You pretty much have to run it through to the end. You can try using
mri_coreg (this is the first step of bbregister). It does not need
anything but two images and will run in a few min.
On 3/3/2022 5:24 AM, Guillem París wrote:
> External Email - Use Caution
>
> Hello,
>
> I'm trying
External Email - Use Caution
Hello,
I'm trying to run a Boundary-based registration by using bbregister. In
the documentation, it is specified that the anatomical image has to be
previously analysed in FreeSurfer. I assume that means to run the
"recon-all" pipeline.
Now, are a
Yea, I've tried that before. It does not work very well. You can
proceed, but it will not be providing you with a very good correction.
On 8/9/2021 9:30 AM, Shane Schofield wrote:
External Email - Use Caution
Hi Freesurfer Experts,
I am trying to obtain coregister diffusion data b0 w
External Email - Use Caution
Hi Freesurfer Experts,
I am trying to obtain coregister diffusion data b0 with T1.
One problem is that I do not have any means to correct for EPI distortions.
Because of this, I am experimenting with DOF = 9 and DOF = 12. The mincost for
12 was consi
On 7/7/2020 3:14 AM, Ellen Ji wrote:
External Email - Use Caution
Dear experts,
I am running bbregister and have a couple questions:
1) I am using freesurfer version 7. My understanding is that I do not
need any --init argument anymore, and without it, by default it uses
init-core
External Email - Use Caution
Dear experts,
I am running bbregister and have a couple questions:
1) I am using freesurfer version 7. My understanding is that I do not
need any --init argument anymore, and without it, by default it uses
init-coreg. Could you confirm this? (I test
to: *Freesurfer support list
*Date: *Wednesday, 3 June 2020 at 17:14
*To: *"freesurfer@nmr.mgh.harvard.edu"
*Subject: *Re: [Freesurfer] Bbregister misalignment {Disarmed}
A couple of things to try:
First, make sure that the whole head and the partial FoV EPIs are in
register wit
rfer support list
*Date: *Wednesday, 3 June 2020 at 14:05
*To: *Freesurfer support list
*Subject: *Re: [Freesurfer] Bbregister misalignment {Disarmed}
*External Email - Use Caution *
Hi Doug,
Thanks for this. However, I can’t seem to access the ftp:
c1749990@l017:~/data/freesurfer/subj
d.ac.uk<mailto:wells...@caerdydd.ac.uk>
Ffôn: 02920 879628
From: on behalf of "Douglas N. Greve"
Reply to: Freesurfer support list
Date: Tuesday, 2 June 2020 at 18:39
To: "freesurfer@nmr.mgh.harvard.edu"
Subject: Re: [Freesurfer] Bbregister misalignment {Disarmed}
If
bost/*: wells...@caerdydd.ac.uk <mailto:wells...@caerdydd.ac.uk>
*/Ffôn/*: 02920 879628
*From: * on behalf of Mason
Wells
*Reply to: *Freesurfer support list
*Date: *Tuesday, 2 June 2020 at 14:06
*To: *Freesurfer support list
*Subject: *Re: [Freesurfer] Bbregister misalignment {Disarmed}
*
.uk>
Ffôn: 02920 879628
From: on behalf of Mason Wells
Reply to: Freesurfer support list
Date: Tuesday, 2 June 2020 at 14:06
To: Freesurfer support list
Subject: Re: [Freesurfer] Bbregister misalignment {Disarmed}
External Email - Use Caution
Hi Doug,
I have FS v6.0 and t
Date: Tuesday, 2 June 2020 at 13:48
To: "freesurfer@nmr.mgh.harvard.edu"
Subject: Re: [Freesurfer] Bbregister misalignment {Disarmed}
Right now, I'm just guessing what the problem is (I'm speculating that it is
FSL FLIRT). You could download just the new bbregister and mri_core
02920 879628
*From: * on behalf of "Douglas
N. Greve"
*Reply to: *Freesurfer support list
*Date: *Monday, 1 June 2020 at 18:02
*To: *"freesurfer@nmr.mgh.harvard.edu"
*Subject: *Re: [Freesurfer] Bbregister misalignment {Disarmed}
What version of FS are you running? That
Ffôn: 02920 879628
From: on behalf of "Douglas N. Greve"
Reply to: Freesurfer support list
Date: Monday, 1 June 2020 at 18:02
To: "freesurfer@nmr.mgh.harvard.edu"
