Hi,
I understand that the models for the hippocampal subfield segmentation were created using high resolution MRI scans. But it sounds like this procedure can be used for scans with 1mm ^3 resolution, right? The resulting values would just need to be divided by 8 in order to get the subfield volumes in 1mm^3 though, since the resulting volumes are reported as 0.5x0.5x0.5mm^3. Is that correct?
Thanks, Tricia Merkley
Hi Tricia,
Yes, that summarizes it neatly. :-)
Koen
On Mon, Jul 4, 2011 at 10:44 PM, Tricia Merkley tmerkle22@yahoo.com wrote:
Hi,
I understand that the models for the hippocampal subfield segmentation were created using high resolution MRI scans. But it sounds like this procedure can be used for scans with 1mm ^3 resolution, right? The resulting values would just need to be divided by 8 in order to get the subfield volumes in 1mm^3 though, since the resulting volumes are reported as 0.5x0.5x0.5mm^3. Is that correct?
Thanks, Tricia Merkley
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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Hi Koen, Look like the outputs (posterior_*.mgz) are probability kind of images. How can I transfer them back into 1x1x1 mm^3 FS space? Maybe merge them into one image without overlapping? Or maybe transfer my own image into this 0.5x0.5x0.5 mm^3 space. How can I achieve this? Thanks, Wayne
On 06/07/11 5:59 AM, "Koen Van Leemput" koen@nmr.mgh.harvard.edu wrote:
Hi Tricia,
Yes, that summarizes it neatly. :-)
Koen
On Mon, Jul 4, 2011 at 10:44 PM, Tricia Merkley tmerkle22@yahoo.com wrote:
Hi,
I understand that the models for the hippocampal subfield segmentation were created using high resolution MRI scans. But it sounds like this procedure can be used for scans with 1mm ^3 resolution, right? The resulting values would just need to be divided by 8 in order to get the subfield volumes in 1mm^3 though, since the resulting volumes are reported as 0.5x0.5x0.5mm^3. Is that correct?
Thanks, Tricia Merkley
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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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Hi Wayne,
You're right: It will be difficult to somehow shoehorn the probability images with voxel size 0.5mm isotropic into the orginal 1mm isotropic FreeSurfer volumes. The other way around, by resampling the 1mm input image onto the correct 0.5mm grid is easy, though:
kvlUpsample nu.mgz 2 kvlResample posterior_left_presubiculum.mgz nu_upsampled_2_2_2.mgz 0 0 0
will result in the files nu_upsampled_2_2_2.mgz and posterior_left_presubiculum_resampled.mgz that are both in the same space and contain 2^3 = 8 times more voxels than the original 1mm voxels.
Hope this helps - please let me know if you need more information.
Koen
On Wed, Jul 6, 2011 at 1:48 PM, Wayne Su wsu@interchange.ubc.ca wrote:
Hi Koen, Look like the outputs (posterior_*.mgz) are probability kind of images. How can I transfer them back into 1x1x1 mm^3 FS space? Maybe merge them into one image without overlapping? Or maybe transfer my own image into this 0.5x0.5x0.5 mm^3 space. How can I achieve this? Thanks, Wayne
On 06/07/11 5:59 AM, "Koen Van Leemput" koen@nmr.mgh.harvard.edu wrote:
Hi Tricia,
Yes, that summarizes it neatly. :-)
Koen
On Mon, Jul 4, 2011 at 10:44 PM, Tricia Merkley tmerkle22@yahoo.com wrote:
Hi,
I understand that the models for the hippocampal subfield segmentation were created using high resolution MRI scans. But it sounds like this procedure can be used for scans with 1mm ^3 resolution, right? The resulting values would just need to be divided by 8 in order to get the subfield volumes in 1mm^3 though, since the resulting volumes are reported as 0.5x0.5x0.5mm^3. Is that correct?
Thanks, Tricia Merkley
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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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.
Or you could use freeview to display them as an overlay without any resampling. What is it you are trying to do?
