Freesurfer

freesurfer@nmr.mgh.harvard.edu

14 participants
30063 discussions

Postdoctoral position in Machine Learning for 3D Histology
by Iglesias Gonzalez, Eugenio 29 Nov '17

29 Nov '17

Dear all, We are looking for a postdoc to work on my ERC Starting Grant project "Building Next-Generation Computational Tools for High Resolution Neuroimaging Studies", at the Translational Imaging Group<http://cmictig.cs.ucl.ac.uk/> (TIG) at University College London<http://ucl.ac.uk/> (UCL). Experience in neuroimaging is definitely a big plus. Details can be found here: https://atsv7.wcn.co.uk/search_engine/jobs.cgi?amNvZGU9MTcwMDA1NiZ2dF90ZW1w… and also here: https://sites.google.com/site/jeiglesias/news/postdocpositionavailable-3 Kind regards, /Eugenio -- Juan Eugenio Iglesias ERC Senior Research Fellow Translational Imaging Group University College London http://www.jeiglesias.com http://cmictig.cs.ucl.ac.uk/

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Erroneous output after recon-all: Bad segmentation and surfaces
by Arsenije Subotic 29 Nov '17

29 Nov '17

Dear experts, I recently finished processing a subject for whom I had performed a skull-strip on the brainmask.mgz volume. I decreased the watershed parameter and re-examined the brainmask and the portion of the skull was gone, although some dura was left over. I did a recon-all using the following command as the troubleshooting tutorial suggested to regenerate the surfaces based on the new brainmask.mgz volume: recon-all -autorecon-pial -subjid <subject name> However, after the subject finished processing the surfaces were generated/outlined on the dura as well. I tried performing a g-cut command but it did not get rid of the dura. I also had issues with the subcortical segmentation as the ventricles were not completely segmented. I've attached screenshots for you to see as well. Would it be necessary to manually erase the extra dura and then re-process the subject? Please let me know. Thank you for your help. Best, Arsenije

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mri_convert partial support of nrrd file format for diffusion MRI data
by Michael Dayan 29 Nov '17

29 Nov '17

Hi, I was pleasantly surprised when I discovered that mri_convert could convert the nrrd file format (to NIFTI in my case). However for diffusion MRI data, while it displays the diffusion gradients information on the terminal, it does not create the associated bval and bvec files. After looking at the mri_convert command-line usage I could not find any option to do so. Would anyone know how to create the bval and bvec files? Best, Michael

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Error with mri_vol2surf
by Elena Theißen 29 Nov '17

29 Nov '17

Hello, I am new to freesurfer and have a problem following the step ,mri_vol2surf‘ as described in your tutorial ,cortical thickness of a Volume-defined ROI‘. During step 3 I always received the error: Could not read (path to) as type 24 The file is a .nii I checked my FS version (6) and redid all the previous steps. Also converting did not help. I tried to convert the nii. in mgz but then error 3 appeared. I would be glad if you could give me a hint how to fix it. Kind regards, Elena Von meinem iPhone gesendet

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[Re] medial wall label in Freesurfer 6
by Sofia Rodriguez Penuela 29 Nov '17

29 Nov '17

Hi, User M del Mar and me belong to same investigation group, so the problem is common. We have 116 subjects and we detected this trouble. However, we tried to repeat the make_average_subject command using a subgroup (only 60 subjects) and label files were correctly created. Maybe, number of subjetcs is the key. Nevertheless, with Freesurfer 5.3 we haven't this problem, no matter number of subjects. Best, Sofia -- Sofía Rodríguez Peñuela, Técnico de Laboratorio. Laboratorio de Neurociencia Funcional Departamento de Fisiología, Anatomía y Biología Celular. Universidad Pablo de Olavide Ctra. de Utrera, Km.1 41013 - Sevilla - España - Movil: 627273085 Email: srodpen(a)upo.es http://www.upo.es/neuroaging/es/

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Re: [Freesurfer] Surface-based kernel operations
by Victor Montal Blancafort 29 Nov '17

29 Nov '17

Thanks Bruce and Doug! Bruce, I think the option of the sphere is the one that better fits my needs, since I need to perform conv operations + derivatives. How should address this issue? I am not very familiar with sphere files (nor metric tensors) and do not know how to open/where to find those files. Thank you once again! Bests, Victor M

