[Freesurfer] Cortical volume parcellation

ortical surface). Thanks for any advice you can provide on this. Best, Mark _______ Mark Wagshul, PhD Albert Einstein College of Medicine Bronx, NY Sent from my iPhone ___ Freesurfer mailing list Freesurfer@nmr.mgh.ha

Re: [Freesurfer] Cortical volume parcellation

Thanks! Mark ___ Mark Wagshul, PhD Albert Einstein College of Medicine Bronx, NY Sent from my iPhone > On Mar 18, 2018, at 3:21 PM, Bruce Fischl wrote: > > Hi Mark > > the easiest thing to do would be to draw the label you want on the > fsaverage

Re: [Freesurfer] Cortical volume parcellation

their extent. Just wanted to know what you thought of this approach (although, to be honest, this might take some time, just to learn how to use tksurfer). Thanks, Mark Mark Wagshul, PhD Associate Professor Gruss Magnetic Resonance Research Center Albert Einstein Colle

[Freesurfer] Extracting DTI/NODDI data from hippocampal subfields

space, or is there a method within Freesurfer to perform the math (e.g. similar to fslmaths)? Thanks, Mark Mark Wagshul, PhD Associate Professor Gruss Magnetic Resonance Research Center Albert Einstein College of Medicine Bronx, NY 10461 Ph: 718-430-4011 FAX: 718-430-3399

Re: [Freesurfer] Extracting DTI/NODDI data from hippocampal subfields

External Email - Use Caution Eugenio, Yes, we are on the same page, thank you so much for the advice. One followup question - is the threshold on the binary masks 50%? Mark ___ Mark Wagshul, PhD Albert Einstein College of Medicine Bronx, NY Sent from my

Re: [Freesurfer] Extracting DTI/NODDI data from hippocampal subfields

University College London http://www.jeiglesias.com http://cmictig.cs.ucl.ac.uk/ From: mailto:freesurfer-boun...@nmr.mgh.harvard.edu>> on behalf of Mark Wagshul mailto:mark.wags...@einstein.yu.edu>> Reply-To: Freesurfer support list mailto:freesurfer@nmr.mgh.harvard.edu>> Date: Wed

Re: [Freesurfer] Extracting DTI/NODDI data from hippocampal subfields

External Email - Use Caution Eugenio, Yes, we are on the same page, thank you so much for the advice. One followup question - is the threshold on the binary masks 50%? Mark ___ Mark Wagshul, PhD Albert Einstein College of Medicine Bronx, NY Sent from my

Re: [Freesurfer] Extracting DTI/NODDI data from hippocampal subfields

External Email - Use Caution Eugenio, Not sure if there is any interest in this, but here is our code for converting the data into T1 NIFTI space. Thanks for the help, Mark Mark Wagshul, PhD Associate Professor Gruss Magnetic Resonance Research Center

[Freesurfer] Linear mixed modeling advice

ation. I'm not sure why this couldn't be done on a voxel-wise or vertex-wise basis, but hopefully someone can enlighten me if I'm being overly naive). Thanks in advance for the advice! Mark ________ Mark Wagshul, PhD Associate Professor Gruss Magnetic Resonance Re

[Freesurfer] Moderation analysis in Freesurfer

provide. Mark Mark Wagshul, PhD Associate Professor Gruss Magnetic Resonance Research Center Albert Einstein College of Medicine Bronx, NY 10461 Ph: 718-430-4011 FAX: 718-430-3399 Email: mark.wags...@einstein.yu.edu<mailto:mark.wags...@einstein.yu.edu> [einstein-logo-rgb

[Freesurfer] Freeview not showing images

the screen resolution settings? Thanks, Mark ____ Mark Wagshul, PhD Associate Professor Gruss Magnetic Resonance Research Center Albert Einstein College of Medicine Bronx, NY 10461 Ph: 718-430-4011 FAX: 718-430-3399 Email: mark.wags...@einstein.yu.edu<mailto:mark.wags...@ei

Re: [Freesurfer] Freeview not showing images

External Email - Use Caution Yes, I’m running it with Xming on Windows. Same thing shows up if I load a volume. Mark Mark Wagshul, PhD Associate Professor Gruss Magnetic Resonance Research Center Albert Einstein College of Medicine Bronx, NY 10461 Ph: 718

Re: [Freesurfer] Freeview not showing images

External Email - Use Caution Yes, that shows up fine. Mark Wagshul, PhD Associate Professor Gruss Magnetic Resonance Research Center Albert Einstein College of Medicine Bronx, NY 10461 Ph: 718-430-4011 FAX: 718-430-3399 Email: mark.wags...@einstein.yu.edu

[Freesurfer] Error running recon-all

iated, thanks. Mark Mark Wagshul, PhD Associate Professor Gruss Magnetic Resonance Research Center Albert Einstein College of Medicine Bronx, NY 10461 Ph: 718-430-4011 FAX: 718-430-3399 Email: mark.wags...@einstein.yu.edu<mailto:mark.wags...@einstein.yu.edu> [einste

