Freesurfer

freesurfer@nmr.mgh.harvard.edu

17 participants
30086 discussions

Re: [Freesurfer] Recon-all error in CA Normalize (FreeSurfer V 7.1)
by Schranzer René 28 May '20

28 May '20

External Email - Use Caution Hi Douglas, First of all, thank you for your help. I forgot to mention that I am already using skull-stripped data for the recon-all processing stream. Therefore, I stopped after -autorecon1 and copied the T1.mgz to brainmask.mgz and brainmask.auto.mgz and continued processing with -autorecon2 and -autorecon3. In some subjects (at some timepoints), the recon-all -autorecon2 -autorecon3 excited with errors, as mentioned below. Now I have used the following command "recon-all -hires -skullstrip -no-wsgcaatlas -s ${sbjID} -i ${sbj} -all" with the skull-stripped data and it worked fine without errors. I also compared the T1.mgz from both approaches and they looked identical. My question, can I use this approach with the "-no-wsgcaatlas" for all subjects or is there something to consider here? Best, René

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lta_convert
by Alshelh, Zeynab 28 May '20

28 May '20

Hi everyone, I am running this version of fs: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 But I am having trouble running lta_convert, it returns with command not found. Is there something I am missing? Thanks ---- Zeynab Alshelh, PhD | Postdoctoral Research Fellow Pain and Neuroinflammation Imaging Laboratory Harvard Medical School | A. A. Martinos Center for Biomedical Imaging Massachusetts General Hospital | 149 Thirteenth Street, Room 1101 Charlestown, MA 02129 +1 (617) 794 6838 zalshelh(a)mgh.harvard.edu | www.nmr.mgh.harvard.edu

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Re: [Freesurfer] ERROR: mri_fill: could not find any points where lh and rh wm are nbrs
by Marina Fernández 28 May '20

28 May '20

External Email - Use Caution Hi Bruce, Yes, everything seems normal in the input files of mri_fill. We review it slice by slice in freeview. Do you know what could have happened? Best regards, Marina ------------------------------------------------------------------------------------------------------------------------------ > Hi Marina > have you looked at the inputs to mri_fill? Does the aseg.auto_noCCseg.mgz and > the wm.mgz look ok? > Bruce > > On Wed, 27 May 2020, Marina Fernández wrote: > External Email - Use Caution Dear Freesurfer experts, When > I run "recon-all -autorecon2-wm -subjid post_006" I get the following > error: ... #-------------------------------------------- > #@# Fill Tue May 26 16:13:33 CEST 2020 > /usr/local/freesurfer/subjects/post_006/mri mri_fill -a > ../scripts/ponscc.cut.log -xform transforms/talairach.lta > -segmentation aseg.auto_noCCseg.mgz wm.mgz filled.mgz logging cutting > plane coordinates to ../scripts/ponscc.cut.log... > INFO: Using transforms/talairach.lta and its offset for Talairach volume > ... > using segmentation aseg.auto_noCCseg.mgz... > reading input volume...done. > searching for cutting planes...voxel to talairach voxel transform > 1.03994 0.01456 0.07738 -16.87541; > -0.02607 1.18971 0.24142 -16.40842; > -0.06544 -0.23822 1.03825 18.09422; > 0.00000 0.00000 0.00000 1.00000; > reading colortable from MGH file... > colortable with 14176 entries read (originally > /usr/local/freesurfer/FreeSurferColorLUT.txt) > voxel to talairach voxel transform > 1.03994 0.01456 0.07738 -16.87541; > -0.02607 1.18971 0.24142 -16.40842; > -0.06544 -0.23822 1.03825 18.09422; > 0.00000 0.00000 0.00000 1.00000; > reading segmented volume aseg.auto_noCCseg.mgz... > mri_fill: could not find any points where lh and rh wm are nbrs > No such file or directory > Linux sleep2014 4.13.0-45-generic #50~16.04.1-Ubuntu SMP Wed May 30 > 11:18:27 > UTC 2018 x86_64 x86_64 x86_64 GNU/Linux recon-all -s post_006 exited with > ERRORS at Tue May 26 16:13:41 CEST 2020 To report a problem, see > http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting I have seen in > other questions that this error may be due to the CC and the > aseg files, and it is interesting because when I load aseg.auto.mgz or > aseg.auto_noCCseg.mgz files in Freeview, the following message in Freeview > terminal is shown in red: > "colortable with 14176 entries read (originally > /usr/local/freesurfer/FreesurferColorLUT.txt)", when I think they should be > 1475 entries. I'm using freesurfer v6.0. Could you help me to solve this > problem? > Thank you in advance! Marina.

