Freesurfer

freesurfer@nmr.mgh.harvard.edu

19 participants
30088 discussions

Voxel dimensions and final recon
by Michael ONeill 04 Dec '18

04 Dec '18

External Email - Use Caution Dear Freesurfer, I'm enquiring about the known effect that pixel spacing has on the reconstructions and final volume estimates produces by Freesurfer. Specifically, is there a range of pixel spacing values that are necessary for accuracy? Secondly, if the pixel spacing and slice thickness are different values (i.e non-isometric voxels) does this have much of an effect on the final recon and volume estimates? All the best, Michael The opinions, conclusions and other information expressed in the above message, or contained within attachments to the above message, are not given or endorsed by Beaumont Hospital unless otherwise indicated by an authorised representative independent of this message. This e-mail message and any files transmitted with it are confidential and intended solely for the use of the individual or entity to whom they are addressed. This e-mail has been scanned for viruses. This e-mail and all attachments are confidential and may be privileged. If you have received this e-mail in error, notify the sender immediately. Do not use, disseminate, store or copy it in any way.

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Postdoc openings on the Connectome 2.0 project
by Yendiki, Anastasia 04 Dec '18

04 Dec '18

https://www.ismrm.org/jobs/j06670.pdf The Connectome 2.0 Project is a new BRAIN initiative-funded effort at the Athinoula A. Martinos Center for Biomedical Imaging, Massachusetts General Hospital and Harvard Medical School. Building on our experience designing the first Connectome scanner, we aim to engineer the next-generation MRI scanner for imaging the circuitry and microstructure of the human brain; and to use the unique data produced by this scanner to develop novel software tools for improving the analysis of more widely available neuroimaging data. We are seeking talented and driven postdoctoral fellows to contribute to this exciting effort. The fellows would join the Martinos Center’s team of leading experts in MRI instrumentation, analysis, and applications, as well as the vibrant neuroimaging community of Boston. We have multiple openings in the following areas: 1. Gradient characterization. The post-doctoral fellow will simulate and design gradient hardware optimized for high-slew rate, ultra-high gradient strength diffusion MRI. The research fellow will develop approaches to characterize and correct for eddy currents. Responsibilities will include mapping the gradient fields, developing gradient nonlinearity correction software, and incorporating information on the gradient coils and eddy currents into the diffusion preprocessing and analysis pipeline. Strong expertise in C/C++ and/or Matlab is highly desirable. 2. Diffusion microstructural modeling and analysis. The post-doctoral fellow will design, acquire, and analyze diffusion microstructural imaging experiments to showcase the capabilities of the next-generation ultra-high gradient 3T MRI scanner. Responsibilities will include acquiring, analyzing and interpreting diffusion microstructural imaging data for in vivo and ex vivo human brain imaging in the next-generation ultra-high gradient MRI system. A strong background in NMR and MRI physics with specific expertise in diffusion MRI and mathematical and computational modeling is essential. 3. Algorithms for connectional anatomy. The post-doctoral fellow will develop software tools that take advantage of the unprecedented diffusion MRI data collected by the Connectome 2.0 to produce the next-generation mapping of the connectional anatomy of the human brain. The fellow will use unique optical and histological ground truth data to validate these methods ex vivo, and will develop algorithms that can be trained on the unprecedented data of the Connectome 2.0 to improve the accuracy of diffusion MRI tractography in routine-quality, widely available in vivo data. Candidates with a strong background in image analysis/computer vision/machine learning are encouraged to apply. Experience in diffusion tractography and/or diffusion microstructural modeling is an asset. For all positions, a Ph.D. in electrical engineering, biomedical engineering, computer science, physics, applied physics, or related field is required. Creativity, initiative, proven ability to publish, and excellent oral and written communication skills are key. The position is full-time with benefits and available immediately. A two-year time commitment is required with a possible extension of another two years. Salary will be based on qualifications and experience. The Massachusetts General Hospital is an Equal Opportunity/Affirmative Action Employer. Applicants should submit a curriculum vitae, the contact information of two references, and a cover letter describing their research background, interests, and professional goals by email to Drs. Susie Huang (syhuang(a)nmr.mgh.harvard.edu) and Anastasia Yendiki (ayendiki(a)mgh.harvard.edu) Please include “Connectome 2.0 postdoctoral position” in the title of your email.