On Jul 12, 2011, at 5:56 AM, Koen Van Leemput koen@nmr.mgh.harvard.edu wrote:
Hi Wayne,
You're right: It will be difficult to somehow shoehorn the probability images with voxel size 0.5mm isotropic into the orginal 1mm isotropic FreeSurfer volumes. The other way around, by resampling the 1mm input image onto the correct 0.5mm grid is easy, though:
kvlUpsample nu.mgz 2 kvlResample posterior_left_presubiculum.mgz nu_upsampled_2_2_2.mgz 0 0 0
will result in the files nu_upsampled_2_2_2.mgz and posterior_left_presubiculum_resampled.mgz that are both in the same space and contain 2^3 = 8 times more voxels than the original 1mm voxels.
Hope this helps - please let me know if you need more information.
Koen
On Wed, Jul 6, 2011 at 1:48 PM, Wayne Su wsu@interchange.ubc.ca wrote:
Hi Koen, Look like the outputs (posterior_*.mgz) are probability kind of images. How can I transfer them back into 1x1x1 mm^3 FS space? Maybe merge them into one image without overlapping? Or maybe transfer my own image into this 0.5x0.5x0.5 mm^3 space. How can I achieve this? Thanks, Wayne
On 06/07/11 5:59 AM, "Koen Van Leemput" koen@nmr.mgh.harvard.edu wrote:
Hi Tricia,
Yes, that summarizes it neatly. :-)
Koen
On Mon, Jul 4, 2011 at 10:44 PM, Tricia Merkley tmerkle22@yahoo.com wrote:
Hi,
I understand that the models for the hippocampal subfield segmentation were created using high resolution MRI scans. But it sounds like this procedure can be used for scans with 1mm ^3 resolution, right? The resulting values would just need to be divided by 8 in order to get the subfield volumes in 1mm^3 though, since the resulting volumes are reported as 0.5x0.5x0.5mm^3. Is that correct?
Thanks, Tricia Merkley
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 mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Thank you Koen. We're investigating the VR Space volume in each hippocampal subfield. Your suggestion is just what I'm looking for, very helpful.
Yes, I can use freeview to display them as an overlay. don't how freeview achieves that. Are you sure no resampling there for the command: freeview nu.mgz \ -p-labels posterior_left_* posterior_Left-Hippocampus.mgz \ -p-labels posterior_right_* posterior_Right-Hippocampus.mgz \ -p-prefix posterior_ -p-lut $FREESURFER_HOME/FreeSurferColorLUT.txt
Wayne
On 12/07/11 5:33 AM, "Bruce Fischl" fischl@nmr.mgh.harvard.edu wrote:
Or you could use freeview to display them as an overlay without any resampling. What is it you are trying to do?
On Jul 12, 2011, at 5:56 AM, Koen Van Leemput koen@nmr.mgh.harvard.edu wrote:
Hi Wayne,
You're right: It will be difficult to somehow shoehorn the probability images with voxel size 0.5mm isotropic into the orginal 1mm isotropic FreeSurfer volumes. The other way around, by resampling the 1mm input image onto the correct 0.5mm grid is easy, though:
kvlUpsample nu.mgz 2 kvlResample posterior_left_presubiculum.mgz nu_upsampled_2_2_2.mgz 0 0 0
will result in the files nu_upsampled_2_2_2.mgz and posterior_left_presubiculum_resampled.mgz that are both in the same space and contain 2^3 = 8 times more voxels than the original 1mm voxels.
Hope this helps - please let me know if you need more information.
Koen
On Wed, Jul 6, 2011 at 1:48 PM, Wayne Su wsu@interchange.ubc.ca wrote:
Hi Koen, Look like the outputs (posterior_*.mgz) are probability kind of images. How can I transfer them back into 1x1x1 mm^3 FS space? Maybe merge them into one image without overlapping? Or maybe transfer my own image into this 0.5x0.5x0.5 mm^3 space. How can I achieve this? Thanks, Wayne
On 06/07/11 5:59 AM, "Koen Van Leemput" koen@nmr.mgh.harvard.edu wrote:
Hi Tricia,
Yes, that summarizes it neatly. :-)
Koen
On Mon, Jul 4, 2011 at 10:44 PM, Tricia Merkley tmerkle22@yahoo.com wrote:
Hi,
I understand that the models for the hippocampal subfield segmentation were created using high resolution MRI scans. But it sounds like this procedure can be used for scans with 1mm ^3 resolution, right? The resulting values would just need to be divided by 8 in order to get the subfield volumes in 1mm^3 though, since the resulting volumes are reported as 0.5x0.5x0.5mm^3. Is that correct?
