Freesurfer

freesurfer@nmr.mgh.harvard.edu

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question for FREESURFER
by hyeyoung park 02 Sep '21

02 Sep '21

External Email - Use Caution Hi, This is hyeyoung Park from Seoul National University in South Korea. I have one question about FREESURFER. I ran recon-all using terminal, and finally I got files such as aseg.stats and aparc.stats. For the next steps, I'd like to extract the measurements like thickness or volume from these files using the terminal or "freesurfer" package in R. But I don't know how should I do for the next steps. How can I get the measurements for several subjects in parallel? I hope you can help me. Thank you, Hyeyoung

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matlab runtime error
by Corinna Bauer 02 Sep '21

02 Sep '21

External Email - Use Caution Hi all, I ran a few subjects successfully through7.1.1, but when I got to check the surfs in freeview I get an error about the Matlab runtime libraries below. However, I already have those libraries and the 2014b runtime environment installed on my Ubuntu 18.04. freeview: /usr/local/MATLAB/MATLAB_Runtime/v97/bin/glnxa64/libQt5X11Extras.so.5: no version information available (required by freeview) freeview: /usr/local/MATLAB/MATLAB_Runtime/v97/bin/glnxa64/libQt5Core.so.5: no version information available (required by freeview) freeview: /usr/local/MATLAB/MATLAB_Runtime/v97/bin/glnxa64/libQt5Gui.so.5: no version information available (required by freeview) freeview: /usr/local/MATLAB/MATLAB_Runtime/v97/bin/glnxa64/libQt5Widgets.so.5: no version information available (required by freeview) freeview: relocation error: freeview: symbol _ZN17QAbstractItemView11eventFilterEP7QObjectP6QEvent version Qt_5 not defined in file libQt5Widgets.so.5 with link time reference I also tried re-installing the 2014b MCR, but get this message: fs_install_mcr R2014b curl: /usr/local/MATLAB/MATLAB_Runtime/v97/bin/glnxa64/libcurl.so.4: no version information available (required by curl) curl: (48) An unknown option was passed in to libcurl Let me know how to best proceed. Thanks! Corinna

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Shiny new 7.2!
by Andy Worth 01 Sep '21

01 Sep '21

External Email - Use Caution Is it true that all that is needed for a new official FS docker container to come into existence is to merge pull request #866 <https://secure-web.cisco.com/10DeE1N6s0_SCCbPo6uqcazn6bfeF4GN2L9n26obY0mrz4…>? That would be so very nice. We like the official release! 4.1K pulls of previous versions on dockerhub can't be wrong. Kind regards, Andy Worth Senior Scientific Solutions Engineer he, him, his <http://secure-web.cisco.com/1q0M-qEiBJlwu49m9WEWx5rGqctEdeZiwaiHNtscHhu8sb1…>

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The Department of Psychology (http://secure-web.cisco.com/1L2oUeS03j4UpCKska-6NzVcNYkUOi4t3lCF7-KCqRL2UzvmuNigg1dexCNUvuS4mfvbONgeHxSnKxGIQ8x58YQo5DFR7RHXerH4W09GqHKfZQm6exjszmcWP9RcfvGe6QsjzBR_NOGCfwUDPHEXauO-vooHLHnSHsnBl0DE_6eQwpeTB9mxwA1WkCUlTXvJd7n89LG4mVwuLdW3r6yj8elx_mQ5tRw3dMvv5Ci8n5zESv2W6U-5I_Vk1V7Fr5gCBRcbgCFmnKzV4-pPB1cl4KA/http%3A%2F%2Fwww.psychology.umd.edu) at the University of Maryland, College Park seeks candidates for positions in Cognitive Neuroscience, Behavioral Neuroscienc
by Tracy Riggins 01 Sep '21