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Re: [Freesurfer] Problem in Installing FreeSurfer on Mint19
by Maedeh Khalilian 04 Dec '18

04 Dec '18

External Email - Use Caution Dear Tim, I did it successfully, Thanks more... Best Maedeh

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Set annotation cluster color
by Ting Li 03 Dec '18

03 Dec '18

External Email - Use Caution Dear Freesurfer Expert, Can I change the color of loading from the annot file in Freeview? Thanks a lot! Best regards, Ting

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When no control points are needed...
by Rosalia Dacosta Aguayo 03 Dec '18

03 Dec '18

External Email - Use Caution Dear Bruce and Bram, After improving the pial surface for my participants, I have seen that some of them do not need control points. My question is: for those ones, should I run -autorecon2 and -autorecon3 or only -autorecon3. Hi Bruce and Bram, I will try to upload two problematic files. When I told you that I have been editing all my participants I was referring that some of them need more editing than others, and the ones that needed the less I just tried to improve the pial surface not too much, but now the results are better than before. Thank you in advance for your help. Yours sincerely, Rosalia

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mris_preproc paired diff outputs 0 values
by Sims, Sara A 03 Dec '18

03 Dec '18

External Email - Use Caution Hello, I am trying to do a paired difference analysis of two runs of probtrackx (I have already put them on the surface). The two conditions are “central” and “far” for each subject. I have already checked the individual subjects data and it does indeed have values. Here is a sample of my subject list: 100206.central 100206.far 100307.central 100307.far 100408.central 100408.far …etc. Here is my mris_preproc script: mris_preproc --target fsaverage --hemi lh --isp $in/FP/100206.central/lhsurf.mgh --isp $in/FP/100206.far/lhsurf.mgh --isp $in/FP/100307.central/lhsurf.mgh --isp $in/FP/100307.far/lhsurf.mgh --isp $in/FP/100408.central/lhsurf.mgh --isp $in/FP/100408.far/lhsurf.mgh … --out $out/preproc_FP_cf_lh/lh.paired-diff.FP_cf.mgh --f $sublist --paired-diff The output log shows no errors, the number of inputs equals the number in the subject list and it creates a file but it’s all zeros. I just have no idea as to why this would happen? Thanks, Sara Sims

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Warping fsaverage maps to MNI152 volume
by Alon Baram 03 Dec '18

03 Dec '18

External Email - Use Caution Hello, I have a significance map I obtained through some analysis I did in Matlab. It's currently in fsaverage space. I want to move it to MNI152 space to compare with other results. From exploring the archives, it seems there are two ways of doing this, and I'm not sure which is better - any advice or correction would be appreciated. *Method 1*: First move to fsaverage volume, then us volumetc registraion to move to MNI152: 1. mri_surf2vol --surfval sigMap.mgh --identity fsaverage --template ./fsaverage/mri/T1.mgz --hemi rh --o sigMap.fsspace.mgz 2. mri_vol2vol --inv --targ sigMap.fsspace.mgz --mov /$FSL_DIR/data/standard/MNI152_T1_2mm.nii.gz --o sigMap_MNI.nii --interp nearest --reg fsaverage/mri/transforms/reg.mni152.2mm.dat *Method 2*: Run recon-all on the MNI152 T1 image. Use mri_surf2surf to map to move sigMap to the MNI152 surface. Then use mri_surf2vol with the --identity flag to move from MIN152 surface to volume. I ran method 1 and it looks OK though in some place it seems the out put doesn't follow white matter super nicely (though generally quite good). See attached image. I haven't ran method 2 yet. Thanks very much! Alon [image: image.png]

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Surface displacement
by 1013364183 03 Dec '18

03 Dec '18

External Email - Use Caution Dear FS, We want to calculate the displacement of different surfaces, what should we do? yours yujunjie

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Recon-all - mghRead could not read rawavg.mgz
by Diamond, Bram Ryder 03 Dec '18

03 Dec '18

Hi Batuhan, Can you please upload the BE2 subject data using our ftp file exchange and let me know the exact command and terminal output when you ran mri_convert? Info on our ftp file exchange: https://surfer.nmr.mgh.harvard.edu/fswiki/FtpFileExchange Thanks, Bram Bram R. Diamond, BSc Research Technician II Laboratory for Computational Neuroimaging Martinos Center for Biomedical Imaging Massachusetts General Hospital 149 13th Street Charlestown, MA 02129 (p): 617-726-6598

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Problem in Installing FreeSurfer on Mint19
by Maedeh Khalilian 03 Dec '18

03 Dec '18

External Email - Use Caution Dear experts, Thank u very much for all the help so far I have mint19 on my system and I have installed FreeSurfer on it. when I run a command like "mri_convert" it is ok. But when I run "recon-all" and some other commands, I see the error below : bash: /usr/local/freesurfer/bin/recon-all: /bin/tcsh: bad interpreter: No such file or directory by the way my default setup file is .bashrc. I really dunno what the problem is.I would be grateful if u could help me. Cheers, Maedeh

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