Freesurfer March 2021

freesurfer@nmr.mgh.harvard.edu

106 participants
144 discussions

Re: [Freesurfer] freesurfer install error
by fsbuild 16 Mar '21

16 Mar '21

External Email - Use Caution It reads like you are trying to install on an Ubuntu system, e.g., Ubuntu 18 or Ubuntu 20? On Ubuntu you can try the install command,$ sudo apt install libjpeg62 Also it would be good to know what freesurfer release you are installing, e.g., 7.1.1. Something may not be right with your environment for remote X programs.  I would check you have the DISPLAY environment variable setup in your xshell or xmanager setup.  On my terminal DISPLAY is set to, $ echo $DISPLAY:0 I don’t know how xshell and xmanager setup your X environment, but I would first try running a simple X windows program like xeyes and get that to work (displays a pair of eyes that track the cursor) before running tksurfer, etc. - R. On Mar 16, 2021, at 07:17, 1248742467 <1248742467(a)qq.com> wrote:        External Email - Use Caution        Hello, FsAfter installing FreeSurfer, use tkregister2, tkmedit, tkurfer, and recon all -- help to verify whether the installation is successful. The first and fourth commands are OK, but the second and third commands display the same error: glut: fatal error in tksurfer.bin : could not open display:  localhost:17.0.I use xshell as a terminal, and I have installed xmanager. I used to be able to use it, but now I have problems.And when I use the Freeview command, an error is reported as follows: freeview.bin : error while loading shared libraries:  libjpeg.so .62: cannot open shared object file: No such file or directoryDo you know how to solve the above problems?Looking forward to your reply_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

1 0

Help
by Murray Howerth 16 Mar '21

16 Mar '21

External Email - Use Caution I am new to this platform and would like some direction as how to obtain adjusted cerebellar volumes, specifically lobular cerebellum structure. With thanks, M

2 1

Aseg missing frontal portions - subcortical okay?
by Laurel Quinlan 16 Mar '21

16 Mar '21

External Email - Use Caution Hi Freesurfer Team, I am checking over the aseg on one of my subjects and notice that there are large portions of cortex missing anteriorly. The omission does not seem to affect any subcortical structures. Do you think that the subcortical values extracted from this subject are okay, even if there is cortex missing? Thanks! Laurel Quinlan Research Specialist Center for Healthy Minds University of Wisconsin-Madison

2 4

Flip image (resize)
by Ramesh Babu 16 Mar '21

16 Mar '21

External Email - Use Caution Dear Experts, The fMRI data, when viewed in SPM, some images have 3x3x4 voxel dimensions and some images have -3x3x4. Should I flip the image (using resize option) so that all images will have the same dimensions? or Should I leave it without flipping? Please give your suggestions. Regards Ramesh

2 1

Absolute volume difference between Freesurfer 6.0 and 7.1
by Lee, Sang Hoon 16 Mar '21

16 Mar '21

External Email - Use Caution I recently installed version 7.1, and I compared absolute volumes with version 6.0, and I realized that there are some significant differences in some brain structures (e.g. Hippocampus and amygdala). In some cases, the differences are more than 7%-14%. I understand that I should not be mixing the version when I process my datasets, but can you let me know what the main reason for the differences is, and how much should I expect? thank you. Sang

2 1

editing surfaces in two different Freesurfer versions
by Lara Foland-Ross 16 Mar '21

16 Mar '21

External Email - Use Caution Hi there, We are making the switch to Freesurfer v7.1 and wondering - can we continue editing surfaces in 7.1 that had previously undergone editing in versions 5.3 or 6.0? Thanks, Lara Lara Foland-Ross, Ph.D. Senior Research Associate and Imaging Lab Manager Center for Interdisciplinary Brain Sciences Research Stanford University School of Medicine 401 Quarry Road, Room 1356 Stanford, CA 94305-5795

