Freesurfer

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30088 discussions

Issue with BBR and Applying CVS Warps to Diffusion Data
by Austin Patrick 06 Mar '20

06 Mar '20

External Email - Use Caution Dear All, I have used CVS to align around 180 scans to a single, representative subject. I have then used BBR to align the mean b0 image to register the diffusion data to the native space T1 and then apply CVS warps; however, the resulting aligned images for calculated maps from the DWIs are very poor with a great deal of heterogeneity, especially at the boundary but also within white matter. The coefficient of variation of the mean b0 BB registered to the T1 is around 30% globally (excluding the edges of the brain) and 40% or greater for FA. I have reviewed the initial rigid registration of the b0s to the T1s for gross misalignment and found that FLIRT performed pretty well and didn’t fail for any of my subjects and didn’t require manual adjustment; however, the result of after applying the CVS warps is quite poor. The data T1s are 1mm (MPnRAGE) and the b0s are at 2mm. The DWIs were corrected for eddy currents, Gibbs’ ringing, rician noise, and B0 distortions and look pretty great. The DWIs are 70x180x180 at 2mm isotropic and the T1s are 256x256x256 at 1mm isotropic. Are there any suggestions for this issue? I have tried re-aligning the DTI parameter maps to the b0s before applying the CVS warps (although they should be in the same space) and I have tried using both the –t2 and –dti, as well as with/out the –fsl-init flag. Is bbregister shifting the origin for the images at all? Any help would be appreciated. Cheers, -Austin -- Austin M. Bazydlo, MS PhD Candidate Dept. of Medical Physics University of Wisconsin-Madison

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registrations
by Octavian Lie 06 Mar '20

06 Mar '20

External Email - Use Caution Dear All, I need to register: 1. T1.mgz to a T1 postresection volume (no contrast), with large resection. Which one should I use, mri_robust_register, or bbregister, if the latter, which is the better initiator (nmi, spm, fsl)? 2. T1.mgz to a 3D FLAIR SPACE sequence (outside of the flair space recon-all flag), which FS registration tool should I use? 3. I then need to mask the coregistered T1 postresection with a T1.mgz mask. I would appreciate commands (either names, or full command lines), please advise. Thank you, Octavian

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group analysis for same group in 2 conditions
by Marco Ninghetto 06 Mar '20

06 Mar '20

External Email - Use Caution Dear experts, I'm performing a study on visual pathways, in which each participant undergoes to 2 different conditions. One in normal sight (NG, i.e.: No Goggles) and second in narrowed sight using special goggles (YG, i.e.: Yes Goggles). I'd like to compare the results between these two conditions (basically, subject A, B, C in cond1 versus subject A, B, C in cond2). I created the FSGD file (attached as "RetinotopyStudy" file) and the contrast matrices, organised as: 1 -1 , named "YG-NG.mtx" > -1 1, named "NG-YG.mtx" In this FSGD sample file, I reported only subjects from 7 to 12. My folders are organised as follows: main >> recon_output >> sub-yy (X folders for X subjects) > >> Contrasts (with contrast files) > >> FSGD (with FSGD files) > >> fsaverage (subjects template > created during recon-all -qcache) > >> pRF_function >> analNG (inside, there are the functionals for > each subject in NG condition) > >> analYG (inside, there are the > functionals for each subject in YG condition) Once I used the pipeline for the retinotopy analysis <http://freesurfer.net/fswiki/FsFastIndividualRetinotopyAnalysis>and I have results for each participant, and now I'd like to make 2nd lev analysis. So the idea would be, as you probably already got it, condition Yes Goggles versus condition No Goggles. I use the command: mris_preproc --fsgd RetinotopyStudy --target fsaverage --hemi ?h --out > outputname.mgh But I'm not sure it would calculate in the right way. The question is: how would I organise the FSGD file or folders in such a way that FREESURFER would know that it has to compare results from the same subjects but from two different folders (analNG vs analYG)? Hoping that's clear, I really look forward to hear from you soon. Thank you for your time, Marco -- --------------------------------------------------- Marco Ninghetto, PhD candidate Laboratory of Neuroplasticity Nencki Institute of Experimental Biology Polish Academy of Sciences 3 Pasteur Street, 02-093 Warsaw, Poland

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Open lab manager position in Perception & Brain Dynamics Laboratory at NYU Medical Center
by Wu, Yuan hao 06 Mar '20

06 Mar '20

External Email - Use Caution Sorry for spamming. The contact email in the previous mail contains a typo The Perception & Brain Dynamics Laboratory (http://www.med.nyu.edu/helab/) at New York University School of Medicine is looking for a lab manager to start in spring/summer 2020. The Laboratory is within the Neuroscience Institute at NYU Langone Health(http://www.med.nyu.edu/neuroscience), affiliated with Departments of Neurology, Neuroscience and Physiology, and Radiology. Our research focus is on understanding the neural bases of perceptual awareness using multimodal imaging (fMRI, MEG, EEG, ECoG) and stimulation (tDCS, TMS) techniques in humans, combined with computational neuroscience approaches. We are looking for a bright and driven candidate with a Bachelor's or Master's degree who is dedicated to neuroscience research. A variety of backgrounds, including neuroscience, biology, psychology, and computer science is possible, and experience with programming is highly desirable. In addition, the ideal candidate has high responsibility and dependability, as well as excellent critical thinking, organizational and leadership skills. Performing independent research is an important aspect of the position, in addition to lab management duties. A minimal commitment of 2 years is required. Interested candidates please send a cover letter, a CV, undergraduate and/or graduate transcript, and names and contacts of two to three referees, to Prof. Biyu J. He at biyu.jade.he(a)gmail.com, with the subject line "Lab manager application 2020". The application is rolling, so please submit your materials as soon as possible.