01 Sep '21

External Email - Use Caution Please post/circulate as appropriate; excuse cross-postings. Thank you. The Department of Psychology (http://secure-web.cisco.com/1L2oUeS03j4UpCKska-6NzVcNYkUOi4t3lCF7-KCqRL2Uzv…) at the University of Maryland, College Park seeks candidates for positions in Cognitive Neuroscience, Behavioral Neuroscience and Clinical Psychology with a starting date of August 2022. The full position announcements and application portal can be found via the employment links below. Assistant Professor in Cognitive Neuroscience https://secure-web.cisco.com/1Z-RRqxsigDpJer5hEkiA6TXEl0hLo4gO1jaUmugWYbggx… Assistant Professor in Behavioral Neuroscience https://secure-web.cisco.com/1kfG6aV4cfooPw7PvLEfDJPvEr2TvVbWiuQYrplqlgnG-v… Assistant or Associate in Clinical Psychology https://secure-web.cisco.com/1eMqsqMGPvfaje54pwO0AmenI9qYEC3SQoGp5sMXsDAAki… Application materials should be submitted through the link above no later than November 1, 2021 and should include: a cover letter, CV, statement of current and future research interests and research philosophy, a statement of teaching philosophy and experience (including evidence of teaching excellence, if available), and contact information for three references. Applicants should provide sample research manuscripts or journal articles in the Supplemental Document 1 field in eJobs. Because the Department of Psychology is committed to increasing the diversity of the campus community and promoting inclusion across campus, materials should address how the candidate will contribute to fostering a diverse and inclusive community. In addition, the Department embraces the values of open and reproducible science, and candidates are encouraged to address how they have pursued and/or plan to pursue these goals in their work. The University of Maryland, College Park, an equal opportunity/affirmative action employer, complies with all applicable federal and state laws and regulations regarding nondiscrimination and affirmative action; all qualified applicants will receive consideration for employment. The University is committed to a policy of equal opportunity for all persons and does not discriminate on the basis of race, color, religion, sex, national origin, physical or mental disability, protected veteran status, age, gender identity or expression, sexual orientation, creed, marital status, political affiliation, personal appearance, or on the basis of rights secured by the First Amendment, in all aspects of employment, educational programs and activities, and admissions. The University of Maryland has made the safety of our students, faculty and staff, and our surrounding communities a top priority. As part of that commitment, the University System of Maryland (USM) recently announced that students, faculty, and staff on USM campuses this fall, including UMD, are required to be vaccinated against COVID. As a prospective and/or a new employee at UMD, you will be required to comply with the University’s vaccination protocol. Proof of full vaccination will be required before the start of employment in order to work at any University of Maryland location. Prospective or new employees may seek a medical or religious exemption to the vaccination requirement at return.umd.edu <https://secure-web.cisco.com/1-xn068vbthEknoIWbkAwOfUqSZoMUsHVaKbCBo2LvGMRk…> and must have an approved exemption prior to the start of their employment. -- Tracy Riggins, Ph.D. Pronouns <https://secure-web.cisco.com/1iLnmQ8Au0eEK07bg8TX8wCNei48kyu0pxlj6dnWl89JgT…>: she/her/hers Associate Professor of Psychology Secretary, Cognitive Development Society 4094 Campus Drive, Biology/Psychology Building 2147J University of Maryland, College Park, MD 20742 ***************************************************** Research info: http://secure-web.cisco.com/1zMjA3wZL1bVISPYhKnp3xSpIOD2J73ZxmIVu46ORRGV5GK… <https://secure-web.cisco.com/1WZVU5oCPDkWjiZlUnNI84I3BX2osoEnVHC_dKT8q5Mzle…> and https://secure-web.cisco.com/1WZVU5oCPDkWjiZlUnNI84I3BX2osoEnVHC_dKT8q5Mzle… Black lives matter in academia <https://secure-web.cisco.com/10nyNX_SDjMsD8Bk7H-wMu9C4SlBSvAEYdvOZdmE_hje2d…> LGBTQIA Ally <https://secure-web.cisco.com/1RCgvgN2MM72_6sY3jVkD_dxYTBgytophWKzs5G-vMmu31…> actions <https://secure-web.cisco.com/1RCgvgN2MM72_6sY3jVkD_dxYTBgytophWKzs5G-vMmu31…>

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TOPO_DEF
by halil ibrahim AKÇAY 31 Aug '21

31 Aug '21

External Email - Use Caution Hi My name is Halil Ibrahim akçay. I am a neurologist. I have been used FreeSurfer for a while. And I cannot understand some part of troubleshooting process. I am sending a screenshot of my question. How can I understand whether gray zone as marked blue circle is a problem or not in this picture? And Should I fill this zone to fix the problem, if this is a problem? Thanx for your helping. I am looking forward to your answer. Best regards

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ERROR: mri_ca_register with non-zero status 11
by 朱子家 31 Aug '21

31 Aug '21

External Email - Use Caution Hello FreeSurfer Developers, when I run the recon-all command: $ export SUBJECTS_DIR=`pwd` $ cd /lustre/home/acct/zjzhu/project/zzu_MRI/T1/test $ ls *nii | parallel --jobs 12 recon-all -s {.} -i {} -all -qcache I get the following error ERROR: mri_ca_register with non-zero status 11 recon-all -s co20160131_165733 exited with ERRORS at Mon Aug 30 13:57:15 CST 2021 I've searched the list and no similar errors have been reported. Does anyone have any thoughts on how to trouble-shoot this one? Also, Ive attached the recon-all.log in case it's of any use. 1) FreeSurfer version: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551 2) Platform: CentOS Linux release 7.7.1908 (Core) 3) Linux login1.pi.sjtu.edu.cn 3.10.0-1062.el7.x86_64 #1 SMP Wed Aug 7 18:08:02 UTC 2019 x86_64 x86_64 x86_64 GNU/Linux 4) recon-all.log: see attached

