I did not see any response. What would be your recommended course of action to resolve these issues? Is there a way to see volumetric measures in the freeview GUI (when clicking a region) to possibly manually trace the missing regions? Thank you for your time,