Freesurfer

freesurfer@nmr.mgh.harvard.edu

15 participants
30064 discussions

Cortical thickness map
by Esteban, Eva(GE Healthcare) 29 Aug '17

29 Aug '17

Hello everyone, I am trying to overlay a cortical thickness map onto a subject but when I try this command freeview -v good_output/mri/T1.mgz good_output/mri/wm.mgz good_output/mri/brainmask.mgz good_output/mri/aseg.mgz:colormap=lut:opacity=0.2 -f good_output/surf/lh.thickness.fsaverage.mgh:edgecolor=blue or this command: freeview -v good_output/mri/T1.mgz good_output/mri/wm.mgz good_output/mri/brainmask.mgz good_output/mri/aseg.mgz:colormap=lut:opacity=0.2 -f good_output/surf/lh.thickness:edgecolor=blue I get an error saying: nquads=1966084, nvertices=599 ERROR: MRISread: file '/home/eva/Downloads/tutorial_data/buckner_data/tutorial_subjs/good_output/surf/lh.thickness' has many more faces than vertices! Probably trying to use a scalar data file as a surface! Do any of you know how to load it properly? Thank you!

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Cortical Thickness of Hippocampus subfields
by Dev vasu 29 Aug '17

29 Aug '17

Dear Sir, I have performed Subfield segmentation of Hippocampus subfields, I would like to how i can calculate thickness of each subfield post segmentation, are the values in the text files *[lr]h.hippoSfVolumes-<T1>-<analysisID>.v10.txt*: indicate estimated volume of each subfield , Is there any way i can obtain thickness of each subfield w.r.t whole hippocampus ?. Thanks Vasudev

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Centos 7 - hippocampal subfield segmentation in freeview
by Vetterman, Richard 29 Aug '17

29 Aug '17

Dear freesurfer experts, after an update of my computer I finally use Centos 7 now. It seems as if some parts of the lateral hippocampal subfield segmentation are not visualized any more when using freesurfer. When using FSL, everything looks fine, though. Do you have any suggestions, what to do? Thanks, Richard

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PETSURFER - mri_gtmpvc option to use SGTM
by M Janani 28 Aug '17

28 Aug '17

Hi Team, Could you please tell me how to modify this command to perform SGTM mri_gtmpvc --i pet.nii.gz --reg template.reg.lta --psf FWHM --seg gtmseg.mgz --default-seg-merge --auto-mask PSF .01 --mgx .01 --o gtmpvc.output I have tried with -sgtm and -sgtmx but it's not working. Regards, Janani ::DISCLAIMER:: ---------------------------------------------------------------------------------------------------------------------------------------------------- The contents of this e-mail and any attachment(s) are confidential and intended for the named recipient(s) only. E-mail transmission is not guaranteed to be secure or error-free as information could be intercepted, corrupted, lost, destroyed, arrive late or incomplete, or may contain viruses in transmission. The e mail and its contents (with or without referred errors) shall therefore not attach any liability on the originator or HCL or its affiliates. Views or opinions, if any, presented in this email are solely those of the author and may not necessarily reflect the views or opinions of HCL or its affiliates. Any form of reproduction, dissemination, copying, disclosure, modification, distribution and / or publication of this message without the prior written consent of authorized representative of HCL is strictly prohibited. If you have received this email in error please delete it and notify the sender immediately. Before opening any email and/or attachments, please check them for viruses and other defects. ----------------------------------------------------------------------------------------------------------------------------------------------------

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Recommended MRI acquisition protocol for Siemens 3.0T Prisma
by Karla Rivera Figueroa 28 Aug '17

28 Aug '17

Hi Freesurfer team, Do you have any recommended MRI protocols for the Siemens 3.0 Prisma? I am analyzing both morphometry and function with ASD subjects. Thank you for your help, Karla <https://www.avast.com/sig-email?utm_medium=email&utm_source=link&utm_campai…> Virus-free. www.avast.com <https://www.avast.com/sig-email?utm_medium=email&utm_source=link&utm_campai…> <#DAB4FAD8-2DD7-40BB-A1B8-4E2AA1F9FDF2>

