Freesurfer

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30132 discussions

Re: [Freesurfer] Registering Anatomical Parcellation to DWI
by Yendiki, Anastasia 05 Dec '18

05 Dec '18

Yes, you can register other modalities to the T1 using bbregister. Then you can use that registration to transform any volume from T1 space to the space of the other modality. Check out the multimodal integration tutorials on the freesurfer wiki. On Dec 5, 2018 2:36 AM, Maedeh Khalilian <M.Khalilian(a)sutech.ac.ir> wrote: External Email - Use Caution Dear FreeSurfer experts, I have a parcellation and a whole brain white matter files which are the outputs of FreeSurfer. I want to register them to my DWI. I mean I want my parcellation and white matter to be in the physical space of my DWI. Can FreeSurfer do it for me? If not , can you suggest me a toolbox that can do it fast? I would be grateful if u could help me. Cheers, Maedeh,

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Map image in MNI onto fsaverage
by john Anderson 05 Dec '18

05 Dec '18

External Email - Use Caution Dear Freesurfer experts, I have the mean PET images for a number of subjects in MNI152 space. For visualization purposes, I would like to map this mean image onto brain surface. How can I do it. I appreciate any suggestion you may provide. Thanks! John

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Outer smoothed surface (lh.pial-outer-smoothed) only partly 'real' outer surface
by M. Jordan 05 Dec '18

05 Dec '18

External Email - Use Caution Hi!, i am using recon-all -s <subj> -localGI to get the outer smoothed surface of the pial files. This works, but when loading the original pial and the smoothed one, some parts of the original pial stand out. Is there any possibility / parameter to avoid this? I need an outer surface which completely covers the brain. Thank you!

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create ctab from annot
by Winkelbeiner, Stephanie A 04 Dec '18

04 Dec '18

External Email - Use Caution Hi freesurfer-experts, I used a customized script that produces a more fine-grained parcellation resulting in an .annot file. I don't seem to have a look-up-table (LUT), however. I tried the following: - mri_annotation2label --> allows me to extract the single labels. But I rather need a .ctab file when I want to read out my values. - mris_anatomical_stats with the -c flag --> to output the colortable as a text file I first need the .ctab file. Is there a way to get the LUT in a text file or the .ctab file just from the annotation file? Thanks a lot in advance! Cheers, Stephanie Stephanie Winkelbeiner, MSc Research Coordinator Psychiatry Research Zucker Hillside Hospital 75-59 263 Street Glen Oaks, NY 11004 Tel: (718) 470-4588 Email: swinkelbei(a)northwell.edu<mailto:swinkelbei@northwell.edu> Northwell Health Visit us at Northwell.edu<http://northwell.edu/> The information contained in this electronic e-mail transmission and any attachments are intended only for the use of the individual or entity to whom or to which it is addressed, and may contain information that is privileged, confidential and exempt from disclosure under applicable law. If the reader of this communication is not the intended recipient, or the employee or agent responsible for delivering this communication to the intended recipient, you are hereby notified that any dissemination, distribution, copying or disclosure of this communication and any attachment is strictly prohibited. If you have received this transmission in error, please notify the sender immediately by telephone and electronic mail, and delete the original communication and any attachment from any computer, server or other electronic recording or storage device or medium. Receipt by anyone other than the intended recipient is not a waiver of any attorney-client, physician-patient or other privilege.

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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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