Freesurfer

freesurfer@nmr.mgh.harvard.edu

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30076 discussions

Freesurfer v7.x and bias correction -3T option not working
by Notestine, Christine 12 Dec '21

12 Dec '21

External Email - Use Caution We recently moved to FreeSurfer 7.1.1 running it on ~ 100 different types of cases using the -3T options, but after a case failure, we looked deeper into the v7.x changes related to bias correction, and it seems that using the -3T option did not produce a different bias corrected outcome than using the default for any cases (see description below). IF this is truly the case, our workaround would be to continue using the MNI N3 approach options we had before (e.g., an expert option file with the line: mri_nu_correct.mni --no-ants-n4), since that improved the correction in our data previously, but would like to make sure we are interpreting the v7 approach correctly. Thoughts on this appreciated, many thanks: * In earlier FreeSurfer versions, we used the options based on the Zheng paper with N3 as recommended for 3T data. So with our switch to v7.1.1 which is now using ANTs N4, we looked into the 3T options with the flags described on the wiki, and used those flags in our runs accordingly. * However, once we had this case failure (which had worked in a prior FS version run with the N3 3T flags), we dug into things and did some test runs. We found that in Freesurfer v7.1.1 when using ANTs N4 (i.e., AntsN4BiasFieldCorrectionFs) [instead of MNI N3 (i.e., nu_correct)], the effect of specifying the recon-all -3T (or -nuintensitycor-3T) option did not change the outcome relative to the default bias correction: * In v7.1.1, it seems that when ANTs N4 is used for bias field correction, the same bias field correction is performed whether the -3T (or -nuintensitycor-3T) option is specified or not. We assessed this by creating nu.mgz difference images (between runs with and without the -3T option) and confirmed by reviewing logs and the mri_nu_correct.mni script. * When the ANTs N4 bias field correction is used with the -3T options, the parameters for stronger bias field correction (i.e., "--n 1 --proto-iters 1000 --distance 50") are passed to mri_nu_correct.mni, but then seem to be dropped by mri_nu_correct.mni and not included in the subsequent call to AntsN4BiasFieldCorrectionFs. * Below are the relevant lines extracted from a mri_nu_correct.mni.log when stronger bias field correction was specified via the -3T (or -nuintensitycor-3T) option to recon-all but the parameters do not seem to be used by ANTs: mri_nu_correct.mni.log: ... /usr/local/freesurfer/bin/mri_nu_correct.mni --no-rescale --i orig.mgz --o orig_nu.mgz --ants-n4 --n 1 --proto-iters 1000 --distance 50 nIters 1 mri_nu_correct.mni 7.1.1 ... AntsN4BiasFieldCorrectionFs -i orig.mgz -o /dev/shm/tmp.mri_nu_correct.mni.2116356/nu0.mgz Using shrink factor: 4 ... -- Christine Fennema-Notestine, Ph.D.

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Questions about contrasts
by Laura Willers de Souza 12 Dec '21

12 Dec '21

External Email - Use Caution Hello FreeSurfer Developers, I want to perform an analysis of the difference between two groups in cortical thickness, having cortisol levels as covariate. This is my model: cortical thickness ~ pathology (CU/CI) + CSF cortisol + pathology*CSF cortisol >From the GLM DODS analysis I want to know if: * the regression coefficient is significant only for the difference between groups, * or only for cortisol, * or for both, * or if the coefficient of the intercept between group and cortisol is significant. Is my FSGD file (attached) correct? What would the contrasts look like? Thanks in advance! Laura Willers de Souza Master Student in Biochemistry Zimmer Lab - Federal University of Rio Grande do Sul - Porto Alegre/RS - Brazil

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Error: recon-all exited with ERRORS: failing without generating all surf files: How to modify wm.mgz to make it work?
by Sumit Sharma 12 Dec '21

