Freesurfer May 2020

freesurfer@nmr.mgh.harvard.edu

111 participants
208 discussions

Fwd: Error in Monte Carlo simulation
by behzad sorouri khorashad 29 May '20

29 May '20

External Email - Use Caution TO: freesurfer(a)nmr.mgh.harvard.edu SUBJECT: Error in Monte Carlo simulation: Error running mri_surfcluster Hello FreeSurfer Developers, I'm attempting to run a longitudinal analysis on structural T1 images for a sample, as described on the freesurfer wiki tutorial ( https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/LongitudinalTutorial) For post processing data, i used qdec option. However, when i want to use the monte carlo correction I receive the following Error: Error in Monte Carlo:Error in running mri_surfcluster If I change the number in /qdec/untitlted/fwhm.dat to the fwhm i have chosen in my analysis, the error is solved. But I wonder whether this is correct way to solve this error or not. 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 error in the terminal in case it's of any use. 1) FreeSurfer version: freesurfer-Darwin-OSX-stable-pub-v6.0-2beb96c 2) Platform: OS X ElCapitan verson 10.11.6 Thanks for your help Yours Behzad

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dimension mismatch longitudinal
by KennethSPrice 28 May '20

28 May '20

External Email - Use Caution Hello Freesurfers! In regards to the link below: https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg36839.html Is there a way to fix a dimension mismatch? Thanks, Ken Sent with [ProtonMail](https://protonmail.com) Secure Email.

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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, The talairach transform is reasonable and the aseg segment the cc correctly. I run with freesurfer dev version the same command (recon all -autorecon-2wm -subjid post_006) and now I have more information about what could be the problem. The output of the terminal (that you can see below) says that there is a vertex in the curv file of each hemisphere that has one vertex number that it is not expected. When I open the curv file in tksurfer there is a 0 in these positions. Maybe this output can be useful to help me solve the problem. What do you think I should do? Thanks in advance! mris_curvature -seed 1234 -thresh .999 -n -a 5 -w -distances 10 10 rh.inflated setting seed for random number generator to 1234 normalizing curvature values. averaging curvature patterns 5 times. sampling 10 neighbors out to a distance of 10 mm 128 vertices thresholded to be in k1 ~ [-0.27 0.70], k2 ~ [-0.10 0.11] total integrated curvature = 0.637*4pi (8.002) --> 0 handles ICI = 1.5, FI = 8.0, variation=142.940 106 vertices thresholded to be in [-0.03 0.02] writing Gaussian curvature to ./rh.inflated.K...thresholding curvature at 99.90% level curvature mean = 0.000, std = 0.001 125 vertices thresholded to be in [-0.16 0.23] done. writing mean curvature to ./rh.inflated.H...curvature mean = -0.017, std = 0.023 done. @#@FSTIME 2020:05:28:10:21:34 mris_curvature N 12 e 52.03 S 0.20 U 51.78 P 99% M 334852 F 0 R 89611 W 0 c 174 w 1 I 0 O 1888 L 2.00 2.00 1.76 @#@FSLOADPOST 2020:05:28:10:22:26 mris_curvature N 12 2.00 2.00 1.77 #----------------------------------------- #@# Curvature Stats lh Thu May 28 10:22:26 CEST 2020 /usr/local/freesurfer/subjects/post_006/surf mris_curvature_stats -m --writeCurvatureFiles -G -o ../stats/lh.curv.stats -F smoothwm post_006 lh curv sulc Toggling save flag on curvature files [ ok ] Outputting results using filestem [ ../stats/lh.curv.stats ] Toggling save flag on curvature files [ ok ] Setting surface [ post_006/lh.smoothwm ] Reading surface... [ ok ] Setting texture [ curv ] Reading texture...error: No such file or directory error: MRISreadNewCurvature: incompatible vertex number in file /usr/local/freesurfer/subjects/post_006/surf/lh.curv ***WARNING!*** Some error has occurred while reading 'lh.curv'. This might be due a vertex incompatibility between the surface 'lh.smoothwm' and curv 'lh.curv'. You might be able to correct this by re-running 'mris_make_surfaces' on this dataset. Skipping this (and any remaining) curvature files. Any measurements / calcuations that depend on the curvature file will be skipped. ************* Calculating Discrete Principal Curvatures... Determining geometric order for vno faces... [####################] [ ok ] Determining KH curvatures... [####################] [ ok ] Determining k1k2 curvatures... [####################] [ ok ] deltaViolations [ 208 ] WARN: S lookup min: -0.238596 WARN: S explicit min: 0.000000 vertex = 1525 @#@FSTIME 2020:05:28:10:22:26 mris_curvature_stats N 11 e 2.95 S 0.14 U 2.79 P 99% M 170736 F 6 R 48708 W 0 c 56 w 7 I 1104 O 7584 L 2.00 2.00 1.77 @#@FSLOADPOST 2020:05:28:10:22:29 mris_curvature_stats N 11 2.00 2.00 1.77 #----------------------------------------- #@# Curvature Stats rh Thu May 28 10:22:29 CEST 2020 /usr/local/freesurfer/subjects/post_006/surf mris_curvature_stats -m --writeCurvatureFiles -G -o ../stats/rh.curv.stats -F smoothwm post_006 rh curv sulc Toggling save flag on curvature files [ ok ] Outputting results using filestem [ ../stats/rh.curv.stats ] Toggling save flag on curvature files [ ok ] Setting surface [ post_006/rh.smoothwm ] Reading surface... [ ok ] Setting texture [ curv ] Reading texture...error: No such file or directory error: MRISreadNewCurvature: incompatible vertex number in file /usr/local/freesurfer/subjects/post_006/surf/rh.curv ***WARNING!*** Some error has occurred while reading 'rh.curv'. This might be due a vertex incompatibility between the surface 'rh.smoothwm' and curv 'rh.curv'. You might be able to correct this by re-running 'mris_make_surfaces' on this dataset. Skipping this (and any remaining) curvature files. Any measurements / calcuations that depend on the curvature file will be skipped. ************* Calculating Discrete Principal Curvatures... Determining geometric order for vno faces... [####################] [ ok ] Determining KH curvatures... [####################] [ ok ] Determining k1k2 curvatures... [####################] [ ok ] deltaViolations [ 190 ] WARN: S lookup min: -0.040471 WARN: S explicit min: 0.000000 vertex = 53

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fs_install_mcr error
by AmirHussein Abdolalizadeh 28 May '20

28 May '20

External Email - Use Caution Hi all, I have installed FS7 (centOS8 version) on ubuntu 18.04. I try to install MATLAB runtime but it gives an error when I type "fs_install_mcr R2014b": Archive: installer.zip End-of-central-directory signature not found. Either this file is not a zipfile, or it constitutes one disk of a multi-part archive. In the latter case the central directory and zipfile comment will be found on the last disk(s) of this archive. unzip: cannot find zipfile directory in one of installer.zip or installer.zip.zip, and cannot find installer.zip.ZIP, period. Since I suspected it might be an access issue, I have used chmod -R 777 on my FreeSurfer installation category. Also, using "sudo" before "fs_install_mcr" causes the bash not to recognise fs_install_mcr command. Any suggestions? Bests, Amir

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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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Freesurfer May 2020