Freesurfer

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30083 discussions

7.1.1 recon-all steps verification
by Jaiashre Sridhar 18 Mar '21

18 Mar '21

External Email - Use Caution Hello, I am using FreeSurfer version v7.1.1. For few subjects who have already been through the complete recon-all pipeline, I would like to re-run the recon steps downstream of “-fill”. I am using the following commands to do so. Can an expert check and let me know if this encompasses all the downstream steps accurately for v7.1.1? ### Recon commands begin ### recon-all -s [subjid] -tessellate -smooth1 -inflate1 -qsphere -fix cd [subdir]/mri #-------------------------------------------- #@# AutoDetGWStats lh mris_autodet_gwstats --o ../surf/autodet.gw.stats.lh.dat --i brain.finalsurfs.mgz --wm wm.mgz --surf ../surf/lh.orig.premesh #-------------------------------------------- #@# AutoDetGWStats rh mris_autodet_gwstats --o ../surf/autodet.gw.stats.rh.dat --i brain.finalsurfs.mgz --wm wm.mgz --surf ../surf/rh.orig.premesh #-------------------------------------------- #@# WhitePreAparc lh mris_place_surface --adgws-in ../surf/autodet.gw.stats.lh.dat --wm wm.mgz --threads 1 --invol brain.finalsurfs.mgz --lh --i ../surf/lh.orig --o ../surf/lh.white.preaparc --white --seg aseg.presurf.mgz --nsmooth 5 #-------------------------------------------- #@# WhitePreAparc rh mris_place_surface --adgws-in ../surf/autodet.gw.stats.rh.dat --wm wm.mgz --threads 1 --invol brain.finalsurfs.mgz --rh --i ../surf/rh.orig --o ../surf/rh.white.preaparc --white --seg aseg.presurf.mgz --nsmooth 5 #-------------------------------------------- #@# CortexLabel lh mri_label2label --label-cortex ../surf/lh.white.preaparc aseg.presurf.mgz 0 ../label/lh.cortex.label #-------------------------------------------- #@# CortexLabel+HipAmyg lh mri_label2label --label-cortex ../surf/lh.white.preaparc aseg.presurf.mgz 1 ../label/lh.cortex+hipamyg.label #-------------------------------------------- #@# CortexLabel rh mri_label2label --label-cortex ../surf/rh.white.preaparc aseg.presurf.mgz 0 ../label/rh.cortex.label #-------------------------------------------- #@# CortexLabel+HipAmyg rh mri_label2label --label-cortex ../surf/rh.white.preaparc aseg.presurf.mgz 1 ../label/rh.cortex+hipamyg.label recon-all -s [subjid] -smooth2 -inflate2 -curvHK -autorecon3 ### Recon commands end ### Additional question – Is there an individual flag that replaces the hardcoded commands above for AutoDetGWStats, CortexLabel, WhitePreAparc and CortexLabel+HipAmyg? According to the [subjid]/scripts/recon-all.cmd file, I see that these additional commands are added to v7.1.1 but are not present in the recon steps listed here for stable 7.1.1 release https://secure-web.cisco.com/1mh5NrCnQZwjol6BqUWZ3zVU1wUDX0ceM5QaWcfAsgmEUH…. Thank you in advance for your response. Sincerely, Jaiashre.

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FreeSurfer brainmask.mgz: B-1 corrected?
by Arman Avesta 18 Mar '21

18 Mar '21

External Email - Use Caution Hi FreeSurfer gang, I'm using ADNI's pre-processed data to train a neural network. Specifically, for each included subject I'm using FreeSurfer Cross-Sectional brainmask.mgz (as input). My question is: are these ADNI pre-processed brainmask.mgz volumes already B1-corrected? (All ADNI subjects that I'm including in my project have B1 acquisition). If not, is there a simple way to perform B1 correction on brainmask.mgz? Thank you so much,Arman Arman Avesta, MD Radiology Resident & PhD Student Yale School of Medicine & Yale Graduate School of Arts and Sciences Email: arman.avesta(a)yale.edu Phone: 617-763-6632

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TRACULA error: missing output volume name
by Shanika Jayakody 18 Mar '21

18 Mar '21

External Email - Use Caution Dear FreeSurfer team I have been running TRACULA for some time now but recently, I come across a message "missing output volume name" and I cannot do preprocessing in new or old subjects (even subjects who completed preprocessing without error) I have not made any change to the configuration files. It is the same format that I have been using. Any advice on this is appreciated. I have attached one of the configuration files. Thanks, Shanika

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Phase encoding direction in Philips
by Benxamin varela lópez 18 Mar '21

18 Mar '21

External Email - Use Caution Hello dear experts. I am conducting a TBSS analysis. My MRI data was acquired by using a Philips Achieva. Since my data is derived from a Philips I am having problems accessing the acquisition parameters. Specifically I am interested in knowing the phase encoded direction. In the DICOM header it is specified "Phase encoding direction" = col, but there is no information about the direction (Anterior-Posterior/Posterior-Anterior). Based on the appearance of my data I assume this is a P-A acquisition but I would like to be sure (attached is a screenshot of my images). Thank you very much in advance. Benxa.

