Freesurfer

freesurfer@nmr.mgh.harvard.edu

17 participants
30086 discussions

Re: [Freesurfer] Updating Freesurfer Version
by Ferraro, Pilar 10 Sep '20

10 Sep '20

External Email - Use Caution Hi Freesurfer experts, I’m trying to update my current Freesurfer version (from 6.0 to 7.1). I’d like to know whether the installation procedure for 7.1 would overwrite the current one (6.0). Many thanks, Pilar > Il giorno 22 ago 2020, alle ore 7:48 AM, freesurfer-request(a)nmr.mgh.harvard.edu ha scritto: > > Send Freesurfer mailing list submissions to > freesurfer(a)nmr.mgh.harvard.edu > > To subscribe or unsubscribe via the World Wide Web, visit > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > or, via email, send a message with subject or body 'help' to > freesurfer-request(a)nmr.mgh.harvard.edu > > You can reach the person managing the list at > freesurfer-owner(a)nmr.mgh.harvard.edu > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of Freesurfer digest..." > > > Today's Topics: > > 1. Global surface area and global thickness values (Palin, Tara) > 2. How to run recon-all for different subjects and each subject > with different sessions ? (Camargo, Aldo) > 3. Postdoctoral scientist positions at UCSF (Tosun, Duygu) > 4. Re: extracting beta coefficients and p-values (Douglas N. Greve) > 5. Re: How to run recon-all for different subjects and each > subject with different sessions ? (Douglas N. Greve) > 6. Re: Global surface area and global thickness values > (Douglas N. Greve) > 7. Re: ROI-wide cortical thickness for each network ! (Martin Juneja) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Fri, 21 Aug 2020 18:55:16 +0000 > From: "Palin, Tara" <Palin(a)kennedykrieger.org> > Subject: [Freesurfer] Global surface area and global thickness values > To: "freesurfer(a)nmr.mgh.harvard.edu" <freesurfer(a)nmr.mgh.harvard.edu> > Cc: "Plotkin, Micah" <PlotkinMic(a)kennedykrieger.org>, "Crocetti, > Deana" <crocetti(a)kennedykrieger.org> > Message-ID: <162876d303f44e7d987ab303c0a11b45(a)kennedykrieger.org> > Content-Type: text/plain; charset="iso-8859-1" > > External Email - Use Caution > > Hello freesurfer experts, > > > I am looking to extract the global surface and global thickness measurements and am curious if my understanding of the output on the aparc.stats (for lh and rh) are correct. When looking at these files, at the very top you will find the Pial Surface Total Area and a Mean Thickness value which I am assuming are the global measures. Below you have all of the ROIs listed (this was not changed by us or generated by us this is what comes out of freesurfer to my understanding) that includes everything EXCEPT the corpus callosum and the unknown. However, I summed all the surface areas and took and average of all the thickness measurements and they are very close to the values printed at the top of the sheet. Another observation I had made was that the total surface area measurement has a decimal and the surface area for the ROIs appears to be rounded and if they were not rounded the values would be the same. For the thickness values, the value I calculated and the one on the sheet are within the average of the standard deviation each other. > > > If my understanding is incorrect please let me know and provide insight into how we may calculate these global measurements correctly. > > > Thank you in advance for your time, > > Tara Palin > > > ---------------------------------------------------------------------- > Disclaimer: > > > The materials in this e-mail are private and may contain Protected Information. Please note that e-mail communication is not encrypted by default. You have the right to request further emails be encrypted by notifying the sender. Your continued use of e-mail constitutes your acknowledgment of these confidentiality and security limitations. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying, distribution, or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this e-mail in error, please immediately notify the sender via telephone or return e-mail. >

2 1

mri_volsynth question
by Nasiriavanaki, Zahra 10 Sep '20

10 Sep '20

Hi I am trying to make a subcortical 5 mm sphere ROI around a talairach coordinate. I am using the below command, but when I visualize it, it doesn’t look at the correct location. I see the same question in forum (https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg67295.html) I should probably use -pdf delta but I don’t know how to get the col, row and slice indices of the vertex where it should go. mri_volsynth --template $SUBJECTS_DIR/fsaverage/mri/brainmask.mgz --c_ras -21.8 -12.2 -10.3 --dim 5 5 5 5 —o new.mgh I appreciate your help. Thanks Mona Zahra (Mona) Nasiriavanaki, M.D. Postdoctoral Research Fellow Department of Psychiatry Massachusetts General Hospital 149 13th Street, 149-2615 Charlestown, MA, USA, 02129

2 9

FLAIR to improve pial segmentation? What are the surfaces used for stat estimation?
by Otília C. d'Almeida 10 Sep '20

