Re: [Freesurfer] mri_vol2vol anatomical to functional

[Douglas N. Greve]

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 wrote:


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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?

Hi Douglas,

thank you for your time; I am trying to get the ribbon at functional 
space resolution (I need it to extract the white matter from my ROIs)


Here I am copying the 2 commands (one using .reg file, the second 
using .lta) I am using, and the terminal terminal outputs. Attached 
you will also find 3 screenshots from freeview with 1) original ribbon 
2) ribbon transformed in functional space using the .reg file and 3) 
ribbon transformed using the .lta file.


(Please Note:  I am using Matlab to integrate this analysis in the 
general pipeline, so the command are started by the s=system() function;)


%%REG

s=system(['mri_vol2vol --reg 'regpath ' --mov 'inputvol ' --targ 
'funcTemp ' --o 'outputvol ]);


regio_read_register: loading lta

Matrix fromregfile:

0.99982  -0.01069 -0.01533  -0.11505;

0.01423  -0.09676 0.99521  -0.84297;

0.01212   0.99525 0.09659  -5.72961;

0.0   0.0 0.0   1.0;

movvol Anatomy_Processed/hum_15477.long.long002/mri/lh.ribbon.mgz

targvol 
FSfast_struc/all_sub/f02_Sess03/bold/ecc_lh/conjunction_pe/v1_trai_vol.nii


outvol Anatomy_Processed/hum_15477.long.long002/mri/lh.ribbon_func.mgz

regfile FSfast_struc/all_sub/f02_Sess03/bold/register.dof6.lta

invert 0

tal 0

talres 2

regheader 0

noresample 0

interp trilinear(1)

precision float(3)

Gdiag_no -1

Synth 0

SynthSeed 1649422337

Final tkRAS-to-tkRASMatrixis:

0.99982  -0.01069 -0.01533  -0.11505;

0.01423  -0.09676 0.99521  -0.84297;

0.01212   0.99525 0.09659  -5.72961;

0.0   0.0 0.0   1.0;

Vox2Vox Matrixis:

2.01888  -0.03096 0.02351   23.93213;

0.02447   0.19504 -2.18955   197.85437;

-0.02873  -2.00955 -0.21287   240.49161;

0.0   0.0 0.0   1.0;

Resampling

Output registrationmatrixisidentity

mri_vol2vol done

%%LTA

s=system(['mri_vol2vol --lta 'ltapath ' --mov 'inputvol ' --targ 
'funcTemp ' --o 'outputvol ]);


Matrix fromLTA:

0.99983  -0.01069 -0.01533  -0.11505;

0.01423  -0.09676 0.99521  -0.84293;

0.01212   0.99525 0.09659  -5.72960;

0.0   0.0 0.0   1.0;

Anatomy_Processed/hum_15477.long.long002/mri/lh.ribbon.mgz 
FSfast_struc/all_sub/f02_Sess03/bold/ecc_lh/conjunction_pe/v1_trai_vol.nii


INFO: src volume infodiffersfromtheonestoredinlta.getsmodifiednow.

volume geometry:

extent  : (256, 256, 256)

voxel   : ( 1., 1.,  1.)

x_(ras) : (-1., -0., -0.)

y_(ras) : ( 0.,  0., -1.)

z_(ras) : (-0.,  1.,  0.)

c_(ras) : ( 0.2540,  9.2232,  8.1562)

file    : Anatomy_Processed/hum_15477.long.long002/mri/lh.ribbon.mgz

volume geometry:

extent  : (104, 104, 69)

voxel   : ( 2.0192, 2.0192,  2.2000)

x_(ras) : (-0.9995, -0.0137,  0.0296)

y_(ras) : ( 0.0126, -0.9991, -0.0397)

z_(ras) : ( 0.0301, -0.0393,  0.9988)

c_(ras) : ( 1.5530, 16.4346, 14.9788)

file    : bold/template.nii.gz

INFO: dst volume infodiffersfromtheonestoredinlta.getsmodifiednow.

volume geometry:

extent  : (104, 104, 69)

voxel   : ( 2.0192,  2.0192,  2.2000)

x_(ras) : (-0.9995, -0.0137,  0.0296)

y_(ras) : ( 0.0126, -0.9991, -0.0397)

z_(ras) : ( 0.0301, -0.0393,  0.9988)

c_(ras) : ( 1.5530, 16.4345, 14.9788)

file    : 
FSfast_struc/all_sub/f02_Sess03/bold/ecc_lh/conjunction_pe/v1_trai_vol.nii


volume geometry:

extent  : (256, 256, 256)

voxel   : ( 1.,  1.,  1.)

x_(ras) : (-1., -0., -0.)

y_(ras) : ( 0.,  0., -1.)

z_(ras) : (-0.,  1.,  0.)

c_(ras) : ( 0.2540, 9.2232,  8.1562)

file    : Anatomy_Processed/hum_15496.long.long002/mri/orig.mgz

movvol Anatomy_Processed/hum_15477.long.long002/mri/lh.ribbon.mgz

targvol 
FSfast_struc/all_sub/f02_Sess03/bold/ecc_lh/conjunction_pe/v1_trai_vol.nii


outvol Anatomy_Processed/hum_15477.long.long002/mri/lh.ribbon_func.mgz

regfile FSfast_struc/all_sub/f02_Sess03/bold/register.dof6.lta

invert 0

tal 0

talres 2

regheader 0

noresample 0

interp trilinear(1)

precision float(3)

Gdiag_no -1

Synth 0

SynthSeed 1649445621

Final tkRAS-to-tkRASMatrixis:

0.99828   0.04446 -0.03809   2.43217;

0.03729   0.01869 0.99913   9.13850;

-0.04513   0.99884 -0.01700   12.13850;

0.0   0.0 0.0   1.0;

Vox2Vox Matrixis:

2.01577  -0.07692 -0.09781   28.12225;

-0.09113  -0.03433 -2.19744   198.19705;

-0.07530  -2.01747 0.04112   244.54424;

0.0   0.0 0.0   1.0;

Resampling

Output registrationmatrixisidentity

mri_vol2vol done

Many thanks again,

Best

Giorgio

Re: [Freesurfer] mri_vol2vol anatomical to functional

[Manenti, Giorgio]

2/mri/orig.mgz
movvol Anatomy_Processed/hum_15477.long.long002/mri/lh.ribbon.mgz
targvol 
FSfast_struc/all_sub/f02_Sess03/bold/ecc_lh/conjunction_pe/v1_trai_vol.nii
outvol Anatomy_Processed/hum_15477.long.long002/mri/lh.ribbon_func.mgz
regfile FSfast_struc/all_sub/f02_Sess03/bold/register.dof6.lta
invert 0
tal0
talres 2
regheader 0
noresample 0
interp  trilinear (1)
precision  float (3)
Gdiag_no  -1
Synth  0
SynthSeed  1649445621

Final tkRAS-to-tkRAS Matrix is:
0.99828   0.04446  -0.03809   2.43217;
0.03729   0.01869   0.99913   9.13850;
-0.04513   0.99884  -0.01700   12.13850;
0.0   0.0   0.0   1.0;

Vox2Vox Matrix is:
2.01577  -0.07692  -0.09781   28.12225;
-0.09113  -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. Greve" 
Subject: Re: [Freesurfer] mri_vol2vol anatomical to functional
To: freesurfer@nmr.mgh.harvard.edu
Message-ID: <50029d97-24be-17a3-2358-3c93982de...@mgh.harvard.edu>
Content-Type: text/plain; charset=UTF-8; format=flowed

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 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 checking via freeview, i am getting the right 
> functional space dimensions but the INPUT and OUTPUT .mgz are never 
> overlapping. Why am i getting this misplacement ? Is this problem due to the 
> register file i provide or maybe it is just a visualisation error (perhaps 
> freeview is not the best way to check the conversion).
>
> I tried to change REGfile by providing the 1) init.register.dof6.dat and 2) 
> register.dof6.lta (changing ??reg with ?lta?). I am getting an almost perfect 
> merge when using the .lta file but still the two volumes are misaligned.
> I tried mri_label2vol as well, but as expected i got worse results.
>
> To provide a minimum more detail, after recon-all i process the anatomy with 
> the longitudinal recon. At that point i use the longitudinal anatomy to 
> register the functional data, which i process by 1) mk-template 2) topup & 
> applytopup.
>
> Many thanks in advance
> Warm regards
>
> Giorgio
>
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Re: [Freesurfer] mri_vol2vol anatomical to functional

[Douglas N. Greve]

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 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 checking via freeview, i am getting the right 
> functional space dimensions but the INPUT and OUTPUT .mgz are never 
> overlapping. Why am i getting this misplacement ? Is this problem due to the 
> register file i provide or maybe it is just a visualisation error (perhaps 
> freeview is not the best way to check the conversion).
>
> I tried to change REGfile by providing the 1) init.register.dof6.dat and 2) 
> register.dof6.lta (changing “—reg with —lta”). I am getting an almost perfect 
> merge when using the .lta file but still the two volumes are misaligned.
> I tried mri_label2vol as well, but as expected i got worse results.
>
> To provide a minimum more detail, after recon-all i process the anatomy with 
> the longitudinal recon. At that point i use the longitudinal anatomy to 
> register the functional data, which i process by 1) mk-template 2) topup & 
> applytopup.
>
> Many thanks in advance
> Warm regards
>
> Giorgio
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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[Freesurfer] mri_vol2vol anatomical to functional

[Manenti, Giorgio]

External Email - Use Caution

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 checking via freeview, i am getting the right 
functional space dimensions but the INPUT and OUTPUT .mgz are never 
overlapping. Why am i getting this misplacement ? Is this problem due to the 
register file i provide or maybe it is just a visualisation error (perhaps 
freeview is not the best way to check the conversion). 

I tried to change REGfile by providing the 1) init.register.dof6.dat and 2) 
register.dof6.lta (changing “—reg with —lta”). I am getting an almost perfect 
merge when using the .lta file but still the two volumes are misaligned. 
I tried mri_label2vol as well, but as expected i got worse results. 

To provide a minimum more detail, after recon-all i process the anatomy with 
the longitudinal recon. At that point i use the longitudinal anatomy to 
register the functional data, which i process by 1) mk-template 2) topup & 
applytopup. 

