Freesurfer

freesurfer@nmr.mgh.harvard.edu

21 participants
30071 discussions

Visualizing and interpreting vertex-wise GLM analysis
by Julian Macoveanu 23 Jun '22

23 Jun '22

External Email - Use Caution <This is an updated repost> Dear Freesurfers, I have a simple design with patients and controls and would like to find regions showing group differences in cortical volume and thickness. I also remove the effect of age, sex and ICV. Running the GLM group analysis by the book I get a few clusters showing significant differences in intercept. 1. I interpret this like patients have smaller “predicted” regional volume at age 0, or at mean age of the group (if demeaned age covariate) compared to controls. How can this finding be described in a more clinically meaningful way? 2. Related to the above, how do I visualize what is going on in the significant clusters? The extracted values from these clusters (ocn.dat) show no group differences in volume when displaying the group means in SPSS (using either age/sex/ICV adjusted or non-adjusted values). Maybe I am misunderstanding something, how can there be differences in intercept but no differences between group means? (slopes not significantly different). How do I best describe and visualize this group difference in a paper? Going through the studies I found on Pubmed that used Freesurfer with vertex-wise GLM, so far, I only found e.g. the “lower thickness” interpretation in one group vs the other and not “lower intercept”. In my case at least, I cannot say this since the extracted values between groups show no group difference. Julian

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Re: [Freesurfer] VM image passcode
by fsbuild 22 Jun '22

22 Jun '22

External Email - Use Caution Please check your email again. - R. On Jun 22, 2022, at 17:38, Sean Kelso <skelso(a)outlook.com> wrote:        External Email - Use Caution        I still have not received the passcode..Thanks,Sean On Jun 20, 2022, at 1:55 PM, Sean Kelso <skelso(a)outlook.com> wrote:Hi, what is the pass code needed to expand the Ubuntu archive? Thanks! Sean_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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VM image passcode
by Sean Kelso 22 Jun '22

22 Jun '22

External Email - Use Caution Hi, what is the pass code needed to expand the Ubuntu archive? Thanks! Sean

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Re: [Freesurfer] 7z virtualbox passcode request
by fsbuild 22 Jun '22

22 Jun '22

External Email - Use Caution How fast/efficient a VM runs on a host usually depends upon how much memory and how many processors you can allocate to the VM and what the host machine is running that competes for those resources.   We can't really predict what the performance will be on each users machine.  But if you can install and run directly onto linux or MacOS, then I suggest using the package installers (if you have sudo/admin privileges) instead of the tar archives. Please note all requests for the VM info are being replied to directly using the email address of the sender, and not being copied to the freesurfer list.  Dr. Gregori should have already received the VM info. - R. On Jun 22, 2022, at 13:33, Bouchra Guelib <bouchra.guelib(a)univ-constantine2.dz> wrote:        External Email - Use Caution        Hi,I already used VMware as virtual machine to install Freesurfer, I would advice you to change your OS to linux or Mac , it won't take the same time as you run Freesurfer on VM, also the installation is easy, just download the freesurfer and use tar commend line to install it.Please let me know if you face problem Le mer. 22 juin 2022 à 17:27, Gregori, Johannes, Prof. Dr. <johannes.gregori(a)h-da.de> a écrit :        External Email - Use Caution        HelloI would like to try out th 7z virtual machine image containing freesurfer. Could you send me the passcode? Thanks in advancemit freundlichen Grüßen / best regardsJohannes Prof. Dr. Johannes Gregorih_daHochschule DarmstadtUniversity of Applied SciencesFachbereich Mathematik und NaturwissenschaftenSchöfferstr. 3D-64295 DarmstadtMailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://secure-web.cisco.com/1WNHPeRkbS3nRlAs5qToJ2vaGrrpV0d79z966n… mailing listFreesurfer(a)nmr.mgh.harvard.eduMailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://secure-web.cisco.com/1lyl_zun4PI5oJRR96Ww6c8fNpeqx9wSphcOiP… 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 Mass General Brigham Compliance HelpLine at MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://secure-web.cisco.com/1IzmRZBWywkssd8SbDBWXR_gcGm8v2UY8Gr_Mg… has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://secure-web.cisco.com/1dqzNt3akI2_u7BpZ7h6IkFGdoyvoBrDTX5e91…; .Please note that this e-mail is not secure (encrypted).  If you do not wish to continue communication over unencrypted e-mail, please notify the sender of this message immediately.  Continuing to send or respond to e-mail after receiving this message means you understand and accept this risk and wish to continue to communicate over unencrypted e-mail. _______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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7z virtualbox passcode request
by Gregori, Johannes, Prof. Dr. 22 Jun '22

