Freesurfer

freesurfer@nmr.mgh.harvard.edu

18 participants
30131 discussions

Can FS use the recon all command to automatically divide it into DKT32 areas?
by 1248742467 26 Mar '21

26 Mar '21

External Email - Use Caution Hello, Fs I saw an article that gave the Dice coefficient and ACC of Freesurfer's automatic segmentation, so I am curious, can Fs automatically divide it into 32 regions?

2 1

cross sectional vs longitudinal TRACULA reliability
by Carissa Nicole Weis 25 Mar '21

25 Mar '21

External Email - Use Caution Hello, I’ve run both longitudinal and cross-sectional TRACULA pipelines on the same dataset, and I’ve found surprisingly low correlations of FA measurements for several tracts (as low as r= .1 in some cases). Which measurement should be considered more reliable? I’m having a hard time deciding which set of results to carry forward to group analysis. Thanks, Carissa

2 1

Re: [Freesurfer] make_average_subject without Talairach transform
by Trisanna Sprung-Much 25 Mar '21

25 Mar '21

External Email - Use Caution Thanks Bruce for your speedy response. I am dealing with chimp scans and therefore am trying to avoid anything to do with Talairach. The surfaces have reconstructed pretty nicely using recon-all, but I’d like to create an average surface now. I will try as you suggest Trisanna Sprung-Much Research Associate McGill University MD Anderson Cancer Centre -- From: <freesurfer-bounces(a)nmr.mgh.harvard.edu> on behalf of "Fischl, Bruce" <BFISCHL(a)mgh.harvard.edu> Reply-To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> Date: Thursday, March 25, 2021 at 10:59 AM To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] make_average_subject without Talairach transform Sure, I guess you can just run mri_average. I think also if you specify the file name for the transform as identity.nofile to any binary that takes an lta file, the code will internally create an identity transform. I won’t look pretty though…. Cheers Bruce From: freesurfer-bounces(a)nmr.mgh.harvard.edu <freesurfer-bounces(a)nmr.mgh.harvard.edu> On Behalf Of Trisanna Sprung-Much Sent: Thursday, March 25, 2021 10:19 AM To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> Subject: [Freesurfer] make_average_subject without Talairach transform External Email - Use Caution External Email - Use Caution Hi there I’d like to know if it is possible to create an average volume and average surface of several subjects without having to incorporate the Talairach transform and no transform at all. Thank you, Trisanna Sprung-Much Research Associate McGill University MD Anderson Cancer Centre --

2 1

read_surf surface
by Shizuka Hayashi 25 Mar '21

25 Mar '21

External Email - Use Caution Dear Freesurfer team, I have a question about the inconsistency between the vertex read from read_surf and vertex shown in Freeview. I have a volume from the hippocampal subfield pipeline and I converted it to surface mesh using mri_tessellate mri/lh.hippoAmygLabels-T1.long.v21.mgz -an surf/lh.hippoAmygLabels-T1.long.v21.surf. Then I smoothed the surface using mris_smooth surf/lh.hippoAmygLabels-T1.long.v21.surf surf/lh.hippoAmygLabels-T1.long.v21.surf Now I want to get the corresponding voxel of lh.hippoAmygLabels-T1.long.v21.mgz with the vertex. In Freeview, for example, the vertex 0 is [5.17, -19.5, 4.83]. I know how to convert this vertex to the corresponding voxel. However, when I read the surf/lh.hippoAmygLabels-T1.long.v21.surf from Matlab using read_surf, the first vertex ( vertex(1,:,:)) is equal to [165.4900,217.3600,-159.7300]. Are there any ways to solve the issue? Thank you. Regards, Shizuka

2 1

Questions regarding atlas labels
by Blanpain, Lou 25 Mar '21

25 Mar '21

External Email - Use Caution Hello, I had the following 2 general questions regarding Freesurfer: 1. Is there an extensive list of anatomical labels for each atlas used? For instance, what are all the potential labels used in wmparc.mgz? I am aware of the extensive list of labels in ‘FreeSurferColorLUT.txt’, but this list does not seem to indicate which labels are included in which atlas. 2. Do we know of Freesurfer users who have already worked on categorizing labels from such atlases? For instance, I would be interested in categorizing labels belonging to the visual system network vs the auditory system network. Thank you so much for your assistance. Warm regards, Lou Blanpain ________________________________ This e-mail message (including any attachments) is for the sole use of the intended recipient(s) and may contain confidential and privileged information. If the reader of this message is not the intended recipient, you are hereby notified that any dissemination, distribution or copying of this message (including any attachments) is strictly prohibited. If you have received this message in error, please contact the sender by reply e-mail message and destroy all copies of the original message (including attachments).