Many thanks in advance 
Warm regards

Giorgio

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 .
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Re: [Freesurfer] mri_vol2vol usage

[Douglas N. Greve]

No, that is the output of bbregister

On 11/11/2020 1:55 PM, RENXI LI wrote:


External Email - Use Caution

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, 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 around with that matrix?


Best,

Renxi

On Nov 11, 2020, at 10:12 AM, Douglas N. Greve 
mailto:dgr...@mgh.harvard.edu>> wrote:


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 the required arguments in this case?


Best,
Renxi

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Re: [Freesurfer] mri_vol2vol usage

[RENXI LI]

External Email - Use Caution

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, 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 around with that matrix?

Best,

Renxi

On Nov 11, 2020, at 10:12 AM, Douglas N. Greve 
mailto:dgr...@mgh.harvard.edu>> wrote:

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 the 
required arguments in this case?

Best,
Renxi

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Re: [Freesurfer] mri_vol2vol usage

[RENXI LI]

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 around with that matrix?

Best,

Renxi

> On Nov 11, 2020, at 10:12 AM, Douglas N. Greve  wrote:
> 
> 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 the 
>> required arguments in this case?
>> 
>> Best,
>> Renxi
>> 
>> ___
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> 
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Re: [Freesurfer] mri_vol2vol usage

[Douglas N. Greve]

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 around with that matrix?
>
> Best,
>
> Renxi
>
>> On Nov 11, 2020, at 10:12 AM, Douglas N. Greve  
>> wrote:
>>
>> 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 
>>> the required arguments in this case?
>>>
>>> Best,
>>> Renxi
>>>
>>> ___
>>> Freesurfer mailing list
>>> Freesurfer@nmr.mgh.harvard.edu
>>> https://secure-web.cisco.com/16aEdFK0Gv5KpgTIRto9q-RCzWSyxP-MUfC9vggf3jWdTQ9yIjrk0s4EtV8XuO_3i2SYtVJ3GUDzmnmPJBG1Smh9GIvW07SWj5ojp4jY5bOjJ2xAHtVSdOINI3szwHFObrgmUyQX4R6R0SPSAretAJQE-br26tS7bp2RGm_m_xKzwOdB0XV7MJrc6aIPUwbWrSYZaiVky5V6UvzWYDMNAfl4kdH3w9Idfz5FIVOgDLbuyw5FoZPwmR3Aiuiw4hxX1MlVKtqFxXds9ZzRMGC4Wyw/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer
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Re: [Freesurfer] mri_vol2vol usage

[Douglas N. Greve]

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 the 
> required arguments in this case?
>
> Best,
> Renxi
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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[Freesurfer] mri_vol2vol usage

[RENXI LI]

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 the 
required arguments in this case?

Best,
Renxi

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Re: [Freesurfer] mri_vol2vol with --inv-morph producing unexpected results

[Douglas N. Greve]

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:


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 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. However, the resulting
outputs produce images with abnormal warpings to the brain. Using
mri_vol2vol to take subject files into mni152 space with the same
m3z file works fine, it seems to be the inverse that is the
problem. Does anyone have thoughts on how I can remedy this issue?

FreeSurfer Version: freesurfer-linux-centos6_x86_64-7.1.1
Platform: Windows Subsystem for Linux - Ubuntu 18.04 LTS

Thank you!
Noriana Jakopin


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Re: [Freesurfer] mri_vol2vol with --inv-morph producing unexpected results

[Noriana Jakopin]

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 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. However, the resulting outputs produce images with abnormal warpings
> to the brain. Using mri_vol2vol to take subject files into mni152 space
> with the same m3z file works fine, it seems to be the inverse that is the
> problem. Does anyone have thoughts on how I can remedy this issue?
>
> FreeSurfer Version: freesurfer-linux-centos6_x86_64-7.1.1
> Platform: Windows Subsystem for Linux - Ubuntu 18.04 LTS
>
> Thank you!
> Noriana Jakopin
>
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[Freesurfer] mri_vol2vol with --inv-morph producing unexpected results

[Noriana Jakopin]

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. However, the resulting outputs produce images with abnormal warpings
to the brain. Using mri_vol2vol to take subject files into mni152 space
with the same m3z file works fine, it seems to be the inverse that is the
problem. Does anyone have thoughts on how I can remedy this issue?

FreeSurfer Version: freesurfer-linux-centos6_x86_64-7.1.1
Platform: Windows Subsystem for Linux - Ubuntu 18.04 LTS

Thank you!
Noriana Jakopin
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Re: [Freesurfer] mri_vol2vol

[Douglas N. Greve]

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:


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.mgz I created, it is apparent tha​t 
surfaces of lh.white and rh.white are not mismatched with the 
wmparc2diff.mgz. This issue is also mentioned by another user. The Web 
link is
/_https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg55788.html. 
_/Could you give me some advice?

Thanks.
He Tao​

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[Freesurfer] mri_vol2vol

[侠义江湖，醉笑人生]

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.mgz I created, it is apparent tha​t surfaces of 
lh.white and rh.white are not mismatched with the wmparc2diff.mgz. This issue 
is also mentioned by another user. The Web link is  
https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg55788.html. ;
  Could you give me some advice? Thanks. He Tao​___
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Re: [Freesurfer] mri_vol2vol

[Benjamin Ineichen]

External Email - Use Caution

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 <
dgr...@mgh.harvard.edu>:

> 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, Benjamin Ineichen wrote:
>
> External Email - Use Caution
> 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:
>>
>> 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 to the
>> average space of the subjects.
>>
>> For this, I first ran mri_vol2vol:
>>
>> mri_vol2vol --talres 1  --interp nearest --mov SW1-2039/BGmaskbin.nii.gz
>> --s SW1-2039/001.nii --targ multiplems_average/mri/T1.mgz --regheader --o
>> BG2039mask_avesp.mgz
>>
>> The output from that was then used to run mri_robust register
>>
>> mri_robust_register --mov BGmask2039_avesp.mgz --dst
>> multiplems_average/mri/T1.mgz --lta BG_2039_reg.lta --mapmov
>> BG_2039_reg.mgz --iscale --satit
>>
>> But this does not seem to do the job.
>>
>> How can I transform and register a mask to the average space?
>>
>> Many thanks for your help!
>>
>> Best regards,
>> Ben
>>
>> Am Fr., 6. März 2020 um 18:33 Uhr schrieb Benjamin Ineichen <
>> bv.ineic...@gmail.com>:
>>
>>> 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
 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 example.mgz --s 001.mgz
 --targ $FREESURFER_HOME/subjects/fsaverage/mri/orig.mgz --regheader --o
 example.mni305.mgz

 The transformed mask (example.mni305) is located in a completely
 different brain region in the MNI template compared to the native mask in
 the native template (see screenshots). How I can I correct this? Do I need
 to register the native and MNI template first?

 Thanks!

 /Ben

 Am Fr., 6. März 2020 um 17:59 Uhr schrieb Douglas N. Greve <
 dgr...@mgh.harvard.edu>:

> 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 order to transform a segmentation mask (example.mgz) from native so
> standard MNI space I ran:
> mri_vol2vol --talres 1  --interp nearest --mov example.mgz --s 001.mgz
> --targ $FREESURFER_HOME/subjects/fsaverage/mri/orig.mgz --regheader --o
> example.mni305.mgz
>
> the output example.mni305.mgz did somehow transform to a different
> space as you can see in Screenshot orig where the native mask is white and
> the transformed mask is red. However, the masks seems to be in a
> completely different brain region in the native MNI space (Screenshot 
> MNI).
> But the point of transforming my segmentation mask is that the segmented
> mask should be in the same brain region but just transformed to the
> standard space. How can I correct this?
>
> Many thanks for the support!
>
> /Ben
>
> --
> 
> Benjamin Victor Ineichen, MD PhD
> Karolinska Institutet
> Center for Molecular Medicine
> Stockholm, Sweden
> ineic...@protonmail.ch
> +41 76 391 04 01
>
> Dr. med. et Dr. rer. nat. ETH Benjamin Victor Ineichen
> Karolinska Institutet
> Center for Molecular Medicine
> Stockholm, Sweden
> ineic...@protonmail.ch
> +41 76 391 04 01
>
> ___
> Freesurfer mailing 
> listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
> ___
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Re: [Freesurfer] mri_vol2vol

[Douglas N. Greve]

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, Benjamin Ineichen wrote:


External Email - Use Caution

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:


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 to the average space of the subjects.

For this, I first ran mri_vol2vol:

mri_vol2vol --talres 1  --interp nearest --mov
SW1-2039/BGmaskbin.nii.gz --s SW1-2039/001.nii --targ
multiplems_average/mri/T1.mgz --regheader --o BG2039mask_avesp.mgz


The output from that was then used to run mri_robust register

mri_robust_register --mov BGmask2039_avesp.mgz --dst
multiplems_average/mri/T1.mgz --lta BG_2039_reg.lta --mapmov
BG_2039_reg.mgz --iscale --satit


But this does not seem to do the job.

How can I transform and register a mask to the average space?

Many thanks for your help!

Best regards,
Ben

Am Fr., 6. März 2020 um 18:33 Uhr schrieb Benjamin Ineichen
mailto:bv.ineic...@gmail.com>>:

the space in which the image was aqcuired.

Am Fr., 6. März 2020 um 18:31 Uhr schrieb Douglas N. Greve
mailto:dgr...@mgh.harvard.edu>>:

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
example.mgz --s 001.mgz --targ
$FREESURFER_HOME/subjects/fsaverage/mri/orig.mgz
--regheader --o example.mni305.mgz

The transformed mask (example.mni305) is located in a
completely different brain region in the MNI template
compared to the native mask in the native template (see
screenshots). How I can I correct this? Do I need to
register the native and MNI template first?

Thanks!

/Ben

Am Fr., 6. März 2020 um 17:59 Uhr schrieb Douglas N.
Greve mailto:dgr...@mgh.harvard.edu>>:

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 order to transform a segmentation mask
(example.mgz) from native so standard MNI space I ran:
mri_vol2vol --talres 1  --interp nearest --mov
example.mgz --s 001.mgz --targ
$FREESURFER_HOME/subjects/fsaverage/mri/orig.mgz
--regheader --o example.mni305.mgz

the output example.mni305.mgz did somehow transform
to a different space as you can see in Screenshot
orig where the native mask is white and the
transformed mask is red. However, the masks seems
to be in a completely different brain region in the
native MNI space (Screenshot MNI). But the point of
transforming my segmentation mask is that the
segmented mask should be in the same brain region
but just transformed to the standard space. How can
I correct this?