Subject: Re: [Freesurfer] Bbregister misalignment {Disarmed}
What version of FS are you running? That fl
to: *Freesurfer support list
*Date: *Monday, 1 June 2020 at 17:38
*To: *"freesurfer@nmr.mgh.harvard.edu"
*Subject: *Re: [Freesurfer] Bbregister misalignment
Sorry for missing your first email. Can you try adding --init-coreg to
your first bbregister command? Make sure to add it AF
d.ac.uk<mailto:wells...@caerdydd.ac.uk>
Ffôn: 02920 879628
From: on behalf of "Douglas N. Greve"
Reply to: Freesurfer support list
Date: Monday, 1 June 2020 at 17:38
To: "freesurfer@nmr.mgh.harvard.edu"
Subject: Re: [Freesurfer] Bbregister misalignment
Sorry fo
Sorry for missing your first email. Can you try adding --init-coreg to
your first bbregister command? Make sure to add it AFTER --feat
On 6/1/2020 12:06 PM, Mason Wells wrote:
External Email - Use Caution
Hi Experts,
I posted earlier, but I believe my message has not been posted due
External Email - Use Caution
Thank you. Can you please clarify, documentation for mri_convert states
default for resampling is -interpolate, does this mean trilinear? Also,
which method is preferable for bbregister (I am applying it for
intrasubject uni and multimodal registration
It will but, it will always be resampled with trilinear interpolation.
On 4/30/2020 12:55 PM, Octavian Lie wrote:
External Email - Use Caution
Dear All,
I have seen bbregister command lines using --o option to get the final
output (say a .nii vol), and others where bbregister is use
External Email - Use Caution
Dear All,
I have seen bbregister command lines using --o option to get the final
output (say a .nii vol), and others where bbregister is used to get an lta
transform, which is used in a follow-up step (mri_convert with -ns 1 (no
scale), and -rl orig.mg
What version of FS are you using? If before 6.0 (eg, 5,3), then it may
be an error with the initialization. This is much improved in version 6.
On 6/18/2019 5:38 PM, Wenzhen Zhao wrote:
> External Email - Use Caution
>
> Dear list,
>
> After running preproc-sess on fmri data, bbr-sum was
External Email - Use Caution
Dear list,
After running preproc-sess on fmri data, bbr-sum was 0.94. After looking
through images of template.nii.gz with register.dof6.lta file, I found that
coronal and axial views of template(w/ registration applied) are switched.
$preproc-sess
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 PM,
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 t
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
https://surfer.nmr.mgh.harvard.edu/f
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 t
reesurfer support list
mailto:freesurfer@nmr.mgh.harvard.edu>>
Date: Friday, February 16, 2018 at 4:17 PM
To: Freesurfer support list
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] bbregister aparc+aseg to diffusion space
Hi Anastasia,
Thank you for the quick response. I did not
ehalf of "Michiko H." <
> michiko...@gmail.com>
> Reply-To: Freesurfer support list
> Date: Friday, February 16, 2018 at 3:57 PM
> To: Freesurfer support list
> Subject: [Freesurfer] bbregister aparc+aseg to diffusion space
>
> Hi,
>
> I understand that b
mr.mgh.harvard.edu>>
Subject: [Freesurfer] bbregister aparc+aseg to diffusion space
Hi,
I understand that bbregister can be used to register diffusion to T1 space but
I'm a lot less certain how this can be done in the reverse way, i.e.
registering the entire aparc+aseg file to diff
Hi,
I understand that bbregister can be used to register diffusion to T1 space
but I'm a lot less certain how this can be done in the reverse way, i.e.
registering the entire aparc+aseg file to diffusion B0? Do I also do:
bbregister
--s $subject --mov bo_brain.nii.gz --reg registration2b0.dat --dt
There is a structural extended package that has the FreeSurfer folders.