22 Jun '22

External Email - Use Caution Hello I would like to try out th 7z virtual machine image containing freesurfer. Could you send me the passcode? Thanks in advance mit freundlichen Grüßen / best regards Johannes Prof. Dr. Johannes Gregori h_da Hochschule Darmstadt University of Applied Sciences Fachbereich Mathematik und Naturwissenschaften Schöfferstr. 3 D-64295 Darmstadt https://secure-web.cisco.com/1_sKuRnSJKjVJJm47O1OBgQL0QQC_DUYx3VfrsIJoKJuO9…

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VM Password
by Jessica Ramamurthy 21 Jun '22

21 Jun '22

External Email - Use Caution Hi, Could you please provide me with the password to expand the archive for FreeSurfer 7.2.0 so I may import it into the virtual machine? Thank you!

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mri_aparc2aseg bad incorrect ROIs
by Benjamin Deck 21 Jun '22

21 Jun '22

External Email - Use Caution Hi Freesurfer experts, I am attempting to turn my surface-based parcellation into a segmentation file using the following command: mri_aparc2aseg --s sub-DAEK --annot yeo2011 --annot-table sub-DAEK_yeoLUT.txt --threads 6 --rip-unknown --volmask However, when I load the resulting volume using my custom LUT the ROIs get labeled to the white matter and subcortical structures leaving the grey matter unlabeled. When I examine the annotation files, they look appropriate and there isn't any overlap. Do I need to include the subcortical structures in my custom LUT to avoid this from happening or is there a better solution? Thank you! -- *Benjamin L. Deck* *Doctoral Student* *Applied Cognitive and Brain Sciences* *Department of Psychological and Brain Sciences* *Drexel University* <https://secure-web.cisco.com/1QkkGrc1M5CNJQjlaL6JN2C_Kh4FZGHEk5bXUEdRCEnkZG…> Virus-free. http://secure-web.cisco.com/12C_QfaDOwg3LKh_yiXvYrqC0D4zGBhxMG0vzRqgBwZzH5m… <https://secure-web.cisco.com/1tDhPrZdlS9NSF2Pe-eEm0Zojd9ScbaKYJdMT0872rwJGr…> <#DAB4FAD8-2DD7-40BB-A1B8-4E2AA1F9FDF2>

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using brain mask from older FreeSurfer version on a newer
by Aaron Tanenbaum 21 Jun '22

21 Jun '22

External Email - Use Caution Our lab is moving from FreeSurfer 5.3 to 7.2. We have thousands of scans to do. I see that you can give freesurfer a brainmask. I was thinking of giving freesurfer a brainmask from the previous from 5.3 to 7.1. Is this a wise idea? Do you have any objections?

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postdoc at Martinos/LCN
by Douglas N. Greve 20 Jun '22

20 Jun '22

A postdoctoral fellow position in the Lab for Computational Neuroimaging (LCN) under Dr. Douglas Greve is available. We are seeking a highly motivated and talented researcher to pursue independent research. The role will be to develop new algorithms within FreeSurfer, including multi-modal, modality-independent surface placement and brain image segmentation (volume and surface) for both cross-sectional and longitudinal analysis. The projects will use conventional Bayesian and machine learning techniques. The work will mostly focus on structural MRI, but there will be applications to PET (PETsurfer) and fMRI (FSFAST). The candidate should be an accomplished computer programmer with experience in brain image analysis, strong analytical skills, and an ability and desire to do independent research. The ideal candidate would hold a Ph.D. degree in Neuroscience, MR Physics, Biomedical Engineering, or a related field; however, strong candidates with other scientific backgrounds will also be considered. The candidate must have an interest in understanding FreeSurfer at a deep level and welcome the opportunity to leverage this understanding into public visibility through helping to maintain and support FreeSurfer. Interested applicants are invited to send a cover letter describing research interests and experience, an up-to-date CV, and names and contact information of three references to: dgreve(a)mgh.harvard.edu This position is full-time with benefits and is available immediately. The Massachusetts General Hospital and Harvard Medical School are an equal opportunity employer, and all qualified applicants will receive consideration for employment without regard to race, color, religion, sex, national origin, disability status, protected veteran status, gender identity, sexual orientation, pregnancy and pregnancy-related conditions or any other characteristic protected by law. best doug

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FreeSurfer Password
by Mattia Pagano 20 Jun '22

20 Jun '22

External Email - Use Caution Good morning, I need the password to expand the archive for Freesurfer 7.2.0 release in Ubuntu. Thanks, Mattia

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