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
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
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 fischl@nmr.mgh.harvard.edu 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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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: 0.000000 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 fischl@nmr.mgh.harvard.edu 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.
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 fischl@nmr.mgh.harvard.edu 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: 0.000000 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 < fischl@nmr.mgh.harvard.edu> 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.
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 <fischl@nmr.mgh.harvard.edu mailto:fischl@nmr.mgh.harvard.edu> 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: 0.000000 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 <fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu>> 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 <mailto: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 <mailto: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
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 fischl@nmr.mgh.harvard.edu 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: 0.000000 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 <fischl@nmr.mgh.harvard.edu> 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.
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 fischl@nmr.mgh.harvard.edu 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 <fischl@nmr.mgh.harvard.edu
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: 0.000000 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 <fischl@nmr.mgh.harvard.edu> 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.
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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@nmr.mgh.harvard.edu
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Bruce Fischl -
Dorsa Haji Ghaffari -
Douglas N Greve