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Longitudinal Registration
by Suzan Maleki 18 Mar '21

18 Mar '21

External Email - Use Caution Hi FS experts, I appreciate it if you help me with a question on your longitudinal processing pipeline. If I use FreeSurfer to generate an unbiased T1 image template from N time points (non-linear registration), then how can I apply the within subject transformation matrix (Jacobian matrix) to that subject's DTI maps. Does FreeSurfer save the transformation matrix from N.Time-Points toward Template image? and if so, in which folder directory it will be saved? Also, given that FS uses vertices, should I first convert that transformation matrix to voxel space (eg. using surf2voxels ?) and then multiply that into different time-points of one's DTI images. Hope my questions are clear and looking forward to hearing from you:-) Best Suzan -- *Suzan Maleki* PhD Student *Brain, Mind and Society Research Hub* *Turner Institute for Brain and Mental Health* School of Psychological Sciences Monash University 770 Blackburn Road Clayton VIC 3800 Australia E: *suzan.maleki(a)monash.edu <suzan.maleki(a)monash.edu>* W: http://secure-web.cisco.com/11rJxuhHbcEcZqCYP3vJeG9D1pvF71PV1NgM7qYlH-yg7b7…

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Troubleshooting: Soft Failures
by 崔鹏程 18 Mar '21

18 Mar '21

External Email - Use Caution Hi FreeSurfer experts, Recently, I used Fresurfer's recon-all toprocess our own T1 MRI brain volumes which is 0.7 m3 isotropic. For most young brain cases, FS performs very well, the segmention is great. But for almost every elderly brain case, the segmention is inaccurate visibly. The figure is the same slice of T1 data and aseg. mgz , the GM is mislabeled as wm-hypointensities. I found some solutions to this problem. But these solutions all require manual editing, which will take a long time. Is there a way to automatically solve this problem by setting some parameters? Thank you for your attention and your help! Cui

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Which pial surface to trust, with or without -FLAIR option
by Xiaojiang Yang 17 Mar '21

17 Mar '21

External Email - Use Caution Dear FS developers, I have run FS’s recon-all on many cases, with and without -FLAIR options. I found the pial surface results (?h.pial) I obtained without -FLAIR option fit to the original image (subjected/mri/orig.mgz) much better than those with -FLAIR option, at least from my visual judgment. See https://secure-web.cisco.com/1jL9MUfd9oLXR_SVyZl8-wPztrX70T9SJxxJaJElRv5e-D… for one example. I know -FLAIR option was introduced to improve the quality of pial surface segmentation. Now for many cases, my intuition is that -FLAIR option decreases the pial quality. My questions are: - Is this intuition correct? - Should I trust the pial surface that’s obtained with or without -FLAIR option in general? In addition, when I use the -FLAIR option, I sometimes get failed when running recon-all. After I did some manual edits to the brainmask image, and re-run the recon-all: recon-all -autorecon-pial -subjid <subjectID> I can get recon-all successful. But if I run recon-all without -FLAIR option, I can get successful results without needing to manually edit the brainmask image. So my last question is: - Should I just run recon-all without -FLAIR option, or, with -FLAIR option + manual edit + re-run with -autorecon-pial? Which is better? Thank you very much! John

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Difference between V1_exvivo.label and v1.predict.label?
by Lee Subin Kristine 17 Mar '21

17 Mar '21

External Email - Use Caution Dear FreeSurfers, I am wondering what is the difference between V1 labels obtained from V1_exvivo.label and v1.predict.label, and what is more exact? When visualizing resutls from both labels, V1_exvivo.label occupies a larger portion than v1.predict label. Thanks, Kristine

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mri_vol2surf; --projfrac-avg and --projfrac-max
by Horn, Mitchell Jacob 17 Mar '21

17 Mar '21

Dear FS Experts, When using --projfrac-max or --projfrac-avg, how is the “min” component defined? If I specify: --projfrac-max -2 1 0.1 Is the min (-2) simply 2x the thickness at each vertex below/inside the GM/WM boundary? Thanks in advance! Mitch

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Post-doctoral Position in Human Perceptual Neuroscience at NYU
by Wu, Yuan hao 17 Mar '21

17 Mar '21

External Email - Use Caution The Perception and Brain Dynamics Laboratory (PI: Biyu J. He, Ph.D.) at New York University is currently recruiting for a post-doctoral fellow to study neural mechanisms of human perception and the interaction between perceptual and cognitive systems. We are looking for a candidate with independent critical thinking, strong analytical and quantitative skills, and good interpersonal skills. We are especially interested in candidates with experience in using advanced neuroimaging data analyses to test theories in perceptual/cognitive neuroscience, and/or candidates with experience in large-scale computational modeling. Our laboratory is located on the medical campus of New York University in Manhattan, NY, and is affiliated with the Neuroscience Institute, Departments of Neurology, Neuroscience & Physiology, and Radiology. The position is expected to start in fall 2021. We provide competitive salary and benefits that adjust for cost of living in New York City. To apply, please send a CV, a cover letter, a statement of scientific and career goals, and names and contacts of three referees to Prof. Biyu Jade He (email: biyu.jade.he(a)gmail.com<mailto:biyu.jade.he@gmail.com>) with the subject line “post-doctoral application 2021”. --------------------------------- Yuan-hao Wu, Ph.D. Postdoctoral Researcher Neuroscience Institute New York University Langone Medical Center New York, NY 10016 ------------------------------------------------------------ This email message, including any attachments, is for the sole use of the intended recipient(s) and may contain information that is proprietary, confidential, and exempt from disclosure under applicable law. Any unauthorized review, use, disclosure, or distribution is prohibited. If you have received this email in error please notify the sender by return email and delete the original message. Please note, the recipient should check this email and any attachments for the presence of viruses. The organization accepts no liability for any damage caused by any virus transmitted by this email. =================================

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