Freesurfer May 2019

freesurfer@nmr.mgh.harvard.edu

95 participants
141 discussions

applyMorph on talairach.m3z
by Peled, Noam 03 May '19

03 May '19

Dear group, How can I apply the talairach.m3z transformation on a list of points? I was trying to use applyMorph on one of my subjects: applyMorph --template $SUBJECTS_DIR/M1/mri/orig.mgz --transform $SUBJECTS_DIR/M1/mri/transforms/talairach.m3z point_list $SUBJECTS_DIR/M1/electrodes/electrodes_to_morph.txt tal.txt a but I got this error: Template name:/autofs/space/thibault_001/users/npeled/subjects//M1/mri/orig.mgz After loading template Template name:/autofs/space/thibault_001/users/npeled/subjects//M1/mri/orig.mgz After loading template extension = m3z terminate called after throwing an instance of 'std::bad_alloc' what(): std::bad_alloc Abort (core dumped) I'm using the FreeSurfer dev version (in martinos), and my SUBJECT_DIR is /autofs/space/thibault_001/users/npeled/subjects/ Thanks! Noam

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recon-all error
by 王梦星 03 May '19

03 May '19

External Email - Use Caution Hello FreeSurfer Developers, I'm attampting to do a structural MRI analysis with the command "recon-all -i sub102.nii.gz -s bert -all", as described in the FreeSurfer Download and Install (http://surfer.nmr.mgh.harvard.edu/fswiki/DownloadAndInstall) But I always met the error as recorded in the recon-all.log, " /home/share/test2/bert/surf mris_curvature -w lh.white.preaparc total integrated curvature = 10.012*4pi (125.809) --> -9 handles ICI = 164.9, FI = 1856.5, variation=28617.761 writing Gaussian curvature to ./lh.white.preaparc.K...done. writing mean curvature to ./lh.white.preaparc.H...done. rm -f lh.white.H ln -s lh.white.preaparc.H lh.white.H Linux wmx 2.6.32-754.12.1.el6.x86_64 #1 SMP Tue Apr 9 14:52:26 UTC 2019 x86_64 x86_64 x86_64 GNU/Linux recon-all -s bert exited with ERRORS at Mon Apr 22 11:44:12 CST 2019 " And then I checked that, the '?.white.preaparc' had been created while the '?h.white.H/K' had not, so I did some steps described in http://surfer.nmr.mgh.harvard.edu/fswiki/ReconAllTableStableV6.0, The commands "mris_curvature -w ?h.white.preaparc " and " mris_curvature -thresh .999 -n -a 5 -w -distances 10 10 ?h.inflated " were done to generate some files successfully. Howevere, when I continue to use "mris_curvature_stats -m --writeCurvatureFiles -G -o ../stats/?h.curv.stats -F smoothwm <subjid> ?h curv sulc ", there were errors below: " mris_curvature_stats -m --writeCurvatureFiles -G -o ../stats/?h.curv.stats -F smoothwm bert ?h curv sulc Toggling save flag on curvature files [ ok ] Outputting results using filestem [ ../stats/?h.curv.stats ] Toggling save flag on curvature files [ ok ] Setting surface [ bert/?h.smoothwm ] Reading surface...MRISread(/home/share/test2/bert/surf/?h.smoothwm): could not open file No such file or directory [ ok ] mris_curvature_stats: could not read surface file /home/share/test2/bert/surf/?h.smoothwm No such file or directory " In fact, the '?h.smoothwm' files exist and I can find it by 'ls' commond. Any help is greatly appreciated. Thanks. Mengxing Wang

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resampling to native space for recons with multiple T1s
by Zimmerman, Jared 02 May '19

02 May '19

External Email - Use Caution Hi Freesurfers, What’s the best way to resample recon data such as aparc+aseg.mgz into scanner space for recons with multiple T1s? Right now I’m using mri_vol2vol with –regheader to resample from orig space to rawavg, then using mri_vol2vol again with the 001.lta, 002.lta etc. registration matrices to get it back to the original scanner space for each T1. Is there a way to do this without two interpolation steps? Thanks, jared

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Failure to import cortical surface extracted with Freesurfer into Matlab using ft_read_headshape
by Darinka Trübutschek 02 May '19

