7:30 AM, Ramesh Babu wrote:
>
> External Email - Use Caution
> Hello,
>
> I want to register JHU-ICBM-tracts-maxprob-thr0-1mm.nii.gz with local
> subject space. For this, I want to generate a registration.dat file which
> will be used for registration with local subje
space. For this, I want to generate a registration.dat file
which will be used for registration with local subject image. But I am
facing an issue which I pasted below.
echo $SUBJECTS_DIR
/usr/local/freesurfer/subjects
bbregister --ss sample-001.mgz --mov
/usr/local/fsl/data/atlases/JHU/JHU-ICBM
External Email - Use Caution
Hello,
I want to register JHU-ICBM-tracts-maxprob-thr0-1mm.nii.gz with local
subject space. For this, I want to generate a registration.dat file which
will be used for registration with local subject image. But I am facing an
issue which I pasted
External Email - Use Caution
The amygdala nuclei labels from segmentHA_T1.sh seem to behave differently in
standard freesurfer registration commands than other labels from
aparc+aseg.mgz: I can't get the amygdala nuclei to register to my functional
space correctly despi
Subject: Re: [Freesurfer] synthmorph for functional registration?
We haven't explored this yet, but I'd be curious to know as well.
From: freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of Josh
Sent: Friday, December 13, 2024 00:12
To: Freesurf
functional registration?
External Email - Use Caution
bbregister is known to be really could at registering functionals to T1w image.
I am curious as to whether synthmorph performs close to bbregister or not when
registering epi to the structural.
___
External Email - Use Caution
bbregister is known to be really could at registering functionals to T1w
image. I am curious as to whether synthmorph performs close to bbregister
or not when registering epi to the structural.
___
Freesurfer
You can invert the gca with somehting like
mri_ca_register -invert-and-save cvs.gca inv.cvs.gca
The apply inv.cvs.gca to map from CVS space back to the native space
On 12/6/2024 3:51 AM, Tanxin Dong wrote:
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To whom this may concern:
Hi, I’ve been working
External Email - Use Caution
To whom this may concern:
Hi, I’ve been working on creating a template for a certain metric using the
applyMorph command to project the calculated metrics onto the CVS template.
However, I'm curious if there’s a way to reverse this process.
Specificall
-all with the -FLAIRpial option.
>
> 1) I wonder whether the FLAIR to T1 registration is handled by recon-all
> or whether I need to supply a FLAIR image already registered to T1.
>
> 2) in case recon-all handles the registration, is there a way I can check
> the registration quali
On 11/12/2024 6:58 AM, Simone Cauzzo wrote:
External Email - Use Caution
Hi all
I am running Freesurfer 7.4
I use recon-all with the -FLAIRpial option.
1) I wonder whether the FLAIR to T1 registration is handled by
recon-all or whether I need to supply a FLAIR image already
External Email - Use Caution
Hi all
I am running Freesurfer 7.4
I use recon-all with the -FLAIRpial option.
1) I wonder whether the FLAIR to T1 registration is handled by recon-all or
whether I need to supply a FLAIR image already registered to T1.
2) in case recon-all handles
External Email - Use Caution
Hi Edward,
From my understanding, since you do not specify the registration model (the
"-m" parameter), it assumes "-m joint", which outputs .nii.gz or .mgz; this
explains your error message. You can use the "-m affin
oun...@nmr.mgh.harvard.edu
> on behalf of Antoine Royer
>
> Sent: Saturday, May 4, 2024 15:06
> To: freesurfer@nmr.mgh.harvard.edu
> Subject: Re: [Freesurfer] Understanding registration with mri_synthmorph
>
> External Email - Use Caution
>
> Thanks Malte!
&g
d.edu
Subject: Re: [Freesurfer] Understanding registration with mri_synthmorph
External Email - Use Caution
Thanks Malte!
Would you recommend anything between saving deform transforms generated from
synthmorph, between .mgz or .nii.gz? Which in my case, are expected to be
passed
: Re: [Freesurfer] Understanding registration with mri_synthmorph
External Email - Use Caution
Thank you very much!!
De : freesurfer-boun...@nmr.mgh.harvard.edu
de la part de Hoffmann, Malte,PhD
Envoyé : 20 avril 2024 11:16
À : freesurfer@nmr.mgh.harvar
bbregister is more sensitive to the smoothing in the PET images. This
can create a confound between atrophy and registration. bbregister
should only be used on non-smoothed data.