2 1

Missing 'brainstemSsLabels.v10.mgz' file
by Taylor, Lisa Marie 25 Mar '21

25 Mar '21

External Email - Use Caution Hi, This is the first time I have encountered this problem. I have a participant that has been through recon all, but when trying to create PET masks, the error that comes up is that the 'brainstemSsLabels.v10.mgz' file is missing in the MRI directory. I am unsure of how to have this label created when it has been created in other participants from freesurfer. Here is the command and the arguments used when running this participant (every one of our participants has had the same command): ${FREESURFER_HOME}/bin/recon-all -s /pub/ltaylor2/*PARTICIPANT* -no-isrunning -all -hippocampal-subfields-T1 -brainstem-structures -qcache Any understanding as to why this particular participant is not having this file created? Any leads would be greatly appreciated! Lisa ________________________________ This message may contain confidential information and is for the sole use of the intended recipient(s). If you are not the intended recipient, do not use, distribute, or copy this e-mail. Please notify the UC Irvine Health – Compliance and Privacy Office via email at hacompliance(a)uci.edu or by phone 888-456-7006 immediately if you have received this e-mail in error. E-mail transmission cannot be guaranteed to be secure or error-free as information could be intercepted, corrupted, lost, destroyed, arrive late or incomplete, or contain viruses. The sender therefore does not accept liability for any errors or omissions in the contents of this message, which arise as a result of e-mail transmission.

2 1

Lesion Heatmap question - follow up
by XY XY 25 Mar '21

25 Mar '21

External Email - Use Caution Thanks Douglas, "mri_convert lesionmap.mgz -at samseg.m3z lesionmap.mni152.mgz" worked fabulously after some tweaks in the command line! What would be the best approach to compare population-wise lesion heat maps between groups of subjects using the output from SAMSEG? (the full FS pipeline cannot process my data due to brain defects and time restrictions). Thanks for all the support for these fantastic tools! Stay safe! ----------------------------------------------------- David Olayinka Kamson, MD PhD Clinical and Research Fellow Joint Neuro-Oncology Program of Johns Hopkins Medicine & National Institutes of Health dkamson1(a)jhmi.edu <mailto:dkamson1@jhmi.edu>

2 1

Re: [Freesurfer] Which pial surface to trust
by Jones, Richard 25 Mar '21

25 Mar '21

External Email - Use Caution A couple of questions:- 1) Do you experience similar variability with the T2 and FLAIR options or is FLAIR more variable due to it's generally lower SNR? 2) Should the spatial resolution of the T2/FLAIR scan match that of the T1 scan? Richard Message: 8 Date: Wed, 17 Mar 2021 17:51:51 -0400 From: "Douglas N. Greve" <dgreve(a)mgh.harvard.edu> Subject: Re: [Freesurfer] Which pial surface to trust, with or without -FLAIR option To: <freesurfer(a)nmr.mgh.harvard.edu> Message-ID: <3c789103-dad7-974a-0d76-58a02cba2992(a)mgh.harvard.edu> Content-Type: text/plain; charset="utf-8" We get a lot of variable results with FLAIR. Sometimes it helps, sometimes it hurts. FLAIR scans themselves can be very variable across sites. If it is looking like it is hurting your results, then just run without it. On 3/12/2021 11:07 AM, Xiaojiang Yang wrote: > > ????????External Email - Use Caution > > Dear FS developers, > > I have run FS?s recon-all on many cases, with and without -FLAIR > options. I found the pial? surface results (?h.pial) I obtained > without -FLAIR option fit to the original image > (subjected/mri/orig.mgz) much better than those with -FLAIR option, at > least from my visual judgment. See *MailScanner has detected a > possible fraud attempt from "secure-web.cisco.com" claiming to be* > https://secure-web.cisco.com/1kdfPWDTAquCY3qAKfDNtc8TRiBI5hNHL96VYA9_mTvUn4… > <https://secure-web.cisco.com/1jL9MUfd9oLXR_SVyZl8-wPztrX70T9SJxxJaJElRv5e-D…>?for > one example. > > I know -FLAIR option was introduced to improve the quality of pial > surface segmentation. Now for many cases, my intuition is that -FLAIR > option decreases the pial quality. My questions are: > > * Is this intuition correct? > * Should I trust the pial surface that?s obtained with or without > -FLAIR option in general? > > In addition, when I use the -FLAIR option, I sometimes get failed when > running recon-all. After I did some manual edits to the brainmask > image, and re-run the recon-all: > > recon-all -autorecon-pial -subjid <subjectID> > > I can get recon-all successful. But if I run recon-all without -FLAIR > option, I can get successful results without needing to manually edit > the brainmask image. > > So my last question is: > > * Should I just run recon-all without -FLAIR option, or, with -FLAIR > option + manual edit + re-run with -autorecon-pial? Which is better? > > Thank you very much! > > John >

