[Freesurfer] Virtual Box Passcode

External Email - Use Caution Good morning, Please send the Virtual Box passcode to unlock the .ova archive file. Thanks, Scott Watkins Systems Analyst Radiology - PACS IT School of Medicine University of Missouri Health (573) 884-9822

Re: [Freesurfer] glmfit sig file all zeros

o you mean it is based on a volumentric sphere? How did you create it? On 10/8/2021 1:24 PM, Pedersen, Walker Scott wrote: If I run without the mask, the output sig file looks normal. If I overlay the surface ROI and the output sig file on the fsaverage, I can see that the maximum absolute p

Re: [Freesurfer] glmfit sig file all zeros

21 9:25 AM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] glmfit sig file all zeros what happens if you run it without the mask? On 9/29/2021 2:33 PM, Pedersen, Walker Scott wrote: I just wanted to follow up on this - based on the output I sent previously, they seem to have the sa

Re: [Freesurfer] glmfit sig file all zeros

be getting good F.nii.gz files, but bad sig.nii.gz files. From: Pedersen, Walker Scott Sent: Thursday, September 23, 2021 1:40 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] glmfit sig file all zeros Here is what I get fo

[Freesurfer] Longitudinal Hypothalamic Subunits

I see that generating the hippocampal subfields in the longitudinal pipeline has its own script (segmentHA_T1_long.sh), but am not seeing a corresponding script or command to do the same for the hypothalamic subunits. Would simply running mri_segment_hypothalamic_subunits on my subject_session

Re: [Freesurfer] glmfit sig file all zeros

dimension of /autofs/cluster/neuromod/NIFTI/OCD_N M/derivatives/fsfast/rois/recall/lIFG_surf_rad10.nii.gz you can check with mri_info On 9/17/2021 8:32 PM, Pedersen, Walker Scott wrote: Hi, I am running glmfit on some functional data (using ces.nii.gz surface files as input) using ROIs and the

[Freesurfer] glmfit sig file all zeros

Hi, I am running glmfit on some functional data (using ces.nii.gz surface files as input) using ROIs and the --mask argument, that I plan to later submit to glmfit-sim for small volume correction. I have some rois that are subcortical and some that are surfaces. For the glmfit run within the

[Freesurfer] MRI RA Position at Ohio State

%2F%2Fthebbal.com%2F>) directed by Dr. Scott Hayes. The B-BAL studies the relationships among aging, physical activity, cognition and the brain [using Magnetic Resonance Imaging (MRI) metrics]. We also examine neural correlates of memory in healthy and clinical populations. The Research Assistant 1 a

[Freesurfer] mris_make_surfaces -aseg filled vs -noaseg (difference v5.3 and v6)

. From the error I am guessing that labels in filled (127 and 255) are not those required. Is it (still) possible to use filled.mgz as the input to -aseg in mris_make_surfaces? Is it perhaps possible to modify the label numbers in filled.mgz to get this working again? Thanks, Scott

[Freesurfer] MRI RA position available at Ohio State Buckeye Brain Aging Lab

/) directed by Dr. Scott Hayes. The B-BAL studies the relationships among aging, physical activity, cognition and the brain [using Magnetic Resonance Imaging (MRI) metrics]. We also examine neural correlates of memory in healthy and clinical populations. The Research Assistant 1 assists in the

[Freesurfer] RA position available at Ohio State University Buckeye Brain Aging Lab (B-BAL)

Brain Aging Lab (B-BAL) directed by Dr. Scott Hayes. The B-BAL studies the relationship among aging, physical activity, cognition and the brain [using Magnetic Resonance Imaging (MRI) metrics]. We also examine neural correlates of memory in healthy and clinical populations. The Research Assistant 1

[Freesurfer] Job posting: 2-year postdoctoral position

External Email - Use Caution Enquires and applications to Dr. Martine Migaud (martine.mig...@inra.fr) Job title: Multi-modal MRI analysis of a large mammalian brain model Structure: A 2-year postdoctoral position is available in the group of Dr. Martine Migaud, at the laboratory

[Freesurfer] RA position at Ohio State

. Scott Hayes. The B-BAL studies the relationship among aging, physical activity, cognition and the brain [using Magnetic Resonance Imaging (MRI) metrics]. We also examine the neural correlates of memory in healthy and clinical populations. The Research Assistant 1 assists in the general coordination and