2 1

Using Aseg atlas/subcortical segmentation with T2 MRI
by Choi, Nuri 16 Mar '21

16 Mar '21

External Email - Use Caution Hi, I was wondering if it is possible for me to use FreeSurfer's subcortical segmentation feature with T2-weighted images. Our lab was hoping to make our own T2-weighted Aseg atlas (which I believe is possible with FreeSurfer) and run the subcortical segmentation using that atlas. However, since FreeSurfer is designed for T1-weighted images, I wasn't sure if it be possible to pass a T2w MRI image instead. We don't need any of the other features available from FreeSurfer, just the subcortical segmentation. Would doing this step for T2 MRI be feasible using FreeSurfer? Thanks, -Nuri _________________________________________ Nu Ri Choi Undergraduate Student, Washington University in St. Louis Computer Science + Math Mobile: 314-327-2303

2 1

mri_surf2surf command error
by 1248742467 16 Mar '21

16 Mar '21

External Email - Use Caution Hello, Fs I want to template some subject to fsaverage5, but now I meet some problems FreeSurfer version: Fs6 Download the files: HLN-12-2.tar.gz    OASIS-TRT-20-1.tar.gz   Twins-2-1.tar.gz  Twins-2-2.tar.gz(https://secure-web.cisco.com/1yywjdkihIUyeuY7hFipb87XklaxLwbZLe2QL2---s_fK-nE83BFo2qLnTIxrpfr03QPbYjK5EiK9CV2zp5j8blIQiOrwLboJ9E6xSpJT3iwQoB4PQpqDg35Zmi8MY0XZCoayc2olZ7KIILnAncgm-NiKtOJYZ6kmhAAJlH2OjNQnuzQuF4FLLUiRhZx7-3PFqoNLT6YIA5nDRnnNcs9JSEc9yJ4TBP4UZziy8kENeniwtUqKhxIKe7yXkWaUzSJNkAAR3ryEXlnSj0aNK-8QiA/https%3A%2F%2Fosf.io%2Fwzqmg%2F) Register the following 5 files into the fsaverage5 space: lh.area            lh.jacobian_white     lh.volume                     lh.labels.DKT31.manual.annot The error message: HLN-12-2: lh.area    lh.volume    lh.jacobian_white                  can't match the surface （148208,146833） OASIS-20-1： lh.labels.DKT31.manual.annot                        here is a problem with the registration of the .annot file， can't allocate memory Twins-2-1/Twins-2-2:                         File missing: lh.area lh.volume lh.jacobian_white template to fsaverage5 space command: mri_surf2surf example 1:   mri_surf2surf --srcsubject Afterthought-1 --sval thickness --src_type curv --trgsubject fsaverage5 --trgsurfval /home/tj/application/freesurfer/subjects/Afterthought-1-target/thickness --trg_type curv --hemi rh example  2:  mri_surf2surf --srcsubject OASIS-TRT-20-1 --trgsubject fsaverage5 --hemi lh --sval-annot /home/tj/application/freesurfer/subjects/OASIS-TRT-20-1/label/lh.labels.DKT31.manual.annot  --tval  /home/tj/application/freesurfer/subjects/min_template/OASIS-TRT-20-1-target/lh.labels.DKT31.manual.annot Do you know how to solve these problem? Could you please download the four folder, and template the four file to fsaverage5 space? Then send the peocessed file to me.  Thank you very much! 从QQ邮箱发来的超大附件 Description.txt (1.2K, 2021年03月04日 10:52 到期)进入下载页面：http://secure-web.cisco.com/1jd2liRa00yonNeFyG9AZ2bcluJP4-ULFyYof… HLN-12-2.tar.gz (313.74M, 2021年04月03日 10:45 到期)进入下载页面：http://secure-web.cisco.com/1J-fWxcdcF6bvpmsz6UIpIJxIGomCAdLkeFoo… OASIS-TRT-20-1.tar.gz (317.69M, 2021年04月03日 10:53 到期)进入下载页面：http://secure-web.cisco.com/11SlUOJyt6MBMrV6J67jeFNISMvisa-dACbQN… Twins-2-1.tar.gz (227.10M, 2021年04月03日 11:02 到期)进入下载页面：http://secure-web.cisco.com/1EXcLgILy53kxZ_CKjJSDkth4O91WhxEdozgc… Twins-2-2.tar.gz (265.12M, 2021年04月03日 11:07 到期)进入下载页面：http://secure-web.cisco.com/1R9eFYoZnJyEzQ0wpWbZLeO41mITjC214u7P8…