2 1

Difference between vox2ras and vox2ras-tkr for subject-specific T1w through FreeSurfer
by Adam Li 25 Mar '21

25 Mar '21

External Email - Use Caution Hi, I am a bit noob on FreeSurfer and coordinate systems and I had a few questions. I am wondering if I have the T1.mgz file of FreeSurfer after running recon-all and this is the 256^3 image re-scaled and re-oriented from your orig.mgz file, then how does one define the fsnative (volume RAS) vs surface RAS (tkras in FreeSurfer)? Assuming there was no preprocessing done on the original scanner nifti, I run the following commands: (base) workstation$ mri_info ~/bids/derivatives/freesurfer/la02/mri/T1.mgz --vox2ras -1.00000 0.00000 0.00000 126.81799 0.00000 -0.00000 1.00000 -121.57332 0.00000 -1.00000 0.00000 159.64563 0.00000 0.00000 0.00000 1.00000 (base) workstation$ mri_info ~/bids/derivatives/freesurfer/la02/mri/T1.mgz --vox2ras-tkr -1.00000 0.00000 0.00000 128.00000 0.00000 0.00000 1.00000 -128.00000 0.00000 -1.00000 0.00000 128.00000 0.00000 0.00000 0.00000 1.00000 *Questions:* 1. Applying the `vox2ras` to any voxel, I would get RAS xyz coordinates right? 2. If I apply `vox2ras-tkr` to any voxel, I would also get RAS xyz coordinates? 3. So what is the difference exactly between these two transforms? Is there anything special / consistent in terms of the definition of the origin and orientation? E.g. Orientation is always RAS, and origin is always... estimated center of the patient's brain? Or is the origin somewhere special like the AC? 3. When would I use one transform over the other? I've searched online and read through the following, but I feel like there is not explicit discussion of the above questions: - https://secure-web.cisco.com/1sKe3PERttYdO2z94AST1tBVsT1X0Q84dpaG1N3eU1eJEW… - http://secure-web.cisco.com/1fnkHZ6-zCUMYrDAnGdeklCU8ErX4aX7Dumo0EB8QRqeu1t… -- Best Regards, Adam Li (he/him) PhD Student in Biomedical Engineering Johns Hopkins University & School of Medicine

2 1

Re: [Freesurfer] Missing 'brainstemSsLabels.v10.mgz' file
by Iglesias Gonzalez, Juan E. 24 Mar '21

24 Mar '21

Dear Lisa, Maybe the brainstem module failed for some reason? If you send us the log files, we can take a look. Cheers, /Eugenio Juan Eugenio Iglesias Senior research fellow CMIC (UCL), MGH (HMS) and CSAIL (MIT) http://www.jeiglesias.com From: <freesurfer-bounces(a)nmr.mgh.harvard.edu> on behalf of "Taylor, Lisa Marie" <ltaylor2(a)hs.uci.edu> Reply-To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> Date: Tuesday, March 23, 2021 at 15:32 To: "freesurfer(a)nmr.mgh.harvard.edu" <freesurfer(a)nmr.mgh.harvard.edu> Subject: [Freesurfer] Missing 'brainstemSsLabels.v10.mgz' file External Email - Use Caution Hi, This is the first time I have encountered this problem. I have a participant that has been through recon all, but when trying to create PET masks, the error that comes up is that the 'brainstemSsLabels.v10.mgz' file is missing in the MRI directory. I am unsure of how to have this label created when it has been created in other participants from freesurfer. Here is the command and the arguments used when running this participant (every one of our participants has had the same command): ${FREESURFER_HOME}/bin/recon-all -s /pub/ltaylor2/*PARTICIPANT* -no-isrunning -all -hippocampal-subfields-T1 -brainstem-structures -qcache Any understanding as to why this particular participant is not having this file created? Any leads would be greatly appreciated! Lisa ________________________________ This message may contain confidential information and is for the sole use of the intended recipient(s). If you are not the intended recipient, do not use, distribute, or copy this e-mail. Please notify the UC Irvine Health – Compliance and Privacy Office via email at hacompliance(a)uci.edu or by phone 888-456-7006 immediately if you have received this e-mail in error. E-mail transmission cannot be guaranteed to be secure or error-free as information could be intercepted, corrupted, lost, destroyed, arrive late or incomplete, or contain viruses. The sender therefore does not accept liability for any errors or omissions in the contents of this message, which arise as a result of e-mail transmission.

2 2

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