Can you send the terminal output and/or the log file?
On 08/22/2018 09:49 AM, Nada Naguib wrote:
>
> External Email - Use Caution
>
> Hello, thank you for your response, yes My terminal is in the tcsh
> shell so I’m not sure why it’s not working
>
> Nada
>
>
> On Aug 22, 2018, at 3:22
External Email - Use Caution
Hello, thank you for your response, yes My terminal is in the tcsh shell so I’m
not sure why it’s not working
Nada
> On Aug 22, 2018, at 3:22 PM, Adam Martersteck wrote:
>
> External Email - Use Caution
>
> Are you sure you're
External Email - Use Caution
Are you sure you're terminal is setup in tcsh or csh? If you're using bash
instead, you want "export SUBJECTS_DIR=/project/bil/Nada"
Take a look at:
https://surfer.nmr.mgh.harvard.edu/fswiki/SetupConfiguration_Mac or
External Email - Use Caution
Hello,
I have been using bbregister in this format
bbregister —mov dkti4d.nii —s NewT2out —init-fsl —bold —lea register.lta
NewT2out is the output of the free surfer processing on the T1 image and
dkti4d.nii is the template file I want to use for
, 2017 at 12:56 PM
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] bbregister error -- Human Connectome Project Data
Okay so if I am going to try and run this option, recon-all must also be
done on the structural scans. I have the pre-processed structural
Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
> Date: Wednesday, December 27, 2017 at 5:55 PM
> To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
>
> Subject: Re: [Freesurfer] bbregister error -- Human Connectome Project
> Data
>
> Matt,
>
r@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] bbregister error -- Human Connectome Project Data
Matt,
Thanks for the quick reply! I'll check out that Wiki document and the 2016
Nature paper first.
The reason I have the pre-processed (but not ICA-FIX'ed) rfMRI data is
because I would like to use th
surfer@nmr.mgh.harvard.edu>
> Date: Wednesday, December 27, 2017 at 4:41 PM
> To: <freesurfer@nmr.mgh.harvard.edu>
> Subject: Re: [Freesurfer] bbregister error -- Human Connectome Project
> Data
>
> As a work-around to the above issue, I did the registrations directly in
> FSL using F
oun...@nmr.mgh.harvard.edu> on behalf of Lana Ruck
<lr...@umail.iu.edu>
Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Date: Wednesday, December 27, 2017 at 4:41 PM
To: <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] bbregister error -- Human Connectome Projec
As a work-around to the above issue, I did the registrations directly in
FSL using FLIRT, and then converted the resultant fsl reg.mat files to
freesurfer reg.dat files (using tkregister2; they all look fine). Now, all
I need is to project these rfMRI data to fsaverage4, and I thought
mri_vol2surf
Hello,
I am currently starting a project with the minimally pre-processed rfMRI
from the Human Connectome Project, but I need to do some additional
processing first. This includes smoothing at 6mm FWHM and projection onto
the fsaverage4 surface. I have smoothed the pre-processed rfMRI data using
mailto:zkauf...@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] bbregister error
To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu
mailto:freesurfer@nmr.mgh.harvard.edu
Message-ID: 555b5e20.6000...@nmr.mgh.harvard.edu
mailto:555b5e20.6000...@nmr.mgh.harvard.edu
Content-Type
Hi Freesurfer users,
I'm trying to run the bbregister command on the brain.mgz file.
Here is the command line and resulting error:
[12239012@psych2 ~/001ER]$ bbregister --s 001ER --mov mri/brain.mgz --reg
register.dat
ERROR: cannot find 001ER in /usr/local/apps/freesurfer/5.1.0/subjects
I need
It looks like the SUBJECTS_DIR environment variable is probably set
incorrectly.
Does /usr/local/apps/freesurfer/5.1.0/subject/001ER exist? What is
SUBJECTS_DIR set to?
SUBJECTS_DIR should be set to the directory containing 001ER.
-Zeke
On 05/19/2015 11:48 AM, Stefani O'Donoghue wrote:
Hi
February 2015 20:02
To: Freesurfer support list
Subject: Re: [Freesurfer] bbregister error [Was: TRACULA mask error]
Hi Amanda - Glad to hear the registration issue got fixed!
If the tract looks like a single line in the volume (in which case you
wouldn't be able to see it 3D in view), it's probably
-boun...@nmr.mgh.harvard.edu
freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Anastasia Yendiki
ayend...@nmr.mgh.harvard.edu
Sent: 11 February 2015 16:21
To: Freesurfer support list
Subject: Re: [Freesurfer] bbregister error [Was: TRACULA mask error]
Hi Amanda - It doesn't look like the new
Yendiki
ayend...@nmr.mgh.harvard.edu
Sent: 11 February 2015 16:21
To: Freesurfer support list
Subject: Re: [Freesurfer] bbregister error [Was: TRACULA mask error]
Hi Amanda - It doesn't look like the new registration was applied to the
aparc+aseg. Can you tell us the exact sequence of steps
From: freesurfer-boun...@nmr.mgh.harvard.edu
freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Douglas N Greve
gr...@nmr.mgh.harvard.edu
Sent: 06 February 2015 19:15
To: Bruce Fischl; Freesurfer support list
Subject: Re: [Freesurfer] bbregister
try --init-spm
On Fri, 6 Feb 2015, Anastasia Yendiki wrote:
Hi Amanda - So it looks like --init-header didn't work, and neither does
--init-fsl. I'll defer to the father of bbregister, Doug, for clues about
how to proceed.
a.y
On Wed, 21 Jan 2015, Worker, Amanda wrote:
Hi Anastasia,
Hi Amanda - So it looks like --init-header didn't work, and neither does
--init-fsl. I'll defer to the father of bbregister, Doug, for clues about
how to proceed.
