[Freesurfer] Tracula trac-all -prep error

s that had this problem, will attempt to reconstruct them # with a different initial guess. # Default: 0 (do not reinitialize) # set reinit = 0 Jake R. Powell, MS, LAT, ATC Doctoral Student - Human Movement Science Matthew Gfeller Sport-Related Traumatic Brain Injury Research Center 2207 St

Re: [Freesurfer] surface/volume editing

External Email - Use Caution Hi again, Doug, I am just checking to make sure that the thread didn't get lost in the pile of requests, and whether or not you have had a chance to look at the surfaces I sent. Thanks Jake Jensen On Tue, Oct 6, 2020 at 10:08 AM Jake Jensen

Re: [Freesurfer] surface/volume editing

Jensen On Wed, Sep 30, 2020 at 8:37 AM Jake Jensen wrote: > Here are some pictures of the pial (red), wm (yellow), and orig.nofix > (green) surfaces with the brainmask.mgz and wm.mgz volumes > > > > On Wed, Sep 30, 2020 at 8:15 AM Douglas N. Greve > wrote: > >>

Re: [Freesurfer] surface/volume editing

wm.mgz volume > > On 9/23/2020 2:11 PM, Jake Jensen wrote: > > External Email - Use Caution > Hello, > > I am attempting to edit a subject, but upon removing voxels where the WM > and pial surfaces should not be, the WM surface does not receed (pictures > are attached

[Freesurfer] Edits to aparc+aseg

. Best regards, Jake ___ 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 it is addressed. If you believe this e-mail was

Re: [Freesurfer] Unknown regions in cortical parcellation

We are using Freesurfer v6.0 Biomedical Engineer, Brain Rehabilitation Research Center Malcolm Randall VA Medical Center, 1601 SW Archer Road, Gainesville, FL 32608 Phone: 1-352-376-1611 ext. 5249, E-mail: jakeri...@gmail.com On Thu, Sep 7, 2017 at 6:17 PM, Douglas N Greve wrote: > what version

Re: [Freesurfer] Pial surface missing GM

Okay, understood. Thanks again for your help. Best regards, Jake On Fri, Jul 28, 2017 at 11:20 AM, Bruce Fischl wrote: > it depends. In this case you want to erase as it creates an incorrect > connection. In others you want to add if there is an incorrect break > On Fri, 28 Jul 2

Re: [Freesurfer] Pial surface missing GM

m.mgz where the defects are located? In other words, defects can be interpreted as areas of misclassified as WM? In this case, it seems that I need to focus on deleting voxels in the wm.mgz that are incorrectly segmented. Thanks, Jake Biomedical Engineer, Brain Rehabilitation Research Center Malcolm Ran

Re: [Freesurfer] Pial surface missing GM

improve pial surface after initial running with just the T1. Thanks again Jake Biomedical Engineer, Brain Rehabilitation Research Center Malcolm Randall VA Medical Center, 1601 SW Archer Road, Gainesville, FL 32608 Phone: 1-352-376-1611 ext. 5249, E-mail: jakeri...@gmail.com On Wed, Jul 26, 2017 at 8

[Freesurfer] average 4d volume

Hi! I tried to use mri_xvolavg to average a 4d nii volume, but does it need me to list each 3d volume separately? Is there a command that I can use to produce an average of a 4d volume, in one 3d image? Thanks in advance!! Jake ___ Freesurfer

[Freesurfer] is there a command to give resolution information?

rrect area in my text search. Also, what if I wanted to confirm slice thickness? Thanks in advance! Jake ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Re: [Freesurfer] Registration file conversion

or occured while reading file: CTRL01_fslreg.mat I feel like I'm missing something obvious.. thanks Jake > use tkregister2, something like > > tkregister2 --mov mov.nii --targ targ.nii --reg register.dat --fslout > fsl.mat --noedit > > and > > tkregister2 --mov mov

Re: [Freesurfer] tkregister2 error

vard.edu wrote: >> Hello, >> >> I am still getting the same error and can't figure out what mistake I >> may >> be making. Any help would be appreciated, >> >> thanks! >> Jake >> >> >> >> >> >> >>> Hi, I c

Re: [Freesurfer] tkregister2 error

Hello, I am still getting the same error and can't figure out what mistake I may be making. Any help would be appreciated, thanks! Jake > Hi, I can't seem to open a window in tkregister2. Any help would be > appreciated, thanks! > > > [striatum:mri] (nmr-st

[Freesurfer] tkregister2 error

Hi, I can't seem to open a window in tkregister2. Any help would be appreciated, thanks! [striatum:mri] (nmr-std-env) tkregister2 --targ orig.mgz --mov /space/amaebi/35/users/ablood/R01_Botox/CD_R01BTX_ctrl2_sess2/bold/020/fmcsm4.bhdr --reg /space/amaebi/35/users/ablood/R01_Botox/CD_R01BTX_ctrl

Re: [Freesurfer] recon surf folder is missing data

Thank you Bruce and Doug > but remember to delete the IsRunning file > > Bruce Fischl wrote: >> Hi Jake >> >> looks like recon-all stopped in the middle of running. You can see >> this because (1) the recon-all.log file is in the middle of the >> surfac