02 May '19

External Email - Use Caution Dear freesurfer community, I am currently trying to import cortical surfaces extracted with freesurfer (version: freesurfer-linux-centos7_x86_64-dev-20190403-dacefd1) into Matlab (version: R2018b) using the fieldtrip function ft_read_headshape (version: 20190329). All of this is run in an Ubuntu 18.04.2 LTS environment. While all of the extracted surfaces seem fine upon visual inspection in freeview, the import into Matlab fails, throwing the following error message: pial = ft_read_headshape('freesurfer/surf/lh.pial'); Error using fread Invalid size. Error in read_surf (line 72) vertex_coords = fread(fid, vnum*3, 'float32') ; Error in ft_read_headshape (line 909) [pos, tri] = read_surf(filename); It is most certainly related to the fact that, both for the number of vertices (vnum) and the number of faces (fnum), the function read_surf returns non-sensible (?) values (i.e., vnum = -1.0263e+09 and fnum = -1.0529e+09). The same code produces no error when run on the same pial surface extracted with a different version of freesurfer (freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c) in a different Ubuntu environment (Ubuntu 16.04 LTS). As visual inspection in Freeview of the 2 surfaces from the two different Freesurfer versions reveals no obvious differences, I am therefore at a loss as where exactly to start to fix this problem and would be grateful for any help. Many thanks! Darinka -- Darinka Trübutschek, PhD Department of Experimental Psychology Anna Watts Building Radcliffe Observatory Quarter Woodstock Road Oxford, OX2 6GG UK website: https://sites.google.com/site/dtruebutschek/

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Research Assistant for Brain Imaging Studies @ Albert Einstein College of Medicine {Disarmed}
by Emily Schwartz 02 May '19

02 May '19

External Email - Use Caution The Position: The Research Assistant will work in the Division of Cognitive and Motor Aging to acquire, manage and process behavioral and brain imaging data in ongoing neuroimaging studies of older adults. Responsibilities • Recruit, screen and accompany older adults to brain imaging studies • Acquire and enter behavioral data into paper and computerized forms, review forms for completeness and accuracy • Maintain computer databases of behavioral and brain imaging data • Read, process, and quality check brain imaging data Qualifications • Bachelor's Degree required • Coursework in Neuroscience, Neuroanatomy, Cognitive Science/Psychology, or Computer science preferred Skills and Competencies • Outstanding interpersonal and computing skills required • Strong database management, and clear understanding of clinical and research databases highly preferred • Previous experience with neuroimaging processing highly preferred. • Proficiency in neuroimaging processing software (FreeSurfer, fsl, SPM) preferred • Previous experience with Linux operating systems and MATLAB software preferred APPLY HERE: https://careers-einstein.icims.com/jobs/11910/psychology-assistant/job?mobi…<https://nam02.safelinks.protection.outlook.com/?url=https%3A%2F%2Fcareers-e…> Helena M. Blumen, PhD. Assistant Professor Department of Medicine (Geriatrics) Department of Neurology (Cognitive and Motor Aging) Albert Einstein College of Medicine E-mail: helena.blumen(a)einstein.yu.edu<mailto:helena.blumen@einstein.yu.edu> Office Phone: (718) 430 3810<tel:%28718%29%20430%203810> http://www.einstein.yu.edu/faculty/12983/helena-blumen/<https://nam02.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.einste…>

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inaccurate segmentation from recon-all
by Mun, Anna 02 May '19

02 May '19

Hi Freesurfer team, I have a question about segmentation. I am working with scans of patients with Down syndrome and the segmentation (aseg.presurf.mgz and aseg.mgz) for a few subjects is slightly inaccurate. It mostly affects the areas that we are specifically interested in - basal ganglia and thalamus. Is there any alternative way to correct the segmentation other than doing it manually? Thank you! Best, Anna

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ERROR! FOV=265.909 > 256
by Anik Dar 02 May '19

