Re: [Freesurfer] question about reslicing

2016-07-26 Thread Dorsa Haji Ghaffari 
Hi,
Yes my original data has 1x1x1mm voxel dimension but I prefer to work with
the upsampled data. I am satisfied with the results I get from Freesurfer
and the results actually look better than the results I get with the 1mm
data, the only problem I have is that the thalamus mask does not keep the
original dimensions in both cases. It is 256x256x256 ,so in terms of the
thalamus position I do not know if it is at the right place. I will need to
combine the STN that I have traced out in Analyze with the thalamus, thats
why I need to make sure everything are in the correct position with respect
to others.

Thank you

Dorsa

On Tue, Jul 26, 2016 at 1:58 PM, Bruce Fischl 
wrote:

> sorry, I'm confused about what you are trying to do. Can you start from
> the beginning and explain? If the data you have is 1mm but upsampled by the
> scanner there is really nothing to be gained by processing the upsampled
> data and it will waste lots of time
>
>
> cheers
> Bruce
>
> On Mon, 25 Jul 2016, Dorsa Haji Ghaffari wrote:
>
> Yes I created it using the higher resolution and I think it looks fine. I
>> attached the aseg.mgz. Is there any way to create the thalamus mask with
>> the
>> original properties ( same as the original mri) at the first place? I need
>> to make sure the size and position of the thalamus corresponds to the
>> original mri.
>>
>> Thank you!
>>
>> Dorsa
>>
>> On Mon, Jul 25, 2016 at 3:29 PM, Bruce Fischl > >
>> wrote:
>>   Hi Dorsa
>>
>>   did you create the aseg.mgz from 1mm data (using the standard
>>   "conform" process), or higher res? The file you sent is higher:
>>
>>   mri_info resliceduncoregtahalmus.nii.gz
>>   Volume information for resliceduncoregtahalmus.nii.gz
>> type: nii
>>   dimensions: 512 x 512 x 288
>>  voxel sizes: 0.488281, 0.488281, 0.625000
>> type: SHORT (4)
>>  fov: 250.000
>>  dof: 0
>>   xstart: -125.0, xend: 125.0
>>   ystart: -125.0, yend: 125.0
>>   zstart: -90.0, zend: 90.0
>>   TR: 8.06 msec, TE: 0.00 msec, TI: 0.00 msec, flip
>>   angle: 0.00 degrees
>>  nframes: 1
>>  PhEncDir: UNKNOWN
>>  FieldStrength: 0.00
>>   ras xform present
>>
>>
>>   it also has strange values in it (-32K and 32K, so probably
>>   things that can't be represented as a short). Does your aseg.mgz
>>   look right?
>>
>>   cheers
>>   Bruce
>>
>>
>>   On Mon, 25 Jul 2016, Dorsa Haji Ghaffari wrote:
>>
>> Hi, This is the command line for reslicing:
>> mri_convert -rl aseg.mgz thalamus.nii
>> resliceduncoregtahalmus.nii
>>
>> thalamus.nii is the thalamus mask obtained by using
>> the following command:
>> mri_binarize --i aseg.mgz --match 10 --o
>> thalamus.mask.nii.gz
>>
>> and I have attached the out put.
>>
>> Thank you!
>>
>> On Mon, Jul 25, 2016 at 12:41 PM, Bruce Fischl
>> 
>> wrote:
>>   Hi Dorsa
>>
>>   you need to give us more details. What was
>> your reslicing
>>   command line? And the screen output?
>>
>>   Bruce
>>   On Mon, 25 Jul 2016, Dorsa Haji Ghaffari
>> wrote:
>>
>>
>> Hi,
>>
>> I re-sliced my left thalamus so that the
>> size and
>> number of slices correspond with the
>> original MRI,
>> but when I open it in freeview, it shows
>> an extra
>> part(
>> like a cube) on the bottom of the image
>> ( I have
>> attached the  mask). do you have any
>> idea how to
>> solve that?
>> Also how can I make sure that the
>> position and size
>> of the thalamus makes sense since the
>> thalamus mask
>> has a different slice size and number
>> than the
>> original mri?
>>
>> Thank you
>>
>> Dorsa
>>
>>
>>
>> ___
>> 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,

Re: [Freesurfer] question about reslicing

2016-07-26 Thread Bruce Fischl 
sorry, I'm confused about what you are trying to do. Can you start from the 
beginning and explain? If the data you have is 1mm but upsampled by 
the scanner there is really nothing to be gained by processing the 
upsampled data and it will waste lots of time


cheers
Bruce

On Mon, 25 Jul 2016, 
Dorsa Haji Ghaffari wrote:



Yes I created it using the higher resolution and I think it looks fine. I
attached the aseg.mgz. Is there any way to create the thalamus mask with the
original properties ( same as the original mri) at the first place? I need
to make sure the size and position of the thalamus corresponds to the
original mri.