12 Dec '21

External Email - Use Caution Hello FreeSurfer Developers, I'm attempting to generate the segmentation files by running the "the recon-all" command. The command is failing and I am getting the below error. ERROR: recon-all -s out_24 exited with ERRORS at Thu I searched and open the wm.mgz and other files using the below command following the tutorials: https://secure-web.cisco.com/1GbbXPOsSqlnYztwVk4vidqb-NyHGtLcthCKOl6FN_kuZ2… https://secure-web.cisco.com/1Da47ZnOFHuJQ-ZILQdgpeHcwfKHsJb7cuOQe4WoXHMu9w… Command: freeview -v out_24/mri/brainmask.mgz \ out_24/mri/wm.mgz:colormap=heat:opacity=0.4:visible=0 \ -f out_24/surf/lh.white:edgecolor=yellow \ out_24/surf/lh.pial:edgecolor=red \ out_24/surf/rh.white:edgecolor=yellow \ out_24/surf/rh.pial:edgecolor=red \ out_24/surf/lh.orig.nofix:visible=0 However, there are no surface files which are mentioned in the above command. The surface folder contains only the below files: lh.defect_borders lh.defect_labels lh.orig.nofix lh.qsphere.nofix rh.defect_borders rh.defect_labels rh.orig.nofix rh.smoothwm.nofix lh.defect_chull lh.inflated.nofix lh.orig.premesh lh.smoothwm.nofix rh.defect_chull rh.inflated.nofix rh.qsphere.nofix Please suggest on how should I modify the wm.mgz file in such case: Below are my doubts: What I understood so far that wm.mgz contains information of white and non-white matter (whether gray matter or CSF), however I could see yellow color pixels of intensity 255 near the corpus callosum cavity which is non-white matter region, however when I modify the voxels in freeview using recon-edit option, I need to give 255 pixel value to the white matter region, I am a little bit confused on how to edit wm.mgz, whether to edit voxels in the white matter region with 255 value and erase in the non white region or do the opposite, Please guide. What is the best way to modify the wm.mgz if the surfaces are not generated? Please advise. 1) FreeSurfer version: freesurfer-linux-centos6_x86_64-7.1.1-20200723-8b40551 2) Platform: ubuntu 3) recon-all.log: (PFA). Thanks and Regards Sumit Sharma ------------------------------------------------------------------------------------------------------------------------------ Sumit Sharma

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Doubts about analysis of hippocampal subfields and nuclei of the amygdala
by Laura Willers de Souza 12 Dec '21

12 Dec '21

External Email - Use Caution Hello FreeSurfer Developers, I would like to know if the analysis of hippocampal subfields and nuclei of the amygdala can only be done through ROI-based analysis or is there any way to perform GLM analysis with these data in freesurfer? Thanks in advance! Laura Willers de Souza Master Student in Biochemistry Zimmer Lab - Federal University of Rio Grande do Sul - Porto Alegre/RS - Brazil

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error in mri_sclimbic_seg
by Zeng, Victor (BIDMC - Keshavan - Psychiatry) 12 Dec '21

12 Dec '21

External Email - Use Caution I receive this error when I try to run mri_sclimbic_seg in dev 2021 12 06 How can I fix this? mri_sclimbic_seg --s 10105_S1200QUM/ --conform /usr/local/freesurfer/dev7/python/scripts/mri_sclimbic_seg --s 10105_S1200QUM/ --conform Excluding seg [853] Using CPU Using 1 thread(s) Loaded lookup table /usr/local/freesurfer/dev7/models/sclimbic.ctab Loaded population stats /usr/local/freesurfer/dev7/models/sclimbic.volstats.csv Segmentation fault Victor Zeng Beth Israel Deaconess Medical Center Keshavan Lab --

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PhD student position in the NCC lab at the European Neuroscience Institute Göttingen, Germany
by Caspar M. Schwiedrzik 12 Dec '21