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Re: [Freesurfer] recon-all exited with ERRORS
by guang 31 Aug '21

31 Aug '21

External Email - Use Caution At 2021-08-05 08:44:11, "guang" <zhaoguang721(a)163.com> wrote: Hello FreeSurfer Developers, I'm trying to analyze aseg.mgz files for each subjects though i have segmented hippocampal subfields and nuclei of the amygdala. Can I make the voxel-by voxel group analysis with the aseg.mgz or the aparc+aseg.mgz files? Thank you for any reply. guang

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Freesurfer Matlab LME tool: problem with function lme_mass_RgGrow
by Bonati, Sara 31 Aug '21

31 Aug '21

External Email - Use Caution Dear FreeSurfer Developers, I'm attempting to analyze thickness changes in a longitudinal design using a mass-univariate approach, as described on the Linear Mixed Effects tutorial at https://secure-web.cisco.com/1HwLf5wG3aIAhV84T5KTL4VUiVpoa1DISeYUypdAqYlExO…. Before starting the tutorial I followed the preprocessing steps described in section 2 at https://secure-web.cisco.com/1DrlLxryQICRHsEOZazZuvsDg0-s9654AX1e3qQgZGXx_G… I now have a dataset folder that contains 1) for each subject-session pair to include in the analysis a .long folder 2) a subject specific base template folder that used all available sessions from that subject. All recon-all.log files, both in the base template folder and the subject-session specific long folders, seem to have finished without error. After that, to prepare files for LME, I created a longitudinal qdec file and used it to prepare thickness.mgh files as described in the beginning of the Linear Mixed Effects tutorial for the mass-univariate approach. When advancing in the analysis the function lme_mass_RgGrow gets stuck: in the terminal the output looks like this ``` Starting region growing algorithm Computing seeds ... ``` and stays like this without advancing. I tried to change the thickness file used (lh.thickness.mgh VS lh.thickness_sm5.mgh VS lh.thickness_sm10.mgh etc..) but unfortunately the error persists. Looking in the mailing list I found an email with a problem that is similar to mine: https://secure-web.cisco.com/166fF5937wdn5yDLqNvdeV6NeSe3cGRWXBnp12bBcQPqvc… . Upon inspection of my lh.thickness.mgh file I also noticed that some columns are all zeros: do you know what could cause such columns of zeros to appear in the thickness files and how the problem with the function could be solved to continue in the analysis? Thank you very much for your help, Kind regards Sara Bonati 1) FreeSurfer version: freesurfer-darwin-macOS-7.2.0-20210713-aa8f76b 2) Platform: macOS Catalina version 10.15.7

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mri is cut off
by Ricardo Adrogue 31 Aug '21

31 Aug '21

External Email - Use Caution Hi y,all, I know that freesurfer is not made to work with MRI scans that are cut off. However, this is the only imaging we have, and we would love to have freesurfer data to analyze from this patient. The posterior third of the scan is missing, so it will not be an easy fix. If anyone has any suggestions on things to try, please let me know. Thanks! Ricardo Adrogue

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Re: [Freesurfer] SAMSEG esitmation error
by Stefano Cerri 31 Aug '21

31 Aug '21

External Email - Use Caution Hi Achille, It sounds like the initial affine registration of the template in SAMSEG is failing for some of your subjects. If that is the case, you will see that "template_coregistered.nii" is probably not aligned with your original data. As the affine registration has been improved in the latest version (FS 7.2), can you try to run a couple of failed segmentations on this new version and see if it solves the issue? If that doesn't work, it would be good if you can send us a couple of representative subjects so that we can see where SAMSEG fails. Best, Stefano Dear experts, We are working with a large MRI dataset (FLAIR, T1) and we are performing SAMSEG pipeline to estimate lesion volumes. We computed the registration between the two input images and the resampling as advised in the SAMSEG page (mri_coreg and mri_vol2vol) which worked perfectly. However, when we do the visual chek on the segmentation after running SAMSEG, it is completely wrong for some subjects. By looking at corresponding mode01_bias_corrected.mgz and mode02_bias_corrected.mgz images, they are too cropped (centered on the cerebellum) compared to the original ones (3D_T1 .nii.gz and 3D_FLAIR.nii.gz). We also noticed a < RuntimeWarning: invalid value encountered in true_divide > during the burn-in phase (in the GMM.py code). Do you have any clue of what is happening with this cropping (can it be linked to the bias field estimation ?) and how we can correct it ? Thanks for your help and I can provide some screenshots of the cropped images to help visualize the issue. Best, Achille Teillac

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Freesurfer