02 May '19

External Email - Use Caution Hello All, I am running recon-all highres on 10 7T MP2RAGE datasets that has been skull striped and in two subjects, I get the following error - I tried the suggested workaround ie I included the flag -cw256 but that didnt help and I got the error again. Can you suggest how to fix this ? Many thanks Ani P.S. The error below For more details, see the log file /Applications/freesurfer6/subjects/HighResT1/scripts/recon-all.log To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting \n**************************************** ERROR! FOV=265.909 > 256 Include the flag -cw256 with recon-all! Inspect orig.mgz to ensure the head is fully visible. ****************************************\n Darwin Kernel Version 15.6.0: Thu Jun 21 20:07:40 PDT 2018; root:xnu-3248.73.11~1/RELEASE_X86_64 x86_64 recon-all -s HighResT1 exited with ERRORS at Mon Apr 22 20:20:31 EDT 2019 For more details, see the log file /Applications/freesurfer6/subjects/HighResT1/scripts/recon-all.log To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting

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Postdoc position available
by Iglesias Gonzalez, Eugenio 02 May '19

02 May '19

External Email - Use Caution Dear all, We are looking for a postdoc in our ERC project, with two main purposes. First, to improve the 3D histology reconstruction tools that we have been developing to build an ultra-high resolution atlas of the brain using histology. And second, to collaborate in the development of segmentation techniques to apply the atlas to the automated analysis of in vivo MRI scans, which hope to integrate with FreeSurfer. Our research line is moving toward the integration of classic model-based algorithms with modern deep learning techniques (see for instance https://arxiv.org/abs/1904.11319) The postdoc will join the Centre for Medical Image Computing (CMIC) at University College London (UCL), which will be soon co-located with the new UCL Artificial Intelligence Centre, located on High Holborn in central London. In addition, the postdoc will have the opportunity of visiting our lab at the Martinos Center in Boston. More information here: www.jeiglesias.com<http://www.jeiglesias.com> https://tinyurl.com/y4hv275f -- Juan Eugenio Iglesias Senior research fellow CMIC (UCL), MGH (HMS) and CSAIL (MIT) http://www.jeiglesias.com

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freeview parcellation error
by Ebru Ayyürek 02 May '19

02 May '19

External Email - Use Caution Hi FreeSurfer Developers, I'm attempting to perform a freeview visualisation and parcellation to my data on Linux. I can open freeview and load surfaces and volumes.But when I want to load a label for parcellation on freeview ,it can not load label.And I've got an error like this on the terminal; freeview: could not scan # of lines from label file � LabelRead failedfreeview: could not scan # of lines from label file freeview: could not parse 1th line '2 G&S_occipital_inf 23 60 180 0' in label file LabelRead failedfreeview: could not parse 1th line '2 G&S_occipital_inf 23 60 180 0' in label file freeview: could not parse 1th line '2 caudalanteriorcingulate 125 100 160 0' in label file LabelRead failedfreeview: could not parse 1th line '2 caudalanteriorcingulate 125 100 160 0' in label file PS:I've update my freeview as described here https://surfer.nmr.mgh.harvard.edu/fswiki/UpdateFreeview I've searched the list and no similar errors have been reported. Does anyone have any thoughts on how to trouble-shoot this one? 1) FreeSurfer version: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0 2) Ubuntu version:18.10 3) uname -a: Linux sid 4.18.0-17-generic #18-Ubuntu SMP Wed Mar 13 14:34:40 UTC 2019 x86_64 x86_64 x86_64 GNU/Linux

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nu_correct crashing in FreeSurfer v6.0
by Jayasekera, Dinal 01 May '19

01 May '19

External Email - Use Caution Dear all, I have been running version 4 of the HCP Pipelines which now used FreeSurfer 6.0. I get the following error when running recon-all using their FreeSurferPipelineBatch script: nu_evaluate: crashed while running minc_modify_header (termination status=134) nu_correct: crashed while running nu_evaluate (termination status=65280) ERROR: nu_correct I didn't get this error previously when running FreeSurfer 5.3.0 on the same set of data. Are the MNI tools distributed through FreeSurfer 6.0 sensitive to the operating system and its version? Does anyone have a record of it working on an Ubuntu 14.04 OS? 1) FreeSurfer version: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0 2) Platform: Ubuntu 14.04 3) recon-all.log: see attached Kind regards, Dinal Jayasekera<https://dinaljay.weebly.com/> PhD Candidate | InSITE Fellow<https://www.insitefellows.org/> Ammar Hawasli Lab<https://hawaslilab.weebly.com/> Department of Biomedical Engineering<https://bme.wustl.edu/Pages/default.aspx> | Washington University in St. Louis<https://wustl.edu/>

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Freesurfer May 2019