10 Sep '20

External Email - Use Caution Hi FS community, I started using FS 7.1.0 for cortical and subcortical parcellation/segmentation. As I found information that FLAIR data could improve pial surfaces creation, I decided to try it on since I have FLAIR images besides MPRAGE, by using the command line form FSwiki: RECON-ALL -SUBJECT NAME -I INPUT_VOLUME.NII -FLAIR FLAIR_VOLUME.NII -FLAIRPIAL -ALL However when I opened Freeview, I overlaid RH.PIAL, and RH.PIAL.FLAIR, RH.PIAL.T1. The first two are quite similar (overlap) and the segmentation is worse than rh.pial.T1. So, my question is, what is really the final surface of recon-all that must be checked for errors and that is used for stats estimation? Thank you in advance. Best regards, Otília

2 3

mean gyrification index
by vittal korann 10 Sep '20

10 Sep '20

External Email - Use Caution Thank you so much, Douglas. Could you please guide me to obtain the global mean gyrification index for each subject? With regards korann

3 16

big difference between ICV same patient....
by Gonzalo Rojas Costa 10 Sep '20

10 Sep '20

External Email - Use Caution Hi: Why I got a big ICV difference between MPRAGE of the same patient (2019: 1775887.317631, 2020: 1566398.53576 mm3), one-year difference acquisition, and the same MRI Skyra 3T equipment? I used freesurfer 5.1.0 on the same computer, and operating system in both cases... I reviewed the coregistration to MNI305 and it is reasonably good in both cases... The case was reviewed by an expert neuroradiologist, and she does not consider that there is a significant visual difference between both sizes. Sincerely Gonzalo Rojas Costa

2 1

mri_cvs_register with sub-millimeter recons
by Noriana Jakopin 10 Sep '20

10 Sep '20

External Email - Use Caution Hello Freesurfer Experts, I have been trying to run mri_cvs_register to bring sub-millimeter data into MNI space, however the final outputs have large deformations to the brain. I have tried with both 0.5 mm and 0.7 mm using their respective sub-milimeter recons. It seems that the issue arises during Step 3(i) as the el_reg_tocvs_avg35_inMNI152.mgz does not have the deformations, but the step1_CVSmorphed_tocvs_avg35_inMNI152_norm.mgz file does. Does anyone have any guidance on how I can troubleshoot this? I have attached the recon-all.log file for the 0.7 mm data. If you need me to share any other files, let me know. FreeSurfer Version: freesurfer-linux-centos6_x86_64-7.1.1 Platform: Windows Subsystem for Linux - Ubuntu 18.04 LTS Thank you, Noriana Jakopin

2 2

job opening: MRI Senior Research Specialist at Ohio State University
by Xiangrui Li 10 Sep '20

10 Sep '20

External Email - Use Caution Sorry if cross-posted. See the attachment for the job detail. Thanks. _____________ Xiangrui Li, Ph.D. Center for Cognitive and Behavioral Brain Imaging The Ohio State University Phone: 614-292-1847

1 0

tksurfer 64bit update?
by Jesse Gomez 10 Sep '20

10 Sep '20

External Email - Use Caution Hello, I noticed tksurfer disappeared in the new 7.1 version of freesurfer. While it's still present in older versions of course, it no longer runs on 64-bit only operating systems (e.g. OSX Catalina). Is tksurfer going to be updated? It seems to be the only way to draw labels and ROIs on a surface. Is there an alternative? Freeview, as far as I can tell, only has volume-based ROI-drawing methods. This surface label feature in tksurfer was fairly critical for many analyses; I do hope it's on its way back. All the best, Jesse

2 4

Re: [Freesurfer] vol2surf: lesion overlap across group into surfaces
by Horn, Mitchell Jacob 10 Sep '20

10 Sep '20

Thanks so much Douglas. Many of the lesions are in the white matter, and many span across WM and GM. In the case where the lesions on not strictly cortical, is this surface mapping not possible? Or perhaps a representative surface map showing the occurrences of lesions in any lobe/ROI? Best, Mitch

1 0

longitudinal MRI and DTI registration
by Zeng, Qi 10 Sep '20

10 Sep '20

External Email - Use Caution Hi, I was conducting a longitudinal DTI analysis. However, MRI and DTI brain scans were scheduled at different time frames. Should I be concerned that for example MRI was taken at 9/1/2006 and nearby DTI was taken on 10/1/2007 or 10/1/2009, which may result in misregistration of DTI given MRI morphology. Best, Qi

2 1

Jump to page:

2026

2025

2024

2023

2022

2021

2020

2019

2018

2017

2016

2015

2014

2013

2012

2011

2010

2009

2008

2007

2006

2005

2004

Freesurfer