[Freesurfer] Job offer - 2 year postdoc France

External Email - Use Caution Applications are invited for a two year, full time postdoctoral position (see below for details). Contact Dr. Martine Migaud (martine.mig...@inra.fr) for questions. Job title: Multi-modal MRI analysis of a large mammalian brain model Structure: A 2-

Re: [Freesurfer] Error in running make_average_subject

Thanks, Andrew! On Tue, Feb 20, 2018 at 11:42 AM, Hoopes, Andrew wrote: > Hi Scott, > > It looks like the mri_aparc2aseg binary in that patch directory was > compiled for centos. The version at the following link was compiled on OS > X: https://surfer.nmr.mgh.harvard.edu/pub/dis

Re: [Freesurfer] Error in running make_average_subject

file not executable. Darwin scott-pruetts-computer.local 17.3.0 Darwin Kernel Version 17.3.0: Thu Nov 9 18:09:22 PST 2017; root:xnu-4570.31.3~1/RELEASE_X86_64 x86_64 recon-all -s 601_10y_av exited with ERRORS at Tue Feb 20 11:04:10 EST 2018 I've attached the recon-all.log file. Any help wou

[Freesurfer] postdoctoral fellowship at Memory Disorders Research Center, VA Boston / Boston University

interests. Please also have three letters of recommendation emailed to Dr. Mieke Verfaellie (v...@bu.edu). Start date is summer 2018. Scott M. Hayes, Ph.D. Associate Director Neuroimaging Research for Veterans Center Memory Disorders Research Center VA Boston Healthcare System Assistant

Re: [Freesurfer] Issue with Freesurfer installation

Thanks, Andrew. That seems to have done the trick! On Thu, Dec 14, 2017 at 9:43 PM, Hoopes, Andrew wrote: > Hi Scott, > > It looks like "/Users/scottpruett/sample-001.mgz" doesn’t exist because > your cp command never ran (you have to specify a destination). Try: > cp

[Freesurfer] Issue with Freesurfer installation

plications/freesurfer/mni scott-pruetts-computer:~ scottpruett$ cp $FREESURFER_HOME/subjects/sample-001.mgz usage: cp [-R [-H | -L | -P]] [-fi | -n] [-apvX] source_file target_file cp [-R [-H | -L | -P]] [-fi | -n] [-apvX] source_file ... target_directory scott-pruetts-computer:~ s

Re: [Freesurfer] General question about freesurfer

sure of the answer for question 3 but it would depend on the format your atlas is already in and how you wanted to use it. Best, Scott > On 15 Feb 2017, at 09:51, Arsene Ella wrote: > > Hi everyone, > > I am a newbie in freesurfer. I went a little bit throughout the tutorials a

Re: [Freesurfer] MPRAGE Data

Hi Bruce, Thanks for your response. I'm writing software that involves processing the data; currently I have one sample set but expect to be working with more in future. Scott > On Jan 7, 2016, at 6:45 AM, Bruce Fischl wrote: > > Hi Scott > > we are almost certainly

[Freesurfer] Freesurfer 6 - matlab crash

have attached two example crash reports one with ‘segmentation violation’ the other common one is ‘Abort signal detection’. What else should we be looking at to fix the problem ? Cheers, Scott matlab_crash_dump.20760-1 Description: application/applefile matlab_crash_dump.20760-1

[Freesurfer] SNR Tracula

Thanks Barbara, that is what I was after. Cheers, Scott ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom

[Freesurfer] SNR Tracula

Hi, Tracula outputs the SNR for each volume in a txt file. I was wondering if anyone can point me to some literature on how the SNR is being calculated? Cheers, Scott Quadrelli ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https

[Freesurfer] TRACULA error related to bvec/bval input

bevy/bval file however I can’t see what the issue is with the data contained within the file. Does the output from dcm2nii need to be reformatted for input to TRACULA ?Cheers,Scott-/Applications/freesurfer/bin/trac-preproc

[Freesurfer] Expediting the pial surface calculation

Hi, We are wondering if there is a faster way to generate lh.pial and rh.pial than running the 24 hour long recon-all function. We took a look at http://surfer.nmr.mgh.harvard.edu/fswiki/ReconAllFilesVsSteps and it seems that the inputs for lh.pial and rh.pial are needed from the recon-all out

Re: [Freesurfer] parcellation of group stats maps?