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Centos 7 - freesurfer hippocampal subfield visualization
by Vetterman, Richard 28 Aug '17

28 Aug '17

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PhD position in collaborative predictive analytics (Munich)
by Dominic Dwyer 28 Aug '17

28 Aug '17

An immediate full-time PhD position is available for an outstanding researcher in the Section for Neurodiagnostic Applications at the Dep. of Psychiatry and Psychotherapy, LMU Munich, directed by Prof. Nikolaos Koutsouleris. The position involves the development of cloud-based predictive applications for an unprecedented Europe-USA international collaborative project called HARMONY (Harmonization of At Risk Multisite Observational Networks for Youth Consortium: Toward the Validation of Biomarkers for Clinical Trials) and for a large-scale Europe-wide project being directed by Prof. Koutsouleris; PRONIA (www.pronia.eu) The main goal is to construct reliable predictive tools that optimally integrate clinical data, neuroimaging, neurocognitive, genetic/metabolic information using state-of-the-art machine learning techniques to predict outcomes of clinical high-risk and first-episode stages of psychosis and depression. The candidate should have experience in MATLAB programming and predictive analytics, machine learning, database management, and model visualization, or some combination of these. These skills are needed to further develop cutting-edge machine-learning techniques being developed at the neurodiagnostics laboratory, including unsupervised and semi-supervised clustering techniques and ensemble learning methods. A profile with evidence of inter-disciplinary flexibility is a positive, evidence of good strategic thinking ability is favourable, and good communication skills are required (fluent English). The minimum degree requirement is M.Sc. (or equivalent) and salary is according the German TV-L E13 scale depending on the academic level of the applicant. The position is initially limited to one year but with the possibility of extension. The position is located at the core of a multi-site international project with a young, dynamic, and multidisciplinary team that is rapidly growing and poised to make significant contributions to the field using unique datasets and cutting-edge methods. Long-standing cooperations also exist with the Section for Biomedical Image Analysis (Christos Davatzikos), the NAPLS 3 coordinating team at Yale University (Ty Cannon), and the Melbourne Neuropsychiatry Centre (Christos Pantelis). Review of applications will begin immediately and will continue until the position is filled. Applicants should send their Curriculum Vitae along with a statement of academic interests and the details of two professional references to: Nikolaos Koutsouleris, nikolaos.koutsouleris(a)med.uni-muenchen.de.

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Recon-all error
by Bronwyn Overs 27 Aug '17

27 Aug '17

Dear mailing list, I am trying to batch a series of 30 MRI images using the following command: recon-all -autorecon2-cp -subjid ID001 -qcache But for each image the process exits with the following errors: --------------------------------------------------- #@# 1/1 ID_001 Wed Aug 16 11:39:12 AEST 2017 -------------- ----------------------- mri_surf2surf --srcsubject ID_001 --srchemi lh --srcsurfreg sphere.reg --trgsubject fsaverage --trghemi lh --trgsurfreg sphere.reg --tval ./tmp.mris_preproc.18138/ID_001.1.mgh --sval /mridata/workingdata/CHD/BAR/PROCESSING/baseline_5.3.fix/ID_001/surf/lh.volume --jac --sfmt curv --noreshape --no-cortex Source registration surface changed to sphere.reg Target registration surface changed to sphere.reg srcsubject = ID_001 srcval = /mridata/workingdata/CHD/BAR/PROCESSING/baseline_5.3.fix/ID_001/surf/lh.volume srctype = curv trgsubject = fsaverage trgval = ./tmp.mris_preproc.18138/ID_001.1.mgh trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = lh trghemi = lh frame = 0 fwhm-in = 0 fwhm-out = 0 label-src = (null) label-trg = (null) OKToRevFaceOrder = 1 Reading source surface reg /mridata/workingdata/CHD/BAR/PROCESSING/baseline_5.3.fix/ID_001/surf/lh.sphere.reg Loading source data Reading curvature file /mridata/workingdata/CHD/BAR/PROCESSING/baseline_5.3.fix/ID_001/surf/lh.volume ERROR: number of vertices in /mridata/workingdata/CHD/BAR/PROCESSING/baseline_5.3.fix/ID_001/surf/lh.volume does not match surface (109952,110385) ERROR: reading curvature file Linux katana.neura.edu.au 2.6.32-504.3.3.el6.x86_64 #1 SMP Wed Dec 17 01:55:02 UTC 2014 x86_64 x86_64 x86_64 GNU/Linux recon-all -s ID_001 exited with ERRORS at Wed Aug 16 11:39:13 AEST 2017 To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> I came across an earlier post in relation to a similar error (https://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/2009-February/009807.… <https://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/2009-February/009807.…>) where it was recommended that you run “recon-all -s subjid -make all” to rebuild all files where the dependency chain is wrong. I ran this for each of the subjects and then tried to rerun my original recon-all command again but got the same error. Do you have any alternate suggestions for fixing this problem? Kind regards, Bronwyn Overs Research Assistant Neuroscience Research Australia Margarete Ainsworth Building Barker Street Randwick Sydney NSW 2031 Australia M 0411 308 769 T +61 2 9399 1883 F +61 2 9399 1265 neura.edu.au <http://neura.edu.au/> <https://twitter.com/neuraustralia> <https://www.facebook.com/NeuroscienceResearchAustralia> <http://www.neura.edu.au/help-research/subscribe>

