Freesurfer

freesurfer@nmr.mgh.harvard.edu

12 participants
30060 discussions

Start a nNew thread

Re: [Freesurfer] Freesurfer Waitlist
by Bess Lam 30 Mar '24

30 Mar '24

1 0

mri_volsynth fails but exits with 0 exit status
by Aaron Tanenbaum 29 Mar '24

29 Mar '24

External Email - Use Caution I am currently running FreeSurfer 7.4. I wrote a script using the program mri_volsynth. I noticed for the first time the program was trying to write files where it did not have write permissions. It outputted a few error messages but gave a 0 exit status. It would be nice to have it exit with a nonzero exit status.

2 1

Extracting significant regions - Longitudinal two stage model
by Liliana Wu 29 Mar '24

29 Mar '24

External Email - Use Caution Hi, I ran a longitudinal two stage model analysis in 83 participants comparing two groups. After applying cluster correction, I am seeing several significant regions, and I was wondering if there is a way to extract each significant cluster from each participant. I appreciate any help! Thank you, Liliana

2 1

autorecon1 issue
by Saifullah Tumrani 29 Mar '24

29 Mar '24

External Email - Use Caution I am using freesurfer to preprocess my t1w 3d Mris using autorecon1 which includes first 5 preprocessing techniques till skullstripping it worked well for 4 different datasets including ixi one from open neuro SRBPS but when i am using it for another dataset which has alsmost same configuration it’s talairach transformation fails for some samples and brain matter is removed in the final brainmask.mgz file moreover i applied autorecon-all for this dataset and even the process stopped for some showing error talaraich failed and for some samples the whole pipeline was executed without any error but in manual inspection i found brain matter removed by freesurfer kindly help me solving this problem. I later found bad skull stripping fix at this link FsTutorial/SkullStripFix_freeview - Free Surfer Wiki <https://secure-web.cisco.com/1W6bcIn5Fy404rUlulLdvgZBsqq1rLSJmG1UU4wSK-ttJn…> using some commands but i am facing errors using these command recon-all -skullstrip -wsthresh -clean-bm -no-wsgcaatlas -subjid skullstrip1_before kindly look into this if you have also experience same issues or have any insight on this. A response will be appriciated. Thanks

2 1

Part brain is missing
by Chen Yang 29 Mar '24

29 Mar '24

External Email - Use Caution Dear FreeSurfer Developers, I am trying to do the processing for structural MRI data. I found that part of brain is missing in one data (see Fig.1). Then I tried to change the watershed parameter, but it didnt work at all (no matter which number I use), the brainmask looks the same as before. So I did the manual editing, cloned voxel from T1.mgz to brainmask.mgz. Then I run the -autorecon-pial, but it froze in this step - fix topology. I checked 'wm.mgz', it contained a lot skull and a lot of WM are missing (see Fig.2). I also tried to manually edit the brainmask.mgz and wm.mgz, then run '-autorecon-wm' but it also froze in -fix topology. I put other might relevant information in the end. I've searched in the mail archive but didn't find similar errors. I am not sure if I did anything wrong. Does anyone have any thoughts on how to trouble-shoot this problem? Also, Ive attached the recon-all.log in case it's of any use. Thanks in advance! Best regards, Chen Other might relevant Information: 1) Coil element is wrong. 'HE2,4;NE2'. 2) I got an error message when I wad doing the recon-all first time: watershed error: indices out of bounds. Then I added the command line 'mri_add_xform_to_header $mdir/transforms/talairach.xfm $mdir/nu.mgz $mir/nu.mgz' based on this page <https://secure-web.cisco.com/1uRXBiwoaszcFJpp3kKMMx2gS1DnuVTXjdvnMG63iVHxJH…>. Then I got another error message in recon-all: mri_em_register: could not open brainmask.mgz so I added some cp to nu.mgz. It worked but the part of brain is missing, as I mentioned in the beginning (Fig.1). 1) FreeSurfer version: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0 2) Platform: Linux 5.10.0-28-amd64 3) uname -a: Linux ramones 5.10.0-28 -amd64 #1 SMP Debian 5.10.209-2 (2024-01-31) x86_64 GNU/Linux 4) recon-all.log: see attached -- Chen Yang PhD Student Independent Research Group 'Milestones of Early Childhood Development' Max Planck Institute for Human Cognitive and Brain Sciences Email:yangc@cbs.mpg.de

2 1

Fw: Discrepancy between mris_preproc and mri_surf2surf results when mapping individual's measures to fsaverage space
by tyzhang＠ibp.ac.cn 29 Mar '24