Thank you!

Dorsa

On Mon, Jul 25, 2016 at 3:29 PM, Bruce Fischl 
wrote:
  Hi Dorsa

  did you create the aseg.mgz from 1mm data (using the standard
  "conform" process), or higher res? The file you sent is higher:

  mri_info resliceduncoregtahalmus.nii.gz
  Volume information for resliceduncoregtahalmus.nii.gz
            type: nii
      dimensions: 512 x 512 x 288
     voxel sizes: 0.488281, 0.488281, 0.625000
            type: SHORT (4)
             fov: 250.000
             dof: 0
          xstart: -125.0, xend: 125.0
          ystart: -125.0, yend: 125.0
          zstart: -90.0, zend: 90.0
              TR: 8.06 msec, TE: 0.00 msec, TI: 0.00 msec, flip
  angle: 0.00 degrees
         nframes: 1
         PhEncDir: UNKNOWN
         FieldStrength: 0.00
  ras xform present


  it also has strange values in it (-32K and 32K, so probably
  things that can't be represented as a short). Does your aseg.mgz
  look right?

  cheers
  Bruce


  On Mon, 25 Jul 2016, Dorsa Haji Ghaffari wrote:

Hi, This is the command line for reslicing:
mri_convert -rl aseg.mgz thalamus.nii
resliceduncoregtahalmus.nii

thalamus.nii is the thalamus mask obtained by using
the following command:
mri_binarize --i aseg.mgz --match 10 --o
thalamus.mask.nii.gz

and I have attached the out put.

Thank you!

On Mon, Jul 25, 2016 at 12:41 PM, Bruce Fischl

wrote:
      Hi Dorsa

      you need to give us more details. What was
your reslicing
      command line? And the screen output?

      Bruce
      On Mon, 25 Jul 2016, Dorsa Haji Ghaffari
wrote:


            Hi,

            I re-sliced my left thalamus so that the
size and
            number of slices correspond with the
original MRI,
            but when I open it in freeview, it shows
an extra
            part(
            like a cube) on the bottom of the image
( I have
            attached the  mask). do you have any
idea how to
            solve that? 
            Also how can I make sure that the
position and size
            of the thalamus makes sense since the
thalamus mask
            has a different slice size and number
than the
            original mri?

            Thank you

            Dorsa



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Re: [Freesurfer] question about reslicing

2016-07-26 Thread Douglas N Greve 
Does this wiki page help?
http://surfer.nmr.mgh.harvard.edu/fswiki/FsAnat-to-NativeAnat

On 07/25/2016 04:22 PM, Dorsa Haji Ghaffari wrote:
> Yes I created it using the higher resolution and I think it looks 
> fine. I attached the aseg.mgz. Is there any way to create the thalamus 
> mask with the original properties ( same as the original mri) at the 
> first place? I need to make sure the size and position of the thalamus 
> corresponds to the original mri.
>
> Thank you!
>
> Dorsa
>
> On Mon, Jul 25, 2016 at 3:29 PM, Bruce Fischl 
> > wrote:
>
> Hi Dorsa
>
> did you create the aseg.mgz from 1mm data (using the standard
> "conform" process), or higher res? The file you sent is higher:
>
> mri_info resliceduncoregtahalmus.nii.gz
> Volume information for resliceduncoregtahalmus.nii.gz
>   type: nii
> dimensions: 512 x 512 x 288
>voxel sizes: 0.488281, 0.488281, 0.625000
>   type: SHORT (4)
>fov: 250.000
>dof: 0
> xstart: -125.0, xend: 125.0
> ystart: -125.0, yend: 125.0
> zstart: -90.0, zend: 90.0
> TR: 8.06 msec, TE: 0.00 msec, TI: 0.00 msec, flip
> angle: 0.00 degrees
>nframes: 1
>PhEncDir: UNKNOWN
>FieldStrength: 0.00
> ras xform present
>
>
> it also has strange values in it (-32K and 32K, so probably things
> that can't be represented as a short). Does your aseg.mgz look right?
>
> cheers
>
> Bruce
>
>
> On Mon, 25 Jul 2016, Dorsa Haji Ghaffari wrote:
>
> Hi, This is the command line for reslicing:
> mri_convert -rl aseg.mgz thalamus.nii resliceduncoregtahalmus.nii
>
> thalamus.nii is the thalamus mask obtained by using the
> following command:
> mri_binarize --i aseg.mgz --match 10 --o thalamus.mask.nii.gz
>
> and I have attached the out put.
>
> Thank you!
>
> On Mon, Jul 25, 2016 at 12:41 PM, Bruce Fischl
> >
> wrote:
>   Hi Dorsa
>
>   you need to give us more details. What was your reslicing
>   command line? And the screen output?
>
>   Bruce
>   On Mon, 25 Jul 2016, Dorsa Haji Ghaffari wrote:
>
>
> Hi,
>
> I re-sliced my left thalamus so that the size and
> number of slices correspond with the original MRI,
> but when I open it in freeview, it shows an extra
> part(
> like a cube) on the bottom of the image ( I have
> attached the  mask). do you have any idea how to
> solve that?
> Also how can I make sure that the position and size
> of the thalamus makes sense since the thalamus mask
> has a different slice size and number than the
> original mri?
>
> Thank you
>
> Dorsa
>
>
>
> ___
> 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
>
>
> 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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> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