1.3 --avgwf $SUBJECTS_DIR/qdec/roiaverages.txt --sum $SUBJECTS_DIR/qdec/roi.sum.txt Best, Scott On Wed, Nov 26, 2014 at 9:29 PM, Douglas Greve wrote: > > You can use mri_segstats with the annotation (--annot) and the cluster sig > map as a mask (--mask , --maskthresh, --masksign), use the

[Freesurfer] parcellation of group stats maps?

group analysis). It seems like this might be possible to accomplish w/ a single command, but we have not been able to pinpoint the exact command w/ the necessary flags. Any guidance would be appreciated. Thanks, Scott ___ Freesurfer mailing list Freesurfer

Re: [Freesurfer] Group analysis over different studies?

Terri On Tue, Jun 17, 2014 at 4:27 AM, Douglas Greve wrote: > > Just run isxconcat-sess for each study, then > > mri_concat study1/gamma.mgh study2/gamma.mgh --o > study1-and-study2-gamma.mgh > > then run mri_glmfit on the above output > > doug > > > > On 6

[Freesurfer] Group analysis over different studies?

Hi all, I want to do a group analysis using subjects that were run in different studies but who have (some of) the same relevant functional contrasts. Is there a way to run something like isxconcat-sess on data from different analysis streams? Or if not, which files do I need to collect and align

[Freesurfer] question about running a post-hoc group analysis

Hello, I'm working with a data set which has been analyzed entirely in the subjects' native spaces in Freesurfer, but now I would like to run a group analysis on the data. Is it necessary to re-run the preprocessing and contrasts in normalized space, or is there a small set of files that are looke

[Freesurfer] Neuroimaging Postdoctoral Research Position in Mild Traumatic Brain Injury and Posttraumatic Stress Disorder

analyses, ASL) and the use of cognitive and MRI outcome measures subsequent to exercise intervention in Veterans with mTBI and PTSD. Dr. Scott Hayes will be the primary mentor, and the fellow will also collaborate with an interdisciplinary team including Drs. Mieke Verfaellie, David Salat, Daniel

[Freesurfer] Neuroimaging Postdoctoral Research Position in Memory, Aging, and Alzheimer's disease

Cognitive Impairment and medial temporal lobe amnesics). Studies will focus on human memory, age- and AD-related changes in memory and the brain, and individual differences (e.g., in cardiovascular fitness) that attenuate age-related decline. Dr. Scott Hayes will be the primary mentor, and the

[Freesurfer] error using selxavg3-sess for resting state connectivity

le as it's definitely there in the directory containing fmcpr.nii can anyone help? many thanks Scott ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail i

[Freesurfer] Freesurfer stats into REDCap

recon-stats to do just that. Hope at least someone else out there can find this useful! Scott Burns Sr. Research Imaging Specialist Education and Brain Science Research Laboratory Vanderbilt University Nashville, TN ___ Freesurfer mailing list Frees

[Freesurfer] error at ex-vivo entorhinal cortex label lh

Hello, I'm new to using freesurfer and I have gotten the following error when running recon-all on a new set of subjects. #@# Ex-vivo Entorhinal Cortex Label lh Tue Jan 15 09:25:23 EST 2013 mris_spherical_average -erode 1 -orig white -t 0.4 -o KAN_adapt_02 label lh.entorhinal lh sphere.reg lh.

[Freesurfer] SPM complications - moving parcels into native space

Dear all, I'm new to freesurfer and I'm trying to move a set of parcels from mni space to the native space of a subject. The parcels were created in SPM but I was going to try to register them to the subject using cvs. I registered my subject to an mni template with cvs. I converted the .img parce

[Freesurfer] Another -use-gpu experiment

Just curious, certainly not a deal-breaker if it doesn't. Thanks for your input. Scott Burns Neuroimaging Analyst Education and Brain Science Lab Kennedy Center Vanderbilt University ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https

Re: [Freesurfer] bedpost failure using tracula

to be running thus far. As Shannon Buckley mentioned previously, it seems like we both encountered the same issues... Best, Scott -- Scott M. Hayes, Ph.D. Memory Disorders Research Center Neuroimaging Research Center VA Boston Healthcare System Assistant Professor Department of Psychiatry Bos

