Freesurfer

freesurfer@nmr.mgh.harvard.edu

11 participants
30080 discussions

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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Color scale error
by Nillo, Ryan Michael R 01 May '19

01 May '19

External Email - Use Caution Hello FreeSurfer Developers. I am using FSv6 and I am having problems loading a colorbar. I am trying to run this code: freeview -f /data/sugrue2/ABCD/fsaverage/surf/rh.pial:overlay=/data/sugrue2/ABCD/temp/testing.mgh:overlay_threshold=0,1:overlay_method=linear -viewport 3d -hide-3d-slices -nocursor —colorscale. The resulting color scale makes no sense in that it does not properly display the min and max values specified. As you can see in the screenshot, the color scale runs from 1e-10 to -1e-10. Configuring the colors from the GUI seems to fix the issue, but Ideally I would like to automate the screenshot process. Any help is greatly appreciated. [cid:2CAB9F39-3B27-4969-8EAF-20F7E1FECFC1@ucsf.edu] Ryan Michael Nillo Staff Research Associate I University of California San Francisco Department of Radiology and Biomedical Imaging

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Hippocampal subfields segmentation template
by Dongsheng Wu 30 Apr '19

30 Apr '19

External Email - Use Caution Dear FS developers, I uesd the ''recon-all command'' to get the volumes of the hippocampal subfields, and we would like to perform further analysis with these subfields in MNI. Could you show us the templates which are used to perform hippocampal segmentation (CA1, CA3, HATA, etc.)? Best wishes, Wu

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