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TRACULA and the IFOF
by Juergen Haenggi 29 Nov '17

29 Nov '17

Dear TRACULA experts I am wondering wheter someone has already implemented the tractography of the inferior fronto-occipital fascicle (IFOF) into TRACULA? if yes, we are interested in this implementation. Regards Jürgen Hänggi ----------------------------------------------------------------------------------------------------- University of Zurich Dr. Jürgen Hänggi, Ph.D. Department of Psychology Division Neuropsychology Binzmuehlestrasse 14, PO Box 25 8050 Zurich, Switzerland 0041 44 635 73 97 (phone office) 0041 76 445 86 84 (phone mobile) 0041 44 635 74 09 (fax office) BIN 4.D.04 (office room number) j.haenggi(a)psychologie.uzh.ch (email) http://www.psychologie.uzh.ch/neuropsy/ (website) http://www.juergenhaenggi.ch (private website) This email (and any attachment/s) contains confidential and/or privileged information. If you are not the intended recipient (or have received this email in error) please notify the sender immediately and destroy this email. Any unauthorised copying, disclosure or distribution of the material in this email is strictly forbidden. -----------------------------------------------------------------------------------------------------

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error in segmentHA_T2.sh
by Cong 29 Nov '17

29 Nov '17

Dear freesurfer experts I am trying segment hippocampal and amygdala subregions in dev version(freesurfer-i386-apple-darwin11.4.2-dev-20171024), the segmentHA_T1.sh works well. However, when I try to add a T2 propeller sequence it doesn’t work. I am sure the T2.nii file is in mri folder, and this T2.nii file works well in 6.0.0 version for segmenting hippocampal subregion. I pasted the wrong scripts, could you tell me what’s wrong? Thanks! Best Regards Cong BrainwaverdeMacBook-Pro:subjects Brainwaver$ segmentHA_T2.sh control004 control004/mri/T2.nii T2 1 #-------------------------------------------- #@# Hippocampal Subfields processing (T1+T2) left 2017年11月29日星期三 17时27分20秒 CST ------------------------------------------ Setting up environment variables --- DYLD_LIBRARY_PATH is .:/Users/Brainwaver/Documents/freesurfer/MCRv80//runtime/maci64:/Users/Brainwaver/Documents/freesurfer/MCRv80//bin/maci64:/Users/Brainwaver/Documents/freesurfer/MCRv80//sys/os/maci64: Warning: application is running on a locale different from the original platform locale. Registering norm.mgz to additional volume znzreadInt: znzread failed znzreadInt: znzread failed niiRead(): error opening file control004/mri/T2.nii mri_robust_register.bin: could not open MRI target control004/mri/T2.nii. /Users/Brainwaver/Documents/freesurfer/bin//mri_robust_register --mov /Users/Brainwaver/Documents/freesurfer/subjects/control004/mri/norm.mgz --maskmov /Users/Brainwaver/Documents/freesurfer/subjects/control004/tmp/hippoSF_T1T2_v20_T2_left//wholeBrainMask.mgz --dst control004/mri/T2.nii --lta /Users/Brainwaver/Documents/freesurfer/subjects/control004/mri/transforms/T1_to_T2.v20.lta --noinit --cost NMI -nosym >/dev/null: Signal 127 ERROR: cannot find transform file /Users/Brainwaver/Documents/freesurfer/subjects/control004/mri/transforms/T1_to_T2.v20.lta gunzip: can't stat: /Users/Brainwaver/Documents/freesurfer/subjects/control004/tmp/hippoSF_T1T2_v20_T2_left//T2resampledLikeT1.mgz (/Users/Brainwaver/Documents/freesurfer/subjects/control004/tmp/hippoSF_T1T2_v20_T2_left//T2resampledLikeT1.mgz.gz): No such file or directory 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 segmentSubjectT1T2_autoEstimateAlveusML (line 198) MATLAB:badSwitchExpression #-------------------------------------------- #@# Hippocampal Subfields processing (T1+T2) right 2017年11月29日星期三 17时27分31秒 CST ------------------------------------------ Setting up environment variables --- DYLD_LIBRARY_PATH is .:/Users/Brainwaver/Documents/freesurfer/MCRv80//runtime/maci64:/Users/Brainwaver/Documents/freesurfer/MCRv80//bin/maci64:/Users/Brainwaver/Documents/freesurfer/MCRv80//sys/os/maci64: Warning: application is running on a locale different from the original platform locale. Registering norm.mgz to additional volume znzreadInt: znzread failed znzreadInt: znzread failed niiRead(): error opening file control004/mri/T2.nii mri_robust_register.bin: could not open MRI target control004/mri/T2.nii. /Users/Brainwaver/Documents/freesurfer/bin//mri_robust_register --mov /Users/Brainwaver/Documents/freesurfer/subjects/control004/mri/norm.mgz --maskmov /Users/Brainwaver/Documents/freesurfer/subjects/control004/tmp/hippoSF_T1T2_v20_T2_right//wholeBrainMask.mgz --dst control004/mri/T2.nii --lta /Users/Brainwaver/Documents/freesurfer/subjects/control004/mri/transforms/T1_to_T2.v20.lta --noinit --cost NMI -nosym >/dev/null: Signal 127 ERROR: cannot find transform file /Users/Brainwaver/Documents/freesurfer/subjects/control004/mri/transforms/T1_to_T2.v20.lta gunzip: can't stat: /Users/Brainwaver/Documents/freesurfer/subjects/control004/tmp/hippoSF_T1T2_v20_T2_right//T2resampledLikeT1.mgz (/Users/Brainwaver/Documents/freesurfer/subjects/control004/tmp/hippoSF_T1T2_v20_T2_right//T2resampledLikeT1.mgz.gz): No such file or directory 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 segmentSubjectT1T2_autoEstimateAlveusML (line 198) MATLAB:badSwitchExpression All done! If you have used results from this software for a publication, please cite: Iglesias, J.E., Augustinack, J.C., Nguyen, K., Player, C.M., Player, A., Wright, M., Roy, N., Frosch, M.P., McKee, A.C., Wald, L.L., Fischl, B., and Van Leemput, K., A computational atlas of the hippocampal formation using ex vivo, ultra-high resolution MRI: Application to adaptive segmentation of in vivo MRI. Neuroimage 115, 2015, 117-137. http://dx.doi.org/10.1016/j.neuroimage.2015.04.042 In addition, if you have used the segmentation of the nuclei of the amygdala, please also cite: Saygin, Z.M. & Kliemann, D. (joint 1st authors), Iglesias, J.E., van der Kouwe, A.J.W., Boyd, E., Reuter, M., Stevens, A., Van Leemput, K., McKee, A., Frosch, M.P., Fischl, B., and Augustinack, J.C., High-resolution magnetic resonance imaging reveals nuclei of the human amygdala: manual segmentation to automatic atlas. Neuroimage 155, 2017, 370-382. http://doi.org/10.1016/j.neuroimage.2017.04.046 BrainwaverdeMacBook-Pro:subjects Brainwaver$