29 Mar '24

External Email - Use Caution Dear FreeSurfer Experts, Sorry, I think I've found the answer. It's because Jacobian correction was performed for mris_preproc, right? Tongyu Zhang -----原始邮件----- 发件人:tyzhang@ibp.ac.cn 发送时间:2024-03-20 16:31:23 (星期三) 收件人: freesurfer(a)nmr.mgh.harvard.edu 抄送: 主题: Discrepancy between mris_preproc and mri_surf2surf results when mapping individual's measures to fsaverage space Dear FreeSurfer Experts, I'm currently working on mapping cortical morphometric measurements from each individual in the HCP dataset to the fsaverage space. I have noticed that both the mris_preproc and mri_surf2surf commands can achieve this function. However, I found that the vertex-level measurements for cortical thickness, sulcal depth, and curvatures are consistent between these two commands, but the results for surface area and gray matter volume are totally different. I am puzzled by this inconsistency and speculate that perhaps these two commands are calculated on different surfaces? I don't understand why the two commands get different results since the inputs are the same. My command are as follows: (Different surface area values will be obtained in lh.area.fsaverage.mgh and lh.area.fsaverage.gii files) mris_preproc --s id --meas area --target fsaverage --hemi lh –out /Results/CorticalFeatures/id/lh.area.fsaverage.mgh mri_surf2surf --srcsubject id --trgsubject fsaverage --hemi lh --sval /HCP/id/surf/lh.area --tval /Results/CorticalFeatures/id/lh.area.fsaverage.gii Thank you so much! Tongyu Zhang

2 1

Discrepancy between mris_preproc and mri_surf2surf results when mapping individual's measures to fsaverage space
by tyzhang＠ibp.ac.cn 29 Mar '24

29 Mar '24

External Email - Use Caution Dear FreeSurfer Experts, I'm currently working on mapping cortical morphometric measurements from each individual in the HCP dataset to the fsaverage space. I have noticed that both the mris_preproc and mri_surf2surf commands can achieve this function. However, I found that the vertex-level measurements for cortical thickness, sulcal depth, and curvatures are consistent between these two commands, but the results for surface area and gray matter volume are totally different. I am puzzled by this inconsistency and speculate that perhaps these two commands are calculated on different surfaces? I don't understand why the two commands get different results since the inputs are the same. My command are as follows: (Different surface area values will be obtained in lh.area.fsaverage.mgh and lh.area.fsaverage.gii files) mris_preproc --s id --meas area --target fsaverage --hemi lh –out /Results/CorticalFeatures/id/lh.area.fsaverage.mgh mri_surf2surf --srcsubject id --trgsubject fsaverage --hemi lh --sval /HCP/id/surf/lh.area --tval /Results/CorticalFeatures/id/lh.area.fsaverage.gii Thank you so much! Tongyu Zhang

2 1

aparc & wm underestimation
by Stanica, Maria 29 Mar '24

29 Mar '24

External Email - Use Caution Hello FS developers, I ran my subjects through skullstripping and recon-all. Everything processed correctly (and exited without errors), except 4 images which have an underestimation in coronal subcortical region. The underestimation is significant and goes on for about 10-12 slices (for one image it was 153-162, for another it was 150-164). After searching the list, we attempted control points, which ended up not working (I don’t believe this was the right method to correct the error). Then we tried white matter edits, and one of the images was resolved, but the other 3 did not get better. Is there anything else we could do to try to resolve the issue? I can provide any other information needed. Any help would be appreciated! 1. Freesurfer version: FreeSurfer/7.1.1-centos7_x86_64 2. Operating System: Red Hat Enterprise Linux 7 3. OS Version: 7.9 (Maipo) Best, Maria Maria Stǎnicǎ, B.A. | Graduate Student Medical/Clinical Psychology Doctoral Program UAB |The University of Alabama at Birmingham mstanica(a)uab.edu<mailto:mstanica@uab.edu> Pronouns: she/her/hers [Image]

2 7

recon-all nu_correct error
by Dong, Yilei 28 Mar '24

28 Mar '24

External Email - Use Caution Hi Freesurfer support, Recently, I submitted a script to run recon-all on 100 MRI images on UCSD's computing cluster. I get an error file that says "nu_correct: Command not found. FREESURFER: Undefined variable." I previously emailed this problem and was told to send my recon-all.log if running the recon-all did not work a 2nd time. I was also told previously that my cluster's Freesurfer can't locate the minc toolkit binaries on my system. How can this error be troubleshooted? Please let me know if you need any other information. Freesurfer version: 7.2.0, but already available as module Platform: Rocky Linux release 8.8 (Green Obsidian) uname -a: Linux login01 4.18.0-477.15.1.el8_8.x86_64 #1 SMP Wed Jun 28 15:04:18 UTC 2023 x86_64 x86_64 x86_64 GNU/Linux Recon-all log: see attached Sincerely, Yilei

3 3

command line options to control appearance in timecourse window
by Proulx, Jean Sebastien 27 Mar '24

27 Mar '24

Dear Fresurfers, I'm visualizing multiple timecourses using the -timecourse window in freeview. I'd like to specify the color of each traces through the command line. Is there a hidden (or easy to implement) feature for that? I use the dev version at the Martinos. Thanks for the help and Have a great day! Sebastien

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