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FS6: Mapping data to fsaverage6
by Tim Schäfer 28 May '20

28 May '20

External Email - Use Caution Dear FreeSurfer experts, I'm trying to resample cortical thickness data onto the fsaverage6 template subject in FreeSurfer v6. I have copied fsaverage6 into my $SUBJECTS_DIR. I tried the following 2 commands: * mris_preproc --s subject1 --target fsaverage6 --hemi lh --meas thickness --fwhm 5 --out lh.thickness.fwhm5.fsaverage6.mgh and alternatively: * recon-all -s subject1 -qcache -measure thickness -target fsaverage6 Both fail because the file subject1/surf/lh.fsaverage6.sphere.reg is missing (see attached recon-all.log file). How can I generate the ?h.fsaverage6.sphere.reg file? I tried: mris_register subject1/surf/lh.sphere fsaverage6/surf/lh.sphere subject1/surf/lh.fsaverage6.sphere.reg However, that fails as well, see attached file mris_reg_output.txt for the error message. All the best, Tim -- Dr. Tim Schäfer Postdoc Computational Neuroimaging Department of Child and Adolescent Psychiatry, Psychosomatics and Psychotherapy University Hospital Frankfurt, Goethe University Frankfurt am Main, Germany

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Postdoctoral position on real-time layer-fMRI at 7T available at MPI in Leipzig
by Romy Lorenz 28 May '20

28 May '20

External Email - Use Caution Postdoctoral position on real-time layer-fMRI at 7T The Max Planck Institute for Human Cognitive and Brain Sciences (MPI CBS) in Leipzig (Germany) invites applications for a Postdoctoral Researcher Positionin the Department of Neurophysics with Dr. Romy Lorenz and Prof. Dr. Nikolaus Weiskopf. We are looking for an ambitious postdoc interested in pushing the frontiers of high-resolution fMRI with the aim to resolve laminar activation in higher-level cognitive brain regions in real-time. In this novel and highly ambitious project, we want to combine real-time fMRI at 7T with machine learning (i.e., neuroadaptive Bayesian optimization) to advance our understanding about the specific functional role of different layers in higher-level brain regions. The postdoc will develop methods for and conduct offline (i.e., not real-time) and online (i.e., real-time) experiments with healthy human participants undergoing different cognitive tasks in the 7T scanner. The postdoc will compare different MR acquisition sequences (e.g., gradient-echo BOLD and VASO) and develop offline as well as real-time laminar analyses pipelines of 7T fMRI data. Dr. Romy Lorenz is also affiliated with the University of Cambridge and Stanford University; the postdoc will have the opportunity to benefit from our network of international collaborators. This project is funded by the Klaus Tschira Foundation (PI: RL) and the Max Planck Society. The ideal candidate should have a strong interest in research on high-level cognition and curiosity for real-time and closed-loop experimentation with machine learning. A strong background in fMRI data analysis is essential. The candidate needs to be proficient in MRI data acquisition (i.e., can operate the scanner and modify scanning protocols) as well as MRI data analyses packages (e.g., FSL/SPM and Freesurfer). Strong programming skills in Bash, Matlab and/or Python are required. Prior experience with 7T functional imaging is highly desirable but not necessary. Equally, experience with machine learning-methods and data/code sharing platforms (e.g. GitHub) are desirable. Candidates are expected to have a PhD in physics, computer science, mathematics, biomedical engineering, or cognitive (neuro)science and psychology. The Max Planck Institute offers a world-leading research environment and the postdoc will have access to the latest cutting-edge MRI hardware (including a Siemens Terra 7T, Prisma 3T, Verio 3T and 3T Connectom equipped with 300mT/m gradients) and other excellent research facilities (306-channel MEG, EEG, virtual reality, eye-tracking, TMS/tES). Dedicated support staff will assist with the recruitment of study participants and a team of MR physicists will support the postdoc in the technical realisation of the project. The Institute offers a vibrant and engaging community of international researchers. The working language is English. Leipzig has been called “Germany’s new cultural hot spot” (The Guardian) and is located just a little over an hour train ride south of the center of Berlin. The starting date for the position is 1st September 2020. The duration of the post is 2 years. Remuneration is based on the pay scale of the Max Planck Society. Female and international applicants are particularly encouraged to apply. The Max-Planck Society is committed to increasing the number of individuals with disabilities in its workforce and therefore encourages applications from such qualified individuals. To apply, please submit a single PDF file containing a curriculum vitae (including publication list), personal statement (describing your personal qualifications, research interests and motivation for applying), contact information of three referees and academic certificates (PhD, Diploma/Master, Bachelor certificates). Please submit your application via our online system at http://www.cbs.mpg.de/vacancies (subject heading: “PD 05/20”). The deadline for application submission is 6th July 2020. Interviews of shortlisted candidates will take place likely via Zoom between 13th-17thJuly 2020. In case of questions, please contact Romy Lorenz at lorenzr(a)cbs.mpg.de. Dr. Romy Lorenz Sir Henry Wellcome Postdoctoral Fellow University of Cambridge & Max-Planck Institute for Human Cognitive and Brain Sciences romylorenz.com

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Postdoc position available - computational modeling and real-time fMRI neurofeedback of language
by Narly Golestani 28 May '20

28 May '20

External Email - Use Caution With the launch of a new ‘NCCR Evolving Language’ (http://www.snf.ch/SiteCollectionDocuments/nfs/Faktenblatt_NCCR_evolvinglang…) which involves nearly 40 different research groups from a large variety of disciplines across Switzerland, we seek to fill a Postdoc position for a four-year project starting in September 2020, or at the selected candidate’s earliest convenience. Our goal is to make progress in understanding the importance of prosody in language processing. To this end, we plan to carry out a set of studies involving both computational modeling of fMRI data and real-time fMRI neurofeedback to understand the mechanisms whereby prosody and rhythm support linguistic processing per se. The computational modeling work will be an extension of our recent work on the neural encoding of acoustic information in speech sounds (https://www.ncbi.nlm.nih.gov/pubmed/31285622) The research will be done in the group of Narly Golestani (www.brainandlanguagelab.org<http://www.brainandlanguagelab.org>) in Geneva, in collaboration with researchers in Switzerland and abroad (Elia Formisano in Maastricht, and Frank Scharnowski in Vienna). Applicants should hold a degree in Biomedical Engineering, Computational Neuroscience, or a related field, and should have solid experience in human brain imaging, and ideally also in computational modelling (i.e. encoding / decoding) of fMRI data, real-time fMRI based neurofeedback, machine learning, statistics and programming. The NCCR places great emphasis on gender diversity and we particularly encourage women to apply. To apply, please send a cover letter, CV, names and contact information of 2-3 references as well as any other relevant documents to Narly.Golestani(a)unige.ch<mailto:Narly.Golestani@unige.ch>. Feel free to contact me should you have any questions. Deadline for application: June 20th 2020 ----------------------------------------------------------------------------------------------------------------------------------------------------------------- Brain and Language Lab Prof. Narly GOLESTANI Department of Psychology Campus Biotech 9 Chemin des Mines, 1202 Genève +41 22 379 53 52 <https://outlook.unige.ch/owa/redir.aspx?SURL=5WTo-p-J-W9FrDydU-0WU4PdMytUGs…>http://www.brainandlanguagelab.org https://twitter.com/brain_lang_lab ----------------------------------------------------------------------------------------------------------------------------------------------------------------- <https://outlook.unige.ch/owa/redir.aspx?SURL=5WTo-p-J-W9FrDydU-0WU4PdMytUGs…>

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Re: [Freesurfer] FreeSurfer 7.1 Matlab error, GLIBC_PRIVATE not defined {Disarmed}
by fsbuild 28 May '20

28 May '20

External Email - Use Caution Hello Alex, I would try unseting LD_LIBRARY_PATH altogether or at least take the matlab paths out of it.  My understanding is freesurfer commands don't need matlab paths in LD_LIBRARY_PATH to use matlab after you have setup the freesurfer environment (set FREESURFER_HOME, and source’d the freesurfer setup script).   It looks like the matlab libraries in LD_LIBRARY_PATH are overriding other binaries trying to find the system libc with the symbols they need (and are instead finding the matlab copy of the system libraries). - R. On May 27, 2020, at 23:22, Alexandru Hanganu <hanganu.alexandru(a)gmail.com> wrote:        External Email - Use Caution        Hello FreeSurfer Developers,I attemting to run brainstem/ hippocampus/ thalamus segmentation with FS 7.1 and there seems to be a problem with environment variables. Based on comments on other forums, I cannot install GlibC (if this is the case) since it's a cluster. Are there any methods that can be used to avoid this limitation?FreeSurfer version: freesurfer-linux-centos7_x86_64-7.1.0Platform: CentOS Linux 7 (Core)uname -a: Linux cedar5.cedar.computecanada.ca 3.10.0-1062.12.1.el7.x86_64 #1 SMP Tue Feb 4 23:02:59 UTC 2020 x86_64 GNU/Linuxerror:Setting up environment variables---grep: relocation error: /lib64/libc.so.6: symbol _dl_starting_up, version GLIBC_PRIVATE not defined in file ld-linux-x86-64.so.2 with link time referenceLD_LIBRARY_PATH is .:/lib64:/home/user/freesurfer/MCRv84//runtime/glnxa64:/home/user/freesurfer/MCRv84//bin/glnxa64:/home/user/freesurfer/MCRv84//sys/os/glnxa64:/home/user/freesurfer/MCRv84//sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/home/user/freesurfer/MCRv84//sys/java/jre/glnxa64/jre/lib/amd64/server:/home/userfreesurfer/MCRv84//sys/java/jre/glnxa64/jre/lib/amd64/client:/home/userfreesurfer/MCRv84//sys/java/jre/glnxa64/jre/lib/amd64:/opt/software/slurm/libod: relocation error: /lib64/libc.so.6: symbol _dl_starting_up, version GLIBC_PRIVATE not defined in file ld-linux-x86-64.so.2 with link time referencetr: relocation error: /lib64/libc.so.6: symbol _dl_starting_up, version GLIBC_PRIVATE not defined in file ld-linux-x86-64.so.2 with link time referenceRegistering imageDump.mgz to mask from ASEGcp: relocation error: /lib64/libc.so.6: symbol _dl_starting_up, version GLIBC_PRIVATE not defined in file ld-linux-x86-64.so.2 with link time referencegzip: relocation error: /lib64/libc.so.6: symbol _dl_starting_up, version GLIBC_PRIVATE not defined in file ld-linux-x86-64.so.2 with link time referenceERROR: problem reading fnameSWITCH expression must be a scalar or string constant.Error in myMRIread>load_mgh (line 550)Error in myMRIread>myMRIread_aux (line 92)Error in myMRIread (line 63)Error in SegmentThalamicNuclei (line 278)MATLAB:badSwitchExpressionrm: relocation error: /lib64/libc.so.6: symbol _dl_starting_up, version GLIBC_PRIVATE not defined in file ld-linux-x86-64.so.2 with link time reference255Best regards,Alex_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Running amygdala segmentation on a warped brain (fsaverage-to-MNI152)
by Elizabeth Haris 27 May '20

27 May '20

External Email - Use Caution Hi guys, I’m wanting to run segmentHA_T1.sh on an MNI152 registered brain. On my subject, I have run recon-all, then run mri_cvs_register to obtain a brain image registered in MNI152 space. My questions are: 1. In recon-all, is there a way to specify registration to MNI152 space, or is it necessary to first run recon-all and then to run mri_cvs_register? 2. Is it possible to run the segmentHA script on the brain registered in MNI152 space? I’m unable to find where I would specify the use the cvs/norm.mgz (instead of the mri/norm.mgz file). And from what I can see in the script, the parameters set in lines 179/180/181 (below) point to fsaverage brain files, which don’t appear to be the correct targets for the new MNI152 brain; however, there are no corresponding output files in the cvs folder, so I am unsure how to define these parameters. 3. Is there anything I have missed and would also need to do to run the segmentHA script on an MNI152 brain? (I have previously run the script on the average brain and all went well.) 179 set ATLASMESH="$FREESURFER_HOME/average/HippoSF/atlas/AtlasMesh.gz"; 180 set ATLASDUMP="$FREESURFER_HOME/average/HippoSF/atlas/AtlasDump.mgz"; 181 set LUT="$FREESURFER_HOME/average/HippoSF/atlas/compressionLookupTable.txt"; Thanks in advance, Elizabeth

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FreeSurfer 7.1 Matlab error, GLIBC_PRIVATE not defined
by Alexandru Hanganu 27 May '20

27 May '20

External Email - Use Caution Hello FreeSurfer Developers, I attemting to run brainstem/ hippocampus/ thalamus segmentation with FS 7.1 and there seems to be a problem with environment variables. Based on comments on other forums, I cannot install GlibC (if this is the case) since it's a cluster. Are there any methods that can be used to avoid this limitation? FreeSurfer version: freesurfer-linux-centos7_x86_64-7.1.0 Platform: CentOS Linux 7 (Core) uname -a: Linux cedar5.cedar.computecanada.ca 3.10.0-1062.12.1.el7.x86_64 #1 SMP Tue Feb 4 23:02:59 UTC 2020 x86_64 GNU/Linux error: Setting up environment variables --- grep: relocation error: /lib64/libc.so.6: symbol _dl_starting_up, version GLIBC_PRIVATE not defined in file ld-linux-x86-64.so.2 with link time reference LD_LIBRARY_PATH is .:/lib64:/home/user/freesurfer/MCRv84//runtime/glnxa64:/home/user/freesurfer/MCRv84//bin/glnxa64:/home/user/freesurfer/MCRv84//sys/os/glnxa64:/home/user/freesurfer/MCRv84//sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/home/user/freesurfer/MCRv84//sys/java/jre/glnxa64/jre/lib/amd64/server:/home/userfreesurfer/MCRv84//sys/java/jre/glnxa64/jre/lib/amd64/client:/home/userfreesurfer/MCRv84//sys/java/jre/glnxa64/jre/lib/amd64:/opt/software/slurm/lib od: relocation error: /lib64/libc.so.6: symbol _dl_starting_up, version GLIBC_PRIVATE not defined in file ld-linux-x86-64.so.2 with link time reference tr: relocation error: /lib64/libc.so.6: symbol _dl_starting_up, version GLIBC_PRIVATE not defined in file ld-linux-x86-64.so.2 with link time reference Registering imageDump.mgz to mask from ASEG cp: relocation error: /lib64/libc.so.6: symbol _dl_starting_up, version GLIBC_PRIVATE not defined in file ld-linux-x86-64.so.2 with link time reference gzip: relocation error: /lib64/libc.so.6: symbol _dl_starting_up, version GLIBC_PRIVATE not defined in file ld-linux-x86-64.so.2 with link time reference ERROR: problem reading fname SWITCH expression must be a scalar or string constant. Error in myMRIread>load_mgh (line 550) Error in myMRIread>myMRIread_aux (line 92) Error in myMRIread (line 63) Error in SegmentThalamicNuclei (line 278) MATLAB:badSwitchExpression rm: relocation error: /lib64/libc.so.6: symbol _dl_starting_up, version GLIBC_PRIVATE not defined in file ld-linux-x86-64.so.2 with link time reference 255 Best regards, Alex

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Circular/cyclic color map for polar data and threshold-ing question in freeview
by Devavrat Vartak 27 May '20

27 May '20

External Email - Use Caution Hello freesurfer community, I had asked this question before, however I am unable to reply to that thread. The question still remains unsolved. I am trying to setup a retinotopy pipeline. I have analysed population receptive field data that generates polar angle and eccentricity maps which I project onto an inflated surface / flattened surface in freeview (Freesurfer 6). MacOS 10.14.6 Freesurfer 6 Nipype (nipype version 1.5.0-rc1 (latest: 1.4.2) I have two queries, which I think are connected. 1) Is there a way to display a circular/cyclic colour map (for the polar angle data) in the overlay screen? The existing 'color wheel' option seems linear(?) (i.e it doesn't not warp around). 2) The distribution of data overlayed changes/shifts compared to the RAW data distribution. I have linked the raw theta values generated from the pRF analysis (in radians) as a histogram and a polarmap - (the figures depict values for both hemispheres) and the distribution when I overlay it on the LH (the distribution for RH is similar) See here for images: imgur[dot]com/a/Wo42DLd This is my processing stream: > The raw theta values based on their voxel coordinates are affined to the functional image and saved as a NIFTI volume. The NIFTI volume in functional space is transformed to the anatomical space and is converted to a surface using > > ! mri_vol2surf --src (input_file_theta.nii.gz) --o theta.mgh --hemi lh --regheader sub-03/freesurfer/recon_all --projfrac 0.5 Any help will be appreciated :-) --- From the old thread, there was this comment: "*Hi!* *Jumping in on this, since it has come up many times but is without a solution so far: the issue is that the color code is now mapped onto a straight color bar, not a circle. At the same time, it is not documented what color refers to which angle. That makes it very difficult to work with this kind of color bar. It would be very helpful to reintroduce the circle, and to explicitly document how angles are mapped to colors. Thank you! - Caspar (**Caspar M. Schwiedrzik)* " Thank you . Cheers, Dev

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