Peace,
Matt.
From: on behalf of Lana Ruck
Reply-To: Freesurfer support list
Date: Thursday, December 28, 2017 at 12:56 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] bbregister error -- Human Connectome
er 27, 2017 at 5:55 PM
> To: Freesurfer support list
>
> 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 rea
this.
Peace,
Matt.
From: on behalf of Lana Ruck
Reply-To: Freesurfer support list
Date: Wednesday, December 27, 2017 at 5:55 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] bbregister error -- Human Connectome Project Data
Matt,
Thanks for the quick reply! I'll chec
data, you can do that
> with wb_command -cifti-smoothing before following the above steps.
>
> Peace,
>
> Matt.
>
> From: on behalf of Lana Ruck <
> lr...@umail.iu.edu>
> Reply-To: Freesurfer support list
> Date: Wednesday, December 27, 2017 at 4:41 PM
> To
: Freesurfer support list
Date: Wednesday, December 27, 2017 at 4:41 PM
To:
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 FLIRT, and then converted the resultant fsl reg.mat files
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
m
Hi Dorit, I'm suspecting that the initial registration is off. Can you
upload the data to somewhere I can get at it?
doug
On 12/18/2017 03:08 PM, Dorit Kliemann wrote:
> Hi,
>
> I’m having some troubles with using bbregister on hemispherectomy
> brains (i.e only one hemisphere; data is success
Hi,
I’m having some troubles with using bbregister on hemispherectomy brains (i.e
only one hemisphere; data is successfully processed with recon-all dev version
- thanks to Bruce).
I use bbregister to create a register.dat for the functional (preprocessed with
fmriprep and registered -but not
Have you tried passing the fs registration matrix to mri_vol2vol instead
of the fsl matrix?
On 07/13/2017 05:02 PM, Paul Glad Mihai wrote:
> Hello,
>
> I'm getting two different results from the coregistration step. When I run
> bbregister on the mean epi it coregisters properly and writes out
glad it worked out
Bruce
On Mon, 17 Jul 2017, Paul Glad Mihai wrote:
> Hello again,
>
> I've found my mistake! Instead of using the brainmask from reconall for
> the target, I used the brain from the fsl ouput of BET. This is a
> mistake, since the two brains aren't aligned. I've corrected the mis
Hello again,
I've found my mistake! Instead of using the brainmask from reconall for
the target, I used the brain from the fsl ouput of BET. This is a
mistake, since the two brains aren't aligned. I've corrected the mistake
and now it works.
Regards,
Glad
On 07/13/2017 11:02 PM, Paul Glad Mihai
Hello Experts,
Just to follow up on my previous posting, here is the information from
the headrs of the different nifti files after the steps performed.
* First, the header of the mean original nifti after realignment:
qto_xyz:1 -1.099422 0.024665 0.025745 65.286888
qto_xyz:2 -0.02
So far it isn't anymore. It's more of a problem with ANTs now.
BBRegister works with --init-header for partial FoV T1 and mean EPI are
more or less in alignment. But if they wouldn't be then one would have a
problem with registration.
On 07/13/2017 12:35 AM, Douglas N Greve wrote:
> Is this still
Is this still a problem?