a.y
On Wed, 21 Jan 2015, Worker, Amanda wrote:
Hi Anastasia,
Yes I have done that. My command line was... bbregister --s
or --init-rr if you don't have matlab/spm
On 02/06/2015 01:49 PM, Bruce Fischl wrote:
try --init-spm
On Fri, 6 Feb 2015, Anastasia Yendiki wrote:
Hi Amanda - So it looks like --init-header didn't work, and neither does
--init-fsl. I'll defer to the father of bbregister, Doug, for clues
Hi Corinna, are you sure that the mri-in-hardi.nii.reg registration is
accurate? the following should look in register:
tkregister2 --reg mri-in-hardi.nii.reg --mov mri-in-hardi.nii --surfs
doug
On 03/25/2013 06:09 PM, Corinna Bauer wrote:
I am trying to get the V1 label to map onto my HARDI
Hello all,
I am attempting to run bbregister on 4D HARDI data that has already been
motion, eddy, and epi-distortion corrected in fsl. I run the command:
bbregister --s lindsay --mov hardi/ffiltered_func_data_01.nii.gz --dti
--init-fsl --reg register.dat and get a number of errors that seem to
Hi Corinna, can you run
fslregister --debug --s lindsay --mov
hardi/ffiltered_func_data_01.nii.gz --reg fsl.reg.dat --niters 1
--maxangle 90 --nobetmov --tmp ./tmp.fslregister --dof 6 --fsvol
brainmask | tee dng.log
and send me the dng.log?
doug
On 03/25/2013 12:39 PM, Corinna Bauer
Can you verify that
/usr/local/freesurfer/subjects/symmetry/lindsay/mri/brainmask.mgz
exists?
doug
On 03/25/2013 12:55 PM, Corinna Bauer wrote:
sure. Here is the dng.log.
Corinna
On Mon, Mar 25, 2013 at 12:45 PM, Douglas N Greve
gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu
yes, this file exists.
On Mon, Mar 25, 2013 at 1:10 PM, Douglas N Greve
gr...@nmr.mgh.harvard.eduwrote:
Can you verify that
/usr/local/freesurfer/**subjects/symmetry/lindsay/mri/**brainmask.mgz
exists?
doug
On 03/25/2013 12:55 PM, Corinna Bauer wrote:
sure. Here is the dng.log.
Corinna, can you edit $FREESURFER_HOME/bin/bbregister? If so, change the
following line
From
set cmd = (fslregister --s $subject --mov $regvol --reg $InitReg \
--niters 1 --maxangle 90 --tmp $tmpdir/fslregister \
--dof $FSLDOF --fsvol $fsvol)
To
set cmd = (fslregister --s
Ok I adjusted the bbregister file to say fsvol.mgz in the location you
specified and got this error a bit later on in the bbregister output:
setenv SUBJECTS_DIR /usr/local/freesurfer/subjects/symmetry
cd /usr/local/freesurfer/subjects/symmetry/lindsay
/usr/local/freesurfer/bin/bbregister --s
Are you sure you made the right edit? It should be --fsvol $fsvol.mgz
It looks like you might have changed it to --fsvol.mgz $fsvol
On 03/25/2013 01:30 PM, Corinna Bauer wrote:
Ok I adjusted the bbregister file to say fsvol.mgz in the location you
specified and got this error a bit later on
yep, looks right
On 03/25/2013 03:12 PM, Corinna Bauer wrote:
Also, I now want to apply the inverse transform to move the T1 into
the HARDI space. Did I do this correctly? It looks good in tkregister.
mri_vol2vol --mov hardi/ffiltered_func_data_01.nii.gz --targ
mri/orig.mgz --reg
Hi Doug,
The brainmask.mgz does exists, and the full recon-all runs normally. The
problem seems to be in the -FLAIRpial sequence only for me. The
registration runs, but doesn't produce mri/FLAIR.mgz.
I have attached the FLAIRraw.dat.log file. Please let me know if you would
like me to upload the
Hi Charles, can you verify that brainmask.mgz exists for that subject?
What do you get if you run
stem2fname $SUBJECTS_DIR/$subject/mri/brainmask
doug
On 3/11/13 4:07 AM, Charles Malpas wrote:
Hi Doug,
I think I am having the same problem, but only when running on our Red
Hut cluster
Hi Doug,
I think I am having the same problem, but only when running on our Red Hut
cluster (CentOS 6 was fine). I have attached the terminal output with
--debug
Many thanks,
- Charles
On 9 March 2013 03:47, Douglas N Greve gr...@nmr.mgh.harvard.edu wrote:
Salil, can you run fslregister
Salil, can you run fslregister with --debug as the first option, capture
the terminal output, and send it to me?
thanks
doug
On 03/07/2013 09:02 PM, Anastasia Yendiki wrote:
Hi Salil - I'm cc-ing Doug who may be able to help. The error happens
when bbregister invokes fslregister, in this
Hi Salil - I'm cc-ing Doug who may be able to help. The error happens when
bbregister invokes fslregister, in this particular line of fslregister:
set refvol = `stem2fname $SUBJECTS_DIR/$subjid/mri/$fsvol`
When run on brainmask.mgz, it returns ERROR: could not determine file.
a.y
On Wed, 6
Hi Priyank, can you send the full terminal output and/or the log file
created?
thanks
doug
On 01/03/2013 03:11 PM, Shukla,Priyank wrote:
Hi,
My bbregistration finished with the warnning
-
Hi,
My bbregistration finished with the warnning
-
WARNING: initial G-W contrast was negative, but expected positive.
If the mov data has a T1 contrast, re-run with --T1
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