On 5/1/2024 5:06 AM, Ruben Dörfel wrote:
External Email - Use Caution
Hi FreeSurfer Team,
I am
External Email - Use Caution
Hi FreeSurfer Team,
I am currently using PETSurfer to analyze FDG data. Following the guide
https://secure-web.cisco.com/11AP3L-fRQ1NyWLwYgy3qW-ObrGxWQsVDEGWJEidxYaLFleo8x6bV-bdH8eLZwLbRkWinVldOV1qDJy0v2d0UB8jW9t6WaSDIlGCVfwxhg2vbtB12Ci8gqdvbKFx-xKQxd
registration with mri_synthmorph
Hi Antoine,
Thanks for reaching out. Unless you're using a dev build of FreeSurfer,
mri_synthmorph may lag behind the dockerized version, which is likely why you
see a different behavior. For affine transforms, we switched to LTA format to
track the source and t
z".
Malte
From: freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of Antoine Royer
Sent: Friday, April 19, 2024 16:08
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] Understanding registration with mri_synthmorph
External Email - Use
the
resulting transform (affine initialization + deform warp) downstream my
pipeline for further registration using ANTs (antsApplyTransforms). I tested
and it seems to work, but i would appreciate an opinion. Does the --insrcgeom
parameter fixes everything for me?
*
Initialization
It looks like if you don't specify a subject (--target subject) as common
space, it will default to 'fsaverage'. See
https://surfer.nmr.mgh.harvard.edu/fswiki/mris_preproc
The input to -surfreg <> is the surface registration to the common space. I
think it should be a sur
ing a custom registration template with
FreeSurfer template
You need to specify a format for the output (eg, ...thickness.mgz)
On 2/26/2024 10:31 AM, Asuka Toyofuku wrote:
External Email - Use Caution
Hi, many thanks for your reply.
Here's the terminal output;
asuka@rigi:/m
ubject:* Re: [Freesurfer] Creating a custom registration template
with FreeSurfer template
Can you include the full terminal output for one of the mris_preproc
commands that is failing?
On 2/22/2024 7:12 AM, Asuka Toyofuku wrote:
*External Email - Use Caution *
Dear Freesurfer experts,
reesurfer-boun...@nmr.mgh.harvard.edu
on behalf of Douglas N. Greve
Sent: 23 February 2024 19:30
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] Creating a custom registration template with
FreeSurfer template
Can you include the full terminal output for one of the mris_preproc com
Can you include the full terminal output for one of the mris_preproc
commands that is failing?
On 2/22/2024 7:12 AM, Asuka Toyofuku wrote:
External Email - Use Caution
Dear Freesurfer experts,
I have issues with creating a custom registration template. (I'm
following
(standard T1 sequence). Both process start
fine but abort at the exact same step with an error in Talairach registration.
The command I use is:
$> recon-all -i sub-20190911.nii.gz -s jjm -all
SUBJECTS_DIR is set correctly; sub-20190911 exists.
I receive the following error:
ERROR: awk
External Email - Use Caution
Dear Freesurfer experts,
I have issues with creating a custom registration template. (I'm following this
instruction:
https://secure-web.cisco.com/1_qfYxT5WNAR-lGRNh895Kl4pqE513hIRdGqZt0w-oDRR8NwLSUh8ataurmBy
External Email - Use Caution
Dear all,
We are pleased to announce that registration is now open for FSL Course 2024,
which will be held in-person June 17th – 21st in Osaka, Japan, co-hosted by the
Riken Center for Biosystems Dynamics Research. You can find details and
an ROI analysis. You mean for
a voxelwise analysis?
On 1/12/2024 5:46 PM, Mirsol Choi wrote:
External Email - Use Caution
Hi there,
Following the first registration step, should I also run
another registration command to put all fa-in
h free surfer?
>>
>> Thank you again for your time.
>>
>> M
>>
>> On Fri, Jan 12, 2024 at 4:05 PM Douglas N. Greve
>> wrote:
>>
>>> oh, I thought you wanted to do an ROI analysis. You mean for a voxelwise
>>> analysis?
>
xelwise
>> analysis?
>>
>> On 1/12/2024 5:46 PM, Mirsol Choi wrote:
>>
>> External Email - Use Caution
>> Hi there,
>>
>>
>> Following the first registration step, should I also run another
>> registration command to put all fa-in-subfie
wanted to do an ROI analysis. You mean for a
voxelwise analysis?
On 1/12/2024 5:46 PM, Mirsol Choi wrote:
External Email - Use Caution
Hi there,
Following the first registration step, should I also run another
registration command to put all fa-in-subfields.mgz
Douglas N. Greve
wrote:
> oh, I thought you wanted to do an ROI analysis. You mean for a voxelwise
> analysis?
>
> On 1/12/2024 5:46 PM, Mirsol Choi wrote:
>
> External Email - Use Caution
> Hi there,
>
>
> Following the first registration step, should I a
Of
*ERNEST KISSI
*Sent:* Thursday, January 11, 2024 3:54 AM
*To:* freesurfer@nmr.mgh.harvard.edu
*Subject:* [Freesurfer] Registration of MPF to FLASH 3D image
*External Email - Use Caution *
Dear Freesurfer team,
I messaged the team
oh, I thought you wanted to do an ROI analysis. You mean for a voxelwise
analysis?
On 1/12/2024 5:46 PM, Mirsol Choi wrote:
External Email - Use Caution
Hi there,
Following the first registration step, should I also run another
registration command to put all fa-in-subfields.mgz
External Email - Use Caution
Hi there,
Following the first registration step, should I also run another
registration command to put all fa-in-subfields.mgz for each subject onto
the same space for inter subject analysis of FA values?
Thanks again,
M
On Fri, Jan 12, 2024 at 3
es in the same
space for me to do a group analysis. However I am unsure what the
order of registration should be for this process to be feasible.
Does this order seem feasible for accurate analysis?
1) recon-all all of my subjects
2) dt_recon all of my subjects (one of the outputs
gister all of my samples in the same space for
> me to do a group analysis. However I am unsure what the order of
> registration should be for this process to be feasible.
>
> Does this order seem feasible for accurate analysis?
>
> 1) recon-all all of my subjects
> 2) dt_
need to register all of my samples in the same space
for me to do a group analysis. However I am unsure what the order of
registration should be for this process to be feasible.
Does this order seem feasible for accurate analysis?
1) recon-all all of my subjects
2) dt_recon all of my subjects (o
] Registration of MPF to FLASH 3D image
External Email - Use Caution
Dear Freesurfer team,
I messaged the team on my MPF map analysis and a suggestion was made that I
register the MPF maps on the T1 MPRAGE images. However, I did not acquire
MPRAGE but FLASH images.
Can I used those
only the T1 FLASH
images and it did not work so I am not sure whether the registration of the
MPF maps on it will work or not. Is there anyway around this?
Thank you.
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https
FA
values from the subfields. However, this is at the individual subject
level.
I will eventually need to register all of my samples in the same space for
me to do a group analysis. However I am unsure what the order of
registration should be for this process to be feasible.
Does this order seem
Have you tried using the "intermediate" option (--int) in bbregister?
The intermediate volume should be a whole brain volume and it should
share a RAS space with the slab volume (eg, if they were acquired in the
same session; load both the slab and the intermediate in freeview to see
if they ar
mgh.harvard.edu"
*Subject: *Re: [Freesurfer] Boundary based registration on partial FoV
to MNI space
Is MRS_201_MT_tfl_stripped.mgz correctly oriented when you view it
in freeview? Also, bbr is meant to be used for within subject
registration. For something like registering to the mni152
Is MRS_201_MT_tfl_stripped.mgz correctly oriented when you view it in
freeview? Also, bbr is meant to be used for within subject registration.
For something like registering to the mni152, try mri_coreg and specify
--dof 12
On 11/20/2023 10:00 AM, Spapens, Jeltje (NP) wrote
Do you just need to change the voxel size for that dimension? If so, you
can use mri_convert, something like
mri_convert -iis newvoxsize input.mgz output.mgz
where -iis means the change the voxel size of the first dimension. Use
-ijs or -iks for the 2nd and 3rd. You may have to play with it to g
7EQ_Afuse434ESbq411FI8DV1o3Sh2NZ3Ke5QHOSKBvNxOKxF8xyaQPDKNFI1PE6WDHeWhcWNeTSsYmmBpk3i7_1TBwmQ6n1XqVH-IwJMHFOmuSbtrsGHwWnj7LV4ZD4huv_yp8b777ivopbUP6AY99fHLyniraYrPhMJWD0rT7gbtUkaNng_SckMJf8EHsHpyWpx1O7hNvClYt9LD4DJq_Ry9s2RExRiWJpi90t2_8PTxfSPMbLsFTyh0ak5KA/https%3A%2F%2Fstackoverflow.com%2Fquestions
: Freesurfer support list
Cc: Maffei, Chiara, PHD ; Yendiki, Anastasia
Subject: Re: [Freesurfer] Error in trac-all prep intra-subject registration:
if: Expression Syntax. brainmask not found.
External Email - Use Caution
Ok, now we know stem2fname is the problem. I can’t reproduce the error
-xBOJ6yQ0TBjjMzxGKeQojzPYME53MhQwIt2Rq_rcHXbAkV3NMfjxZvvtrICQCv6QrXBdAX9xMR0IqW0uqjjVP1vDsXuQQ/https%3A%2F%2Fstackoverflow.com%2Fquestions%2F71441883%2Fhow-to-get-transformation-affine-from-itk-registration)
registration_ras = flip_LPS_RAS @ registration_lps @ flip_LPS_RAS
registration_lps is ants.txt read
...@nmr.mgh.harvard.edu
On Behalf Of Lawless, Dylan
Sent: Wednesday, October 11, 2023 10:39 AM
To: Freesurfer support list
Subject: Re: [Freesurfer] Error in trac-all prep intra-subject registration:
if: Expression Syntax. brainmask not found.
External Email - Use Caution
I ran this
oun...@nmr.mgh.harvard.edu
on behalf of Huang, Yujing
Sent: Wednesday, October 11, 2023 9:32 AM
To: Freesurfer support list
Cc: Maffei, Chiara, PHD ; Yendiki, Anastasia
Subject: Re: [Freesurfer] Error in trac-all prep intra-subject registration:
if: Expression Syntax. brainmask not found.
Exter
ylan
Sent: Wednesday, October 11, 2023 10:01 AM
To: Freesurfer support list
Subject: Re: [Freesurfer] Error in trac-all prep intra-subject registration:
if: Expression Syntax. brainmask not found.
External Email - Use Caution
Could you point me towards the correct log file? I am unable to loca
Sent: Tuesday, October 10, 2023 10:29 AM
To: Freesurfer support list
Subject: Re: [Freesurfer] Error in trac-all prep intra-subject registration:
if: Expression Syntax. brainmask not found.
External Email - Use Caution
There should be a log for the command you ran.
I’m wondering
...@nmr.mgh.harvard.edu
On Behalf Of Lawless, Dylan
Sent: Tuesday, October 10, 2023 10:29 AM
To: Freesurfer support list
Subject: Re: [Freesurfer] Error in trac-all prep intra-subject registration:
if: Expression Syntax. brainmask not found.
External Email - Use Caution
Sure thing, I have attached the
on behalf of Huang, Yujing
Sent: Tuesday, October 10, 2023 9:23 AM
To: Freesurfer support list
Subject: Re: [Freesurfer] Error in trac-all prep intra-subject registration:
if: Expression Syntax. brainmask not found.
External Email - Use Caution
The error that you cut and paste
: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] Error in trac-all prep intra-subject registration: if:
Expression Syntax. brainmask not found.
External Email - Use Caution
Hello,
I am attempting to create a freesurfer v7.2.0 docker container that can run
tracula on the freesurfer outputs
External Email - Use Caution
Hello,
I am attempting to create a freesurfer v7.2.0 docker container that can run
tracula on the freesurfer outputs, however, I am unable to get past the
intra-subject registration step without receiving the following error:
--s sub-01 --mov
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
External Email - Use Caution
Hi there,
I have an animal brain's MRI with 3 volumes, each with a good resolution in one
of the planes.
(i. 768x768x88, ii. 768x768x150, iii. 768x768x140)
As far as I understand freeSurfere doesn't have a 3D ihgh-res reconstruction
tool, right?
S
External Email - Use Caution
Hi Yujing,
I'll try to explain it more explicitly, I rerun my Code and show the
results beyond attaching the Registration files too.
Consider a 3D-Nifti image called "Image.nii" the steps bellow executed in
order:
0- Every time we
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"
(N
send me a license if
I take a snapshot
with everything I should fill in the registration website？
Best!
Lizhao Du
School of Biomedical Engineering, Shanghai Jiao Tong University
lizhao...@sjtu.edu.cn
From: lizhao...@sjtu.edu.cn
Date: 2023-09-07 10:00
To: freesurfer
Subject: Re: [Freesurfer
Engineering, Shanghai Jiao Tong University
lizhao...@sjtu.edu.cn
From: fsbuild
Date: 2023-09-07 09:04
To: freesurfer
Subject: Re: [Freesurfer] registration error (reCAPTCHA not checked)
External Email - Use Caution
The captcha authentication will not work if javascript is
quot;secure-web.cisco.com" claiming to
behttps://surfer.nmr.mgh.harvard.edu/registration.html, a
registration error occured (see below). Is there something wrong for
my internet? Or what could I do to get the license? A few
words from you may help me a lot. Thanks in
advance.<Catch7EDF(09
-XwaFXcCSQ/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Fregistration.html,
a registration
error occured (see below). Is there something wrong for my internet? Or what
could I do to get the license?
A few words from you may help me a lot. Thanks in advance.
Best!
Lizhao Du
School of
External Email - Use Caution
Dear all,
Registration is now open for FSL Course 2023, which will be held fully online,
11th - 22nd September 2023. You can find details and registration info here:
https://secure-web.cisco.com
ore
You don't have to be an INCF member to participate, but this is a good
occasion to become one - r
to a T1-weighted scan? What I am interested is the forward
field only, not the quality of the registration per se. But I imagine these are
connected, and having poor coregistration will result in a poor forward field.
Many thanks in advance!Codrin
On the PETsurfer wiki,
https://surfer.nmr.mgh.harvard.edu/fswiki/PetSurfer, I had recommended
using mri_coreg to register your PET to the FS anatomical using the
following command line:
mri_coreg --s subject --mov template.nii.gz --reg template.reg.lta
This works well for PET scans that do not
It all must be done.
There is no tissue type segmentation per se. You can get it from the
aseg.mgz
The 3rd question is about FSL commands. you should contact FSL
On 12/5/2022 5:50 PM, Zeng, Qi wrote:
External Email - Use Caution
Hi Freesurfer experts,
If I just want to normalize, re
External Email - Use Caution
Hi Freesurfer experts,
If I just want to normalize, register, and segment the T1-weighted images
to the GM, WM, and CSF tissues, can certain steps be skipped from
recon-all, such as the inflation process? What is the output for the
segmentation of GM,
blems with the Talairach registration.
I believe that I should be able to check the Talairach registration, using this
command:
tkregisterfv --s $sub_id --fstal
Since I have not run autorecon2 yet, I leave out the --surf orig flag as
instructed here:
*MailScanner has detected a possible
External Email - Use Caution
Hello Freesurfer,
I am trying to run recon-all on a dataset, and a subset of appear to have
problems with the Talairach registration.
I believe that I should be able to check the Talairach registration, using this
command:
tkregisterfv --s $sub_id
External Email - Use Caution
Dear Freesurfer Experts
I am trying use segmentHA_T1.sh:
During the registration of imageDump.mgz to target
hippoAmygBinaryMask_autoCropped.mgz, I get the warning:
* WARNING: Registration did not converge in 5 steps!
* Problem might be
External Email - Use Caution
Dear all,
We are pleased to announce that registration is open for FSL course 2022 to be
held in-person, Sept 19th - 23rd, in Oxford, UK. You can find details and
registration info here:
https://secure-web.cisco.com
On 6/15/2022 1:26 PM, Kuo, Yi-Ling wrote:
Hello,
The below solutions sounded like data need to be analyzed with
Freesurfer individually to get the registration file?
The anatomical must be analyzed in FS, but not the fMRI. See eg
https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial
:12 PM, Kuo, Yi-Ling wrote:
Hi Freesurfer experts,
I am trying to use the Freeview GUI to load fMRI BOLD activation data
(analyzed in FSL) and project on the inflated surface. I used the
feature “Overlay/Load generic” and was prompted to select overlay file
and/or apply registration. The
Hi Freesurfer experts,
I am trying to use the Freeview GUI to load fMRI BOLD activation data (analyzed
in FSL) and project on the inflated surface. I used the feature “Overlay/Load
generic” and was prompted to select overlay file and/or apply registration. The
selected overlay file didn’t seem
On 3/28/2022 2:39 PM, Salar Dini, Elaheh wrote:
External Email - Use Caution
Thanks Douglas. I have read the freesurfer official page on surface
co-registration, but I still can't grasp where the .lta file comes
from in case of surface co-registration. I suspect that you can&
External Email - Use Caution
Thanks Douglas. I have read the freesurfer official page on surface
co-registration, but I still can't grasp where the .lta file comes from in case
of surface co-registration. I suspect that you can't use the same lta file that
you used f
similar as volumetric co-registration but for
surfaces. To be exact, I have moved a subject's brainmask.mgz,
orig.mgz, aparc+aseg.mgz, and T1 mgz to a new coordinate using
mri_coreg and subsequently vol2vol, but the surfaces are still in the
original coordinate and doesn't match the v
External Email - Use Caution
Dear Freesurfer experts,
Is there a way to move lh.white of a subject to a new coordinate? Something
quite similar as volumetric co-registration but for surfaces. To be exact, I
have moved a subject's brainmask.mgz, orig.mgz, aparc+aseg.mgz, a
n the acquired
dwi intensity at each voxel).
I was told that if you just translate the image and don't rotate it during
co-registration, the quality of the image won't drop, because you don't cut
through the existing voxels on the original image in resampling process to fit
i
you are right! Just fixed it.
thanks
On 2/18/2022 2:15 PM, Gomez, Daniel wrote:
> There is a minor bug/typo in mri_surf2vol that was leading to registration
> issues if the "--fillribbon" flag is used, like in my case.
>
> https://github.com/freesurfer/freesurfer
You can use something like
mris_apply_reg --lta lh.white reg.lta lh.white.reg
The direction of reg.lta does not matter -- it will figure out the right
direction based on the geometry info
On 2/16/2022 12:20 PM, Gomez, Daniel wrote:
> Dear FS users,
>
> I’m trying to get surface indices from surf
There is a minor bug/typo in mri_surf2vol that was leading to registration
issues if the "--fillribbon" flag is used, like in my case.
https://github.com/freesurfer/freesurfer/blob/dev/mri_surf2vol/mri_surf2vol.cpp#L373
The call to MRIcopyHeader(OutVol,VtxVol); has to happen after t
Dear FS users,
I’m trying to get surface indices from surfaces generated with recon-all into a
volume in native functional/EPI space. I’m using mri_surf2vol for that, though
if there is a better alternative solution, I’m happy to take it.
My issue is that the output index volume (vtxvol) I get
PRAGE-file, which was registered in
freesurfer-space. Now I want to register other sequences like T2 in
the same space using the registration matrix. What is the best way to
do this?
In bbregister I didn't found an option to give the registration matrix
which should be used, so applywarp w
External Email - Use CautionHi,
I ran recon-all on a MPRAGE-file, which was registered in freesurfer-space. Now I want to register other sequences like T2 in the same space using the registration matrix. What is the best way to do this?
In bbregister I didn't found an o
implement this average surface into FS
to perform surface registration of my individual labels to the average
surface.
Thanks!
Trisanna
--
*From:* freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of Fischl, Bruce
*Sent
summer and I was running into one
problem after the next and unfortunately no one answered my questions. So, we
have a new MNI chimp average surface and I would like to know if I can somehow
implement this average surface into FS to perform surface registration of my
individual labels to the
ember 4, 2021 10:00 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] question about surface registration to an average
surface
External Email - Use Caution
Thanks Bruce Yes I am working with chimp data.
Any other things I could try?
Trisanna
Sent from my G
ubject: Re: [Freesurfer] question about surface registration to an average
surface
Oh, then no, that won’t work
From: freesurfer-boun...@nmr.mgh.harvard.edu
On Behalf Of Trisanna Sprung-Much
Sent: Saturday, December 4, 2021 10:48 AM
To: Freesurfer support list
Subject: Re: [Freesurfer] ques
Oh, then no, that won't work
From: freesurfer-boun...@nmr.mgh.harvard.edu
On Behalf Of Trisanna Sprung-Much
Sent: Saturday, December 4, 2021 10:48 AM
To: Freesurfer support list
Subject: Re: [Freesurfer] question about surface registration to an average
surface
External Email
ssage
From: "Fischl, Bruce"
Date: 2021-12-04 10:27 a.m. (GMT-05:00)
To: Freesurfer support list
Subject: Re: [Freesurfer] question about surface registration to an average
surface
Hi Trisanna
Can you run mris_sphere on it to create a spherical surface? You could then
regis
conformed one will be ok
Cheers
Bruce
From: freesurfer-boun...@nmr.mgh.harvard.edu
On Behalf Of Trisanna Sprung-Much
Sent: Friday, December 3, 2021 6:42 PM
To: Freesurfer support list
Subject: [Freesurfer] question about surface registration to an average surface
External Email - Use
associated with it. There is no volume associated with it to run in recon-all.
According to the instructions for mri_surf2surf I need the sphere.reg file,
which is generated during recon-all. I wonder if there is a way to undergo
surface registration in my situation? I found the following documentation
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