> *From:* freesurfer-boun...@nmr.mgh.harvard.edu <
> freesurfer-boun...@nmr.mgh.harvard.edu> *On Behalf Of *Yazdan Rezaee
> Jouryabi
> *Sent:* Sunday, October 8, 2023 10:04 AM
> *To:* Freesurfer support list
> *Subject:* Re: [Freesurfer] lta_convert issue with ants Registrat
...@nmr.mgh.harvard.edu
On Behalf Of Yazdan Rezaee Jouryabi
Sent: Sunday, October 8, 2023 10:04 AM
To: Freesurfer support list
Subject: Re: [Freesurfer] lta_convert issue with ants Registration Matrix
External Email - Use Caution
Hi Yujing,
Sure.
the results of applying mri_info are attached
rvard.edu <
> freesurfer-boun...@nmr.mgh.harvard.edu> *On Behalf Of *Yazdan Rezaee
> Jouryabi
> *Sent:* Friday, September 29, 2023 12:19 PM
> *To:* Freesurfer support list
> *Subject:* Re: [Freesurfer] lta_convert issue with ants Registration
> Matrix
>
>
>
> *
...@nmr.mgh.harvard.edu
On Behalf Of Yazdan Rezaee Jouryabi
Sent: Friday, September 29, 2023 12:19 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] lta_convert issue with ants Registration Matrix
External Email - Use Caution
Hi Yujing,
I'll try to explain it more explicitly, I rerun my
>
> Hi Yazdan,
>
>
>
> I’m trying to understand the issues.
>
>
>
> Can you specify the commands used to generate the matrices attached to
> your email? And give more details of the issues you are seeing?
>
>
>
> Best,
>
>
>
> Yujing
>
>
Behalf Of Yazdan Rezaee Jouryabi
Sent: Monday, September 25, 2023 1:49 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] lta_convert issue with ants Registration Matrix
External Email - Use Caution
Dear all, Hi
for checking registration i used fsl applyxfm on an Image(1)(Called
External Email - Use Caution
Dear all, Hi
for checking registration i used fsl applyxfm on an Image(1)(Called
Image.nii ) with specific Registration Matrice (Which we suppose to receive
when we apply registration Methods) and Generate the "fsl_resampled.nii.gz"
(Note: Image Orien
External Email - Use Caution
Dear all, Hi
for checking registration i used fsl applyxfm on an Image(1)(Called
Image.nii ) with specific Registration Matrice (Which we suppose to receive
when we apply registration Methods) and Generate the "fsl_resampled.nii.gz"
(Note: Image Orien
lta_convert was not introduced until 6.0. You can just copy it from 6.0
into 5.3
On 5/28/2020 11:24 AM, Alshelh, Zeynab wrote:
Hi everyone,
I am running this version of
fs: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0
But I am having trouble running lta_convert, it returns with command
Hi everyone,
I am running this version of fs:
freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0
But I am having trouble running lta_convert, it returns with command not found.
Is there something I am missing?
Thanks
Zeynab Alshelh, PhD | Postdoctoral Research Fellow
Pain and Neuroinfla
d.edu
on behalf of Christopher Markiewicz
Sent: Tuesday, October 17, 2017 12:11:52 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] lta_convert does not produce ITK transforms that are
correctly applied by antsApplyTransforms
Hi Martin,
I've uploaded a .tgz file with a T1w vo
tober 17, 2017 9:32:54 AM
To: Freesurfer support list
Subject: Re: [Freesurfer] lta_convert does not produce ITK transforms that are
correctly applied by antsApplyTransforms
Hi Chris,
thanks, can you send the images and the exact commands. We have had success in
the past, could be that you h
on behalf of Douglas Greve
>
> Sent: Monday, October 16, 2017 12:39:28 PM
> To: freesurfer@nmr.mgh.harvard.edu
> Subject: Re: [Freesurfer] lta_convert does not produce ITK transforms that
> are correctly applied by antsApplyTransforms
>
> Not sure I understand. If the two
Chris
From: freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of Douglas Greve
Sent: Monday, October 16, 2017 12:39:28 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] lta_convert does not produce ITK transforms that are
correctly appli
Not sure I understand. If the two transforms are only off by less than
the 5th decimal, then why are the registrations off so much. As for why
it would be off at the 5ht dec, it probably has to do with the way we
store the matrix. When a volume is read in, the matrix is decomposed
into translat
Hi,
I've used `bbregister` to generate a transform `bold2T1.lta` from `bold.nii` to
`T1.mgz` (assume we have a `T1.nii` as well for the sake of ANTs).
The following produces a well-aligned output:
mri_convert --apply_transform bold2T1.lta bold.nii bold_space-T1.nii
As does the following:
Thanks
Xiaomin
On Mon, Mar 2, 2015 at 11:51 AM -0800, "Douglas N Greve"
wrote:
try this
ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/lta_convert
On 02/26/2015 12:48 PM, Xiaomin Yue wrote:
> Hi,
>
> Is it possible to download lta_convert?
>
> Thanks,
>
> Xiaomin
>
>
>
>
> O
try this
ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/lta_convert
On 02/26/2015 12:48 PM, Xiaomin Yue wrote:
> Hi,
>
> Is it possible to download lta_convert?
>
> Thanks,
>
> Xiaomin
>
>
>
>
> On Thu, Feb 26, 2015 at 9:35 AM -0800, "David Grayson"
> mailto:dgray...@ucdavis.edu>>
Hi,
Is it possible to download lta_convert?
Thanks,
Xiaomin
On Thu, Feb 26, 2015 at 9:35 AM -0800, "David Grayson"
wrote:
ok, great.
so let's say I have a linear transformation or a full warp field to go
between the freesurfer processed image and the unprocessed brain. is there
a way that I
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