On 07/11/2017 09:51 AM, Paul Glad Mihai wrote:
> Hi Bruce,
>
> Thanks for the quick reply. I've just finished rerunning it with spm,
> fsl and header init and the latter seemed to work if I write out a
> _bbreg.nii file. The former two failed, however. Apparently using the
sure. I'll leave the rest to Doug except to say that a full head EPI is a
pretty cheap and useful thing to get, and that it is not surprising the
using the header (assuming they are same session) works better than
anything else
cheers
Bruce
On Tue, 11 Jul 2017, Paul Glad Mihai wrote:
> Hi Bru
Hi Glad
can you send us the full command line you are using and screen output?
thanks
Bruce
On
Tue, 11 Jul 2017, Paul Glad Mihai wrote:
> Dear List,
>
> I've been quite frustrated with the BBRegister results when trying to
> register a partial field of view EPI mean functional image to a T1 sc
Dear List,
I've been quite frustrated with the BBRegister results when trying to
register a partial field of view EPI mean functional image to a T1 scan.
I've tried different init arguments (fsl, spm, header) and none really
work. I've found that the initial registration is causing the problem,
si
there is not an mri_spmregister (there is spmregister). If you have an
FA map, then I would use bbregister
On 2/25/17 8:03 PM, John Anderson wrote:
Hi Doug, thank you for the detailed response. Highly appreciated!
Kindly. I want to register FA map to structural T1 image using the
command mri_
In those cases the cost of coreg is quite close to the optimal, for
example, 0.366088 vs 0.366089. I guess the final results won't differ much
if I used --init-coreg instead of --init-best.
Best,
Feilong
On Fri, Mar 17, 2017 at 10:04 PM, Douglas Greve
wrote:
> what happened in the ones that co
what happened in the ones that coreg was not the best? what is the
nature of the data?
On 3/17/17 6:39 PM, Feilong Ma wrote:
Thanks, Doug! I've run bbregister with --init-best on my data
comparing coreg, fsl, rr, and header; most of the times the choice is
coreg as you said (59 out of 88 tot
Thanks, Doug! I've run bbregister with --init-best on my data comparing
coreg, fsl, rr, and header; most of the times the choice is coreg as you
said (59 out of 88 total runs).
Best,
Feilong
On Fri, Mar 17, 2017 at 4:11 PM, Douglas N Greve
wrote:
> Hi Feilong, you do not need to use --init-bes
Hi Feilong, you do not need to use --init-best with bbregister anymore.
It automatically uses --init-coreg (a remake of the spm coreg) which is
the best as far a I can tell
On 03/17/2017 02:47 PM, Feilong Ma wrote:
> Hi FreeSurfer Developers,
>
> I'm having trouble using bbregister with the `--
Awesome! Thanks for your help!
Best,
Feilong
On Fri, Mar 17, 2017 at 2:57 PM, Z K wrote:
> It seems that a freesurfer user just submitted a pull request yesterday
> that fixes this bug:
>
> https://github.com/freesurfer/freesurfer/pull/24
>
> Feel free to download the fixed version:
>
> ht
It seems that a freesurfer user just submitted a pull request yesterday
that fixes this bug:
https://github.com/freesurfer/freesurfer/pull/24
Feel free to download the fixed version:
https://github.com/freesurfer/freesurfer/blob/dev/scripts/bbregister
On 03/17/2017 02:47 PM, Feilong Ma
Hi FreeSurfer Developers,
I'm having trouble using bbregister with the `--init-best` flag, a minimal
example and error message is like this:
$> bbregister --s ag00 --mov data/ag00/align/raiders/run00_ref.nii.gz
--init-best --bold --lta data/ag00/align/raiders/run00_ref_to_anat.lta
ERROR: cannot sp
Hi Antonin,
mni152reg was just meant to replicate the affine registration used by
other software and to provide users with a fast-and-easy way to do
volume-based (subcortical) analysis in FS. I would prefer to use CVS for
everything, but, as you mention, it does have a huge computational
footp
Dear Doug,
thank you for the feedback. In this context I would like to ask you to share
your opinion on the mri_cvs_register. This tool should be far the most accurate
for the registration to MNI, than any of affine-based registration tools,
shouldn't be? Are there any pitfalls/disadvantages (a
You can do the masking with mri_mask
On 2/26/17 7:04 AM, Shane Schofield wrote:
Dear Doug,
If I want to create a new volume that is registered to the MNIspace
(using mni1525reg), can I mask out other voxels that are not part of
the mni template brain? It is a PET volume (already in individua
I have not actually tested it on the mni152 reg. It might (probably
does) work fine.
On 2/25/17 5:33 PM, Antonin Skoch wrote:
Dear Doug,
I was wondering, why do you prefer mni152reg to mri_coreg for
gregistration to MNI? According to help, mri_coreg is also able to do
12 DOF registration.
Dear Doug,
If I want to create a new volume that is registered to the MNIspace (using
mni1525reg), can I mask out other voxels that are not part of the mni template
brain? It is a PET volume (already in individual space using bbregister) that
has noisy signals in non-brain regions.
Thank you.
Hi Doug, thank you for the detailed response. Highly appreciated!
Kindly. I want to register FA map to structural T1 image using the command
mri_spmregister as follow:
mri_spmregister move FA.nii --s subj1 --reg reg dat --o FA_2_T1.nii.gz
Is this correct?
Original Message ---
Dear Doug,
I was wondering, why do you prefer mni152reg to mri_coreg for gregistration to
MNI? According to help, mri_coreg is also able to do 12 DOF registration.
Antonin
mri_coreg is the FS implementation of spm_coreg (spmregister) both of which
use normalized mutual info. bbregister uses
mri_coreg is the FS implementation of spm_coreg (spmregister) both of
which use normalized mutual info. bbregister uses the BBR cost function
and is preferred for all MRI. For registration to MNI space, we usually
use mni152reg (a wrapper around fsl's flirt)
On 2/25/17 8:49 AM, John Anderson
Dear Freesurfer experts,
I see that the tool "mri_coreg" has been implemented recently in Free Surfer 6
and I really wanted to know what are the differences between the registration
tools "bbregister", " spmregister" and "mri_coreg"! Kindly:
1. Are these tools similar? if not what are the differe
"
To: "Freesurfer support list"
Subject: Re: [Freesurfer] bbregister
Hi John
one of the many nice things about bbregister is that it is quite
resistant to non-brain tissue, since it's just trying to place the
gray/white (and optionally the pial surface) at a reasonable spot in the
For version 6, it should not matter.
On 2/10/17 3:59 PM, John Anderson wrote:
Hi FS experts,
I want to register T1 image to its freesurfer space (i.e. wmparc.mgz)
using the command
bbregister --t1 --mov T1.nii --init-fsl --reg t1.reg.dat --s subj
do I need to apply brain extraction tools bef
Hi John
one of the many nice things about bbregister is that it is quite
resistant to non-brain tissue, since it's just trying to place the
gray/white (and optionally the pial surface) at a reasonable spot in the
volume. I guess it might make the initialization less robust, not sure, but
I ex
Hi FS experts,
I want to register T1 image to its freesurfer space (i.e. wmparc.mgz) using the command
bbregister --t1 --mov T1.nii --init-fsl --reg t1.reg.dat --s subj
do I need to apply brain extraction tools before this step or bb register can accept non-brain extracted images?
Best,
the pial surface is not currently used. It is possible in the current
version to use pial surface if you want to
On 01/12/2017 04:35 PM, Christopher Markiewicz wrote:
> Hi all,
>
> According to
> https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg25476.html,
> bbregister uses the w
Hi all,
According to
https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg25476.html,
bbregister uses the white matter surface and cortical thickness measures to
perform its registrations, though there was some possibility of using the
pial surface in further releases. I just want to ver
Dear Doug,
yes, the point is, that my_initial_lta.lta does not have subject name in it.