Many thanks for the support!

/Ben

-- 


Benjamin Victor Ineichen, MD PhD
Karolinska Institutet
Center for Molecular Medicine
Stockholm, Sweden
ineic...@protonmail.ch 
+41 76 391 04 01

Dr. med. et Dr. rer. nat. ETH Benjamin Victor Ineichen
Karolinska Institutet
Center for Molecular Medicine
Stockholm, Sweden
ineic...@protonmail.ch 
+41 76 391 04 01

  

Re: [Freesurfer] mri_vol2vol

[Benjamin Ineichen]

External Email - Use Caution

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:
>
> 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 to the
> average space of the subjects.
>
> For this, I first ran mri_vol2vol:
>
> mri_vol2vol --talres 1  --interp nearest --mov SW1-2039/BGmaskbin.nii.gz
> --s SW1-2039/001.nii --targ multiplems_average/mri/T1.mgz --regheader --o
> BG2039mask_avesp.mgz
>
> The output from that was then used to run mri_robust register
>
> mri_robust_register --mov BGmask2039_avesp.mgz --dst
> multiplems_average/mri/T1.mgz --lta BG_2039_reg.lta --mapmov
> BG_2039_reg.mgz --iscale --satit
>
> But this does not seem to do the job.
>
> How can I transform and register a mask to the average space?
>
> Many thanks for your help!
>
> Best regards,
> Ben
>
> Am Fr., 6. März 2020 um 18:33 Uhr schrieb Benjamin Ineichen <
> bv.ineic...@gmail.com>:
>
>> 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
>>> 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 example.mgz --s 001.mgz
>>> --targ $FREESURFER_HOME/subjects/fsaverage/mri/orig.mgz --regheader --o
>>> example.mni305.mgz
>>>
>>> The transformed mask (example.mni305) is located in a completely
>>> different brain region in the MNI template compared to the native mask in
>>> the native template (see screenshots). How I can I correct this? Do I need
>>> to register the native and MNI template first?
>>>
>>> Thanks!
>>>
>>> /Ben
>>>
>>> Am Fr., 6. März 2020 um 17:59 Uhr schrieb Douglas N. Greve <
>>> dgr...@mgh.harvard.edu>:
>>>
 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 order to transform a segmentation mask (example.mgz) from native so
 standard MNI space I ran:
 mri_vol2vol --talres 1  --interp nearest --mov example.mgz --s 001.mgz
 --targ $FREESURFER_HOME/subjects/fsaverage/mri/orig.mgz --regheader --o
 example.mni305.mgz

 the output example.mni305.mgz did somehow transform to a different
 space as you can see in Screenshot orig where the native mask is white and
 the transformed mask is red. However, the masks seems to be in a
 completely different brain region in the native MNI space (Screenshot MNI).
 But the point of transforming my segmentation mask is that the segmented
 mask should be in the same brain region but just transformed to the
 standard space. How can I correct this?

 Many thanks for the support!

 /Ben

 --
 
 Benjamin Victor Ineichen, MD PhD
 Karolinska Institutet
 Center for Molecular Medicine
 Stockholm, Sweden
 ineic...@protonmail.ch
 +41 76 391 04 01

 Dr. med. et Dr. rer. nat. ETH Benjamin Victor Ineichen
 Karolinska Institutet
 Center for Molecular Medicine
 Stockholm, Sweden
 ineic...@protonmail.ch
 +41 76 391 04 01

 ___
 Freesurfer mailing 
 listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


 ___
 Freesurfer mailing list
 Freesurfer@nmr.mgh.harvard.edu
 https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>>
>>>
>>>
>>> --
>>> 
>>> Benjamin Victor Ineichen, MD PhD
>>> Karolinska Institutet
>>> Center for Molecular Medicine
>>> Stockholm, Sweden
>>> ineic...@protonmail.ch
>>> +41 76 391 04 01
>>>
>>> Dr. med. et Dr. rer. nat. ETH Benjamin Victor Ineichen
>>> Karolinska Institutet
>>> Center for Molecular Medicine
>>> Stockholm, Sweden
>>> ineic...@protonmail.ch
>>> +41 76 391 04 01
>>>
>>> ___
>>> Freesurfer mailing 
>>> listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>>
>>>
>>> ___
>>> Freesurfer maili

Re: [Freesurfer] mri_vol2vol

[Douglas N. Greve]

What do you mean by "the average space of the subjects"?

On 3/24/2020 2:01 PM, Benjamin Ineichen wrote:


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 to 
the average space of the subjects.


For this, I first ran mri_vol2vol:

mri_vol2vol --talres 1  --interp nearest --mov 
SW1-2039/BGmaskbin.nii.gz --s SW1-2039/001.nii --targ 
multiplems_average/mri/T1.mgz --regheader --o BG2039mask_avesp.mgz



The output from that was then used to run mri_robust register

mri_robust_register --mov BGmask2039_avesp.mgz --dst 
multiplems_average/mri/T1.mgz --lta BG_2039_reg.lta --mapmov 
BG_2039_reg.mgz --iscale --satit



But this does not seem to do the job.

How can I transform and register a mask to the average space?

Many thanks for your help!

Best regards,
Ben

Am Fr., 6. März 2020 um 18:33 Uhr schrieb Benjamin Ineichen 
mailto:bv.ineic...@gmail.com>>:


the space in which the image was aqcuired.

Am Fr., 6. März 2020 um 18:31 Uhr schrieb Douglas N. Greve
mailto:dgr...@mgh.harvard.edu>>:

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 example.mgz
--s 001.mgz --targ
$FREESURFER_HOME/subjects/fsaverage/mri/orig.mgz --regheader
--o example.mni305.mgz

The transformed mask (example.mni305) is located in a
completely different brain region in the MNI template
compared to the native mask in the native template (see
screenshots). How I can I correct this? Do I need to register
the native and MNI template first?

Thanks!

/Ben

Am Fr., 6. März 2020 um 17:59 Uhr schrieb Douglas N. Greve
mailto:dgr...@mgh.harvard.edu>>:

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 order to transform a segmentation mask (example.mgz)
from native so standard MNI space I ran:
mri_vol2vol --talres 1  --interp nearest --mov
example.mgz --s 001.mgz --targ
$FREESURFER_HOME/subjects/fsaverage/mri/orig.mgz
--regheader --o example.mni305.mgz

the output example.mni305.mgz did somehow transform to a
different space as you can see in Screenshot orig where
the native mask is white and the transformed mask is
red. However, the masks seems to be in a
completely different brain region in the native MNI
space (Screenshot MNI). But the point of transforming my
segmentation mask is that the segmented mask should be
in the same brain region but just transformed to the
standard space. How can I correct this?

Many thanks for the support!

/Ben

-- 


Benjamin Victor Ineichen, MD PhD
Karolinska Institutet
Center for Molecular Medicine
Stockholm, Sweden
ineic...@protonmail.ch 
+41 76 391 04 01

Dr. med. et Dr. rer. nat. ETH Benjamin Victor Ineichen
Karolinska Institutet
Center for Molecular Medicine
Stockholm, Sweden
ineic...@protonmail.ch 
+41 76 391 04 01

___
Freesurfer mailing list
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___
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-- 


Benjamin Victor Ineichen, MD PhD
Karolinska Institutet
Center for Molecular Medicine
Stockholm, Sweden
ineic...@protonmail.ch 
+41 76 391 04 01

Dr. med. et Dr. rer. nat. ETH Benjamin Victor Ineichen
Karol

Re: [Freesurfer] mri_vol2vol

[Benjamin Ineichen]

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 to the
average space of the subjects.

For this, I first ran mri_vol2vol:

mri_vol2vol --talres 1  --interp nearest --mov SW1-2039/BGmaskbin.nii.gz
--s SW1-2039/001.nii --targ multiplems_average/mri/T1.mgz --regheader --o
BG2039mask_avesp.mgz

The output from that was then used to run mri_robust register

mri_robust_register --mov BGmask2039_avesp.mgz --dst
multiplems_average/mri/T1.mgz --lta BG_2039_reg.lta --mapmov
BG_2039_reg.mgz --iscale --satit

But this does not seem to do the job.

How can I transform and register a mask to the average space?

Many thanks for your help!

Best regards,
Ben

Am Fr., 6. März 2020 um 18:33 Uhr schrieb Benjamin Ineichen <
bv.ineic...@gmail.com>:

> 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
>> 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 example.mgz --s 001.mgz
>> --targ $FREESURFER_HOME/subjects/fsaverage/mri/orig.mgz --regheader --o
>> example.mni305.mgz
>>
>> The transformed mask (example.mni305) is located in a completely
>> different brain region in the MNI template compared to the native mask in
>> the native template (see screenshots). How I can I correct this? Do I need
>> to register the native and MNI template first?
>>
>> Thanks!
>>
>> /Ben
>>
>> Am Fr., 6. März 2020 um 17:59 Uhr schrieb Douglas N. Greve <
>> dgr...@mgh.harvard.edu>:
>>
>>> 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 order to transform a segmentation mask (example.mgz) from native so
>>> standard MNI space I ran:
>>> mri_vol2vol --talres 1  --interp nearest --mov example.mgz --s 001.mgz
>>> --targ $FREESURFER_HOME/subjects/fsaverage/mri/orig.mgz --regheader --o
>>> example.mni305.mgz
>>>
>>> the output example.mni305.mgz did somehow transform to a different space
>>> as you can see in Screenshot orig where the native mask is white and the
>>> transformed mask is red. However, the masks seems to be in a
>>> completely different brain region in the native MNI space (Screenshot MNI).
>>> But the point of transforming my segmentation mask is that the segmented
>>> mask should be in the same brain region but just transformed to the
>>> standard space. How can I correct this?
>>>
>>> Many thanks for the support!
>>>
>>> /Ben
>>>
>>> --
>>> 
>>> Benjamin Victor Ineichen, MD PhD
>>> Karolinska Institutet
>>> Center for Molecular Medicine
>>> Stockholm, Sweden
>>> ineic...@protonmail.ch
>>> +41 76 391 04 01
>>>
>>> Dr. med. et Dr. rer. nat. ETH Benjamin Victor Ineichen
>>> Karolinska Institutet
>>> Center for Molecular Medicine
>>> Stockholm, Sweden
>>> ineic...@protonmail.ch
>>> +41 76 391 04 01
>>>
>>> ___
>>> Freesurfer mailing 
>>> listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>>
>>>
>>> ___
>>> Freesurfer mailing list
>>> Freesurfer@nmr.mgh.harvard.edu
>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>
>>
>>
>> --
>> 
>> Benjamin Victor Ineichen, MD PhD
>> Karolinska Institutet
>> Center for Molecular Medicine
>> Stockholm, Sweden
>> ineic...@protonmail.ch
>> +41 76 391 04 01
>>
>> Dr. med. et Dr. rer. nat. ETH Benjamin Victor Ineichen
>> Karolinska Institutet
>> Center for Molecular Medicine
>> Stockholm, Sweden
>> ineic...@protonmail.ch
>> +41 76 391 04 01
>>
>> ___
>> Freesurfer mailing 
>> listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>
>>
>> ___
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
>
> --
> 
> Benjamin Victor Ineichen, MD PhD
> Karolinska Institutet
> Center for Molecular Medicine
> Stockholm, Sweden
> ineic...@protonmail.ch
> +41 76 391 04 01
>
> Dr. med. et Dr. rer. nat. ETH Benjamin Victor Ineichen
> Karolinska Institutet
> Center for Molecular Medicine
> Stockholm, Swe

Re: [Freesurfer] mri_vol2vol

[Benjamin Ineichen]

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
> 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 example.mgz --s 001.mgz
> --targ $FREESURFER_HOME/subjects/fsaverage/mri/orig.mgz --regheader --o
> example.mni305.mgz
>
> The transformed mask (example.mni305) is located in a completely different
> brain region in the MNI template compared to the native mask in the native
> template (see screenshots). How I can I correct this? Do I need to register
> the native and MNI template first?
>
> Thanks!
>
> /Ben
>
> Am Fr., 6. März 2020 um 17:59 Uhr schrieb Douglas N. Greve <
> dgr...@mgh.harvard.edu>:
>
>> 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 order to transform a segmentation mask (example.mgz) from native so
>> standard MNI space I ran:
>> mri_vol2vol --talres 1  --interp nearest --mov example.mgz --s 001.mgz
>> --targ $FREESURFER_HOME/subjects/fsaverage/mri/orig.mgz --regheader --o
>> example.mni305.mgz
>>
>> the output example.mni305.mgz did somehow transform to a different space
>> as you can see in Screenshot orig where the native mask is white and the
>> transformed mask is red. However, the masks seems to be in a
>> completely different brain region in the native MNI space (Screenshot MNI).
>> But the point of transforming my segmentation mask is that the segmented
>> mask should be in the same brain region but just transformed to the
>> standard space. How can I correct this?
>>
>> Many thanks for the support!
>>
>> /Ben
>>
>> --
>> 
>> Benjamin Victor Ineichen, MD PhD
>> Karolinska Institutet
>> Center for Molecular Medicine
>> Stockholm, Sweden
>> ineic...@protonmail.ch
>> +41 76 391 04 01
>>
>> Dr. med. et Dr. rer. nat. ETH Benjamin Victor Ineichen
>> Karolinska Institutet
>> Center for Molecular Medicine
>> Stockholm, Sweden
>> ineic...@protonmail.ch
>> +41 76 391 04 01
>>
>> ___
>> Freesurfer mailing 
>> listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>
>>
>> ___
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
>
> --
> 
> Benjamin Victor Ineichen, MD PhD
> Karolinska Institutet
> Center for Molecular Medicine
> Stockholm, Sweden
> ineic...@protonmail.ch
> +41 76 391 04 01
>
> Dr. med. et Dr. rer. nat. ETH Benjamin Victor Ineichen
> Karolinska Institutet
> Center for Molecular Medicine
> Stockholm, Sweden
> ineic...@protonmail.ch
> +41 76 391 04 01
>
> ___
> Freesurfer mailing 
> listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer



-- 

Benjamin Victor Ineichen, MD PhD
Karolinska Institutet
Center for Molecular Medicine
Stockholm, Sweden
ineic...@protonmail.ch
+41 76 391 04 01

Dr. med. et Dr. rer. nat. ETH Benjamin Victor Ineichen
Karolinska Institutet
Center for Molecular Medicine
Stockholm, Sweden
ineic...@protonmail.ch
+41 76 391 04 01
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Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
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Re: [Freesurfer] mri_vol2vol

[Douglas N. Greve]

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 example.mgz --s 001.mgz 
--targ $FREESURFER_HOME/subjects/fsaverage/mri/orig.mgz --regheader 
--o example.mni305.mgz


The transformed mask (example.mni305) is located in a completely 
different brain region in the MNI template compared to the native mask 
in the native template (see screenshots). How I can I correct this? Do 
I need to register the native and MNI template first?


Thanks!

/Ben

Am Fr., 6. März 2020 um 17:59 Uhr schrieb Douglas N. Greve 
mailto:dgr...@mgh.harvard.edu>>:


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 order to transform a segmentation mask (example.mgz) from
native so standard MNI space I ran:
mri_vol2vol --talres 1  --interp nearest --mov example.mgz --s
001.mgz --targ $FREESURFER_HOME/subjects/fsaverage/mri/orig.mgz
--regheader --o example.mni305.mgz

the output example.mni305.mgz did somehow transform to a
different space as you can see in Screenshot orig where the
native mask is white and the transformed mask is red. However,
the masks seems to be in a completely different brain region in
the native MNI space (Screenshot MNI). But the point of
transforming my segmentation mask is that the segmented mask
should be in the same brain region but just transformed to the
standard space. How can I correct this?

Many thanks for the support!

/Ben

-- 


Benjamin Victor Ineichen, MD PhD
Karolinska Institutet
Center for Molecular Medicine
Stockholm, Sweden
ineic...@protonmail.ch 
+41 76 391 04 01

Dr. med. et Dr. rer. nat. ETH Benjamin Victor Ineichen
Karolinska Institutet
Center for Molecular Medicine
Stockholm, Sweden
ineic...@protonmail.ch 
+41 76 391 04 01

___
Freesurfer mailing list
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___
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--

Benjamin Victor Ineichen, MD PhD
Karolinska Institutet
Center for Molecular Medicine
Stockholm, Sweden
ineic...@protonmail.ch 
+41 76 391 04 01

Dr. med. et Dr. rer. nat. ETH Benjamin Victor Ineichen
Karolinska Institutet
Center for Molecular Medicine
Stockholm, Sweden
ineic...@protonmail.ch 
+41 76 391 04 01

___
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Re: [Freesurfer] mri_vol2vol

[Douglas N. Greve]

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 order to transform a segmentation mask (example.mgz) from native so 
standard MNI space I ran:
mri_vol2vol --talres 1  --interp nearest --mov example.mgz --s 001.mgz 
--targ $FREESURFER_HOME/subjects/fsaverage/mri/orig.mgz --regheader 
--o example.mni305.mgz


the output example.mni305.mgz did somehow transform to a different 
space as you can see in Screenshot orig where the native mask is white 
and the transformed mask is red. However, the masks seems to be in a 
completely different brain region in the native MNI space (Screenshot 
MNI). But the point of transforming my segmentation mask is that the 
segmented mask should be in the same brain region but just transformed 
to the standard space. How can I correct this?


Many thanks for the support!

/Ben

--

Benjamin Victor Ineichen, MD PhD
Karolinska Institutet
Center for Molecular Medicine
Stockholm, Sweden
ineic...@protonmail.ch 
+41 76 391 04 01

Dr. med. et Dr. rer. nat. ETH Benjamin Victor Ineichen
Karolinska Institutet
Center for Molecular Medicine
Stockholm, Sweden
ineic...@protonmail.ch 
+41 76 391 04 01

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Re: [Freesurfer] mri_vol2vol

[Greve, Douglas N.,Ph.D.]

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:

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.nii  --initi-fsl --reg 
register.dat
4- mri_label2vol --seg --ROI.nii --temp meanfuctional.nii --reg register.dat 
--fillthresh 0.5 --o ROI_2.nii

I was wondering if you could check and verify the steps?
As another question is the ROI_2.nii coregistered with meanfunctional.nii?

Best Regards,
Rihana

On Fri, Aug 16, 2019 at 2:09 AM Greve, Douglas N.,Ph.D. 
mailto:dgr...@mgh.harvard.edu>> wrote:
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 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.nii --targ beta_01.nii --regheader --o
> ROI_in_beta.nii
> Multiplying ROI_in_mask.nii by GLM beta, results in NaN over some
> voxels. Can anyone help me solve the problem?
>
> Best regards,
> Rihana
>
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
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Re: [Freesurfer] mri_vol2vol

[Rihana Rayan]

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.nii  --initi-fsl --reg
register.dat
4- mri_label2vol --seg --ROI.nii --temp meanfuctional.nii --reg
register.dat --fillthresh 0.5 --o ROI_2.nii

I was wondering if you could check and verify the steps?
As another question is the ROI_2.nii coregistered with meanfunctional.nii?

Best Regards,
Rihana

On Fri, Aug 16, 2019 at 2:09 AM Greve, Douglas N.,Ph.D. <
dgr...@mgh.harvard.edu> wrote:

> 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 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.nii --targ beta_01.nii --regheader --o
> > ROI_in_beta.nii
> > Multiplying ROI_in_mask.nii by GLM beta, results in NaN over some
> > voxels. Can anyone help me solve the problem?
> >
> > Best regards,
> > Rihana
> >
> >
> >
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Re: [Freesurfer] mri_vol2vol

[Greve, Douglas N.,Ph.D.]

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 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.nii --targ beta_01.nii --regheader --o 
> ROI_in_beta.nii
> Multiplying ROI_in_mask.nii by GLM beta, results in NaN over some 
> voxels. Can anyone help me solve the problem?
>
> Best regards,
> Rihana
>
>
>
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[Freesurfer] mri_vol2vol

[Rihana Rayan]

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.nii --targ beta_01.nii --regheader --o ROI_in_beta.nii

Multiplying ROI_in_mask.nii by GLM beta, results in NaN over some voxels.
Can anyone help me solve the problem?

Best regards,
Rihana
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Re: [Freesurfer] mri_vol2vol

[Nasiriavanaki, Zahra]

Thank you very much


Zahra (Mona) Nasiriavanaki

Postdoctoral Research Fellow

Martinos Center for Biomedical Imaging

Massachusetts General Hospital

149 13th Street, 149-2615

Charlestown, MA, USA, 02129




From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on 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 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/fsaverage/mri/orig.mgz --o $SUBJECTS_DIR/${subj}/mri/${ROI}.mgz 
--talres 2 --interp nearest --regheader


Thanks

Mona


Zahra (Mona) Nasiriavanaki

Postdoctoral Research Fellow

Martinos Center for Biomedical Imaging

Massachusetts General Hospital

149 13th Street, 149-2615

Charlestown, MA, USA, 02129





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Re: [Freesurfer] mri_vol2vol

[Greve, Douglas N.,Ph.D.]

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:


mri_vol2vol --mov ./${ROI}/ROI4.mgz  --targ 
$SUBJECTS_DIR/fsaverage/mri/orig.mgz --o $SUBJECTS_DIR/${subj}/mri/${ROI}.mgz 
--talres 2 --interp nearest --regheader


Thanks

Mona


Zahra (Mona) Nasiriavanaki

Postdoctoral Research Fellow

Martinos Center for Biomedical Imaging

Massachusetts General Hospital

149 13th Street, 149-2615

Charlestown, MA, USA, 02129





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[Freesurfer] mri_vol2vol

[Nasiriavanaki, Zahra]

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/fsaverage/mri/orig.mgz --o $SUBJECTS_DIR/${subj}/mri/${ROI}.mgz 
--talres 2 --interp nearest --regheader


Thanks

Mona


Zahra (Mona) Nasiriavanaki

Postdoctoral Research Fellow

Martinos Center for Biomedical Imaging

Massachusetts General Hospital

149 13th Street, 149-2615

Charlestown, MA, USA, 02129


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Re: [Freesurfer] mri_vol2vol --mni152reg flips volume

[Douglas N Greve]

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,
>
> 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 $SUBJECTS_DIR/fsaverage/mri/orig.mgz --mni152reg --o 
> fsaverage.orig.MNI152.nii.gz
>
> ends up yielding the attached image (red is the output file and 
> background is FSL MNI152 template). Anything obvious he's doing wrong?
>
> Cheers,
>
> Melanie
>
>
>
>
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[Freesurfer] mri_vol2vol --mni152reg flips volume

[Melanie Ganz]

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 $SUBJECTS_DIR/fsaverage/mri/orig.mgz --mni152reg --o 
fsaverage.orig.MNI152.nii.gz


ends up yielding the attached image (red is the output file and 
background is FSL MNI152 template). Anything obvious he's doing wrong?


Cheers,

Melanie


--
Melanie Ganz-Benjaminsen, MSc, Ph.D.
Neurobiology Research Unit
University of Copenhagen
Rigshospitalet
Rockefeller Center
Juliane Maries Vej 28/30, 3.
DK-2100 Copenhagen
Denmark

phone:  +45 3545 6718
e-mail: melanie.g...@nru.dk
web: http://melanie.clausundmelanie.de/

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Re: [Freesurfer] mri_vol2vol question

[pfotiad]

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_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  --targ  --lta
> ./.lta --o 
>
> However, I keep getting the error:
> MatrixAsciiReadFrom: could not scanf parms
>
> Do you happen to know what is the cause of that error?
>
> Thanks in advance.
>
> Best,
> Panos
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[Freesurfer] mri_vol2vol question

[pfotiad]

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  --targ  --lta
./.lta --o 

However, I keep getting the error:
MatrixAsciiReadFrom: could not scanf parms

Do you happen to know what is the cause of that error?

Thanks in advance.

Best,
Panos
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Re: [Freesurfer] mri_vol2vol binary mask

[Douglas Greve]

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 _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 something wrong?

Thanks

Jinsong





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Re: [Freesurfer] mri_vol2vol binary mask

[Jinsong Tang]

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
>
> cheers
> Bruce
>
>  On Wed, 23 Sep 2015, 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
>> _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 something wrong?
>>
>> Thanks
>>
>> Jinsong
>>
>>
>>
>>
>>
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-- 
Jinsong Tang, MD
Institute of Mental Health
The Second Xiangya Hospital , Central South University
139 Renmin Road, Changsha Hunan 410011, P.R. China
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Re: [Freesurfer] mri_vol2vol binary mask

[Bruce Fischl]

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 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 something wrong?

Thanks

Jinsong




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[Freesurfer] mri_vol2vol binary mask

[Jinsong Tang]

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 something wrong?

Thanks

Jinsong
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[Freesurfer] mri_vol2vol from subject space to fsaverage space

[Rodriguez-Thompson, Anais]

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 volume map to the subject's volume space using 
bbregister (naming the reg file register{subject}.dat), and then transformed 
them into a new volume file using the mri_vol2vol command, and referencing the 
file generated by bbregister.

This is the command I used:

mri_vol2vol --mov 
$SUBJECTS_DIR/NNC_PMOD_LoganRef_BPnd/fs_NNC112_0045_RBV_MC_s10v3_LoganRef_BPnd.nii
 (**this is the original volume file**) --fstarg --reg register0045.dat --o 
$SUBJECTS_DIR/NNC_PMOD_LoganRef_BPnd/fs_NNC112_0045_RBV_MC_s10v3_LoganRef_BPnd_reg.nii

When I visualize this file using tkmedit, the map looks fine (and is not cut 
off).

However, after transforming this file into fsaverage space, it becomes cut off.

First I copied each individual volume file into each subject's mri folder. Then 
I used this command to transform the individual files into mni305 space:

mri_vol2vol --mov fs_NNC112_0045_RBV_MC_s10v3_LoganRef_BPnd_reg.nii --targ 
$FREESURFER_HOME/average/mni305.cor.subfov2.mgz --xfm transforms/talairach.xfm 
--o fs_NNC112_0045_RBV_MC_s10v3_LoganRef_BPnd_reg_mni305.subfov2.mgz

Do you know why some of the volume maps are being cut off after transforming 
them into fsaverage space?

Thanks for your help,
Anais


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[Freesurfer] mri_vol2vol

[Rodriguez-Thompson, Anais]

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 volume map to the subject's volume space using 
bbregister (naming the reg file register{subject}.dat), and then transformed 
them into a new volume file using the mri_vol2vol command, and referencing the 
file generated by bbregister.  

This is the command I used:

mri_vol2vol --mov 
$SUBJECTS_DIR/NNC_PMOD_LoganRef_BPnd/fs_NNC112_0045_RBV_MC_s10v3_LoganRef_BPnd.nii
 (**this is the original volume file**) --fstarg --reg register0045.dat --o 
$SUBJECTS_DIR/NNC_PMOD_LoganRef_BPnd/fs_NNC112_0045_RBV_MC_s10v3_LoganRef_BPnd_reg.nii

When I visualize this file using tkmedit, the map looks fine (and is not cut 
off). 

However, after transforming this file into fsaverage space, it becomes cut off. 

First I copied each individual volume file into each subject's mri folder. Then 
I used this command to transform the individual files into mni305 space:

mri_vol2vol --mov fs_NNC112_0045_RBV_MC_s10v3_LoganRef_BPnd_reg.nii --targ 
$FREESURFER_HOME/average/mni305.cor.subfov2.mgz --xfm transforms/talairach.xfm 
--o fs_NNC112_0045_RBV_MC_s10v3_LoganRef_BPnd_reg_mni305.subfov2.mgz

Do you know why some of the volume maps are being cut off after transforming 
them into fsaverage space?

Thanks for your help,
Anais


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Re: [Freesurfer] mri_vol2vol

[Douglas N Greve]

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 looking at the output. This has caused confusion for 
a long time ...

On 07/14/2015 02:05 PM, Celine Louapre wrote:
> 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 //dmri/xfms/anatorig2diff.bbr.dat
> --o /mri/dtifit_MD_registered.nii.gz
>
> Thanks a lot
> Celine
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MGH-NMR Center
gr...@nmr.mgh.harvard.edu
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Fax: 617-726-7422

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[Freesurfer] mri_vol2vol

[Celine Louapre]

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 //dmri/xfms/anatorig2diff.bbr.dat
--o /mri/dtifit_MD_registered.nii.gz

Thanks a lot
Celine
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Re: [Freesurfer] mri_vol2vol

[Douglas Greve]

Try something like this. Run mri_vol2vol with --help to get info about 
each of the flags


mri_vol2vol --mov $invol --reg $reg \
  --tal --talres $res --talxfm $talxfm --interp $interp \
  --no-save-reg --o $outvol

On 4/15/15 10:03 AM, Xiaomin Yue wrote:

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 original 
functional?


On 4/14/15 10:30 PM, Xiaomin Yue wrote:

yes, that's precisely what I want.  the reason is the following.
 A subject was scanned multiple times across days with slightly
different slice position for each time.  What I need is to extract
a peak response when a stimuli was presented.   In order to make
the voxels match from one scan to another, I thought that all
scans have to be in same space, so that the data extracted for a
voxel from different scans match.   Could there be a better way to
do this?

Thanks,
Xiaomin


Date: Tue, 14 Apr 2015 21:08:15 -0400
From: gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu>
To: freesurfer@nmr.mgh.harvard.edu
<mailto: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
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 that?


On 4/14/15 8:20 PM, Xiaomin Yue wrote:

Thanks for your response.  The command you gave will generate
a new function data with the spatial resolution of the
anatomical data, which in my case is much higher than those of
functional data.  What i want is to generate a new functional
data in the anatomical space, with spatial resolution of the
original function data. Is it possible?  I thought that
--fstalres would give me a choice to keep the spatial
resolution of the original function data.

Xiaomin


Date: Tue, 14 Apr 2015 18:22:00 -0400
From: gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu>
To: freesurfer@nmr.mgh.harvard.edu
<mailto: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 --fstarg



On 4/14/15 11:36 AM, Xiaomin Yue wrote:

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 the help document, with same error.  I am
using fs5.3.  the command is: mdi_vol2vol --mov
res-001.nii --fstarg --fstal 1.5 --o res-001.t1.space.nii
--reg register.dof6.dat

Thanks,
Xiaomin


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Re: [Freesurfer] mri_vol2vol

[Xiaomin Yue]

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 original
functional? 



On 4/14/15 10:30 PM, Xiaomin Yue wrote:



  
  yes, that's precisely what I want.  the reason is
the following.  A subject was scanned multiple times across days
with slightly different slice position for each time.  What I
need is to extract a peak response when a stimuli was presented.
  In order to make the voxels match from one scan to another, I
thought that all scans have to be in same space, so that the
data extracted for a voxel from different scans match.   Could
there be a better way to do this?



Thanks,
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 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 that?





On 4/14/15 8:20 PM, Xiaomin
  Yue wrote:



  
  Thanks for your response.  The command you
gave will generate a new function data with the spatial
resolution of the anatomical data, which in my case is
much higher than those of functional data.  What i want
is to generate a new functional data in the anatomical
space, with spatial resolution of the original function
data. Is it possible?  I thought that --fstalres would
give me a choice to keep the spatial resolution of the
original function data. 



Xiaomin 

  

  
Date: Tue, 14 Apr 2015
18:22:00 -0400

From: gr...@nmr.mgh.harvard.edu

To: 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
--fstarg







On 4/14/15 11:36 AM,
  Xiaomin Yue wrote:



  
  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 the help document,
  with same error.  I am using fs5.3.  the
  command is: mdi_vol2vol --mov res-001.nii
  --fstarg --fstal 1.5 --o res-001.t1.space.nii
  --reg register.dof6.dat



Thanks,
Xiaomin 
  
  

  
  

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Partners 

Re: [Freesurfer] mri_vol2vol

[Douglas Greve]

But why do you need to have the same resolution as the original functional?

On 4/14/15 10:30 PM, Xiaomin Yue wrote:
yes, that's precisely what I want.  the reason is the following.  A 
subject was scanned multiple times across days with slightly different 
slice position for each time.  What I need is to extract a peak 
response when a stimuli was presented.   In order to make the voxels 
match from one scan to another, I thought that all scans have to be in 
same space, so that the data extracted for a voxel from different 
scans match.   Could there be a better way to do this?


Thanks,
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 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 that?



On 4/14/15 8:20 PM, Xiaomin Yue wrote:

Thanks for your response.  The command you gave will generate a
new function data with the spatial resolution of the anatomical
data, which in my case is much higher than those of functional
data.  What i want is to generate a new functional data in the
anatomical space, with spatial resolution of the original function
data. Is it possible?  I thought that --fstalres would give me a
choice to keep the spatial resolution of the original function data.

Xiaomin


Date: Tue, 14 Apr 2015 18:22:00 -0400
From: gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu>
To: freesurfer@nmr.mgh.harvard.edu
<mailto: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 --fstarg



On 4/14/15 11:36 AM, Xiaomin Yue wrote:

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 the help document,
with same error.  I am using fs5.3.  the command is:
mdi_vol2vol --mov res-001.nii --fstarg --fstal 1.5 --o
res-001.t1.space.nii --reg register.dof6.dat

Thanks,
Xiaomin


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Re: [Freesurfer] mri_vol2vol

[Xiaomin Yue]

yes, that's precisely what I want.  the reason is the following.  A subject was 
scanned multiple times across days with slightly different slice position for 
each time.  What I need is to extract a peak response when a stimuli was 
presented.   In order to make the voxels match from one scan to another, I 
thought that all scans have to be in same space, so that the data extracted for 
a voxel from different scans match.   Could there be a better way to do this?
Thanks,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
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 that?





On 4/14/15 8:20 PM, Xiaomin Yue wrote:



  
  Thanks for your response.  The command you gave
will generate a new function data with the spatial resolution of
the anatomical data, which in my case is much higher than those
of functional data.  What i want is to generate a new functional
data in the anatomical space, with spatial resolution of the
original function data. Is it possible?  I thought that
--fstalres would give me a choice to keep the spatial resolution
of the original function data. 



Xiaomin 

  

  
Date: Tue, 14 Apr 2015 18:22:00 -0400

From: gr...@nmr.mgh.harvard.edu

To: 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 --fstarg







On 4/14/15 11:36 AM, Xiaomin
  Yue wrote:



  
  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 the help document, with
  same error.  I am using fs5.3.  the command is:
  mdi_vol2vol --mov res-001.nii --fstarg --fstal 1.5 --o
  res-001.t1.space.nii --reg register.dof6.dat



Thanks,
Xiaomin 
  
  

  
  

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Re: [Freesurfer] mri_vol2vol

[Douglas Greve]

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 that?



On 4/14/15 8:20 PM, Xiaomin Yue wrote:
Thanks for your response.  The command you gave will generate a new 
function data with the spatial resolution of the anatomical data, 
which in my case is much higher than those of functional data.  What i 
want is to generate a new functional data in the anatomical space, 
with spatial resolution of the original function data. Is it possible? 
 I thought that --fstalres would give me a choice to keep the spatial 
resolution of the original function data.


Xiaomin


Date: Tue, 14 Apr 2015 18:22:00 -0400
From: gr...@nmr.mgh.harvard.edu
To: 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 --fstarg




On 4/14/15 11:36 AM, Xiaomin Yue wrote:

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 the help document, with same
error.  I am using fs5.3.  the command is: mdi_vol2vol --mov
res-001.nii --fstarg --fstal 1.5 --o res-001.t1.space.nii --reg
register.dof6.dat

Thanks,
Xiaomin


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but does not contain patient information, please contact the sender and properly
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Re: [Freesurfer] mri_vol2vol

[Xiaomin Yue]

Thanks for your response.  The command you gave will generate a new function 
data with the spatial resolution of the anatomical data, which in my case is 
much higher than those of functional data.  What i want is to generate a new 
functional data in the anatomical space, with spatial resolution of the 
original function data. Is it possible?  I thought that --fstalres would give 
me a choice to keep the spatial resolution of the original function data. 
Xiaomin 

Date: Tue, 14 Apr 2015 18:22:00 -0400
From: gr...@nmr.mgh.harvard.edu
To: 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 --fstarg







On 4/14/15 11:36 AM, Xiaomin Yue wrote:



  
  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 the
  help document, with same error.  I am using fs5.3.  the
  command is: mdi_vol2vol --mov res-001.nii --fstarg --fstal 1.5
  --o res-001.t1.space.nii --reg register.dof6.dat



Thanks,
Xiaomin 
  
  

  
  

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Re: [Freesurfer] mri_vol2vol

[Douglas Greve]

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 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 the help document, with same error.  I am 
using fs5.3.  the command is: mdi_vol2vol --mov res-001.nii --fstarg 
--fstal 1.5 --o res-001.t1.space.nii --reg register.dof6.dat


Thanks,
Xiaomin


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[Freesurfer] mri_vol2vol

[Xiaomin Yue]

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 the help document, with 
same error.  I am using fs5.3.  the command is: mdi_vol2vol --mov res-001.nii 
--fstarg --fstal 1.5 --o res-001.t1.space.nii --reg register.dof6.dat
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Re: [Freesurfer] mri_vol2vol error "--o: command not found"

[Douglas N Greve]

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 same data and on 
> additional data, I've encountered an error in which the log reports an 
> "ERROR: Option unknown" and also "--o: command not found."
>
> I am hoping to resolve this issue; does anyone see where my issue is 
> arising from?  This is especially strange given that I've gotten it to 
> work before, and I don't think I made any changes to the script 
> besides changing the directory locations for different subjects' data.
>
> Here is the mri_vol2vol command as I currently have it:
>
> mri_vol2vol --reg ${iSub}_bbregister.dat --mov 
> ${iSub}_Tempfiltered_mean.nii --targ 
> ${DataDir}/S1/${iSub}/${iSub}_brainmask.gcuts.nii \
> --o ${iSub}_mean_epi_inT1.nii
>
> The cd is ${DataDir}/S1/${iSub} , which contains the 
> ${iSub}_bbregister.dat , ${iSub}_Tempfiltered_mean.nii , and 
> ${iSub}_brainmask.gcuts.nii files.
>
> Thanks for your help,
>
> Ben Mooneyham
>
> -- 
> Graduate Student
> UCSB - Department of Psychological & Brain Sciences
> Building 429 Room 102
> (210) 912-6076
> bwmooney...@gmail.com 
>
>
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Fax: 617-726-7422

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[Freesurfer] mri_vol2vol error "--o: command not found"

[Ben Mooneyham]

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
unknown" and also "--o: command not found."

I am hoping to resolve this issue; does anyone see where my issue is
arising from?  This is especially strange given that I've gotten it to work
before, and I don't think I made any changes to the script besides changing
the directory locations for different subjects' data.

Here is the mri_vol2vol command as I currently have it:

mri_vol2vol --reg ${iSub}_bbregister.dat --mov
${iSub}_Tempfiltered_mean.nii --targ
${DataDir}/S1/${iSub}/${iSub}_brainmask.gcuts.nii \
--o ${iSub}_mean_epi_inT1.nii

The cd is ${DataDir}/S1/${iSub} , which contains the ${iSub}_bbregister.dat
, ${iSub}_Tempfiltered_mean.nii , and ${iSub}_brainmask.gcuts.nii files.

Thanks for your help,

Ben Mooneyham

-- 
Graduate Student
UCSB - Department of Psychological & Brain Sciences
Building 429 Room 102
(210) 912-6076
bwmooney...@gmail.com
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Re: [Freesurfer] mri_vol2vol memory error

[Louis Nicholas Vinke]

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. 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 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 pre-processing pipeline, I am trying to
>> transform my subjects' functional volumes (206 TRs of 2sec) into this
>> MNI space by 1) transforming the functional volumes into subject T1
>> space using mri_vol2vol, and 2) applying the nonlinear warp (from
>> ANTs) to the volumes in subject-T1 space to ultimately have my
>> subjects' functional data in MNI space.
>>
>> However, I am getting an error while running mri_vol2vol, where it
>> "cannot allocate region."  I gather from looking around online that
>> this is a memory issue, but I am not sure how to fix it. Thoughts? It
>> is crucial that I be able to translate my functional data into common
>> MNI space before performing second-level analyses...
>>
>> I do not encounter this issue when performing this transformation on
>> functional connectivity maps (where I take an ROI defined in MNI
>> space, transform it into T1, and then subject-EPI space, calculate the
>> FC with the rest of the brain, and then invert the process by
>> transforming back into T1, and finally MNI space).  How can I get this
>> to work with a larger file?
>>
>> Thank you in advance for your help,
>>
>> Ben Mooneyham
>>
>> --
>> Graduate Student
>> UCSB - Department of Psychological & Brain Sciences
>> Building 429 Room 102
>> (210) 912-6076
>> bwmooney...@gmail.com 
>>
>>
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>
>
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Re: [Freesurfer] mri_vol2vol memory error

[Douglas N Greve]

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 your response.  Would you perhaps be able to suggest an 
> alternative approach that may work for my situation?
>
> - Ben M
>
> -- 
> Graduate Student
> UCSB - Department of Psychological & Brain Sciences
> Building 429 Room 102
> (210) 912-6076
> bwmooney...@gmail.com 

-- 
Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
www.nmr.mgh.harvard.edu/facility/filedrop/index.html
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Re: [Freesurfer] mri_vol2vol memory error

[Douglas N Greve]

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 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 pre-processing pipeline, I am trying to 
> transform my subjects' functional volumes (206 TRs of 2sec) into this 
> MNI space by 1) transforming the functional volumes into subject T1 
> space using mri_vol2vol, and 2) applying the nonlinear warp (from 
> ANTs) to the volumes in subject-T1 space to ultimately have my 
> subjects' functional data in MNI space.
>
> However, I am getting an error while running mri_vol2vol, where it 
> "cannot allocate region."  I gather from looking around online that 
> this is a memory issue, but I am not sure how to fix it. Thoughts? It 
> is crucial that I be able to translate my functional data into common 
> MNI space before performing second-level analyses...
>
> I do not encounter this issue when performing this transformation on 
> functional connectivity maps (where I take an ROI defined in MNI 
> space, transform it into T1, and then subject-EPI space, calculate the 
> FC with the rest of the brain, and then invert the process by 
> transforming back into T1, and finally MNI space).  How can I get this 
> to work with a larger file?
>
> Thank you in advance for your help,
>
> Ben Mooneyham
>
> -- 
> Graduate Student
> UCSB - Department of Psychological & Brain Sciences
> Building 429 Room 102
> (210) 912-6076
> bwmooney...@gmail.com 
>
>
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-- 
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MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
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[Freesurfer] mri_vol2vol memory error

[Ben Mooneyham]

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 pre-processing pipeline, I am trying to transform my subjects'
functional volumes (206 TRs of 2sec) into this MNI space by 1) transforming
the functional volumes into subject T1 space using mri_vol2vol, and 2)
applying the nonlinear warp (from ANTs) to the volumes in subject-T1 space
to ultimately have my subjects' functional data in MNI space.

However, I am getting an error while running mri_vol2vol, where it "cannot
allocate region."  I gather from looking around online that this is a
memory issue, but I am not sure how to fix it. Thoughts? It is crucial that
I be able to translate my functional data into common MNI space before
performing second-level analyses...

I do not encounter this issue when performing this transformation on
functional connectivity maps (where I take an ROI defined in MNI space,
transform it into T1, and then subject-EPI space, calculate the FC with the
rest of the brain, and then invert the process by transforming back into
T1, and finally MNI space).  How can I get this to work with a larger file?

Thank you in advance for your help,

Ben Mooneyham

-- 
Graduate Student
UCSB - Department of Psychological & Brain Sciences
Building 429 Room 102
(210) 912-6076
bwmooney...@gmail.com
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Re: [Freesurfer] mri_vol2vol call problem

[Douglas N Greve]

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_vol2vol --targ 816 --m3z combined_to816_elreg_afteraseg-norm.m3z 
> --noDefM3zPath --reg 
> /study5/aa-scratch/TEENEMO/twins_tracula/recons/821/dmri/xfms/anatorig2diff.bbr.dat
>  --mov 
> /study5/aa-scratch/TEENEMO/twins_tracula/recons/821/dmri/dtifit_FA.nii.gz --o 
> test --no-save-reg
>
> spits out
> Using the m3z file as it is; no assumed location.
> movvol 
> /study5/aa-scratch/TEENEMO/twins_tracula/recons/821/dmri/dtifit_FA.nii.gz
> targvol 816
> outvol test
> regfile 
> /study5/aa-scratch/TEENEMO/twins_tracula/recons/821/dmri/xfms/anatorig2diff.bbr.dat
> invert 0
> tal 0
> talres 2
> regheader 0
> noresample 0
> interp trilinear (1)
> precision float (3)
> Gdiag_no -1
> Morphing
> InvertMorph 0
> Synth 0
> SynthSeed 1362252270
> corRead(): can't open file 
> /study5/aa-scratch/TEENEMO/twins_freesurfer/816/COR-.info
>
> i know i have not seen a file COR-.info in the top level
> subject directory in the modern age of the universe.
>
> i know i saw this before but my notes from the last time
> i figured this out got lost in a file system cleanup.
>
> can one of you tell me where i went astray ?
>
> thank you
>
> Greg
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>

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MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
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[Freesurfer] mri_vol2vol call

[Gregory Kirk]

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/mri/norm.mgz 
--m3z 
/study5/aa-scratch/TEENEMO/twins_freesurfer/822/cvs/combined_to816_elreg_afteraseg-norm.m3z
 --noDefM3zPath --reg 
/study5/aa-scratch/TEENEMO/twins_tracula/recons/822/dmri/xfms/anatorig2diff.bbr.dat
 --mov /study5/aa-scratch/TE
ENEMO/twins_tracula/recons/822/dmri/dtifit_FA.nii.gz --o 
/study5/aa-scratch/TEENEMO/twins_freesurfer/822/cvs/FA.mgz --no-save-reg
done


thanks
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[Freesurfer] mri_vol2vol call problem

[Gregory Kirk]

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.bbr.dat
 --mov 
/study5/aa-scratch/TEENEMO/twins_tracula/recons/821/dmri/dtifit_FA.nii.gz --o 
test --no-save-reg

spits out 
Using the m3z file as it is; no assumed location.
movvol /study5/aa-scratch/TEENEMO/twins_tracula/recons/821/dmri/dtifit_FA.nii.gz
targvol 816
outvol test
regfile 
/study5/aa-scratch/TEENEMO/twins_tracula/recons/821/dmri/xfms/anatorig2diff.bbr.dat
invert 0
tal 0
talres 2
regheader 0
noresample 0
interp trilinear (1)
precision float (3)
Gdiag_no -1
Morphing
InvertMorph 0
Synth 0
SynthSeed 1362252270
corRead(): can't open file 
/study5/aa-scratch/TEENEMO/twins_freesurfer/816/COR-.info

i know i have not seen a file COR-.info in the top level
subject directory in the modern age of the universe.

i know i saw this before but my notes from the last time
i figured this out got lost in a file system cleanup.

can one of you tell me where i went astray ?

thank you

Greg
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Re: [Freesurfer] mri_vol2vol

[Andrew Bock]

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.

Instead, I can run xhemireg on all my subjects, and then resample the left
hemisphere overlay of fsaverage to the left and /xhemi (right) hemispheres
for each subject.  It will take a bit longer, but it should be fine.

Andrew

On Tue, Oct 2, 2012 at 3:05 PM, Douglas N Greve
wrote:

> 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 creating norm.mgz for fsaverage to see if
>> xhemireg works.  Even if it doesn't, xhemireg does work for my other
>> subjects, so I'll be able to find a solution.
>>
>> Thanks for your help,
>>
>> Andrew
>>
>> On Tue, Oct 2, 2012 at 12:19 PM, Douglas N Greve <
>> gr...@nmr.mgh.harvard.edu 
>> >
>> wrote:
>>
>> 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_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.mni --i orig.mgz --o nu.mgz --n 2 --uchar
>> transforms/talairach.xfm
>> mri_ca_normalize -mask brainmask.mgz nu.mgz
>> $FREESURFER_HOME/average/RB_**all_2008-03-26.gca
>> transforms/talairach.lta norm.mgz
>>
>> Andrew
>>
>>
>> On Mon, Oct 1, 2012 at 8:32 PM, Douglas Greve
>> > > >
>> >
>> >>
>> wrote:
>>
>>
>> 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
>>
>> 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, but could not find it on the ftp site.  Any
>> suggestions?
>>
>> Andrew
>>
>>
>>
>>
>> __**_
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>> 
>> > >
>> 
>> >
>> 
>> > >>
>> https://mail.nmr.mgh.harvard.**edu/mailman/listinfo/**
>> freesurfer 
>>
>>
>>
>> __**_
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>> 
>> > >
>> 
>> >
>> 
>> > >>
>>
>> 
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>>
>>
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>> person to
>> whom it is
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>> the e-mail
>> contains patient information, please contact the Partners
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Re: [Freesurfer] mri_vol2vol

[Douglas N Greve]

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 creating norm.mgz for fsaverage to see if xhemireg 
> works.  Even if it doesn't, xhemireg does work for my other subjects, 
> so I'll be able to find a solution.
>
> Thanks for your help,
>
> Andrew
>
> On Tue, Oct 2, 2012 at 12:19 PM, Douglas N Greve 
> mailto:gr...@nmr.mgh.harvard.edu>> wrote:
>
> 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_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.mni --i orig.mgz --o nu.mgz --n 2 --uchar
> transforms/talairach.xfm
> mri_ca_normalize -mask brainmask.mgz nu.mgz
> $FREESURFER_HOME/average/RB_all_2008-03-26.gca
> transforms/talairach.lta norm.mgz
>
> Andrew
>
>
> On Mon, Oct 1, 2012 at 8:32 PM, Douglas Greve
> mailto:gr...@nmr.mgh.harvard.edu>
>  >> wrote:
>
>
> 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
>
> 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, but could not find it on the ftp site.  Any
> suggestions?
>
> Andrew
>
>
>
>
> ___
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> 
>  >
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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>
>
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> 
>  >
>
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
> The information in this e-mail is intended only for the
> person to
> whom it is
> addressed. If you believe this e-mail was sent to you in
> error and
> the e-mail
> contains patient information, please contact the Partners
> Compliance HelpLine at
> http://www.partners.org/complianceline . If the e-mail was sent to
> you in error
> but does not contain patient information, please contact the
> sender and properly
> dispose of the e-mail.
>
>
>
> -- 
> Douglas N. Greve, Ph.D.
> MGH-NMR Center
> gr...@nmr.mgh.harvard.edu 
> Phone Number: 617-724-2358 
> Fax: 617-726-7422 
>
> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
> 
> FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html
> 
>
>
>
>

-- 
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MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

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Re: [Freesurfer] mri_vol2vol

[Andrew Bock]

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 my other subjects, so I'll be
able to find a solution.

Thanks for your help,

Andrew

On Tue, Oct 2, 2012 at 12:19 PM, Douglas N Greve
wrote:

> 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_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.mni --i orig.mgz --o nu.mgz --n 2 --uchar
>> transforms/talairach.xfm
>> mri_ca_normalize -mask brainmask.mgz nu.mgz $FREESURFER_HOME/average/RB_*
>> *all_2008-03-26.gca transforms/talairach.lta norm.mgz
>>
>> Andrew
>>
>>
>> On Mon, Oct 1, 2012 at 8:32 PM, Douglas Greve 
>> > gr...@nmr.mgh.harvard.**edu >> wrote:
>>
>>
>> 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
>>>
>>> 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, but could not find it on the ftp site.  Any
>>> suggestions?
>>>
>>> Andrew
>>>
>>>
>>>
>>>
>>> __**_
>>> Freesurfer mailing list
>>> Freesurfer@nmr.mgh.harvard.edu  >> harvard.edu >
>>> 
>>> https://mail.nmr.mgh.harvard.**edu/mailman/listinfo/**freesurfer
>>>
>>
>>
>> __**_
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu > harvard.edu >
>>
>> 
>> https://mail.nmr.mgh.harvard.**edu/mailman/listinfo/**freesurfer
>>
>>
>> The information in this e-mail is intended only for the person to
>> whom it is
>> addressed. If you believe this e-mail was sent to you in error and
>> the e-mail
>> contains patient information, please contact the Partners
>> Compliance HelpLine at
>> 
>> http://www.partners.org/**complianceline.
>>  If the e-mail was sent to
>> you in error
>> but does not contain patient information, please contact the
>> sender and properly
>> dispose of the e-mail.
>>
>>
>>
> --
> Douglas N. Greve, Ph.D.
> MGH-NMR Center
> gr...@nmr.mgh.harvard.edu
> Phone Number: 617-724-2358
> Fax: 617-726-7422
>
> Bugs: 
> surfer.nmr.mgh.harvard.edu/**fswiki/BugReporting
> FileDrop: 
> www.nmr.mgh.harvard.edu/**facility/filedrop/index.html
>
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Re: [Freesurfer] mri_vol2vol

[Douglas N Greve]

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_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.mni --i orig.mgz --o nu.mgz --n 2 --uchar 
> transforms/talairach.xfm
> mri_ca_normalize -mask brainmask.mgz nu.mgz 
> $FREESURFER_HOME/average/RB_all_2008-03-26.gca 
> transforms/talairach.lta norm.mgz
>
> Andrew
>
>
> On Mon, Oct 1, 2012 at 8:32 PM, Douglas Greve 
> mailto:gr...@nmr.mgh.harvard.edu>> wrote:
>
>
> 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
>>
>> 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, but could not find it on the ftp site.  Any
>> suggestions?
>>
>> Andrew
>>
>>
>>
>>
>> ___
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>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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>
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> The information in this e-mail is intended only for the person to
> whom it is
> addressed. If you believe this e-mail was sent to you in error and
> the e-mail
> contains patient information, please contact the Partners
> Compliance HelpLine at
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> you in error
> but does not contain patient information, please contact the
> sender and properly
> dispose of the e-mail.
>
>

-- 
Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html

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Re: [Freesurfer] mri_vol2vol

[Andrew Bock]

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.mni --i orig.mgz --o nu.mgz --n 2 --uchar
transforms/talairach.xfm
mri_ca_normalize -mask brainmask.mgz nu.mgz
$FREESURFER_HOME/average/RB_all_2008-03-26.gca transforms/talairach.lta
norm.mgz

Andrew


On Mon, Oct 1, 2012 at 8:32 PM, Douglas Greve wrote:

>
> 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
>
> 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, but could not find it on the ftp site.  Any suggestions?
>
> Andrew
>
>
>
>
> ___
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> e-mail
> contains patient information, please contact the Partners Compliance
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Re: [Freesurfer] mri_vol2vol

[Douglas Greve]

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


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, but could not find it on the ftp site.  Any suggestions?


Andrew




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[Freesurfer] mri_vol2vol

[Andrew Bock]

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, but could not find it on the ftp site.  Any suggestions?

Andrew
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[Freesurfer] mri_vol2vol not downsampling when applying a morph and a rigid registration matrix

[Alex Kell]

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 their anatomical using bbregister and registered
the subject's anatomical to cvs_avg35 space using mri_cvs_normalize.  Here
is the mri_vol2vol call that I am using to move a volume from cvs space to
native functional space:

mri_vol2vol --targ $roi_in_cvs_space\
--mov $func_vol_file\
--reg-final $bbreg_file   \
--inv   \
--inv-morph \
--m3z $morph_file   \
--o $roi_in_native_func_space  \
--interp nearest\
--noDefM3zPath

This call seems to register the cvs space to the native functional
space accurately -- the mask that I am projecting is in a reasonable
position in the functional space.  However, the voxel size for this output
volume is not the same size as the functional voxels.  The voxel size is
still the same as the size in cvs space.  (Or it could be the anatomical
space, since both are 1 mm isotropic.)

My question: How do I get mri_vol2vol to downsample?  I have no problem
getting mri_vol2vol to downsample from native anatomical to native
functional by applying the inverse of the bbregister-generated matrix, but
I am struggling to get the appropriate downsampling here.  Any suggestions?

And FYI: I'm using this version of
freesurfer: freesurfer-Linux-centos4_x86_64-dev-20120104.

Thanks in advance!


Best,

Alex Kell
Kanwisher Lab Manager
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Re: [Freesurfer] mri_vol2vol

[Lilla Zollei]

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 from 
tkregister2 does not contain the solution from bbregister. Do you have 
both of them saved? Could you apply the bbregister solution alone to your 
T1 and see whether you are getting an acceptable solution? If my 
hypothesis is true, then you will probably need to concatenate the two 
solutions and apply that registration to the T1 to get the desired answer.

--Lilla

On Mon, 12 Sep 2011, Constantin Anastasopoulos wrote:

> 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 .dat
> --surf
>
> As far as I understand the aparc+aseg was the target and the b0 the space 
> difining image. Now again the T1 should be the target and the b0 should 
> remain constant.
> You mean that even if I want to register the T1 to the b0 i have to set the 
> b0 as target?
>
> Thanks
> Constantin
>
>
>
>
>
> Quoting Lilla Zollei :
>
>> 
>> 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 were doing.
>> 
>> Lilla
>> 
>> On Mon, 12 Sep 2011, Constantin Anastasopoulos wrote:
>> 
>> > 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 was the b0image
>> > --targ was the aparc+aseg and T1 respectively
>> > --o was the output (a .nii in both cases)
>> > --reg was the .dat file
>> > and at the and --inv.
>> > 
>> > While the aparc+aseg registration to the b0 worked, the
>> > T1-registration gave a false result (altough it had the same
>> > dimensions and was in the same space with the aparc+aseg).
>> > 
>> > What am I doing wrong? Is the mri_vol2vol command the wrong one? I
>> > want to apply the same changes as to the aparc+aseg, as they are saved
>> > in the .dat file.
>> > 
>> > Thanks a lot,
>> > Constantin
>> > 
>> > 
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>> > 
>> > 
>> > 
>> 
>> 
>> The information in this e-mail is intended only for the person to whom it 
>> is
>> addressed. If you believe this e-mail was sent to you in error and the 
>> e-mail
>> contains patient information, please contact the Partners Compliance
>> HelpLine at
>> http://www.partners.org/complianceline . If the e-mail was sent to you
>> in error
>> but does not contain patient information, please contact the sender and
>> properly
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Re: [Freesurfer] mri_vol2vol

[Constantin Anastasopoulos]

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 .dat
--surf

As far as I understand the aparc+aseg was the target and the b0 the  
space difining image. Now again the T1 should be the target and the b0  
should remain constant.
You mean that even if I want to register the T1 to the b0 i have to  
set the b0 as target?

Thanks
Constantin





Quoting Lilla Zollei :

>
> 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 were doing.
>
> Lilla
>
> On Mon, 12 Sep 2011, Constantin Anastasopoulos wrote:
>
>> 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 was the b0image
>> --targ was the aparc+aseg and T1 respectively
>> --o was the output (a .nii in both cases)
>> --reg was the .dat file
>> and at the and --inv.
>>
>> While the aparc+aseg registration to the b0 worked, the
>> T1-registration gave a false result (altough it had the same
>> dimensions and was in the same space with the aparc+aseg).
>>
>> What am I doing wrong? Is the mri_vol2vol command the wrong one? I
>> want to apply the same changes as to the aparc+aseg, as they are saved
>> in the .dat file.
>>
>> Thanks a lot,
>> Constantin
>>
>>
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>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>
>>
>>
>
>
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> HelpLine at
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Re: [Freesurfer] mri_vol2vol

[Lilla Zollei]

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 were doing.

Lilla

On Mon, 12 Sep 2011, Constantin Anastasopoulos wrote:

> 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 was the b0image
> --targ was the aparc+aseg and T1 respectively
> --o was the output (a .nii in both cases)
> --reg was the .dat file
> and at the and --inv.
>
> While the aparc+aseg registration to the b0 worked, the
> T1-registration gave a false result (altough it had the same
> dimensions and was in the same space with the aparc+aseg).
>
> What am I doing wrong? Is the mri_vol2vol command the wrong one? I
> want to apply the same changes as to the aparc+aseg, as they are saved
> in the .dat file.
>
> Thanks a lot,
> Constantin
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
>
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addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
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[Freesurfer] mri_vol2vol

[Constantin Anastasopoulos]

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 was the b0image
--targ was the aparc+aseg and T1 respectively
--o was the output (a .nii in both cases)
--reg was the .dat file
and at the and --inv.

While the aparc+aseg registration to the b0 worked, the  
T1-registration gave a false result (altough it had the same  
dimensions and was in the same space with the aparc+aseg).

What am I doing wrong? Is the mri_vol2vol command the wrong one? I  
want to apply the same changes as to the aparc+aseg, as they are saved  
in the .dat file.

Thanks a lot,
Constantin


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The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.