[Freesurfer] Reposting a Question RE: Hippocampal/Amygdala subfield segmentation - Anterior Amygdala Area / Medial Nucleus Errors
External Email - Use Caution Hello FreeSurfer Experts, I wanted to re-post this question (posted June 4th), yet did not receive your guidance: I have visually checked 116 subjects that have been processed using Freesurfer's latest hippocampal/amygdala subfield segmentation algorithm (Development version 20180518 <https://surfer.nmr.mgh.harvard.edu/fswiki/HippocampalSubfieldsAndNucleiOfAmygdala>) and came across 5 cases that failed the QC. My T1s had been processed using FS 5.3, and I used the command "segmentHA_T1.sh" from the latest Dev version. - 3 subjects are missing a mask of the anterior amygdaloid area (AAA), but in the volumetric output, there are values for the regions. - 2 subjects' medical nuclei masks are located in the Putamen region (more superior/detached from the rest of the amygdala). I found the exact same inquiry RE: AAA region 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, -- David S. Lee Research Specialist Center for Healthy Minds University of Wisconsin - Madison (608) 890-1115 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] Hippocampal/Amygdala subfield segmentation - Anterior Amygdala Area / Medial Nucleus Errors
External Email - Use Caution Hello FreeSurfer Experts, I have visually checked 116 subjects that have been processed using Freesurfer's latest hippocampal/amygdala subfield segmentation algorithm (Development version 20180518 <https://surfer.nmr.mgh.harvard.edu/fswiki/HippocampalSubfieldsAndNucleiOfAmygdala>) and came across 5 cases that failed the QC. My T1s had been processed using FS 5.3, and I used the command "segmentHA_T1.sh" from the latest Dev version. - 3 subjects are missing a mask of the anterior amygdaloid area (AAA), but in the volumetric output, there are values for the regions. - 2 subjects' medical nuclei masks are located in the Putamen region (more superior/detached from the rest of the amygdala). I found the exact same inquiry RE: AAA region 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, -- David S. Lee Research Specialist Center for Healthy Minds University of Wisconsin - Madison (608) 890-1115 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] GM and WM intensity thresholds (Manual Edits)
External Email - Use Caution Hello FreeSurfer Experts! I currently supply inhomogeneity-corrected (via N4 biascorrection) 3T T1w scans through recon-all pipeline. The correction has solved many segmentation errors which reduced the time spent on manual editing. I have several questions related to this: 1. I am aware of the "3T" flag that can be supplied to recon-all command. It seems redundant to use this flag for already-bias-corrected 3T scans (testing from my end also confirms this), but do you recommend any other bias-correction steps? 2. What are the minimum and maximum intensity thresholds set for GM and WM during recon-all? In the official control point tutorial <https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/ControlPointsV6.0>, it suggests that WM should be "close" to intensity of 110, but I wanted to know the exact thresholds 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 S. Lee Research Specialist Center for Healthy Minds University of Wisconsin - Madison (608) 890-1115 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Gray Matter Manual Edit Reverting
External Email - Use Caution Hello Bruce, Thank you for the quick response. I unchecked "do not draw on voxels in the range of" in the "Recon Edit" window, and I was able to get the clone to work nicely. Thank you for your time! David On Mon, Nov 19, 2018 at 1:38 PM David S Lee wrote: > Hello Experts, > > I am currently using FreeSurfer version 6.0 to make manual edits to T1w > images. In an earlier version 5.3, when GM has been erroneously removed, I > used the "clone tool" to bring back voxels based on the original T1w. > 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 > Center for Healthy Minds > University of Wisconsin - Madison > (608) 890-1115 > -- David S. Lee Research Specialist Center for Healthy Minds University of Wisconsin - Madison (608) 890-1115 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] Gray Matter Manual Edit Reverting
External Email - Use Caution Hello Experts, I am currently using FreeSurfer version 6.0 to make manual edits to T1w images. In an earlier version 5.3, when GM has been erroneously removed, I used the "clone tool" to bring back voxels based on the original T1w. 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 Center for Healthy Minds University of Wisconsin - Madison (608) 890-1115 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] 3T Intensity Normalization (Re-Submission)
External Email - Use Caution Hello Experts, I believe -3T Flag can be used with "recon-all" on scans collected by 3T scanners. I believe it performs intensity normalization to set white matter intensity threshold at 110. I am hoping to learn more about the flag 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 mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] FreeSurfer Manual Edit Sequence
External Email - Use Caution Hello Experts, When performing manual edits on brain masks, white matter, and gray matter, do I have to strictly follow the sequences(process stages) listed here <https://surfer.nmr.mgh.harvard.edu/fswiki/recon-all>? For instance, the link suggests 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 Minds University of Wisconsin - Madison (608) 890-1115 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] ASEG Extraction Inquiry
External Email - Use Caution Hi FreeSurfer Experts, I have extracted ASEG volumes using "asegstats2table" and have a few questions about the output. 1. I get values of "0" for Left and Right "WM-hypointensities" as well as "non-WM-hypointensities". Does the ASEG segmentation for WM-hypointensities only produce whole brain measures (Left and Right combined) ? 2. Most measures are separated by Left and Right, but some are not. So, are these values pertinent to both hemispheres (whole brain?) 3. Is there a reference page I can check 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.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] (Follow-Up) Interaction Contrast
External Email - Use Caution Dear Douglas, Thank you for your guidance. I am following-up on your response with regards to setting up DODS matrix to test interaction between two continous covariates. If I understand your recommendation correctly (please correct me if I am wrong), I am averegaing slopes for the new interaction covairate (age*weight), while regressing out slope estimates for age and weight. I am curious to know why regressing out the two original covariates is recommended. Thanks for your time! David _ You 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 variable (age X weight). Myfsgd looks like this: /GroupDescriptorFile 1/ /Title Cortical Thickness Interaction between Age and Weight/ /Class class1 plus blue/ /Class class2 circle green/ /Variable Demean Age X Demean Weight/ /Input001Class1500/ /Input002Class2433/ /.../ I want to test for an interaction between age and weight while controlling forgroup. Instead ofputting-inage and weight separately, I multiply them to test for interaction. Can 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 <tel:%28608%29%20890-1115> ___ Freesurfer mailing listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine athttp://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] QDEC Interaction of Two Covariates
External Email - Use Caution Hi FreeSurfer Experts, I want to test the relationship between cortical thickness and two continuous covariates (interaction) while controlling for one categorical variable. In QDEC, I can only choose one covariate, so I created a new variable 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 Associate Research Specialist Center for Healthy Minds University of Wisconsin - Madison (608) 890-1115 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] Group Analysis Contrast (Follow-up)
Hi Douglas, Thank you for your reply. To follow up, I am setting up GLM analysis with 1 categorical variable and 1 continuous variable (age X weight). My fsgd looks like this: *GroupDescriptorFile 1* *Title Cortical Thickness Interaction between Age and Weight* *Class class1 plus blue* *Class class2 circle green* *Variable Demean Age X Demean Weight* *Input 001 Class1 500* *Input 002 Class2 433* *...* I want to test for an interaction between age and weight while controlling for group. Instead of putting-in age and weight separately, I multiply them to test for interaction. Can 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 list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] Group Analysis Design Matrix
Hi FreeSurfer Experts, I have two groups (Male and Female) and two covariates (Age and Weight). I want to test change of cortical thickness with age and weight, after removing effects of Group. In other words, is there an interaction between age and weight, regressing out the effects of groups. 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://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] FreeSurfer Error Edit Sequence
Hello Experts, Do you suggest FreeSurfer users to *strictly* follow the *error edit sequence* (Brain Mask --> WM --> GM --> Control Points) listed here (link below)? https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/TroubleshootingData If not, can users follow this sequence instead: 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 - Madison (608) 890-1115 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[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 people to absolutely stick to this particular sequence? Thanks for your time, David ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