12 Dec '21

External Email - Use Caution The NCC Lab at ENI Göttingen is looking for an outstanding *PhD student (f/m/d)* Specialization: interested in studying face perception and predictive processing in non-human primates Limitation: Appointment until 31.12.2025 Working period: 65 % (25,025h/week) Tariff: Entgelt nach TV-L Announcement published on 10.12.2021 Vacancy from 12.08.2021 Application deadline: 14.01.2022 At the University of Göttingen, a new Collaborative Research Center (CRC) 1528 “Cognition of Interaction” will be established with funding from the German Research Foundation (DFG). In 22 projects, the CRC 1528 “Cognition of Interaction” investigates how fundamental cognitive functions and their neurobiological foundations contribute to human and nonhuman primate social behavior and social interactions. The CRC is formed by a highly interdisciplinary consortium formed by systems and computational neuroscientists, data scientists, psychologists and behavioral and cognitive biologists. Partner institutions are the University of Göttingen, the University Medical Center, the German Primate Center, the Max Planck Institute for Dynamics and Self-Organization, the University Hospital Hamburg-Eppendorf and the Weizmann Institute of Science. In the context of this CRC, the Neural Circuits and Cognition Lab of Caspar Schwiedrzik at the European Neuroscience Institute Göttingen is looking for an outstanding PhD student interested in studying face perception and predictive processing. The project investigates neural mechanisms of face perception and predictive processing at the level of circuits and single cells, utilizing functional magnetic resonance imaging (fMRI) in combination with electrophysiology and pharmacology in non-human primates. The Neural Circuits and Cognition Lab seeks to understand the cortical basis and computational principles of visual perception and experience-dependent plasticity in the macaque and human brain. To this end, we use a multimodal approach including fMRI-guided electrophysiological recordings in non-human primates and fMRI and iEEG in humans. The PhD student will play a key role in our research efforts in this area. The lab is located at the European Neuroscience Institute Göttingen (https://secure-web.cisco.com/1M4ih3bIajicoiya9v-lqOnKTS2CbqlGDKae_4HyuGj9V4…) and the German Primate Center ( https://secure-web.cisco.com/1e7PDNnx3vJ0Ki_w3J2EmcwNhCg10VhPvan20Jo38LbRUq…) which are interdisciplinary research centers with international faculty and students pursuing cutting-edge research in neuroscience. Further scientific exchange within the CRC and the Leibniz ScienceCampus ‘Primate Cognition’ (https://secure-web.cisco.com/1UjuTZ8yx1wgmVQdVS8O0yc_fODUaQGXoFT7_Mfln9abC9…) ensures a broad interdisciplinary framework for networking and cooperation. The PhD student will have access to a dedicated imaging center with a dedicated 3T research scanner, state-of-the-art electrophysiology, and behavioral setups. For an overview of our work and representative publications, please see our website https://secure-web.cisco.com/1gqoIp_WsMnNp-n-3I7LUzUkns35bMM3Vw8vYQBUosgdje… The position is funded until 31.12.2025. The successful candidate will join one of the many excellent graduate schools on the Göttingen Campus.Candidates should have a degree (master, diploma or equivalent) in a relevant field (e.g., neuroscience, psychology, biology), and ideally prior experience with non-human primates, strong quantitative, programming, and experimental skills, and share a passion for understanding the neural basis of visual perception and its plasticity. A good command of English is a requirement, but fluency in German is not essential. Interested candidates should send their curriculum vitae, a description of their scientific interests and the names and contact information of two references who are able to comment on your academic background and who agreed to be contacted to Caspar M. Schwiedrzik (cschwie3(a)gwdg.de) The University Medical Center Göttingen is committed to professional equality. We therefore seek to increase the proportion of under-represented genders. Applicants with disabilities and equal qualifications will be given preferential treatment. We look forward to receiving your application by 14.01.2022: University Medical Center Göttingen European Neuroscience Institute Göttingen Dr. Caspar Schwiedrzik Group Leader Grisebachstr. 5 37077 Göttingen Tel.: +49 0551/39-61371 E-Mail: cschwie3(a)gwdg.de Web: http://secure-web.cisco.com/1-7988TeJhnzxuk_F1uUcu7-YL8le_tn5NmaUJxD5RVg9Ta… Contact person: For questions about the position or project, please contact Caspar M. Schwiedrzik (cschwie3(a)gwdg.de) For questions about the application procedure, please contact Christiane Becker (c.becker(a)eni-g.de) Please send your application via e-mail in PDF-format or via mail in copy and not in folders.

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Freesurfer recon-all error “mri_convert: extra argument”
by William McCuddy AZ-Phoenix 11 Dec '21