2 1

Two questions about FDR correction
by Funk, Quentin 16 Mar '21

16 Mar '21

External Email - Use Caution Freesurfer experts, I have two questions that probably show my lack of understanding of many things related to thickness comparisons. I have a group of controls and a single subject with pathology. I'd like to run a thickness analysis comparing them. I realize this is not ideal from a statistical standpoint, but due to the rarity of the disease, we'd like to see the results anyways. Currently I'm using mri_glmfit followed by mri_fdr to do this comparison. My questions are: 1) Is this FDR tool robust enough to handle this type of one-vs-many analysis? Is there a better way? 2) Generally, for one-vs-many analyses, I'd like to use a z-score. Is there a good way to convert this -log10(p) value from sig.mgh into a threshold for z.mgh instead? The dumb thing of back converting from p-value to z-score doesn't give the same maps once thresholded (there is probably an obvious reason for this that I'm missing). thank you for any help you can provide! quentin funk Houston Methodist. Leading Medicine. Houston Methodist is ranked by U.S. News & World Report as the No. 1 hospital in Texas for patient care and safety and one of the top 20 hospitals in the nation. In addition, we are nationally ranked in 11 specialties, the most in the state, and have been national leaders throughout the COVID-19 pandemic in research, offering innovative treatments and surpassing CDC safety standards. For more than 100 years, Houston Methodist has provided the best — and safest — clinical care, advanced technology and patient experience. That is our promise of leading medicine. houstonmethodist.org twitter.com/MethodistHosp facebook.com/HoustonMethodist ***CONFIDENTIALITY NOTICE*** This e-mail is the property of Houston Methodist and/or its relevant affiliates and may contain restricted and privileged material for the sole use of the intended recipient(s). Any review, use, distribution or disclosure by others is strictly prohibited. If you are not the intended recipient (or authorized to receive for the recipient), please contact the sender and delete all copies of the message. Thank you.

2 1

Recon-all Ending Fast
by A.R. Sekar 16 Mar '21

16 Mar '21

External Email - Use Caution Hello, I am trying to run the recon-all function and the whole process is completing within a minute or so. I was told that the whole process would take between 6-24 hours. This is the output I am getting after entering the command: Akilas-MacBook-Air:Sub01 akilasekar$ recon-all -s sub_01 -i sub1.fspgr.nii Subject Stamp: freesurfer-darwin-macOS-7.1.1-20200811-8b40551 Current Stamp: freesurfer-darwin-macOS-7.1.1-20200811-8b40551 INFO: SUBJECTS_DIR is /Applications/freesurfer/7.1.1/subjects Actual FREESURFER_HOME /Applications/freesurfer/7.1.1 Darwin Akilas-MacBook-Air.local 20.3.0 Darwin Kernel Version 20.3.0: Thu Jan 21 00:07:06 PST 2021; root:xnu-7195.81.3~1/RELEASE_X86_64 x86_64 /Applications/freesurfer/7.1.1/subjects/sub_01 \n mri_convert /Users/akilasekar/Desktop/Cambridge/Data/Sub01/sub1.fspgr.nii /Applications/freesurfer/7.1.1/subjects/sub_01/mri/orig/001.mgz \n mri_convert /Users/akilasekar/Desktop/Cambridge/Data/Sub01/sub1.fspgr.nii /Applications/freesurfer/7.1.1/subjects/sub_01/mri/orig/001.mgz reading from /Users/akilasekar/Desktop/Cambridge/Data/Sub01/sub1.fspgr.nii... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (0, -1, 0) j_ras = (0, 0, 1) k_ras = (1, 0, 0) writing to /Applications/freesurfer/7.1.1/subjects/sub_01/mri/orig/001.mgz... /Applications/freesurfer/7.1.1/subjects/sub_01/mri/transforms /Applications/freesurfer/7.1.1/subjects/sub_01 /Applications/freesurfer/7.1.1/subjects/sub_01 Started at Tue Mar 16 14:41:43 EAT 2021 Ended at Tue Mar 16 14:41:49 EAT 2021 #@#%# recon-all-run-time-hours 0.002 recon-all -s sub_01 finished without error at Tue Mar 16 14:41:49 EAT 2021 done It would great if you can help me out! Thank you! Akila

2 1

← Newer
1
...
7
8
9
10
11
12
13
14
15
Older →

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 March 2021