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Surface-based kernel operations
by Victor Montal Blancafort 28 Nov '17

28 Nov '17

Dear Freesurfer experts, I would like to preform several operations in surface files using spatial kernels (i.e mean value in a 3x3 grid, nearest neighbour value, etc). In summary, perform operations in the surface such as a 2D matrix/image. Is it possible to do it with Freesurfer? I tried to open the surfaces using Python and Matlab, but as far as I am concerned, the vertex orders does not follow any "continous" or topological order. Any insight would be very appreciated. Thanks in advance! Victor M

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MacOS Sierra 10.12.5 dyld lazy symbol binding error
by Kelly Martin 28 Nov '17

28 Nov '17

Hi all, I have Freesurfer version freesurfer-i386-apple-darwin11.4.2-stable6-20170119 installed on my MacOS Sierra 10.12.5 environment, and am experiencing similar library issues to what others have reported. I have tried previously offered suggestions to update and test MacPorts, as well as $ sudo -E fs_update. I am trying to run a Connectome Workbench command, but the errors I am receiving involve incompatibilities with the Freesurfer libraries. I was however able to run recon-all without a problem. Does anyone have a recommendation on how to proceed? This is the error: dyld: lazy symbol binding failed: Symbol not found: ___emutls_get_address Referenced from: /Users/username/Applications/freesurfer/bin/../lib/gcc/lib/libgomp.1.dylib Expected in: /usr/lib/libSystem.B.dylib Thank you, Kelly -- Kelly Martin Graduate Student Interdisciplinary Program in Neuroscience Georgetown University

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