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Error with recon-all long
by Bronwyn Overs 27 Aug '17

27 Aug '17

Dear freesurfer mailing list, I have been running the recon-all -long command and received the following errors: #-------------------------------------------- #@# Surf Reg lh Wed Aug 16 18:07:26 AEST 2017 /mridata/workingdata/CHD/BAR/PROCESSING/longitudinal.fix/TPID_001.long.BASEID_001/scripts mris_register -curv -nosulc -norot /mridata/workingdata/CHD/BAR/PROCESSING/longitudinal.fix/BASEID_001/surf/lh.sphere.reg /usr/local/FREESURFER/freesurfer5.3.0/average/lh.average.curvature.filled.buckner40.tif ../surf/lh.sphere.reg using smoothwm curvature for final alignment disabling initial sulc alignment... disabling initial rigid alignment... $Id: mris_register.c,v 1.59 2011/03/02 00:04:33 nicks Exp $ $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $ reading surface from /mridata/workingdata/CHD/BAR/PROCESSING/longitudinal.fix/BASEID_001/surf/lh.sphere.reg... reading template parameterization from /usr/local/FREESURFER/freesurfer5.3.0/average/lh.average.curvature.filled.buckner40.tif... mrisReadTriangleFile(/mridata/workingdata/CHD/BAR/PROCESSING/longitudinal.fix/BASEID_001/surf/lh.smoothwm): surface doesn't match /mridata/workingdata/CHD/BAR/PROCESSING/longitudinal.fix/BASEID_001/surf/lh.sphere.reg No such file or directory mrisReadTriangleFile failed. No such file or directory MRISreadOriginalProperties: could not read surface file smoothwm No such file or directory ERROR -5 from MRISreadOriginalProperties(). Linux katana.neura.edu.au 2.6.32-504.3.3.el6.x86_64 #1 SMP Wed Dec 17 01:55:02 UTC 2014 x86_64 x86_64 x86_64 GNU/Linux recon-all -s TPID_001.long.BASEID_001 exited with ERRORS at Wed Aug 16 18:07:29 AEST 2017 To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> I checked the surf folder and the lh.sphere.reg file does not appear to be there. Do you know how this could have happened and how I can fix the problem? Kind regards, Bronwyn Overs Research Assistant Neuroscience Research Australia Margarete Ainsworth Building Barker Street Randwick Sydney NSW 2031 Australia M 0411 308 769 T +61 2 9399 1883 F +61 2 9399 1265 neura.edu.au <http://neura.edu.au/> <https://twitter.com/neuraustralia> <https://www.facebook.com/NeuroscienceResearchAustralia> <http://www.neura.edu.au/help-research/subscribe>

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Reliability of labeling procedure in the same scan
by anonymous anonymous 26 Aug '17

26 Aug '17

Hi all, Without noticing I run recon-all twice on the same scan of the same subject and we noticed there are some differences, at least in the hippocampal volume estimation. Is it normal? If it is, why is it so? Thank you so much for your help This is a great community!

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