-- 
Douglas N. Greve, Ph.D.
MGH-NMR Center

Re: [Freesurfer] question about reslicing

2016-07-25 Thread Bruce Fischl 

Hi Dorsa

did you create the aseg.mgz from 1mm data (using the standard "conform" 
process), or higher res? The file you sent is higher:


mri_info resliceduncoregtahalmus.nii.gz
Volume information for resliceduncoregtahalmus.nii.gz
  type: nii
dimensions: 512 x 512 x 288
   voxel sizes: 0.488281, 0.488281, 0.625000
  type: SHORT (4)
   fov: 250.000
   dof: 0
xstart: -125.0, xend: 125.0
ystart: -125.0, yend: 125.0
zstart: -90.0, zend: 90.0
TR: 8.06 msec, TE: 0.00 msec, TI: 0.00 msec, flip angle: 0.00 
degrees

   nframes: 1
   PhEncDir: UNKNOWN
   FieldStrength: 0.00
ras xform present


it also has strange values in it (-32K and 32K, so probably things that 
can't be represented as a short). Does your aseg.mgz look right?


cheers
Bruce


On 
Mon, 25 Jul 2016, 
Dorsa Haji Ghaffari wrote:



Hi, This is the command line for reslicing:
mri_convert -rl aseg.mgz thalamus.nii resliceduncoregtahalmus.nii

thalamus.nii is the thalamus mask obtained by using the following command:
mri_binarize --i aseg.mgz --match 10 --o thalamus.mask.nii.gz

and I have attached the out put.

Thank you!

On Mon, Jul 25, 2016 at 12:41 PM, Bruce Fischl 
wrote:
  Hi Dorsa

  you need to give us more details. What was your reslicing
  command line? And the screen output?

  Bruce
  On Mon, 25 Jul 2016, Dorsa Haji Ghaffari wrote:


Hi,

I re-sliced my left thalamus so that the size and
number of slices correspond with the original MRI,
but when I open it in freeview, it shows an extra
part(
like a cube) on the bottom of the image ( I have
attached the  mask). do you have any idea how to
solve that? 
Also how can I make sure that the position and size
of the thalamus makes sense since the thalamus mask
has a different slice size and number than the
original mri?

Thank you

Dorsa



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e-mail
contains patient information, please contact the Partners Compliance
HelpLine at
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but does not contain patient information, please contact the sender
and properly
dispose of the e-mail.



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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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but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

Re: [Freesurfer] question about reslicing

2016-07-25 Thread Bruce Fischl 

Hi Dorsa

you need to give us more details. What was your reslicing command line? 
And the screen output?


Bruce
On Mon, 25 Jul 2016, Dorsa Haji Ghaffari wrote:



Hi,

I re-sliced my left thalamus so that the size and number of slices correspond 
with the original MRI, but when I open it in freeview, it shows an extra part(
like a cube) on the bottom of the image ( I have attached the  mask). do you 
have any idea how to solve that? 
Also how can I make sure that the position and size of the thalamus makes sense 
since the thalamus mask has a different slice size and number than the
original mri?

Thank you

Dorsa


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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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