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Open lab manager position in Perception & Brain Dynamics Laboratory at NYU Medical Center
by Wu, Yuan hao 06 Mar '20

06 Mar '20

External Email - Use Caution The Perception & Brain Dynamics Laboratory (http://www.med.nyu.edu/helab/) at New York University School of Medicine is looking for a lab manager to start in spring/summer 2020. The Laboratory is within the Neuroscience Institute at NYU Langone Health(http://www.med.nyu.edu/neuroscience), affiliated with Departments of Neurology, Neuroscience and Physiology, and Radiology. Our research focus is on understanding the neural bases of perceptual awareness using multimodal imaging (fMRI, MEG, EEG, ECoG) and stimulation (tDCS, TMS) techniques in humans, combined with computational neuroscience approaches. We are looking for a bright and driven candidate with a Bachelor's or Master's degree who is dedicated to neuroscience research. A variety of backgrounds, including neuroscience, biology, psychology, and computer science is possible, and experience with programming is highly desirable. In addition, the ideal candidate has high responsibility and dependability, as well as excellent critical thinking, organizational and leadership skills. Performing independent research is an important aspect of the position, in addition to lab management duties. A minimal commitment of 2 years is required. Interested candidates please send a cover letter, a CV, undergraduate and/or graduate transcript, and names and contacts of two to three referees, to Prof. Biyu J. He at biyu.jade.he(a)gmail.com, with the subject line "Lab manager application 2020". The application is rolling, so please submit your materials as soon as possible.

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Fwd: FreeSurfer Course @ Caltech information - FOLLOW UP
by Paul Wighton 06 Mar '20

06 Mar '20

External Email - Use Caution Hi FreeSurfer friends, Does anybody have experience getting FreeView to run on Windows 10? Any suggestions on how to resolve this issue below? Or, are there any other installation notes you could pass along? Thanks, -Paul I’ve installed FreeSurfer on a Windows 10 machine with a WSL (Ubuntu 18.04 LTS) and Xming for graphical display. It generally works. However, when testing the installation using the examples on the website it fails to display the output volumes from Example 4 (see screenshot below). Do you have any idea what the problem might be? Thank you! Tessa

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some basic questions regarding longitudinal analyses in Freesurfer
by Lara Foland-Ross 06 Mar '20

06 Mar '20

External Email - Use Caution Hello, I'm analyzing a large dataset using an LME model to examine longitudinal changes in brain structure that vary as a function of group (patients vs controls). Because some participants were scanned several years apart in early childhood, the intra-subject registration failed in the longitudinal processing stream. For this reason, my data were not initially processed using the longitudinal processing stream within Freesurfer. However, per this thread - https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg55847.html - I still plan to use the LME model. As I understand it, this model assumes that the longitudinal processing stream was conducted. Therefore, I have the following questions: 1. would the "base" (aka within-subject template) for each subject be = time point 1? 2. would the "long run" for each subject be = each subject's individual time points? 3. assuming #1 and 2 are correct, would I need to set my directory structure to match that used in the longitudinal processing stream? For example, if I have 2 time points for subject 1234, and they are initially labeled "1234.time1" and "1234.time2", then in order to run the LME model, I would create a copy of "1234.time1" and rename the copy as "1234" to indicate to the software that this should be used as the base. And, I would also need to rename "1234.time1" and "1234.time2" as "1234.time1.long.1234" and "1234.time2.long.1234" to indicate that these folders should be used as the longitudinal time points. Does this seem appropriate? Thanks in advance for your help, Lara Lara Foland-Ross, Ph.D. Senior Research Associate and Imaging Lab Manager Center for Interdisciplinary Brain Sciences Research Stanford University School of Medicine 401 Quarry Road, Room 1356 Stanford, CA 94305-5795

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Could not login in "https://mail.nmr.mgh.harvard.edu/NMRAuth/GLOBAL/LOGIN"
by ZhangBo 06 Mar '20

06 Mar '20

External Email - Use Caution Hi teams, I could not login in "Could not login in "https://mail.nmr.mgh.harvard.edu/NMRAuth/GLOBAL/LOGIN"". Thanks.

1 0

recon-all with errors
by Laboratorio de Neurociencia Funcional 05 Mar '20

05 Mar '20

External Email - Use Caution Dear Freesurfer experts, After running the recon-all in one of my subjets, part of the temporal lobe was partially excluded. Then, I tried to use the watershed algorithm to be less agressive in the skull stripping as follows: recon-all -skullstrip -wsthresh 35 -clean-bm -no-wsgcaatlas -subjid sub_001 The problem was solved in the brainmask.mgz but not in the cortical surfaces. To handle this issue, I edited the white matter and run the recon-all (-autorecon2-wm -autorecon3) without success. I also placed control points but the following error appeared after running the recon-all -autorecon2-cp -autorecon3: recon-all -s sub_001 existed with errors I noted that white matter of this part of the temporal lobe has high values (up to 132). What can I do to solve the problem with this subject? Thank you in advance. Best regards, Marina

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8 Gb of ram
by Ian 05 Mar '20

05 Mar '20

External Email - Use Caution Hey guys. I'm running Freesurfer on an AWS EC2 instance, in a docker container (t3.large specifically.) Would you expect 8Gb of ram to *always* be enough to run recon-all on a 280x280x240 T1 image? The instance is running Ubuntu; the container image is based on Ubuntu; and nothing else is being explicitly run on the instance while recon-all is running. Thanks, Ian -- *Ian Hardingham*

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