[Freesurfer] Freesurfer linear mixed models - viewing results

sults projected onto lhsphere. We would like to view these results in a more conventional manner, e.g. projected onto the inflated cortex of fsaverage. Is this possible? Thanks for any advice you can provide. Best, Mark ________ Mark Wagshul, PhD Associate Professor Gruss Magneti

Re: [Freesurfer] Freesurfer linear mixed models - viewing results {Disarmed}

? Our first attempt at this failed, saying that this was not a valid surface. Any advice would be most welcome. Best, Mark P.S. I see that you responded to a similar question from my student Daliah, so no need to continue that thread. Mark Wagshul, PhD Associate Professor

[Freesurfer] Cluster sizes discrepancy for mri_surfcluster vs mri_segstats

mri_segstats command which is not printing out the actual anatomical locations for each cluster?). Mark ____ Mark Wagshul, PhD Associate Professor Gruss Magnetic Resonance Research Center Albert Einstein College of Medicine Bronx, NY 10461 Ph: 718-430-4011 FAX: 718-430-3399 Ema

Re: [Freesurfer] Cluster sizes discrepancy for mri_surfcluster vs mri_segstats

External Email - Use Caution Thanks! Mark Mark Wagshul, PhD Associate Professor Gruss Magnetic Resonance Research Center Albert Einstein College of Medicine Bronx, NY 10461 Ph: 718-430-4011 FAX: 718-430-3399 Email: mark.wags...@einstein.yu.edu This email

Re: [Freesurfer] Cluster sizes discrepancy for mri_surfcluster vs mri_segstats

implement this in segstats? Thanks, Mark ___ Mark Wagshul, PhD Albert Einstein College of Medicine Bronx, NY Sent from my iPhone > On Jul 18, 2019, at 11:50 AM, Greve, Douglas N.,Ph.D. > wrote: > > When you run mri_surfcluster, save an output cluster number (--oc

[Freesurfer] Running FSL randomise on FS cortical thickness data

F statistics at each vertex) into a format which can be read into randomise? Thanks for any advice you can provide. Best, Mark ___ Mark Wagshul, PhD Albert Einstein College of Medicine Bronx, NY Sent from my iPhone ___ Freesurfer

Re: [Freesurfer] Running FSL randomise on FS cortical thickness data

External Email - Use Caution Great, thanks! Mark ___ Mark Wagshul, PhD Albert Einstein College of Medicine Bronx, NY Sent from my iPhone On Jul 27, 2019, at 2:43 PM, Antonin Skoch mailto:a...@ikem.cz>> wrote: External Email - Use Caution

Re: [Freesurfer] Running FSL randomise on FS cortical thickness data {Disarmed}

time than manually running the simulations. Your thoughts? Thanks for the help. Mark ___ Mark Wagshul, PhD Albert Einstein College of Medicine Bronx, NY Sent from my iPhone On Jul 28, 2019, at 4:11 PM, Greve, Douglas N.,Ph.D. mailto:dgr...@mgh.harvard.edu>> wrote: Free

Re: [Freesurfer] Running FSL randomise on FS cortical thickness data {Disarmed} {Disarmed}

External Email - Use Caution Anderson, Thanks! Mark Mark Wagshul, PhD Associate Professor Gruss Magnetic Resonance Research Center Albert Einstein College of Medicine Bronx, NY 10461 Ph: 718-430-4011 FAX: 718-430-3399 Email: mark.wags...@einstein.yu.edu

[Freesurfer] Extracting LME results from label regions

ommands for performing this (or alternatively Matlab commands), or is there a simpler way or extracting these values? Thanks for any advice you can give us on this. Mark ____ Mark Wagshul, PhD Associate Professor Gruss Magnetic Resonance Research Center Albert Einstein College of Medicin

Re: [Freesurfer] Extracting LME results from label regions {Disarmed}

External Email - Use Caution Perfect, thanks so much for the quick response! Mark Mark Wagshul, PhD Associate Professor Gruss Magnetic Resonance Research Center Albert Einstein College of Medicine Bronx, NY 10461 Ph: 718-430-4011 FAX: 718-430-3399 Email

[Freesurfer] Voxel-wise volumes vs APARC volumes

m perfect (R2 ~ 0.86). So, I'm obviously missing something here. What is the difference between the two volume calculation methods which could explain these discrepancies? Any help with this would be MOST appreciated! Best, Mark [cid:image004.jpg@01D6F59B.DA0205F0] ____ Ma

Re: [Freesurfer] Voxel-wise volumes vs APARC volumes

the help! Mark Mark Wagshul, PhD Associate Professor Gruss Magnetic Resonance Research Center Albert Einstein College of Medicine Bronx, NY 10461 Ph: 718-430-4011 FAX: 718-430-3399 Email: mark.wags...@einsteinmed.org<mailto:mark.wags...@einsteinmed.org> [einstein-lo

[Freesurfer] Postdoc opportunity - fMRI and EEG in childhood leukemia

External Email - Use Caution Postdoctoral Fellow position available at Albert Einstein College of Medicine in NYC The departments of Neuroscience (Dr. Elyse Sussman) and Radiology (Dr. Mark Wagshul) at the Albert Einstein College of Medicine in New York City are seeking a full