11 Dec '21

External Email - Use Caution Hello Freesurfer Community, I'm new to freesurfer and could use some help with recon-all on a single subject. The input file is a 3D T1 WAND from a Philips scanner. I used dcm2niix to convert from dicom to nifti. I can open the nifti file and everything looks normal. nNfti header info displayed in screenshot below and computer specs are listed in the attached recon-all log file (shortened). Not sure what the “mri_convert: extra argument” problem is. If anyone knows what I’m doing wrong, I would love some assistance! Thanks, Travis Original T1 (after conversion from dicom) [image: image.png] Fri Dec 10 20:43:44 MST 2021 cd /usr/local/freesurfer/7.2.0/subjects/KH setenv SUBJECTS_DIR /usr/local/freesurfer/7.2.0/subjects /usr/local/freesurfer/7.2.0/bin/recon-all -s KH -i KH_T1.nii.gz -all -parallel -openmp 6 subjid KH setenv SUBJECTS_DIR /usr/local/freesurfer/7.2.0/subjects FREESURFER_HOME /usr/local/freesurfer/7.2.0 Actual FREESURFER_HOME /usr/local/freesurfer/7.2.0 build-stamp.txt: freesurfer-linux-ubuntu18_x86_64-7.2.0-20210721-aa8f76b Linux BarrowPrismProcess 5.11.0-41-generic #45~20.04.1-Ubuntu SMP Wed Nov 10 10:20:10 UTC 2021 x86_64 x86_64 x86_64 GNU/Linux total used free shared buff/cache available Mem: 31Gi 4.8Gi 4.1Gi 24Mi 22Gi 25Gi Swap: 2.0Gi 2.0Mi 2.0Gi ######################################## program versions used 7.2.0 (freesurfer-linux-ubuntu18_x86_64-7.2.0-20210721-aa8f76b) 7.2.0 ####################################### GCADIR /usr/local/freesurfer/7.2.0/average GCA RB_all_2020-01-02.gca GCASkull RB_all_withskull_2020_01_02.gca AvgCurvTif folding.atlas.acfb40.noaparc.i12.2016-08-02.tif GCSDIR /usr/local/freesurfer/7.2.0/average GCS DKaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs ####################################### /usr/local/freesurfer/7.2.0/subjects/KH mri_convert /home/prism/Desktop/Processed Data/KH_T1.nii.gz /usr/local/freesurfer/7.2.0/subjects/KH/mri/orig/001.mgz mri_convert /home/prism/Desktop/Processed Data/KH_T1.nii.gz /usr/local/freesurfer/7.2.0/subjects/KH/mri/orig/001.mgz mri_convert: extra argument ("/usr/local/freesurfer/7.2.0/subjects/KH/mri/orig/001.mgz") type mri_convert -u for usage Command exited with non-zero status 1 @#@FSTIME 2021:12:10:20:43:45 mri_convert N 3 e 0.00 S 0.00 U 0.00 P 100% M 6284 F 0 R 247 W 0 c 0 w 1 I 0 O 0 L 0.32 0.25 0.21 @#@FSLOADPOST 2021:12:10:20:43:45 mri_convert N 3 0.32 0.25 0.21 Linux BarrowPrismProcess 5.11.0-41-generic #45~20.04.1-Ubuntu SMP Wed Nov 10 10:20:10 UTC 2021 x86_64 x86_64 x86_64 GNU/Linux recon-all -s KH exited with ERRORS at Fri Dec 10 20:43:45 MST 2021 To report a problem, see http://secure-web.cisco.com/13ddiImmrJeyHcBtuL-2JQaEFuG60p6qT6OFYGZt3WA_uSv… -- *William T. McCuddy, PhD* Clinical Neuropsychologist Department of Clinical Neuropsychology Joint Appointment in Neuroradiology *Barrow Neurological Institute* *Dignity Health I St. Joseph’s Hospital and Medical Center* 222 W. Thomas Rd, Suite 315 Phoenix, AZ 85013 602.406.3671 (O) 602.406.6115 (F) *Caution**: This email is both proprietary and confidential, and not intended for transmission to or receipt by any unauthorized persons. If you believe that it has been received by you in error, do not read any attachments. Instead, kindly reply to the sender stating that you have received the message in error. Then destroy it and any attachments. Thank you.* Caution: This email is both proprietary and confidential, and not intended for transmission to (or receipt by) any unauthorized person(s). If you believe that you have received this email in error, do not read any attachments. Instead, kindly reply to the sender stating that you have received the message in error. Then destroy it and any attachments. Thank you.

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VirtualBox Ubuntu Password Request
by Zhengyu LIN 11 Dec '21

11 Dec '21

External Email - Use Caution Hello, Could you please send me the password for the "developer" account ofthe Ubuntu virtual machine please. Thank you very much. Yours sincerely, LIN Zhengyu MSc. Medical Resident Center for Functional Neurosurgery, Ruijin Hospital, Shanghai Jiao Tong University, School of Medicine, Shanghai, China Mail: hrfrerrare(a)sjtu.edu.cn zhenyu.lin95(a)outlook.com Telephone: +86 18816500519

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White matter
by Paul, Rahul 10 Dec '21

10 Dec '21

Hi FreeSurfer experts, I know that FreeSurfer genrates WM information (area/volume) for smaller cortical regions (e.g, superiortemporal, supramarginal) along with the GM information. But, I was wondering is there a way to generate larger WM structures (e.g., temporal lobe or parietal lobe) using freesurfer? Thank you, Rahul

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question about surface registration to an average surface
by Trisanna Sprung-Much 10 Dec '21

10 Dec '21

External Email - Use Caution Hi there I have a bunch of labels on individual subjects and would like to register them to an average surface that we have created here at the MNI. So, this average has not gone through recon-all and there are no freesurfer recon-all files associated with it. There is no volume associated with it to run in recon-all. According to the instructions for mri_surf2surf I need the sphere.reg file, which is generated during recon-all. I wonder if there is a way to undergo surface registration in my situation? I found the following documentation, but this seems to be for creating a new average. I have the average already. https://secure-web.cisco.com/1hQ9hS6yFMKayjbN2TstCM6s3-2VxHitXzaDRkJ6eA1mJJ… SurfaceRegAndTemplates - Free Surfer Wiki<https://secure-web.cisco.com/1hQ9hS6yFMKayjbN2TstCM6s3-2VxHitXzaDRkJ6eA1mJJ…> The output from registration is yet another version of the subject's surface mesh, typically named ?h.sphere.reg, with the x,y,z vertex positions still on a sphere, but warped so that the subject's curvature pattern best aligns with the template data.Here is the same convexity data, now plotted on the lh.sphere.reg surface. Similar pattern, but "stretched around". surfer.nmr.mgh.harvard.edu Thank you, Trisanna -- Trisanna Sprung-Much, PhD Research Associate McGill University Montreal Neurological Institute

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