Re: [Freesurfer] Coregister the CT image and MRI image

2016-06-15 Thread Douglas Greve 

use mri_vol2vol, like
mri_vol2vol --mov CT.nii --reg v1t2.lta --fstarg --o CT-in-anat.nii


On 6/15/16 9:58 AM, HARI GURAGAIN wrote:

Dear Douglas,

With the suggestions from Zeke, the mri_coreg is working now. I have 
one last question:
I got the new v1to2.lta. How to apply this transformation to the CT 
image? Is it by using mri_convert?

Something like below?

mri_convert -at v1to2.lta CT.nii new_CT.nii


Any suggestion will be greatly appreciated.
Thank you again,
Hari Guragain


On Jun 9, 2016, at 5:53 PM, HARI GURAGAIN > wrote:


Dear Douglas,

I have used the same file as you pointed, but it keeps on showing the 
same error message. I copied the file to my 
/Applications/freesurfer/bin directory but it still shows the same 
error message:
‘dyld: Library not loaded: 
@executable_path/../lib/gcc/lib/libgomp.1.dylib’

Referenced from: /Applications/freesurfer/bin/mri_coreg.mac
Reason: image not found
Trace/BPT trap:5



Does it have something to do with the library issue with mac?
Any help is appreciated.
Thank you,


On Jun 9, 2016, at 5:45 PM, Douglas N Greve 
> wrote:


try
ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_coreg.mac



On 06/09/2016 06:21 PM, HARI GURAGAIN wrote:

Dear Douglas,

The executable is not working as it says ‘Library not loaded: 
@executable_path/../lib/gcc/lib/libgomp.1.dylib’

Referenced from: /Applications/freesurfer/bin/mri_coreg.mac
Reason: image not found
Trace/BPT trap:5

I am currently using the freeview: Version 1.0 and the operating 
system is: OS X EI Captain Version: 10.11.5
I wonder if the file you pointed works for the mac? Should I 
reinstall the freeview?

Any help would be greatly appreciated.

Thank you,

Hari


On Jun 9, 2016, at 4:28 PM, Douglas N Greve 
 wrote:


No, it is not the same command line. If you run it without args, 
it will

give you some info, but it is basically

mri_coreg --mov vol1.nii --targ vol2.nii --reg v1to2.lta


On 06/09/2016 05:22 PM, HARI GURAGAIN wrote:

Thank you Douglas.
One more thing: Is there any syntax how to use it? I wonder if it 
is same as the mri_robust_register?



On Jun 9, 2016, at 3:43 PM, Douglas N Greve 
 wrote:


I don't think robust register will do cross-modal. You may be 
better off

using mri_coreg, which you can get from here

ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_coreg


On 06/09/2016 01:58 PM, HARI GURAGAIN wrote:

Dear Freesurfer community,

I am relatively new to this community.

I was trying to register the CT image and the MRI images (MRI 
as a the

target volume and CT as the movable volume). I used the
mri_robust_register to to do the registration as below:

/mri_robust_register --mov vol1.nii --dst vol2.nii --lta v1to2.lta
--mapmov v1to2.nii --weights v1to2-weights.mii --iscale —satit /

The problem is that:  after register, the new image (v1to2.nii) 
is not

exactly aligned with the original MRI image (vol2.nii). It gives a
very different output. I wonder if I am missing anything here or I
need to do some extra steps after the above command in order to get
the correct alignment of the two images. I was hoping to get the
resultant image should be well orient with the target volume image
(vol2.nii image in my case).

I really appreciate any help here.

Hari Guragain



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--
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
Outgoing: 
ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/


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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.


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--
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

Re: [Freesurfer] Coregister the CT image and MRI image

2016-06-15 Thread HARI GURAGAIN 
Dear Douglas,

With the suggestions from Zeke, the mri_coreg is working now. I have one last 
question:
I got the new v1to2.lta. How to apply this transformation to the CT image? Is 
it by using mri_convert?
Something like below?
mri_convert -at v1to2.lta CT.nii new_CT.nii