Re: [Freesurfer] bedpost failure using tracula

Hi, The following files & directories are listed directly under dmri.bedpostX: bvals commands.txtlogs nodif_brain_mask.nii.gz bvecs diff_slices monitor xfms --Scott Anastasia Yendiki Fri, 16

[Freesurfer] bedpost failure using tracula

tes: Queuing parallel processing stage 0 slices processed 1 slices processed 1 slices processed etc... Any insight as to what might be causing the issue? Thanks, Scott ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvar

Re: [Freesurfer] tracula failed to find header file for -t

Hi, I'm using FSL 4.1.4 On Mon, Dec 12, 2011 at 12:43 PM, Anastasia Yendiki wrote: > > Hi Scott - Which version of FSL are you using? I cannot replicate this > behavior of fslstats on our data. > > Thanks, > a.y > > > On Mon, 12 Dec 2011, Scott Hayes wrote:

[Freesurfer] tracula failed to find header file for -t

ula config file. Running locally on mac os 10.6.8. Any suggestions would be appreciated. Thanks, Scott ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mai

[Freesurfer] trac-all flag for doing all 3 processing steps?

c ConfigFile Is there a way to specify all three steps w/ one command? That is, could I specify: >trac-all -all -C ConfigFile (I don't see it stated in the help, but maybe it's implicitly understood to work this way?) Thanks for your guidance. Best, Scott _

[Freesurfer] pre-bedposted data in tracula

Hello, If I already ran bedpostx on my diffusion data, how can I skip this step in tracula and still get it to run smoothly. Thank you, Scott ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo

[Freesurfer] Bug in mri_info?

orrectly reading MPRAGE_new.nii as float data. Not an earth shattering bug by any means, but I thought I'd let you know anyways. Scott Burns Kuperberg Lab Martinos Center for Biomedical Imaging sbu...@nmr.mgh.harvard.edu The information in this e-mail is intended only for the person to who

Re: [Freesurfer] selxavg3 can't find image that exists

preprocessing but not actually recompute anything because there's no update needed (assuming I've recently run preproc-sess)? scott On Apr 10, 2011, at 10:40 PM, Douglas Greve wrote: > Hi Scott, the problem is that you specified the "funcstem" as a full filename >

[Freesurfer] selxavg3 can't find image that exists

tions 4 parname atlloc.par RefEventDur 2 timewindow 40.00 prestim 0 TER 0.05 spmhrf 0 stimulusdelay 0 Condition 1 Condition01 Condition 2 Condition02 Condition 3 Condition03 Condition 4 Condition04 nuisreg mcprextreg 3 Thanks for the help. Scott Burns Kuperberg Lab Martinos Center for Biomedi

Re: [Freesurfer] display multiple functional overlays simultaneously

2, 3), and give them the color you want. > 4. mri_seg2annot --seg binmap12.nii --ctab yourcolortable ... > > doug > > Scott Hayes wrote: >> >> Hi Doug, >> I was trying to load the maps so I could examine each map and the >> overlap, as in the attached example (in thi

[Freesurfer] display multiple functional overlays simultaneously

rom the freeview crash if that helps. Any suggestions/guidance would be appreciated. Thanks, Scott Process: freeview.bin [36175] Path: /Applications/freesurfer/bin/Freeview.app/Contents/MacOS/freeview.bin Identifier: freeview.bin Version: 'latest trunk' ('l

[Freesurfer] Questionable T1 sequence

Hi All, Is the following T1 sequence suitable for surface generation? "T1-weighted 3D SPGR (echo time 5 minimum; repetition time = 24 msec; flip angle = 30; field of view = 24 centimeters; slice thickness = 3 millimeters) collected in the axial plane." It's that 3 mm slice thickness that mos

[Freesurfer] RA position available at VA Boston

information can be obtained via e-mail or by phone at (857) 364-4143, or visit the websites: http://www.bu.edu/traumamemorylab/ http://www.bu.edu/brainlab/ -- Scott M. Hayes, Ph.D. Memory Disorders Research Center Neuroimaging Research Center VA Boston Healthcare System Assistant Professor

Re: [Freesurfer] running in the background?

You can make it work with nohup? In the past I've had trouble and my thinking was that because recon-all starts many child processes, the currently continues after the terminal is closed, but any subsequent process can't start. That's why I've been using screen, but YMMV. S

Re: [Freesurfer] running in the background?

mand prompt to reattach to the screen session you created previously. A new terminal will open and will contain all the output from the recon pipeline. Good luck. Scott Burns Kuperberg Lab Martinos Center, MGH sbu...@nmr.mgh.harvard.edu The information in this e-mail is intended only for the p

[Freesurfer] previous release compatibility and reliability set up

ate directories, or should we reimport the duplicate volumes and start from scratch? Thank you all for your help, -Scott ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

[Freesurfer] problem converting .ima files

h I was not able to find the final solution: http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg00890.html Any guidance would be appreciated. Thanks, Scott -- Scott M. Hayes, Ph.D. Memory Disorders Research Center Neuroimaging Research Center VA Boston Healthcare System Ass

[Freesurfer] Postdoctoral Research Position in Neuroimaging/Neuropsychology at VA Boston

three letters of recommendation sent to: Mieke Verfaellie, Ph.D. Memory Disorders Research Center VA Boston Healthcare System (151A) 150 S Huntington Avenue Boston MA 02130 v...@bu.edu 857-364-4031 The Department of Veterans Affairs is an Equal Opportunity Employer. -- Scott M. Hayes, Ph.D

Re: [Freesurfer] fs-fast smoothing

h, in that case the easiest thing to do is to smooth the raw data on the surface. If you have a development version of freesurfer, you can do this with preproc-sess using the -surf-fwhm option doug Scott Gorlin wrote: Thanks Doug, though I'm still a bit confused: I'd like to see

Re: [Freesurfer] fs-fast smoothing

ignificance map the equivalent of smoothing the data, then recreating the significance in the sphere space? This didn't seem true to me, which is why I tried to recreate the significance maps as below. Thanks, -S Doug Greve wrote: Hi Scott, you should skip steps 2-6 (that is the old st

[Freesurfer] fs-fast smoothing

ce via func2sph. Thanks, Scott ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

[Freesurfer] fsfast file question

n my case, is over 1 gb). I don't see this folder described anywhere in the fsfast documentation. I presume these are the residuals after the glm analysis? Are they necessary for any other fsfast/freesurfer commands, or are they safe to delete if i don't need to examine the residu

Re: [Freesurfer] Black digits and black background

i had the same problem on ubuntu after i upgraded to the latest drivers on my ati video card. i could only get proper white labels by switching to an older driver, which wasn't a good solution for other reasons. i switched to an nvidia card and this resolved the issue. Juergen Haenggi wrote:

[Freesurfer] tksurfer overlay scale bar color

Hi, Is there a way to change the text color of the overlay scale bar labels in tksurfer? I see them as black text on a black background - completely unreadable unless i move the brain under the scale bar. Thanks, Scott ___ Freesurfer mailing list

Re: [Freesurfer] CentOS 5.1 and freesurfer and tksurfer

i just fixed something like this on ubuntu 7.10 with an ati radeon x600.  the latest drivers run on aiglx which conflicts with the previous versions which run on xgl.  this sometimes even caused X to crash when running tksurfer and even glxgears. on my system this was resolved by simply remov

[Freesurfer] mris_thickness_diff ERROR

it is -1. Any help on this issue would be greatly appreciated. Thanks. -Scott Beeman ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

[Freesurfer] tksurfer overlay scale bar label colors

7 2007 17:25:01 CVS: $Id: tksurfer.c,v 1.276.2.5 2007/09/16 23:37:27 greve Exp $ User: scott Machine: Renoir Platform: Linux PlatformVersion: 2.6.22-14-generic CompilerName: GCC CompilerVersion: 30200 tksurfer --all-info on my v.3 returns: ProgramName: tksurfer.bin ProgramArguments:

[Freesurfer] File Conversion Inquiry

r and eccentricity mapping data simulateously or can one display (eg. polar mapping) data separately? Thank you very much for your time and any help Sincerely, Gregory Scott ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu

[Freesurfer] mri_convert problem

02 003 and each contains a 124 slice spgr consecutively numbered starting with I.001 "orig" also contains empty anat1 anat2 anat3 dirs Many thanks, Scott ___ Freesurfer mailing list [EMAIL PROTECTED] https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer