Have you visually verified that the registration is correct (only work
with LTAs) using tkregisterfv ?
How are you viewing the combined anatomical/functional in pics? If you
just load the functional without a registration file, then that is not
right.
On 3/29/2022 11:28 AM, Manenti, Giorgio wr
.09113 -0.03433 -2.19744 198.19705;
-0.07530 -2.01747 0.04112 244.54424;
0.0 0.0 0.0 1.0;
Resampling
Output registration matrix is identity
mri_vol2vol done
Many thanks again,
Best
Giorgio
Message: 10
Date: Sun, 27 Mar 2022 17:16:25 -0400
From: "Douglas N.
I'm not sure I understand what you are saying or what the problem is.
Can you provide the actual command line you are using, all the terminal
output, and a picture that shows what the problem is?
On 3/23/2022 2:46 PM, Manenti, Giorgio wrote:
> External Email - Use Caution
>
> Dear Frees
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Dear Freesurfer experts,
I am getting problems to transform my xh.ribbon.mgh from anatomical 256x256x256
to functional 104x104x69 space.
When converting the ribbon via “ mri_vol2vol —reg REGfile —mov INPUT —targ
funcTEMPLATE —o OUTPUT “ and checki
No, that is the output of bbregister
On 11/11/2020 1:55 PM, RENXI LI wrote:
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Wouldn’t --reg still require the registration matrix file in
bbregister?
Best,
Renxi
On Nov 11, 2020, at 11:40 AM, Douglas N. Greve
mailto:dgr...@mgh.harvard.edu>> wrote:
Ye
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Wouldn’t --reg still require the registration matrix file in
bbregister?
Best,
Renxi
On Nov 11, 2020, at 11:40 AM, Douglas N. Greve
mailto:dgr...@mgh.harvard.edu>> wrote:
Yes, use bbregister, run with --help to get docs
On 11/11/2020 11:36 AM, RE
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So I think my functional image processed by SPM12 does not come with any
registration matrix file that is required for mri_vol2vol, is there a way to
get around with that matrix?
Best,
Renxi
> On Nov 11, 2020, at 10:12 AM, Douglas N. Greve wrote:
Yes, use bbregister, run with --help to get docs
On 11/11/2020 11:36 AM, RENXI LI wrote:
> External Email - Use Caution
>
> So I think my functional image processed by SPM12 does not come with any
> registration matrix file that is required for mri_vol2vol, is there a way to
> get aroun
Try --help to get docs and examples
On 11/8/2020 5:07 PM, RENXI LI wrote:
> External Email - Use Caution
>
> Hi FreeSurfer Experts:
>
> I am trying to register the subject’s functional image processed by SPM12 to
> the Freesurfer subject anatomical space using mri_vol2vol, what would be
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Hi FreeSurfer Experts:
I am trying to register the subject’s functional image processed by SPM12 to
the Freesurfer subject anatomical space using mri_vol2vol, what would be the
required arguments in this case?
Best,
Renxi
__
Can you try using mri_convert? Like,
mri_convert mni152.nii.gz --apply_inverse_transform xform.m3z subject.mgz
Let me know if that works
On 9/8/2020 8:28 PM, Noriana Jakopin wrote:
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Hello,
I just wanted to follow up on this and see if anyone had any
suggest
External Email - Use Caution
Hello,
I just wanted to follow up on this and see if anyone had any suggestions,
as I still have not resolved the issue.
Best,
Noriana Jakopin
On Tue, Aug 18, 2020 at 12:54 PM Noriana Jakopin
wrote:
> Hello FreeSurfer Developers,
> I am attempting t
External Email - Use Caution
Hello FreeSurfer Developers,
I am attempting to use the inverse of the final m3z registration file
produced by mri_cvs_register to take files in mni152 space back into my
subject's space. I used mri_vol2vol with the --inv-morph flag to accomplish
this.
First, check the overall registration with
tkregisterfv --mov lowb.nii.gz --reg register.lta
On 8/14/2020 12:30 PM, 侠义江湖，醉笑人生 wrote:
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Hi, freesurfer experts.
I am running dt_recon and mri_vol2vol to obtain FA values of ROI.
Everything is OK after running
External Email - Use Caution
Hi, freesurfer experts. I am running dt_recon and mri_vol2vol to obtain FA
values of ROI. Everything is OK after running the dt_recon command. But some
subjects in my study show an issue with mri_vol2vol registration. When
checking the wmparc2diff.
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Thanks, but I want to transform my ROI to the average space from my
subjects (as created by make_average_subject). How do i get the xfm file to
convert my ROI to this average space?
/Ben
Am Fr., 27. März 2020 um 16:27 Uhr schrieb Douglas N. Greve <
dg
oK, this will not be that pretty, but you can
mri_vol2vol --mov yourRoi.mgz --targ orig.mgz --interp nearest
--regheader --o yourRoiOrig.mgz
mri_convert yourRoiOrig.mgz yourRoiOrigAverageSpace.mgz
--apply_transform subject/mri/transforms/talairach.xfm -rt nearest
On 3/27/2020 11:03 AM, Benjam
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The space i created from all subjects using make_average_subject.
Douglas N. Greve schrieb am Fr. 27. März 2020 um
15:32:
> What do you mean by "the average space of the subjects"?
>
>
> On 3/24/2020 2:01 PM, Benjamin Ineichen wrote:
>
> Exte
What do you mean by "the average space of the subjects"?
On 3/24/2020 2:01 PM, Benjamin Ineichen wrote:
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Dear Freesurfer experts,
I am aware that these are busy times. Please still allow me to repost
my FreeSurfer problem:
I created manual masks on the F
External Email - Use Caution
Dear Freesurfer experts,
I am aware that these are busy times. Please still allow me to repost my
FreeSurfer problem:
I created manual masks on the Freesurfer input 001.mgz for several
subjects. I would like to to transform all these individual masks
External Email - Use Caution
the space in which the image was aqcuired.
Am Fr., 6. März 2020 um 18:31 Uhr schrieb Douglas N. Greve <
dgr...@mgh.harvard.edu>:
> what is "native space"?
>
> On 3/6/2020 12:09 PM, Benjamin Ineichen wrote:
>
> External Email - Use Caution
> ex
what is "native space"?
On 3/6/2020 12:09 PM, Benjamin Ineichen wrote:
External Email - Use Caution
example.mgz is just some example mask created on a template in native
space. And I would need to transform it to MNI space. Thus, I ran:
mri_vol2vol --talres 1 --interp nearest --mov e
What is example.mgz?
If you want to transfer the orig.mgz, you can do it with
mri_vol2vol --tal --talres 1 --interp nearest --mov orig.mgz --s subject
--o example.mni305.mgz
On 2/20/2020 3:53 PM, Benjamin Ineichen wrote:
External Email - Use Caution
Dear Freesurfer experts,
In or
yes, that looks right. The one question is about the fill threshold. You may
need to play with it a little to get a good looking ROI_2.nii (which should be
in registration with the functional -- but you should check it)
On 8/24/2019 2:56 PM, Rihana Rayan wrote:
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External Email - Use Caution
Dear Dr. Greve,
Thank you so much for your prompt response.
I included your advice in the processing steps as bellow:
1- recon all
2- mri_binarize --i aparc.a2009s+aseg.mgz --o ROI.nii --match min max
3- bbregister --s --sub01 --mov meanfuctional.n
You shoul use mri_label2vol with ROI.nii as the --seg input. How do you
know that --regheader is right?
On 8/15/19 3:13 PM, Rihana Rayan wrote:
>
> External Email - Use Caution
>
> Dear FS users,
> I have performed recon-all on structural data and created ROIs (using
> mri_binarize), I w
External Email - Use Caution
Dear FS users,
I have performed recon-all on structural data and created ROIs (using
mri_binarize), I want to mask functional data (GLM beta) with ROIs. To
match the file sizes, I resampled the ROI.nii by performing the command:
mri_vol2vol --mov ROI.ni
behalf of Greve, Douglas N.,Ph.D.
Sent: Monday, January 28, 2019 3:17:36 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] mri_vol2vol
that should work
On 1/28/19 2:44 PM, Nasiriavanaki, Zahra wrote:
Dear Freesurfers
Hi
I am trying to project a subcortical volume , that I manually
that should work
On 1/28/19 2:44 PM, Nasiriavanaki, Zahra wrote:
Dear Freesurfers
Hi
I am trying to project a subcortical volume , that I manually made, from
fsaverage to individual subject's space.
I was wondering if it's ok if I use mri_vol2vol for this purpose. I copied my
command below:
Dear Freesurfers
Hi
I am trying to project a subcortical volume , that I manually made, from
fsaverage to individual subject's space.
I was wondering if it's ok if I use mri_vol2vol for this purpose. I copied my
command below:
mri_vol2vol --mov ./${ROI}/ROI4.mgz --targ
$SUBJECTS_DIR/fsave
You need something like this
mri_vol2vol --targ $SUBJECTS_DIR/fsaverage/mri/orig.mgz --mov
$FSLDIR/data/standard/MNI152_T1_2mm.nii.gz --o
fsaverage.orig.MNI152.nii.gz --inv --reg
$SUBJECTS_DIR/fsaverage/mri/transforms/reg.mni152.2mm.dat
On 04/03/2017 10:36 AM, Melanie Ganz wrote:
> Hi all,
>
>
Hi all,
my colleague Vincent wanted to register a volume in MNI305 to MNI152,
unfortunately the final image appears flipped up-down and
anterior-posterior when using the --mni152reg flag with mri_vol2vol. For
example, trying to resample fsaverage orig.mgz to MNI152 using
mri_vol2vol --mov $S
Sorry for the follow up email, but I realized my mistake. When running the
mri_robust_register command even though I used the lta flag for the output
register file, I gave the extension .dat to the file. It seems like this
is what caused the problem.
Panos
> Dear FS community,
>
> I used mri_rob
Dear FS community,
I used mri_robust_register to register a volume to the fsaverage space,
and then tried to use the resulting .lta file to register another vol on
the same space as the original volume, to fsaverage, using mri_vol2vol.
The structure of the command I used is:
mri_vol2vol --mov --t
Add --interp nearest to use nearest neighbor interpolation instead of
trilinear
On 9/24/15 1:48 AM, Jinsong Tang wrote:
Hello,
I am try to convert some binary mask (0,1) to native space.
I use this command line:
mri_vol2vol --mov bin_mask.mgz --targ rawavg.mgz --regheader --o
bin_mask _ra
Hello Bruce,
Yes, this works.
Thanks,
Jinsong
On Thu, Sep 24, 2015 at 5:35 AM, Bruce Fischl
wrote:
> Hi Jinsong
>
> do you mean some of the values are not 1? By default I believe vol2vol
> uses trilinear interpolation. Try including the option --nearest to use
> nearest neighbor instead
>
> c
Hi Jinsong
do you mean some of the values are not 1? By default I believe vol2vol uses
trilinear interpolation. Try including the option --nearest to use nearest
neighbor instead
cheers
Bruce
On Wed, 23 Sep 2015, Jinsong Tang wrote:
Hello,
I am try to convert some binary mask (0,1) to na
Hello,
I am try to convert some binary mask (0,1) to native space.
I use this command line:
mri_vol2vol --mov bin_mask.mgz --targ rawavg.mgz --regheader --o bin_mask
_rawavg.nii.gz –no-save-reg
I found some result of “ bin_mask _rawavg.nii.gz” with intensity of 0.988
instead of 1.
Is there som
Hi Freesurfer experts,
We are analyzing data for a simultaneous PET-MRI study, and are having trouble
registering individual subject BPnd maps to fsaverage space. I attached a photo
of a post-registration subject (the left side is cut off). I had previously
registered each individual BPnd volum
Hi Freesurfer experts,
We are analyzing data for a simultaneous PET-MRI study, and are having trouble
registering individual subject BPnd maps to fsaverage space. I attached a photo
of a post-registration subject (the left side is cut off). I had previously
registered each individual BPnd volum
Anastasia would know better but she is away for a week or two. But
looking at it, I would say that your command line is correct. The
registration does map the anat to the diffusion space, but mri_vol2vol
understands this and simply inverts the matrix. You should just verify
it for yourself by l
Hi Freesurfer experts
I am always a little confused with the registration matrices from tracula
output. If we need to have the DTI maps like dtifit_MD.nii.gz in the recon
space, do we use the matrix anatorig2diff.bbr.dat?
mri_vol2vol --mov //dmri/dtifit_MD.nii.gz --targ
//mri/brainmask.mgz --reg /
0.25 will generate a huge data.
Xiaomin
Date: Wed, 15 Apr 2015 09:11:10 -0400
From: gr...@nmr.mgh.harvard.edu
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] mri_vol2vol
But why do you need to have the same
Because resampling from 1.5 to 0.25 will generate a huge data.
Xiaomin
Date: Wed, 15 Apr 2015 09:11:10 -0400
From: gr...@nmr.mgh.harvard.edu
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] mri_vol2vol
But why do you need to have the same resolution as the
hanks,
Xiaomin
Date: Tue, 14 Apr 2015 21:08:15 -0400
From: gr...@nmr.mgh.harvard.edu
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] mri_vol2vol
So you want it to be in a volume with field of view 256mm in all
d.edu
Subject: Re: [Freesurfer] mri_vol2vol
So you want it to be in a volume with field of view 256mm in all
three dimensions, but the voxel size to be that of the functional
data? It is possible to do, but not easy to set up. Can you say why
you would want to do
: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] mri_vol2vol
sorry, I don't understand. fstal would imply that you want talairach
space. If you want to map the functional into the anatomical space, then
mri_vol2vol --mov res-001.nii --o res-001.t1.space.nii --reg
register.dof6.dat --f
: [Freesurfer] mri_vol2vol
sorry, I don't understand. fstal would imply that you want talairach
space. If you want to map the functional into the anatomical space,
then
mri_vol2vol --mov res-001.nii --o res-001.t1.space.nii --reg
register.dof6.dat --f
sorry, I don't understand. fstal would imply that you want talairach
space. If you want to map the functional into the anatomical space, then
mri_vol2vol --mov res-001.nii --o res-001.t1.space.nii --reg
register.dof6.dat --fstarg
On 4/14/15 11:36 AM, Xiaomin Yue wrote:
Hi Doug,
I like to c
Hi Doug,
I like to convert a native functional data into the anatomical space using
mri_vol2vol with --fstal, so that the resample data has same spatial resolution
as the original function data. However, mri_vol2vol give a error: --fstal
unknown. I also tried using --fstalres as suggested in t
please send the command line without variables
On 05/28/2014 02:02 PM, Ben Mooneyham wrote:
> Hi all,
>
> I'm trying to transform a mean functional image into subject (T1)
> space using mri_vol2vol. Originally, my code worked successfully, but
> in attempts to re-run the procedure, both on the
Hi all,
I'm trying to transform a mean functional image into subject (T1) space
using mri_vol2vol. Originally, my code worked successfully, but in
attempts to re-run the procedure, both on the same data and on additional
data, I've encountered an error in which the log reports an "ERROR: Option
u
Hi Ben,
There should be a procsurffast flag called -volproj_lowmem which avoids
this mri_vol2vol memory issue.
-Louis
On Wed, 21 May 2014, Douglas N Greve wrote:
>
> mri_vol2vol when used in this way does not manage memory very well. It
> resamples the time series into a 256^3 volume of floats.
Hi Ben, please post questions to the list and not to us personally.
Thanks! I do not have an alternative. I think you are using Thomas Yeo's
stream which we are not supporting. He just uses binaries from FS.
doug
On 05/22/2014 12:16 PM, Ben Mooneyham wrote:
> Hi Douglas,
>
> Thank you for you
mri_vol2vol when used in this way does not manage memory very well. It
resamples the time series into a 256^3 volume of floats. Even for a
small number of time points, this becomes unmanagebly huge
On 05/21/2014 06:06 PM, Ben Mooneyham wrote:
> Hello all,
>
> I am doing pre-processing for re
Hello all,
I am doing pre-processing for resting-state fMRI volumes, but I have
encountered an error and am unsure of how to correct it:
I have previously determined the nonlinear warping transformations from my
subjects' anatomical (T1) space to the 2mm MNI template using ANTs. At the
end of my
Hi Greg, the target (--targ) should be a volume, not the name of a
subject (eg, 816/mri/orig.mgz)
doug
On 02/21/2013 02:23 PM, Gregory Kirk wrote:
> Greetings lords of freesurfer!
>
> I am having a problem getting a combined cvs warp+bbregister to map an FA
> volume
> onto a template.
>
> mri_vol
Hi
I found my old notes ( re my message earlier)
I think this is now correct for mapping subject 822 FA onto my template 816, I
know
the cvs technology is recent, so just asking to make sure there is now a
newer/prefered way.
mri_vol2vol --targ /study5/aa-scratch/TEENEMO/twins_freesurfer/816/
Greetings lords of freesurfer!
I am having a problem getting a combined cvs warp+bbregister to map an FA volume
onto a template.
mri_vol2vol --targ 816 --m3z combined_to816_elreg_afteraseg-norm.m3z
--noDefM3zPath --reg
/study5/aa-scratch/TEENEMO/twins_tracula/recons/821/dmri/xfms/anatorig2diff
I have a custom overlay on the left hemisphere of fsaverage, I wanted to
resample that overlay onto the right hemisphere. I thought it would save
time to run xhemireg once for fsaverage, and then resample the left and
right fsaverage overlays onto the left and right hemispheres for all my
subjects
why are you running xhemireg for fsaverage?
On 10/02/2012 06:04 PM, Andrew Bock wrote:
> I updated all the xhemi scripts following:
> http://www.freesurfer.net/fswiki/Xhemi but unfortunately the problem
> persists for fsaverage, since norm.mgz does not exist for fsaverage.
> I'm going to try c
I updated all the xhemi scripts following:
http://www.freesurfer.net/fswiki/Xhemi but unfortunately the problem
persists for fsaverage, since norm.mgz does not exist for fsaverage. I'm
going to try creating norm.mgz for fsaverage to see if xhemireg works.
Even if it doesn't, xhemireg does work for
when did you update the xhemi scripts last? Do a search on our wiki for
xhemi to get pointers to the most recent ones
On 10/02/2012 01:59 PM, Andrew Bock wrote:
> Thanks Doug!
>
> However, now I'm getting the following error:
>
> /Resampling
> Output registration matrix is identity
>
> mri_vol2vo
Thanks Doug!
However, now I'm getting the following error:
*Resampling
Output registration matrix is identity
mri_vol2vol done
ERROR: canot find norm*
I am running:
*xhemireg --s fsaverage --reg*
Any suggestions? Should I run the following from
$SUBJECTS_DIR/fsaverage/mri/?
mri_nu_correct.mn
I just put a new version here:
ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_vol2vol
doug
On 10/1/12 10:56 PM, Andrew Bock wrote:
Hello,
I'm having a problem similar to the one outlined here:
https://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/2012-June/024182.html
Hello,
I'm having a problem similar to the one outlined here:
https://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/2012-June/024182.html
When I run xhemireg I receive the error "ERROR: Option --keep-precision
unknown"
I looked for the newer version of mri_vol2vol described in the previous
post,
Hi Freesurfers,
I am struggling to get mri_vol2vol to downsample when I apply an inverse
morph and an inverse registration matrix.
Specifically, I am bringing a volume in cvs_avg35 space back into an
individual subject's functional space. I have already registered the
subject's functional to the
Hi Constantin,
No, now I understand what you were doing. The T1 / aparc+asge space is
your target and the diffusion space is the moving one. Your mri_vol2vol
setup should be accurate as you indicated originally. I think the problem
might be that the 2nd registration file that you are saving fr
Hello Lilla,
thanks for the answer. I first used
bbregister
--s (Freesurfer Directory)
--mov b0.nii
--reg .dat
--dti
--init-fsl
Afterwards I made some minor spatial changes to the aparc+aseg,
bringing it closer to what i believed its position was on the b0space:
tkregister2
--mov b0.img
--reg
Hi Constantin,
When you used tkregister2 which volume was the target? Acoording to what
you write it was the b0 volume. So when you apply the registration to the
T1 volume, you should keep it that way.
--mov T1
--targ b0image
and no -inv is necessary.
Let me know if I misunderstood what you w
Hellom
I coregistered manually a aparc+aseq.nii file to my DWI-space with
tkregister2. I saved the .dat file and applied it later to the T1
image in order to apply the same spatial coregistration as to the
aparc+aseg. For woth the aparc+aseg and the T1 I used the command
mri_vol2vol
--mov
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