[Freesurfer] recon-all error - MRISlabel2Mask()

: 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...@einsteinmed.

[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] 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 to debug this. Mark ____

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.wags

[Freesurfer] MGH35 template

) as 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 10461 Ph

[Freesurfer] MGH35 template in tracula

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 m

[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 Medic

[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

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

Re: [Freesurfer] recon-all errors

. 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: 718-430-3399 Email

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, PhD

Re: [Freesurfer] recon-all errors

: 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: 718-430-4011 FAX: 718

[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] Voxel-wise volumes vs APARC volumes

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: 718-430-3399 Email: mark.wags...@einsteinmed.org<mailto:mark.wags...@einsteinmed.org> [einstein-lo

[Freesurfer] Voxel-wise volumes vs APARC volumes

). 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] Mark Wagshul, PhD Associate

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] Extracting LME results from label regions

mmands 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 Medicine Bro

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

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

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

[Freesurfer] Running FSL randomise on FS cortical thickness data

(these are 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] 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

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

[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] 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] 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

[Freesurfer] Error running recon-all

, 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> [einstein-lo

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

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

[Freesurfer] Freeview not showing images

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...@einstein.yu.

[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-lo

[Freesurfer] Linear mixed modeling advice

. 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 Research Center Albert

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

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

Fellow Translational Imaging Group University College London http://www.jeiglesias.com http://cmictig.cs.ucl.ac.uk/ From: <freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>> on behalf of Mark Wagshul <mark.wags...@einstein.yu.edu<mailto:mark

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

[Freesurfer] Extracting DTI/NODDI data from hippocampal subfields

, 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 Email

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 College

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 <fis...@nmr.mgh.harvard.edu> wrote: > > Hi Mark > > the easiest thing to do would be to dr

[Freesurfer] Cortical volume parcellation

). 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.harvard.edu https