Freesurfer

freesurfer@nmr.mgh.harvard.edu

14 participants
30083 discussions

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

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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

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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…

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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.

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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

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Thalamic nuclei segmentation - PuM nucleus mis-segmentation?
by Gronow, Franziska 16 Mar '21

16 Mar '21

External Email - Use Caution Dear Eugenio, here are the zipped norm.mgz and automated segmentations for two subjects: https://secure-web.cisco.com/1NFOUrkRWZ6w5iEt9PtCxQNkjFZr9fIybWKJt1Rx3T_PB7… Hope this helps! Best regards, Franziska

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freesurfer install error
by 1248742467 16 Mar '21

16 Mar '21

External Email - Use Caution Hello, Fs After 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 directory Do you know how to solve the above problems? Looking forward to your reply

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license file not working
by Saemann, Philipp 16 Mar '21

16 Mar '21

External Email - Use Caution Hi FreeSurfer specalists, for some historical reconstruction I had to download an old FS5.3-Version, on a Linux System, untarred etc. - it seems there was no .license = hidden license file coming with the download, and no license.txt file. I requested one (usual link) and received a license.txt file, and put that into the FS home folder. When using the command mri_convert I get the error message that an invalid License file is used. Questions: (1) Is a .license file (so, a hidden file) needed for itself or in addition? (2) Why does a freshly delivered license.txt file not work? (3) Any other solutions or ideas? Bw, Philipp

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Thalamic nuclei segmentation - PuM nucleus mis-segmentation?
by Gronow, Franziska 15 Mar '21

15 Mar '21

External Email - Use Caution Dear Eugenio, do you mean the "ThalamicNuclei.v12.T1.mgz" files? Best regards, Franziska ___________________________ Date: Thu, 11 Mar 2021 16:29:45 +0000 From: "Iglesias Gonzalez, Juan E." <JIGLESIASGONZALEZ(a)mgh.harvard.edu> Subject: Re: [Freesurfer] Thalamic nuclei segmentation - PuM nucleus mis-segmentation? To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> Dear Franziska, Can you please send the automated segmentations as well? Cheers, /Eugenio Juan Eugenio Iglesias Senior research fellow CMIC (UCL), MGH (HMS) and CSAIL (MIT) http://secure-web.cisco.com/141gcV3WY5mJIjV2uPDoq59J1j9A_zAepv_kVvEZA1jJ2mu…

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Postdoctoral Researcher in Neuroimaging at Karolinska Institute, Stockholm, Sweden
by Joana Braga Pereira 15 Mar '21

15 Mar '21

External Email - Use Caution Dear all, We are looking for a Postdoc to work in an interdisciplinary and internationally competitive environment at Karolinska Institute, one of the top medical universities in the world and the home for the Nobel Prize in Medicine. We combine imaging analyses, statistical tools, machine learning algorithms, biofluid assays and genetics to study brain aging and the earliest signs of Alzheimer’s and Parkinson’s diseases. This project will be carried out under the supervision of Assistant Professor Joana B. Pereira and it will involve analyzing cross-sectional and longitudinal imaging data, combining clinical measures and cerebrospinal fluid biomarkers, as well as writing manuscripts and presenting results in international conferences. The fellow is expected to be independent, develop his or her own projects, supervise students and show an interest in approaches based on graph theory. In addition, he/she will have the opportunity to develop new skills, analyze large datasets, apply for grants and develop a wide network of collaborations. The ideal candidate should have the following qualities: - A PhD in neuroimaging, computational science, neuropsychology, physics, statistics or a related field; - Experience in statistical techniques, programming, or scripting; - Experience with structural MRI, DTI, fMRI or PET imaging analyses; - Clinical or research experience with aging and/or neurodegenerative disorders. - Good record of scientific publications. The Postdoctoral studies will be performed for 1 year, with possible extension for an additional year. There are also possibilities for a longer appointment after this 2-year period. To apply please go to: https://secure-web.cisco.com/1YHeKp4uDUxxiD2mZPjaEegL3DgIC_jwTdckTsrl1c73dr… (Deadline: 31/03/2021) For further information or general inquires, please contact Joana B. Pereira at jbragapereira(a)gmail.com or joana.pereira(a)ki.se. Best wishes, Joana

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