Any suggestion will be greatly appreciated.
Thank you again,
Hari Guragain


> On Jun 9, 2016, at 5:53 PM, HARI GURAGAIN  wrote:
> 
> Dear Douglas,
> 
> I have used the same file as you pointed, but it keeps on showing the same 
> error message. I copied the file to my /Applications/freesurfer/bin directory 
> but it still shows the same error message:
>>> ‘dyld: Library not loaded: @executable_path/../lib/gcc/lib/libgomp.1.dylib’
>>> Referenced from: /Applications/freesurfer/bin/mri_coreg.mac
>>> Reason: image not found
>>> Trace/BPT trap:5
> 
> 
> Does it have something to do with the library issue with mac?
> Any help is appreciated.
> Thank you,
> 
> 
>> On Jun 9, 2016, at 5:45 PM, Douglas N Greve  
>> wrote:
>> 
>> try
>> ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_coreg.mac
>> 
>> 
>> 
>> On 06/09/2016 06:21 PM, HARI GURAGAIN wrote:
>>> Dear Douglas,
>>> 
>>> The executable is not working as it says ‘Library not loaded: 
>>> @executable_path/../lib/gcc/lib/libgomp.1.dylib’
>>> Referenced from: /Applications/freesurfer/bin/mri_coreg.mac
>>> Reason: image not found
>>> Trace/BPT trap:5
>>> 
>>> I am currently using the freeview: Version 1.0 and the operating system is: 
>>> OS X EI Captain Version: 10.11.5
>>> I wonder if the file you pointed works for the mac? Should I reinstall the 
>>> freeview?
>>> Any help would be greatly appreciated.
>>> 
>>> Thank you,
>>> 
>>> Hari
>>> 
>>> 
 On Jun 9, 2016, at 4:28 PM, Douglas N Greve  
 wrote:
 
 No, it is not the same command line. If you run it without args, it will
 give you some info, but it is basically
 
 mri_coreg --mov vol1.nii --targ vol2.nii --reg v1to2.lta
 
 
 On 06/09/2016 05:22 PM, HARI GURAGAIN wrote:
> Thank you Douglas.
> One more thing: Is there any syntax how to use it? I wonder if it is same 
> as the mri_robust_register?
> 
> 
>> On Jun 9, 2016, at 3:43 PM, Douglas N Greve  
>> wrote:
>> 
>> I don't think robust register will do cross-modal. You may be better off
>> using mri_coreg, which you can get from here
>> 
>> ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_coreg
>> 
>> 
>> On 06/09/2016 01:58 PM, HARI GURAGAIN wrote:
>>> Dear Freesurfer community,
>>> 
>>> I am relatively new to this community.
>>> 
>>> I was trying to register the CT image and the MRI images (MRI as a the
>>> target volume and CT as the movable volume). I used the
>>> mri_robust_register to to do the registration as below:
>>> 
>>> /mri_robust_register --mov vol1.nii --dst vol2.nii --lta v1to2.lta
>>> --mapmov v1to2.nii --weights v1to2-weights.mii --iscale —satit /
>>> 
>>> The problem is that:  after register, the new image (v1to2.nii) is not
>>> exactly aligned with the original MRI image (vol2.nii). It gives a
>>> very different output. I wonder if I am missing anything here or I
>>> need to do some extra steps after the above command in order to get
>>> the correct alignment of the two images. I was hoping to get the
>>> resultant image should be well orient with the target volume image
>>> (vol2.nii image in my case).
>>> 
>>> I really appreciate any help here.
>>> 
>>> Hari Guragain
>>> 
>>> 
>>> 
>>> ___
>>> Freesurfer mailing list
>>> Freesurfer@nmr.mgh.harvard.edu
>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>> -- 
>> 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
>> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
>> 
>> ___
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.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

Re: [Freesurfer] Coregister the CT image and MRI image

2016-06-14 Thread Z K 
Hello Hari,

In order to use mri_coreg on Mac, you will need to download the 
"Development Version" of freesurfer. See the following page under 
Development Version:

   https://surfer.nmr.mgh.harvard.edu/fswiki/Download

Once downloaded, uncompress the .tar.gz file to some directory on your 
machine and set the FREESURFER_HOME environment variable appropriately. 
Also, you will want to copy over your license file as well. Then you 
should be able to use the mri_coreg binary as Doug mentions below.

-Zeke

On 06/09/2016 06:53 PM, HARI GURAGAIN wrote:
> Dear Douglas,
>
> I have used the same file as you pointed, but it keeps on showing the same 
> error message. I copied the file to my /Applications/freesurfer/bin directory 
> but it still shows the same error message:
>>> ‘dyld: Library not loaded: @executable_path/../lib/gcc/lib/libgomp.1.dylib’
>>> Referenced from: /Applications/freesurfer/bin/mri_coreg.mac
>>> Reason: image not found
>>> Trace/BPT trap:5
>
>
> Does it have something to do with the library issue with mac?
> Any help is appreciated.
> Thank you,
>
>
>> On Jun 9, 2016, at 5:45 PM, Douglas N Greve  
>> wrote:
>>
>> try
>> ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_coreg.mac
>>
>>
>>
>> On 06/09/2016 06:21 PM, HARI GURAGAIN wrote:
>>> Dear Douglas,
>>>
>>> The executable is not working as it says ‘Library not loaded: 
>>> @executable_path/../lib/gcc/lib/libgomp.1.dylib’
>>> Referenced from: /Applications/freesurfer/bin/mri_coreg.mac
>>> Reason: image not found
>>> Trace/BPT trap:5
>>>
>>> I am currently using the freeview: Version 1.0 and the operating system is: 
>>> OS X EI Captain Version: 10.11.5
>>> I wonder if the file you pointed works for the mac? Should I reinstall the 
>>> freeview?
>>> Any help would be greatly appreciated.
>>>
>>> Thank you,
>>>
>>> Hari
>>>
>>>
 On Jun 9, 2016, at 4:28 PM, Douglas N Greve  
 wrote:

 No, it is not the same command line. If you run it without args, it will
 give you some info, but it is basically

 mri_coreg --mov vol1.nii --targ vol2.nii --reg v1to2.lta


 On 06/09/2016 05:22 PM, HARI GURAGAIN wrote:
> Thank you Douglas.
> One more thing: Is there any syntax how to use it? I wonder if it is same 
> as the mri_robust_register?
>
>
>> On Jun 9, 2016, at 3:43 PM, Douglas N Greve  
>> wrote:
>>
>> I don't think robust register will do cross-modal. You may be better off
>> using mri_coreg, which you can get from here
>>
>> ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_coreg
>>
>>
>> On 06/09/2016 01:58 PM, HARI GURAGAIN wrote:
>>> Dear Freesurfer community,
>>>
>>> I am relatively new to this community.
>>>
>>> I was trying to register the CT image and the MRI images (MRI as a the
>>> target volume and CT as the movable volume). I used the
>>> mri_robust_register to to do the registration as below:
>>>
>>> /mri_robust_register --mov vol1.nii --dst vol2.nii --lta v1to2.lta
>>> --mapmov v1to2.nii --weights v1to2-weights.mii --iscale —satit /
>>>
>>> The problem is that:  after register, the new image (v1to2.nii) is not
>>> exactly aligned with the original MRI image (vol2.nii). It gives a
>>> very different output. I wonder if I am missing anything here or I
>>> need to do some extra steps after the above command in order to get
>>> the correct alignment of the two images. I was hoping to get the
>>> resultant image should be well orient with the target volume image
>>> (vol2.nii image in my case).
>>>
>>> I really appreciate any help here.
>>>
>>> Hari Guragain
>>>
>>>
>>>
>>> ___
>>> Freesurfer mailing list
>>> Freesurfer@nmr.mgh.harvard.edu
>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>> --
>> 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
>> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
>>
>> ___
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.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

Re: [Freesurfer] Coregister the CT image and MRI image

2016-06-09 Thread HARI GURAGAIN 
Dear Douglas,

I have used the same file as you pointed, but it keeps on showing the same 
error message. I copied the file to my /Applications/freesurfer/bin directory 
but it still shows the same error message:
>> ‘dyld: Library not loaded: @executable_path/../lib/gcc/lib/libgomp.1.dylib’
>> Referenced from: /Applications/freesurfer/bin/mri_coreg.mac
>> Reason: image not found
>> Trace/BPT trap:5


Does it have something to do with the library issue with mac?
Any help is appreciated.
Thank you,


> On Jun 9, 2016, at 5:45 PM, Douglas N Greve  wrote:
> 
> try
> ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_coreg.mac
> 
> 
> 
> On 06/09/2016 06:21 PM, HARI GURAGAIN wrote:
>> Dear Douglas,
>> 
>> The executable is not working as it says ‘Library not loaded: 
>> @executable_path/../lib/gcc/lib/libgomp.1.dylib’
>> Referenced from: /Applications/freesurfer/bin/mri_coreg.mac
>> Reason: image not found
>> Trace/BPT trap:5
>> 
>> I am currently using the freeview: Version 1.0 and the operating system is: 
>> OS X EI Captain Version: 10.11.5
>> I wonder if the file you pointed works for the mac? Should I reinstall the 
>> freeview?
>> Any help would be greatly appreciated.
>> 
>> Thank you,
>> 
>> Hari
>> 
>> 
>>> On Jun 9, 2016, at 4:28 PM, Douglas N Greve  
>>> wrote:
>>> 
>>> No, it is not the same command line. If you run it without args, it will
>>> give you some info, but it is basically
>>> 
>>> mri_coreg --mov vol1.nii --targ vol2.nii --reg v1to2.lta
>>> 
>>> 
>>> On 06/09/2016 05:22 PM, HARI GURAGAIN wrote:
 Thank you Douglas.
 One more thing: Is there any syntax how to use it? I wonder if it is same 
 as the mri_robust_register?
 
 
> On Jun 9, 2016, at 3:43 PM, Douglas N Greve  
> wrote:
> 
> I don't think robust register will do cross-modal. You may be better off
> using mri_coreg, which you can get from here
> 
> ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_coreg
> 
> 
> On 06/09/2016 01:58 PM, HARI GURAGAIN wrote:
>> Dear Freesurfer community,
>> 
>> I am relatively new to this community.
>> 
>> I was trying to register the CT image and the MRI images (MRI as a the
>> target volume and CT as the movable volume). I used the
>> mri_robust_register to to do the registration as below:
>> 
>> /mri_robust_register --mov vol1.nii --dst vol2.nii --lta v1to2.lta
>> --mapmov v1to2.nii --weights v1to2-weights.mii --iscale —satit /
>> 
>> The problem is that:  after register, the new image (v1to2.nii) is not
>> exactly aligned with the original MRI image (vol2.nii). It gives a
>> very different output. I wonder if I am missing anything here or I
>> need to do some extra steps after the above command in order to get
>> the correct alignment of the two images. I was hoping to get the
>> resultant image should be well orient with the target volume image
>> (vol2.nii image in my case).
>> 
>> I really appreciate any help here.
>> 
>> Hari Guragain
>> 
>> 
>> 
>> ___
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> -- 
> 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
> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
> 
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.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.
> 
 ___
 Freesurfer mailing list
 Freesurfer@nmr.mgh.harvard.edu
 https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
 
 
>>> -- 
>>> 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
>>>

Re: [Freesurfer] Coregister the CT image and MRI image

2016-06-09 Thread Douglas N Greve 
try
ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_coreg.mac



On 06/09/2016 06:21 PM, HARI GURAGAIN wrote:
> Dear Douglas,
>
> The executable is not working as it says ‘Library not loaded: 
> @executable_path/../lib/gcc/lib/libgomp.1.dylib’
> Referenced from: /Applications/freesurfer/bin/mri_coreg.mac
> Reason: image not found
> Trace/BPT trap:5
>
> I am currently using the freeview: Version 1.0 and the operating system is: 
> OS X EI Captain Version: 10.11.5
> I wonder if the file you pointed works for the mac? Should I reinstall the 
> freeview?
> Any help would be greatly appreciated.
>
> Thank you,
>
> Hari
>
>
>> On Jun 9, 2016, at 4:28 PM, Douglas N Greve  
>> wrote:
>>
>> No, it is not the same command line. If you run it without args, it will
>> give you some info, but it is basically
>>
>> mri_coreg --mov vol1.nii --targ vol2.nii --reg v1to2.lta
>>
>>
>> On 06/09/2016 05:22 PM, HARI GURAGAIN wrote:
>>> Thank you Douglas.
>>> One more thing: Is there any syntax how to use it? I wonder if it is same 
>>> as the mri_robust_register?
>>>
>>>
 On Jun 9, 2016, at 3:43 PM, Douglas N Greve  
 wrote:

 I don't think robust register will do cross-modal. You may be better off
 using mri_coreg, which you can get from here

 ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_coreg


 On 06/09/2016 01:58 PM, HARI GURAGAIN wrote:
> Dear Freesurfer community,
>
> I am relatively new to this community.
>
> I was trying to register the CT image and the MRI images (MRI as a the
> target volume and CT as the movable volume). I used the
> mri_robust_register to to do the registration as below:
>
> /mri_robust_register --mov vol1.nii --dst vol2.nii --lta v1to2.lta
> --mapmov v1to2.nii --weights v1to2-weights.mii --iscale —satit /
>
> The problem is that:  after register, the new image (v1to2.nii) is not
> exactly aligned with the original MRI image (vol2.nii). It gives a
> very different output. I wonder if I am missing anything here or I
> need to do some extra steps after the above command in order to get
> the correct alignment of the two images. I was hoping to get the
> resultant image should be well orient with the target volume image
> (vol2.nii image in my case).
>
> I really appreciate any help here.
>
> Hari Guragain
>
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
 -- 
 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
 Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

 ___
 Freesurfer mailing list
 Freesurfer@nmr.mgh.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.

>>> ___
>>> Freesurfer mailing list
>>> Freesurfer@nmr.mgh.harvard.edu
>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>>
>>>
>> -- 
>> 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
>> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
>>
>> ___
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu
>> https://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
>
>

-- 
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
Outgoing:

Re: [Freesurfer] Coregister the CT image and MRI image

2016-06-09 Thread HARI GURAGAIN 
Dear Douglas,

The executable is not working as it says ‘Library not loaded: 
@executable_path/../lib/gcc/lib/libgomp.1.dylib’ 
Referenced from: /Applications/freesurfer/bin/mri_coreg.mac 
Reason: image not found
Trace/BPT trap:5

I am currently using the freeview: Version 1.0 and the operating system is: OS 
X EI Captain Version: 10.11.5
I wonder if the file you pointed works for the mac? Should I reinstall the 
freeview? 
Any help would be greatly appreciated.

Thank you,

Hari 


> On Jun 9, 2016, at 4:28 PM, Douglas N Greve  wrote:
> 
> No, it is not the same command line. If you run it without args, it will 
> give you some info, but it is basically
> 
> mri_coreg --mov vol1.nii --targ vol2.nii --reg v1to2.lta
> 
> 
> On 06/09/2016 05:22 PM, HARI GURAGAIN wrote:
>> Thank you Douglas.
>> One more thing: Is there any syntax how to use it? I wonder if it is same as 
>> the mri_robust_register?
>> 
>> 
>>> On Jun 9, 2016, at 3:43 PM, Douglas N Greve  
>>> wrote:
>>> 
>>> I don't think robust register will do cross-modal. You may be better off
>>> using mri_coreg, which you can get from here
>>> 
>>> ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_coreg
>>> 
>>> 
>>> On 06/09/2016 01:58 PM, HARI GURAGAIN wrote:
 Dear Freesurfer community,
 
 I am relatively new to this community.
 
 I was trying to register the CT image and the MRI images (MRI as a the
 target volume and CT as the movable volume). I used the
 mri_robust_register to to do the registration as below:
 
 /mri_robust_register --mov vol1.nii --dst vol2.nii --lta v1to2.lta
 --mapmov v1to2.nii --weights v1to2-weights.mii --iscale —satit /
 
 The problem is that:  after register, the new image (v1to2.nii) is not
 exactly aligned with the original MRI image (vol2.nii). It gives a
 very different output. I wonder if I am missing anything here or I
 need to do some extra steps after the above command in order to get
 the correct alignment of the two images. I was hoping to get the
 resultant image should be well orient with the target volume image
 (vol2.nii image in my case).
 
 I really appreciate any help here.
 
 Hari Guragain
 
 
 
 ___
 Freesurfer mailing list
 Freesurfer@nmr.mgh.harvard.edu
 https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>> -- 
>>> 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
>>> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
>>> 
>>> ___
>>> Freesurfer mailing list
>>> Freesurfer@nmr.mgh.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.
>>> 
>> 
>> ___
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>> 
>> 
> 
> -- 
> 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
> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
> 
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


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Re: [Freesurfer] Coregister the CT image and MRI image

2016-06-09 Thread Douglas N Greve 
No, it is not the same command line. If you run it without args, it will 
give you some info, but it is basically

mri_coreg --mov vol1.nii --targ vol2.nii --reg v1to2.lta


On 06/09/2016 05:22 PM, HARI GURAGAIN wrote:
> Thank you Douglas.
> One more thing: Is there any syntax how to use it? I wonder if it is same as 
> the mri_robust_register?
>
>
>> On Jun 9, 2016, at 3:43 PM, Douglas N Greve  
>> wrote:
>>
>> I don't think robust register will do cross-modal. You may be better off
>> using mri_coreg, which you can get from here
>>
>> ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_coreg
>>
>>
>> On 06/09/2016 01:58 PM, HARI GURAGAIN wrote:
>>> Dear Freesurfer community,
>>>
>>> I am relatively new to this community.
>>>
>>> I was trying to register the CT image and the MRI images (MRI as a the
>>> target volume and CT as the movable volume). I used the
>>> mri_robust_register to to do the registration as below:
>>>
>>> /mri_robust_register --mov vol1.nii --dst vol2.nii --lta v1to2.lta
>>> --mapmov v1to2.nii --weights v1to2-weights.mii --iscale —satit /
>>>
>>> The problem is that:  after register, the new image (v1to2.nii) is not
>>> exactly aligned with the original MRI image (vol2.nii). It gives a
>>> very different output. I wonder if I am missing anything here or I
>>> need to do some extra steps after the above command in order to get
>>> the correct alignment of the two images. I was hoping to get the
>>> resultant image should be well orient with the target volume image
>>> (vol2.nii image in my case).
>>>
>>> I really appreciate any help here.
>>>
>>> Hari Guragain
>>>
>>>
>>>
>>> ___
>>> Freesurfer mailing list
>>> Freesurfer@nmr.mgh.harvard.edu
>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>> -- 
>> 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
>> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
>>
>> ___
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.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.
>>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>

-- 
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
Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

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Re: [Freesurfer] Coregister the CT image and MRI image

2016-06-09 Thread HARI GURAGAIN 
Thank you Douglas.
One more thing: Is there any syntax how to use it? I wonder if it is same as 
the mri_robust_register?


> On Jun 9, 2016, at 3:43 PM, Douglas N Greve  wrote:
> 
> I don't think robust register will do cross-modal. You may be better off 
> using mri_coreg, which you can get from here
> 
> ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_coreg
> 
> 
> On 06/09/2016 01:58 PM, HARI GURAGAIN wrote:
>> Dear Freesurfer community,
>> 
>> I am relatively new to this community.
>> 
>> I was trying to register the CT image and the MRI images (MRI as a the 
>> target volume and CT as the movable volume). I used the 
>> mri_robust_register to to do the registration as below:
>> 
>> /mri_robust_register --mov vol1.nii --dst vol2.nii --lta v1to2.lta 
>> --mapmov v1to2.nii --weights v1to2-weights.mii --iscale —satit /
>> 
>> The problem is that:  after register, the new image (v1to2.nii) is not 
>> exactly aligned with the original MRI image (vol2.nii). It gives a 
>> very different output. I wonder if I am missing anything here or I 
>> need to do some extra steps after the above command in order to get 
>> the correct alignment of the two images. I was hoping to get the 
>> resultant image should be well orient with the target volume image 
>> (vol2.nii image in my case).
>> 
>> I really appreciate any help here.
>> 
>> Hari Guragain
>> 
>> 
>> 
>> ___
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> 
> -- 
> 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
> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
> 
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.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.
> 


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Re: [Freesurfer] Coregister the CT image and MRI image

2016-06-09 Thread Douglas N Greve 
I don't think robust register will do cross-modal. You may be better off 
using mri_coreg, which you can get from here

ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_coreg


On 06/09/2016 01:58 PM, HARI GURAGAIN wrote:
> Dear Freesurfer community,
>
> I am relatively new to this community.
>
> I was trying to register the CT image and the MRI images (MRI as a the 
> target volume and CT as the movable volume). I used the 
> mri_robust_register to to do the registration as below:
>
> /mri_robust_register --mov vol1.nii --dst vol2.nii --lta v1to2.lta 
> --mapmov v1to2.nii --weights v1to2-weights.mii --iscale —satit /
>
> The problem is that:  after register, the new image (v1to2.nii) is not 
> exactly aligned with the original MRI image (vol2.nii). It gives a 
> very different output. I wonder if I am missing anything here or I 
> need to do some extra steps after the above command in order to get 
> the correct alignment of the two images. I was hoping to get the 
> resultant image should be well orient with the target volume image 
> (vol2.nii image in my case).
>
> I really appreciate any help here.
>
> Hari Guragain
>
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

-- 
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
Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

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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.