Re: [Freesurfer] WM/GM boundary changes and control points

[EK Kim]

Bruce, and other experts, thank you for your time :)

I'm now uploading the data folder (before cp and after cp) to the
freesurfer incoming directory.


We obtained the 3D-SPGR axial images using 3T GE system which have 8HRBRAIN
receiving coil.
Data acquisition matrix is 320-by192, FOV is 200-by-200.

Other parameters;
slice thickness =1.5
TR=5.924
TE=1.472
Flip angle: 20
Inversion Time=400
Imaging Frequency 127.88
Percent Phase FOV =80

Sincerely,

EK



2012/10/11 Bruce Fischl 

> Hi EK
>
> that is a really low-contrast image. Can you tell me about the acquisition
> parameters and resolution? Also, I can't diagnose your problem from just
> the volume I'll need the entire (tarred and gzipped) subject directory.
> Finally, please cc the list on these emails so that others can help you!
>
> Bruce
>
> On Thu, 11 Oct 2012, EK Kim wrote:
>
>  I uploaded the files to transfer/incoming folder.
>>
>>
>> Best,
>>
>> EK
>>
>> 2012/10/11 Bruce Fischl 
>>   If you upload the subject to our FTP site I will take a look
>> Bruce
>>
>>
>>
>> On Oct 10, 2012, at 9:29 PM, EK Kim  wrote:
>>
>>   Thank you for your answer.
>> I'm not sure I understand your question right,
>> but I just processed the file using following procedures.
>> 1. recon-all -autorecon1 -nuintensitycor-3T (because mine was
>> 3T)
>> 2. skullstripping brain mask using gcuts
>> 3. adding control points (only on the left hemisphere)
>> 4. recon-all -autorecon2-cp
>> and this figure was made by a commnad line, [tkmedit wm.mgz -aux
>> brain.mgz -surfs].
>> Best,
>> EK.
>>
>> 2012/10/10 Bruce Fischl 
>>   what was the name of the file that you transferred?
>>   On Wed, 10 Oct 2012, EK Kim wrote:
>>
>> I already uploaded this problem 2 days
>> ago, reprocessing the subject to make
>> sure about control points.
>> However when I added the control points
>> to the left hemisphere,
>> the right hemisphere surface was changed
>> severely.
>> I used the command line, recon-all
>> -autorecon2-cp -s subjectID.
>> Could you tell me why does it occur and
>> how to deal with it?
>>
>>
>> Best,
>>
>> EK
>>
>>
>>
>>
>> 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
>>
>>
>>
>>
___
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.

Re: [Freesurfer] WM/GM boundary changes and control points

[Bruce Fischl]

how long is the scan? Probably pretty short with a TR that short. It's 
*very* low CNR so it's going to be tough to get much out of it


On Sat, 13 Oct 2012, EK Kim wrote:


Bruce, and other experts, thank you for your time :)
 
I'm now uploading the data folder (before cp and after cp) to the freesurfer
incoming directory.
 
 
We obtained the 3D-SPGR axial images using 3T GE system which have 8HRBRAIN
receiving coil.
Data acquisition matrix is 320-by192, FOV is 200-by-200.
 
Other parameters;
slice thickness =1.5
TR=5.924
TE=1.472
Flip angle: 20
Inversion Time=400
Imaging Frequency 127.88
Percent Phase FOV =80
 
Sincerely,
 
EK


 
2012/10/11 Bruce Fischl 
  Hi EK

  that is a really low-contrast image. Can you tell me about the
  acquisition parameters and resolution? Also, I can't diagnose
  your problem from just the volume I'll need the entire (tarred
  and gzipped) subject directory. Finally, please cc the list on
  these emails so that others can help you!

  Bruce
  On Thu, 11 Oct 2012, EK Kim wrote:

I uploaded the files to transfer/incoming folder.
 
 
Best,
 
EK

2012/10/11 Bruce Fischl 
      If you upload the subject to our FTP site I
will take a look
Bruce



On Oct 10, 2012, at 9:29 PM, EK Kim
 wrote:

      Thank you for your answer.
I'm not sure I understand your question right,
but I just processed the file using following
procedures.
1. recon-all -autorecon1 -nuintensitycor-3T (because
mine was
3T)
2. skullstripping brain mask using gcuts
3. adding control points (only on the left
hemisphere)
4. recon-all -autorecon2-cp
and this figure was made by a commnad line, [tkmedit
wm.mgz -aux
brain.mgz -surfs].
Best,
EK.

2012/10/10 Bruce Fischl 
      what was the name of the file that you
transferred?
      On Wed, 10 Oct 2012, EK Kim wrote:

            I already uploaded this problem 2 days
            ago, reprocessing the subject to make
            sure about control points.
            However when I added the control points
            to the left hemisphere,
            the right hemisphere surface was changed
            severely. 
            I used the command line, recon-all
            -autorecon2-cp -s subjectID.
            Could you tell me why does it occur and
            how to deal with it?


            Best,

            EK 




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





___
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.