Your suggestion to rearrange parameters in bbregister indeed helped to get
further, however, later ended with error in bbregister execution in call of
mri_segreg, which does not pass the subject parameter a
does my_initial_lta.lta have the subject name in it? If not, then put
that argument before the --s
On 12/05/2016 10:34 AM, Antonin Skoch wrote:
> Dear experts,
>
> I am having trouble using --init-reg option in bbregister (FreeSurfer
> v6 beta version). It exits with error: must supply subject
Dear experts,
I am having trouble using --init-reg option in bbregister (FreeSurfer v6 beta
version). It exits with error: must supply subject id.
My command line is:
bbregister --mov my_moveable.nii.gz --s my_subject_id --lta my_lta_out.lta
--dti --init-reg my_initial_lta.lta
I traced the p
I have no idea. You can try copying the 5.3 version of mri_segreg to 5.1
On 07/28/2016 04:10 AM, Fred Sampedro wrote:
> Hi Douglas,
>
>
> Thanks a lot for your help, I understand. I tried replacing the
> mri_convert in 5.1 from the 5.3 and the bbregister command went a
> little bit further. Unfo
Hi Douglas,
Thanks a lot for your help, I understand. I tried replacing the mri_convert
in 5.1 from the 5.3 and the bbregister command went a little bit further.
Unfortunately, it segfaulted again when computing the relative costs.
I'm attaching the output of the same command in 5.3 and in 5.1.
Sorry, I have no idea and I'm not going to try to dig in to 5.1 to see.
You can just copy mri_convert from 5.3 into 5.1 (make a backup first)
On 7/25/16 12:31 PM, Fred Sampedro wrote:
Hi Douglas,
Thank you very much for answering. Unfortunately, I can read all the
files without any problem i
Hi Douglas,
Thank you very much for answering. Unfortunately, I can read all the files
without any problem in FSL/SPM, and I still have more than 40GB of free
space. In fact, running the exact same instruction in freesurfer 5.3 works
fine.
:(
On Mon, Jul 25, 2016 at 5:21 PM, Douglas Greve
wro
It looks like one of two things:
1. The files SUBJ_ID.nii.gz is corrupted. See if another tool (FSL, SPM,
AFNI) can read the file
2. You have run out of disk space
On 7/24/16 10:52 AM, Fred Sampedro wrote:
Dear FS experts,
I've installed freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0 an
Dear FS experts,
I've installed freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0 and I'm
trying to run bbregister to register a AV45-PET image to its corresponding
FS processed T1 image. For that, I'm trying to run:
bbregister --s SUBJ_ID --mov SUBJ_PET --reg register.dat --init-fsl --t1
And I
Thanks for the follow up about the new tool you developed! I look forward
to using it and I will remove the --init-spm option.
Just as a follow up I did add the pathway for freesurfer/matlab and it ran
properly for hippocampal subfields, so I do not think that is the issue.
Thanks,
Ajay
On We
--epi-mask is a simple flag without any options. It tells bbregsiter
to exclude certain regions from the surface-based parcellation
(?h.aparc.annot). The regions can be gleened from the code below
B0Annots[0] = CTABentryNameToAnnotation("middletemporal",lhwm->ct);
B0Annots[1] = CTA
Is $FREESURFER_HOME/matlab in your matlab path? Also, I wrote a new
program called mri_coreg that replicates the functionality of
spmregister. This is now the default (no need to spec an init method),
and I encourage you to use it.
On 4/6/16 12:03 AM, Ajay Kurani wrote:
Hi Freesurfer Experts,
Hello Freesurfer Experts,
As a follow up question for bbregister, I used the --tmp and --epi-mask
options, but I did not see a mask in the directory. I wanted to see if
there is any way to output the B0/edge excluded epi-mask used in bbregister?
Thanks,
Ajay
On Tue, Apr 5, 2016 at 11:03 PM,
Hi Freesurfer Experts,
I was running bbregister and came across an issue. I have used previous
versions of bbregister (FS 5.3.0 with spm8) with the --init-spm at it
worked perfectly for a specific subject.