[Freesurfer] recon surf folder is missing data

/R01BTX_recons/CD_R01BTX_pat2_sess4_recon_missing_surfdata Any help would be greatly appreciated, thanks Jake ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

[Freesurfer] preprocessing error

>>>/autofs/space/amaebi_035/users/ablood/R01_Botox/CD_R01BTX_ctrl1_sess1/bold >>>ipfsl -i 016/fmc5 -o 016/fmcsm5 -pct .1 -fwhm 5 -fmt bhdr >>>-- >>>ERROR: cannot find /usr/pubsw/packages/

[Freesurfer] stable3

as of yet. Thanks, Jake ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

[Freesurfer] diffusion unpacksdcmdir error-wrong run!

following after bugr. Thanks in advance! Jake BUGR: FREESURFER_HOME: /usr/local/freesurfer/stable3 Build stamp: freesurfer-Linux-centos4-stable-v3.0.5-20070717 RedHat release: CentOS release 5 (Final) Kernel info: Linux 2.6.18-8.1.15.el5 i686 NMR Center info (/space/freesurfer exists): machine

[Freesurfer] unpacking from CD backup

Hi, Could someone please explain how to unpack an old session saved on a CD? What command line should be used? thank you in advance, Jake ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo

[Freesurfer] Old scanning sessions, are they gone?

results. Are the data actually there? Thanks in advance for you help, Jake ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

[Freesurfer] tkregister2

shown that the registration (created from autoreg-sess) has warped the functional data. I would like to run tkregister2 without the register.dat file, so I can use the orignal unwarped data. Is there a simple way to do so? Thanks in advance , Jake

[Freesurfer] recon with only 1 mprage?

in advance, Jake ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

[Freesurfer] ipfsl failed

Hello, I received the following error: (csh executable, ran from /autofs/homes/014/jake/AnalysisPrograms/CD_DMRFASL_ctrl2_ContrastAnalysis.csh) /autofs/space/amaebi_035/users/ablood/DMRF_ASL/CD_DMRFASL_ctrl2 Mon May 19 10:16:02 EDT 2008 /autofs/space/amaebi_035/users/ablood/DMRF_ASL

[Freesurfer] unpacksdcmdir issue

ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2008/05/09-14:51:51-GMT BuildTimeStamp: May 8 2008 03:44:12 CVS: $Id: mri_convert.c,v 1.146.2.2 2008/03/02 02:53:20 nicks Exp $ User: jake Machine: striatum Platform: Linux PlatformVersion: 2.6.18-8.1.15.el5 CompilerName: GCC

Re: [Fwd: Re: [Freesurfer] Error]

I apologize, the csh file is located in the home directory, /homes/14/jake/AnalysisPrograms Thanks > Hi, > > Thanks for the bugr command. Here is my information, Thank you! > > > Please include the following additional information in your report: > > 1) subject nam

[Fwd: Re: [Freesurfer] Error]

rfer exists): machine: striatum SUBJECTS_DIR: /space/sake/3/users/inverse/subjects ***(this is set to be /space/meso/18/users/ablood/cerv by the .csh script) PWD: /homes/14/jake/Analy

[Freesurfer] Error

Hi, We are getting an error where our preprocessing step seems to be failing, any help would be greatly appreciated, thank you! *running from the following directory /autofs/homes/014/jake/AnalysisPrograms *using the following command (which sources /usr/local/freesurfer/nmr-stable3-env

[Freesurfer] Copying control points file?

If I have the same subject on 2 different computers, but I edited the control points on one, can I just copy the tmp/control.dat file over to the other computer and rerun autorecon2-cp, or are there other files it refrences? Thanks-- -Jake ___ Freesurfer

[Freesurfer] Bad File Descriptor?

; root:xnu-792.6.76.obj~1/RELEASE_PPC Power Macintosh powerpc recon-all exited with ERRORS at Tue Aug 8 07:03:55 PDT 2006 Thanks -Jake ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

[Freesurfer] Recon all finished with errors, How do I see what errors?

53 PDT 2006; root:xnu-792.6.76.obj~1/RELEASE_PPC Power Macintosh powerpc recon-all exited with ERRORS at Mon Aug 7 11:12:31 PDT 2006 Thanks -Jake ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

[Freesurfer] Would adjusting watershed parameters change pial surface?

I was wondering if setting the watershed parameters higher and rerunning autorecon2 would expand the pial surface line if the outer rim of the brain is being left out? Or would this not fix the problem? Thanks -- -Jake ___ Freesurfer mailing list

[Freesurfer] Queue tasks?

use to do this kind of thing? Thanks -- -Jake ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

[Freesurfer] Expanding pial outline

line or what is the best way to edit the files so more brain is included. I was looking at the threshold tools and couldn't see a way to convert say anything with a value of 30-40 to 60, so I was wondering if that was also possible. Thanks --

[Freesurfer] Question concerning orientation

it to get it to work. Thanks Jake ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer