Freesurfer February 2021

freesurfer@nmr.mgh.harvard.edu

98 participants
118 discussions

Recommendation for FreeSurfer BIDS derivatives?
by Francois Tadel, Mr [Affiliate] 05 Feb '21

05 Feb '21

External Email - Use Caution Hello In the BIDS-examples, we're trying to figure out whether we should use: 1) derivatives/freesurfer/sub-01/ses-01/ or 2) derivatives/freesurfer/sub-01_ses-01/ ? According to the FreeSurfer wiki, option #2 is recommended: https://secure-web.cisco.com/1sCCtE6LTMa-49XUNxEx--YIegNS1bF7eTcXR_u4FqKST7… But since the last time this page was edited was in 2018, we were wondering if this info is still up-to-date. Could someone comment directly on this pending PR? https://secure-web.cisco.com/1tQpQxw5ftUz9Yde9DKP1YMlGQWO1XQjNCa6L7RxMhdB2q… Thanks! Francois

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Issue with the hypothalamic segmentation
by Langan, Mackenzie 05 Feb '21

05 Feb '21

External Email - Use Caution Good Morning, I have been trying to run the hypothalamic segmentation and get the following error: *aalqadi@athena:/zstore/data/aalqadi/aalqadi/mPFC/data$ mri_segment_hypothalamic_subunits --s S05486* *Traceback (most recent call last):* * File "/usr/local/freesurfer_dev/freesurfer/python/scripts/mri_segment_hypothalamic_subunits", line 10, in <module>* * import freesurfer as fs* * File "/usr/local/freesurfer_dev/freesurfer/python/packages/freesurfer/__init__.py", line 8, in <module>* * from . import bindings* *ImportError: /lib/x86_64-linux-gnu/libcrypt.so.1: version `XCRYPT_2.0' not found (required by /usr/local/freesurfer_dev/freesurfer/python/packages/freesurfer/* *bindings.cpython-36m-x86_64-linux-gnu.so* <http://secure-web.cisco.com/1hzKok6ieorAQWILbwXrHm4nWv5aGVWrgLXUjICNL0HcYQD…>*)* We installed the development version of freesurfer to see if that would work to run this, but that didn't work. We then installed XCRYPT_2.0 but still got the same error. We have two versions of python on our machine which we amended to fix the problem, but still get the same error. I am at a loss as to what I should try next to implement this. Any help would be great. Thanks Best, Mackenzie

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Lazy_symbol_error libstdc++.6.dylib: stable Version 6 Release
by Costanza Parodi 05 Feb '21

05 Feb '21

External Email - Use Caution Hello Freesurfer Developers, I was attempting to use the mri_cvs_register command ( mri_cvs_register -- mov subjid -- mni) and I received this error: asegfname aseg Using m3z type morph files. dyld: lazy symbol binding failed: Symbol not found: ___emutls_get_address Referenced from: /Applications/freesurfer/bin/../lib/gcc/lib/libgomp.1.dylib Expected in: /usr/lib/libSystem.B.dylib dyld: Symbol not found: ___emutls_get_address Referenced from: /Applications/freesurfer/bin/../lib/gcc/lib/libgomp.1.dylib Expected in: /usr/lib/libSystem.B.dylib Abort I resolved the issue by downloading the Freeview_6.0.0_MacOS patch, but a new error came up : Error opening file dyld: lazy symbol binding failed: Symbol not found: ___emutls_get_address Referenced from: /Volumes/NAME/Applications/freesurfer/bin/../lib/gcc/lib/libstdc++.6.dylib Expected in: /usr/lib/libSystem.B.dylib dyld: Symbol not found: ___emutls_get_address Referenced from: /Volumes/NAME/Applications/freesurfer/bin/../lib/gcc/lib/libstdc++.6.dylib Expected in: /usr/lib/libSystem.B.dylib I did not find similar errors in the archive. Should I disable SIP? Could you help me trouble-shoot this error? My freesurfer is installed on an external hard disk and I am processing my subjects on my Mac desktop. 1) Freesurfer version: freesurfer-Darwin-OSX-stable-pub-v6.0.0-2beb96c 2) MacOs High Sierra version 10.13.6 3)Darwin MacBook-Air.local 17.7.0 Darwin Kernel Version 17.7.0: Thu Jun 18 21:21:34 PDT 2020; root:xnu-4570.71.82.5~1/RELEASE_X86_64 x86_64 4)Xquartz 2.7.11

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Re: [Freesurfer] FIR Analysis and task regressor
by Doll, Laura 05 Feb '21

05 Feb '21

External Email - Use Caution Hi Doug, Thanks for your response. No, I did not demean the task regressor... do I have to? Exactly. When I try to run tksurfer-sess, it complains about the missing file "h". When I rename the "h-offset" file to "h", I can run tksurfer-sess and I do see a map. The time course viewer opens as well but it only shows one time point. I can also continue to run the group analysis. During "isxconcat-sess" it while again complain about the missing file but mri_glmfit and following commands still work. So I do get a group map but I am not sure what it shows. Best, Laura Did you demean the task regressor? Is the problem that you cannot run tksurfer-sess? Or are you reporting multiple problems? On 2/3/2021 8:32 AM, Doll, Laura wrote: External Email - Use Caution Hi everyone, Is it possible to do an FIR analysis using a task regressor instead of (or additional to) a paradigm file? More precisely, we want to use pupil size as task regressor. It was recorded during an auditory detection task (event related). This works when I use "-spmhrf" or other HRF options. However, for FIR I cannot get the expected time course in the single subjects data. Tksurfer ends with an error because it cannot find the file h.nii.gz: ERROR: could not determine file for [...]/S01_3/bold/PupilFIR.lh/h This file indeed does not exist, there is only one called "h-offset". The commands I used until that point are (here neglecting the original task, but using -event-related etc instead of no task results in the same error): mkanalysis-sess -fsd bold -stc up -surface fsaverage lh -fwhm 5 -notask -fir 4 20 -TR 2 -polyfit 2 -analysis PupilFIR.lh -per-run -taskreg Pupil 1 selxavg3-sess -s S01_3 -analysis PupilFIR.lh tksurfer-sess -s S01_3 -analysis PupilFIR.lh -call -tksurfer Is there any solution for this? Or any reason why it should not be done that way? Best, Laura

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Post doctoral position available Johns Hopkins University
by Arnold Bakker 05 Feb '21

05 Feb '21

External Email - Use Caution Post-Doctoral position: Functional Neuroimaging in Human Neurocognitive Aging A full-time position is available for an outstanding, highly motivated post-doctoral fellow in the laboratory of Arnold Bakker, Ph.D. in the Division of Psychiatric Neuroimaging at Johns Hopkins University School of Medicine. The laboratory focuses on the use of high-resolution functional and structural neuroimaging methods to investigate the neural basis of learning and memory in both young and older adults and in individuals with memory complaints, neurodegenerative or psychiatric conditions. Our studies focus primarily on the role of the medial temporal lobe and particularly the hippocampus in memory function, age- and disease-related memory impairment and neuropsychiatric conditions. The Division of Psychiatric Neuroimaging is part of the Department of Psychiatry and Behavioral Sciences at the Johns Hopkins University School of Medicine and is affiliated with the Johns Hopkins Alzheimer’s Disease Research Center (JHADRC), the Division of Geriatric Psychiatry and Neuropsychiatry, the Kirby Center for Brain Imaging, and the Center for Imaging Science (CIS). These affiliations and the Johns Hopkins community in general provide a rich and unique environment for collaboration and education for candidates interested in learning and memory in aging and disease, and neuropsychiatry. The fellow will have responsibility for specific projects, particularly involving image processing and analysis, and lead the preparation of manuscripts for publication and presentation of results at scientific meetings. The successful candidate will have strong academic training in cognitive or computational neuroscience and will have significant experience with functional MRI. A Ph.D. or M.D/Ph.D. in Neuroscience, Cognitive Science or Psychology or a relevant discipline is required. The successful candidate will have excellent writing and communication skills with evidence of successful manuscript productivity as well as the ability to work independently and as part of a collaborative interdisciplinary team. Preference will be given to candidates with experience in clinical research. Review of applications will begin immediately and will continue until the position is filled. Applicants should send their Curriculum Vitae, a statement of academic interests and the names and addresses of three professional references to: Dr. Arnold Bakker (abakker(a)jhu.edu<mailto:abakker@jhu.edu>). The Johns Hopkins University is an equal opportunity/affirmative action employer committed to recruiting, supporting, and fostering a diverse community of outstanding faculty, staff, and students. All applicants who share this goal are encouraged to apply. Division of Psychiatric Neuroimaging Department of Psychiatry and Behavioral Sciences The Johns Hopkins University School of Medicine 600 N. Wolfe Street / Phipps 300 Baltimore, MD 21287 Email: pni(a)jhu.edu<mailto:pni@jhu.edu> | Fax: 410-614-3676

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Multiple subjects with segmentHA_T1.sh
by Wei Shao 05 Feb '21

05 Feb '21

External Email - Use Caution Hi, Dear Freesurfer team I'm wondering is there any command/information that can help to run multiple subjects with segmentHA_T1.sh at one time? Thanks Best, Wei

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Lesion heat map question
by XY XY 04 Feb '21

04 Feb '21

External Email - Use Caution Dear Freesurfers, I’m working on generating a heat map of white matter lesions in a disease group. I have the lesion probability maps for each individual generated in SAMSEG and I was wondering what the best method would be to place the maps of each individual in standard space to generate a population-wise probability map. Any recommendation? Any input is appreciated! Best, David Kamson > On Feb 3, 2021, at 12:00 PM, freesurfer-request(a)nmr.mgh.harvard.edu wrote: > > Send Freesurfer mailing list submissions to > freesurfer(a)nmr.mgh.harvard.edu > > To subscribe or unsubscribe via the World Wide Web, visit > https://secure-web.cisco.com/14lrtjNnm3PEC-7QaJQn7C68uWUGABowPO95pcu1Ff1UbD… > or, via email, send a message with subject or body 'help' to > freesurfer-request(a)nmr.mgh.harvard.edu > > You can reach the person managing the list at > freesurfer-owner(a)nmr.mgh.harvard.edu > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of Freesurfer digest..." > > > Today's Topics: > > 1. Re: Hypothalamus segmentation - Freesurfer 7.1 > (Lab of Autism and Developmental Neuroscience, Lab of Autism and Developmental Neuroscience) > 2. Re: Hypothalamus segmentation - Freesurfer 7.1 (Hoopes, Andrew) > 3. Re: White matter parcellation (Graterol) > 4. define freeview colormap from command line (Simone Cauzzo) > 5. FIR Analysis and task regressor (Doll, Laura) > 6. Re: define freeview colormap from command line (Wang, Ruopeng) > 7. Re: FIR Analysis and task regressor (Douglas N. Greve) > 8. Issue with the hypothalamic segmentation (Langan, Mackenzie) > 9. Re: Issue with the hypothalamic segmentation (Hoopes, Andrew) > 10. Re: white matter volume (Douglas N. Greve) > 11. Re: Issue with the hypothalamic segmentation (Langan, Mackenzie) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Tue, 2 Feb 2021 13:07:50 -0500 > From: "Lab of Autism and Developmental Neuroscience, Lab of Autism and > Developmental Neuroscience" <ladn(a)email.gwu.edu> > Subject: Re: [Freesurfer] Hypothalamus segmentation - Freesurfer 7.1 > To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> > Message-ID: > <CACE7MB++y95_6mkUOwsJo1dexN=Ww7X9-Ve4g_mkG_nTsjgesw(a)mail.gmail.com> > Content-Type: text/plain; charset="utf-8" > > External Email - Use Caution > > Thank you for your help! > > I have tested the hypothalamus segmentation on the development version of > FS, and this was the error output that I got (see below). How should I > proceed to fix this? > > :~/Documents$ mri_segment_hypothalamic_subunits --s UCL55003_srs2 > > Using 1 thread > > 2021-02-02 12:19:04.878273: I > tensorflow/core/platform/cpu_feature_guard.cc:141] Your CPU supports > instructions that this TensorFlow binary was not compiled to use: AVX2 > 2021-02-02 12:19:04.899000: I > tensorflow/core/platform/profile_utils/cpu_utils.cc:94] CPU Frequency: > 2999995000 Hz > 2021-02-02 12:19:04.899178: I > tensorflow/compiler/xla/service/service.cc:150] XLA service 0x20b88f0 > executing computations on platform Host. Devices: > 2021-02-02 12:19:04.899215: I > tensorflow/compiler/xla/service/service.cc:158] StreamExecutor device > (0): <undefined>, <undefined> > processing 1/1 > Traceback (most recent call last): > File > "/home/ladn/Documents/freesurfer/python/scripts/mri_segment_hypothalamic_subunits", > line 1464, in <module> > main() > File > "/home/ladn/Documents/freesurfer/python/scripts/mri_segment_hypothalamic_subunits", > line 91, in main > threads=args.threads > File > "/home/ladn/Documents/freesurfer/python/scripts/mri_segment_hypothalamic_subunits", > line 165, in predict > net = build_model(path_model, model_input_shape, len(label_list)) > File > "/home/ladn/Documents/freesurfer/python/scripts/mri_segment_hypothalamic_subunits", > line 579, in build_model > net.load_weights(model_file, by_name=True) > File > "/home/ladn/Documents/freesurfer/python/lib/python3.6/site-packages/tensorflow/python/keras/engine/network.py", > line 1514, in load_weights > saving.load_weights_from_hdf5_group_by_name(f, self.layers) > File > "/home/ladn/Documents/freesurfer/python/lib/python3.6/site-packages/tensorflow/python/keras/engine/saving.py", > line 839, in load_weights_from_hdf5_group_by_name > original_keras_version = f.attrs['keras_version'].decode('utf8') > AttributeError: 'str' object has no attribute 'decode' > > Also, what's the best way for me to run a second version of Freesurfer on > the same computer? I used a virtualbox, but is there a way to run it > outside of that? > > Thank you so much for the help and stay safe, > Alex > > > > On Sat, Jan 30, 2021 at 1:25 PM Douglas N. Greve <dgreve(a)mgh.harvard.edu> > wrote: > >> It is not in version 7. You'll have to download a development version of >> FS to run it. >> >> On 1/29/2021 9:26 PM, Lab of Autism and Developmental Neuroscience, Lab of >> Autism and Developmental Neuroscience wrote: >> >> External Email - Use Caution >> Dear Freesurfer experts, >> >> I am having some trouble getting the hypothalamus segmentation recognized >> on the command line for FreeSurfer 7.1.0. Is it even available for this >> version? If not, will it work on the 6.0 or the 7.1.1 version? >> >> Thanks and stay safe! >> >> All the best, >> Alex >> >> _______________________________________________ >> Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer(a)nmr.mgh.harvard.edu >> https://secure-web.cisco.com/1FvwK2Q4o_omzwWs74PFlbrtdw14YNUieN1tko0x72qG2l… >

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comparing long and cross FS aparc+aseg
by Michele Valotti 04 Feb '21

04 Feb '21

External Email - Use Caution Hi all, I am running a test of long FS on some subjects to see if I can improve the segmentation accuracy compared to cross FS. The aparc+aseg.mgz output of long FS, however, is not aligned with the original timepoint structural scan, but rather to the T1 image in the "base" folder (which I believe is an average of the original timepoints). I was wondering if there was a way to directly compare the results of long FS segmentation to those of cross FS segmentation, essentially having both the original aparc+aseg image and the new one in the same space and aligned, or if that does not make sense since we are doing the long FS segmentation on an effectively new image. Thank you, Michele

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Freesurfer VirtualBox password
by Gabriel Mackie 04 Feb '21

04 Feb '21

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Two Research Fellow or Senior Research Fellow Positions (Methods) Available at WCHN, London, UK
by Guillaume Flandin 04 Feb '21

04 Feb '21

External Email - Use Caution (apologies for cross-posting) * --------------------------------------------------------------------------------* *UCL Queen Square Institute of Neurology* *Wellcome Centre for Human Neuroimaging* *(Senior) Research Fellow: Methods developer (x2)* *--------------------------------------------------------------------------------* We are looking for two post-doctoral researchers to join the Centre's Methods group. They will work on methodological research to define, implement and deploy strategies for analysing high-resolution functional neuroimaging data from ultra-high magnetic field MRI (7T or more). Since 2019, in-house facilities of the WCHN include a 7T Siemens Terra MRI scanner with parallel transmission capability, providing access to functional and anatomical information about the human brain in vivo with very high precision, spatial specificity and interpretability. The Centre has pioneered many neuroimaging methodologies, including Statistical Parametric Mapping (SPM) and Dynamic Causal Modelling (DCM). The Methods Group specialises in the development of a broad range of image processing methods based on principled generative models of image data and statistical analyses aimed at interpreting neural signals, see: https://secure-web.cisco.com/1GSdlHnnAPyRJX7sjSshoYzIX4pp-j-k8HK4t5xa4G1ZsL… The appointees will engage in their own research projects with flexibility to shape their research directions, in line with the overall goals of the Centre. The developed methods will be made available to Centre researchers, as well as others in the international research community, through the widely used SPM software, which is developed in the Centre. Examples of possible projects include: * Development and optimisation of analysis techniques exploiting 7T fMRI data to probe discrete units of neuronal computation such as layers, columns, stripes and small sub-nuclei; * Development of generative models of anatomically-informed fMRI analyses, for layer-specific, surface-based investigation of cortical processing at 7T; * Devising correction schemes to mitigate imaging artefacts caused by magnetic field inhomogeneities, motion and physiology; * Development of a statistical framework for the multiple testing problem in the context of laminar-specific fMRI analyses. The appointees will liaise closely with the Centre’s Methods, Physics and Computational Anatomy teams to provide solutions to challenges posed by ultra-high field imaging that integrate both acquisition and modelling strategies. Collaboration with neuroscientists from other disciplines working at the Centre is another important aspect of the role, including the provision of advice and guidance on best practice neuroimaging strategies. The posts are available immediately and are funded by a grant from the Wellcome Trust until 30 November 2023 in the first instance. Applicants must have a PhD (Senior Research Fellow) or, if not already held, the PhD must be obtained by the agreed start-date (Research Fellow applicants only) in a topic related to numerical computing and methods development. Strong programming expertise (e.g. MATLAB or C/C++) and experience with ultra-high field MRI are essential. Senior Research Fellow applicants must also have demonstrable experience in relevant areas of methodological development and of leading projects to completion. Appointments will be on UCL Grade 7 (Research Fellow), the salary for which ranges from £36,028 to £43,533 per annum (including London Allowance) or UCL Grade 8 (Senior Research Fellow), the salary for which ranges from £44,737 to £52,764 per annum (including London Allowance). Appointment at Grade 7 is dependent upon having been awarded a PhD; if this is not the case, initial appointment will be at research assistant Grade 6B (salary £31,542 - £33,257 per annum) with payment at Grade 7 being backdated to the date of final submission of the PhD thesis. For more details and to apply see: https://secure-web.cisco.com/1041mkJdpaWZphvMxlX8g815xdLpwOIwvAjIYQx1W8OLEl… or search via UCL's online recruitment – _http://http://secure-web.cisco.com/1HbsF6Jr04MH6tbgBDUOMFvMha5pd-0lf1oTYPl… you can download a job description and person specification using ref: 1874477. For queries regarding the application process, please contact Oksana Shapoval, HR Officer, UCL Queen Square Institute of Neurology (email: _ion.hradmin(a)ucl.ac.uk <mailto:ion.hradmin@ucl.ac.uk>_). Informal enquiries to Dr Guillaume Flandin (email: g.flandin(a)ucl.ac.uk <mailto:g.flandin@ucl.ac.uk>)*.* Closing Date: 23 Feb 2021* * -- Guillaume Flandin, PhD Wellcome Centre for Human Neuroimaging UCL Queen Square Institute of Neurology London WC1N 3BG

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Freesurfer February 2021