I recently installed FS dev 6.0 with SPM12b and ran bbregister --init-spm
option with th
Thanks Martin and Doug,
I'll give both robust_register with robent and mri_coreg a try.
RE: Doug
The PET tracer is Avid's amyloid compound -- F18-florbetapir (aka amyvid,
aka AV45).
The asymmetric signal is a result of the population -- individuals with a
non-amnestic language dementia with under
btw, what tracer is this? And the asymmetry you are talking about is
between the hemispheres? Is that typical for this tracer or is this a
phenomena with this subject (or population)?
On 03/30/2016 03:41 PM, Adam Martersteck wrote:
> Hi Freesurfer team,
>
> I’m encountering a problem using bbreg
Try using mri_coreg
ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_coreg
On 03/30/2016 04:20 PM, Martin Reuter wrote:
> Hi Adam,
>
> not sure robust_register robent will work on this type of stuff (never
> tested it). I would recommend to keep the radius small (2,or 3), but
>
Hi Adam,
not sure robust_register robent will work on this type of stuff (never
tested it). I would recommend to keep the radius small (2,or 3), but
switch on --entcorrection.
You can also try robust_register with normalized mutual information
(NMI) or simple MI to see how that works.
You
Hi Freesurfer team,
I’m encountering a problem using bbregister on PET data:
-- When I attempt to register a PET volume to T1-space the asymmetric
tracer uptake of the PET throws off proper registration. (Treating the PET
as a T1 because of the non-specific white matter uptake > grey matter
sign
Thank you Douglas!
mri_coreg did an awesome job and the registration look good.
On Mon, Feb 22, 2016 at 7:51 PM, Douglas Greve
wrote:
> If you have spm, you can use --init-spm. Alternatively, you can use
> mri_coreg instead of bbr (bbr is not as effective on blurry data)
>
> ftp://surfer.nmr.mg
If you have spm, you can use --init-spm. Alternatively, you can use
mri_coreg instead of bbr (bbr is not as effective on blurry data)
ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_coreg
mri_coreg --s $fs --mov ${pet_ext}_LIA.nii --lta output.lta
Also, why is the top of the
It is masked in, ie, it only uses the vertices that are in the label.
On 09/03/2015 04:26 PM, Sebastien Proulx wrote:
>
> Quick question :
>
> When using --label with bbregister, does the specified label file mask
> in or out (is the the voxels that are out or in of the label file that
> are exc
Quick question :
When using --label with bbregister, does the specified label file mask in or
out (is the the voxels that are out or in of the label file that are excluded
from the analysis)?
Thanks a lot!!
Sebastien
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Great, thank you for your help!
On 8/4/15, 2:36 PM, "freesurfer-boun...@nmr.mgh.harvard.edu on behalf of
Douglas N Greve" wrote:
>Yes, it is for 12dof. It is not hidden for any particular purpose
>(except maybe that I'm lazy). In general, I don't think it is a good
>idea to use 12 or 9 dof unles
Yes, it is for 12dof. It is not hidden for any particular purpose
(except maybe that I'm lazy). In general, I don't think it is a good
idea to use 12 or 9 dof unless you have an explicit reason to.
On 08/04/2015 01:54 PM, Perea Camargo, Rodrigo Dennis wrote:
> Hi all,
> I am using a previous scr
Hi all,
I am using a previous script to update a pipeline for pre-processing diffusion
data. My objective related to this question is the (what I think is a hidden)
argument “- -12” when using bbregister (v. 1.49.2.3 FreeSurfer 5.3). Will this
denote 12 degrees of freedom for my registration? I
(Joseph Andreano)
>
>
> ----------
>
> Message: 1
> Date: Tue, 19 May 2015 12:00:32 -0400
> From: Z K <mailto:zkauf...@nmr.mgh.harvard.edu>>
> Subject: Re: [Freesurfer] bbregister error
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
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
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