Re: [Freesurfer] recon-all errors

.0/bin/fsvglrun: line 20: `if [[ ! -v FS_ALLOW_VGLRUN ]]; then' [mwagshul@loginnode2 mri]$ Thanks for any advice on the issue here. Mark ________ Mark Wagshul, PhD Associate Professor Gruss Magnetic Resonance Research Center Albert Einstein College of Medicine Bronx, NY 10461 Ph: 7

Re: [Freesurfer] recon-all errors

External Email - Use Caution It works fine in 6.0, was in 7.1. The registration looks fine (the FLAIR is brain extracted, while the orig.mgz is not, is this expected, or was that my error, I don't recall which FLAIR image I fed in). Mark Mark Wagshul

Re: [Freesurfer] recon-all errors

tion fault. Not sure if that helps, or why this error wouldn't show up in the log file. Thanks for the help! Mark ________ Mark Wagshul, PhD Associate Professor Gruss Magnetic Resonance Research Center Albert Einstein College of Medicine Bronx, NY 10461 Ph: 718-430-4011 FAX

Re: [Freesurfer] recon-all errors

External Email - Use Caution Doug, Following up on this. Where can I upload the data for you to take a look? Thanks, Mark Mark Wagshul, PhD Associate Professor Gruss Magnetic Resonance Research Center Albert Einstein College of Medicine Bronx, NY 10461 Ph

[Freesurfer] fMRI-EEG Postdoctoral Position at Albert Einstein COM in NYC

External Email - Use Caution Drs. Elyse Sussman and Mark Wagshul, of the Departments of Neuroscience and Radiology at the Albert Einstein College of Medicine in NY, are seeking a full-time postdoctoral research associate to work on an NIH-funded project exploring the neural

[Freesurfer] Postdoctoral Research Fellow in New York – MR correlates of Gait and Falls in multiple sclerosis

CV, a brief statement of their research interests and career goals, and the names and contact info of three references to Mark Wagshul (mark.wags...@einsteinmed.edu). Review of applications will begin immediately and continue until the position is filled. The Albert Einstein College of Medicine

[Freesurfer] Postdoctoral position in Neuroimaging and Aging at Albert Einstein College of Medicine

information. Einstein seeks candidates whose skills, and personal and professional experience, have prepared them to contribute to our commitment to diversity and excellence, and the communities we serve. Mark Mark Wagshul, PhD Associate Professor Gruss Magnetic Resonance

[Freesurfer] recon-all error - MRISlabel2Mask()

ERROR: MRISlabel2Mask(): label vertex 150145 is >= nvertices 150145 Mark ____ Mark Wagshul, PhD Associate Professor Gruss Magnetic Resonance Research Center Albert Einstein College of Medicine Bronx, NY 10461 Ph: 718-430-4011 FAX: 718-430-3399 Email: mark.wags...@einstei

[Freesurfer] MGH35 template in tracula

Mark Mark Wagshul, PhD Associate Professor Gruss Magnetic Resonance Research Center Albert Einstein College of Medicine Bronx, NY 10461 Ph: 718-430-4011 FAX: 718-430-3399 Email: mark.wags...@einsteinmed.edu<mailto:mark.wags...@einsteinmed.edu> [einstein-logo-rgb] This email

[Freesurfer] MGH35 template

s the MGH35_HCP_FA_template image which is used in TRACULA? Does such a template exist, and if so, would it be possible to share? Thanks so much! Mark Mark Wagshul, PhD Associate Professor Gruss Magnetic Resonance Research Center Albert Einstein College of Medicine Bronx, NY 1046

Re: [Freesurfer] Freesurfer Digest, Vol 228, Issue 26

External Email - Use Caution Thanks, that's perfect. Mark Mark Wagshul, PhD Associate Professor Gruss Magnetic Resonance Research Center Albert Einstein College of Medicine Bronx, NY 10461 Ph: 718-430-4011 FAX: 718-430-3399 Email: mark

[Freesurfer] MSM error

+ Write permissions in that folder are fine, so I'm not sure what this is coming from. I'm also puzzled that it is trying to create a directory with so many "+" signs, there are no currect L.logdir folders in there. Thank you in advance for any thoughts on how

[Freesurfer] Recon-all failing

t.mni.1410486/nu0.mgz mul Segmentation fault (core dumped) Thanks so much in advance for any advice! Best, Mark Mark Wagshul, PhD Associate Professor Gruss Magnetic Resonance Research Center Albert Einstein College of Medicine Bronx, NY 10461 Ph: 718-430-4011 FAX: 718-430-3399

Re: [Freesurfer] Error in longitudinal hippocampal fields

External Email - Use Caution This is a single case, all of my other subjects ran through without a problem. Thanks! Mark Mark Wagshul, PhD Associate Professor Gruss Magnetic Resonance Research Center Albert Einstein College of Medicine Bronx, NY 10461 Ph