Thanks, Tricia Merkley
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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it of course resamples for overlay, but it doesn't downsample - just uses the vox2ras matrices from the two volumes to compute a common space
On Tue, 12 Jul 2011, Wayne Su wrote:
Thank you Koen. We're investigating the VR Space volume in each hippocampal subfield. Your suggestion is just what I'm looking for, very helpful.
Yes, I can use freeview to display them as an overlay. don't how freeview achieves that. Are you sure no resampling there for the command: freeview nu.mgz \ -p-labels posterior_left_* posterior_Left-Hippocampus.mgz \ -p-labels posterior_right_* posterior_Right-Hippocampus.mgz \ -p-prefix posterior_ -p-lut $FREESURFER_HOME/FreeSurferColorLUT.txt
Wayne
On 12/07/11 5:33 AM, "Bruce Fischl" fischl@nmr.mgh.harvard.edu wrote:
Or you could use freeview to display them as an overlay without any resampling. What is it you are trying to do?
On Jul 12, 2011, at 5:56 AM, Koen Van Leemput koen@nmr.mgh.harvard.edu wrote:
Hi Wayne,
You're right: It will be difficult to somehow shoehorn the probability images with voxel size 0.5mm isotropic into the orginal 1mm isotropic FreeSurfer volumes. The other way around, by resampling the 1mm input image onto the correct 0.5mm grid is easy, though:
kvlUpsample nu.mgz 2 kvlResample posterior_left_presubiculum.mgz nu_upsampled_2_2_2.mgz 0 0 0
will result in the files nu_upsampled_2_2_2.mgz and posterior_left_presubiculum_resampled.mgz that are both in the same space and contain 2^3 = 8 times more voxels than the original 1mm voxels.
Hope this helps - please let me know if you need more information.
Koen
On Wed, Jul 6, 2011 at 1:48 PM, Wayne Su wsu@interchange.ubc.ca wrote:
Hi Koen, Look like the outputs (posterior_*.mgz) are probability kind of images. How can I transfer them back into 1x1x1 mm^3 FS space? Maybe merge them into one image without overlapping? Or maybe transfer my own image into this 0.5x0.5x0.5 mm^3 space. How can I achieve this? Thanks, Wayne
On 06/07/11 5:59 AM, "Koen Van Leemput" koen@nmr.mgh.harvard.edu wrote:
Hi Tricia,
Yes, that summarizes it neatly. :-)
Koen
On Mon, Jul 4, 2011 at 10:44 PM, Tricia Merkley tmerkle22@yahoo.com wrote:
Hi,
I understand that the models for the hippocampal subfield segmentation were created using high resolution MRI scans. But it sounds like this procedure can be used for scans with 1mm ^3 resolution, right? The resulting values would just need to be divided by 8 in order to get the subfield volumes in 1mm^3 though, since the resulting volumes are reported as 0.5x0.5x0.5mm^3. Is that correct?
Thanks, Tricia Merkley
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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Thanks. Does freeview use same approach as what Koen described? Look like both ways need upsampling nu to 0.5x0.5x0.5.
Wayne
On 12/07/11 10:29 AM, "Bruce Fischl" fischl@nmr.mgh.harvard.edu wrote:
it of course resamples for overlay, but it doesn't downsample - just uses the vox2ras matrices from the two volumes to compute a common space
On Tue, 12 Jul 2011, Wayne Su wrote:
Thank you Koen. We're investigating the VR Space volume in each hippocampal subfield. Your suggestion is just what I'm looking for, very helpful.
Yes, I can use freeview to display them as an overlay. don't how freeview achieves that. Are you sure no resampling there for the command: freeview nu.mgz \ -p-labels posterior_left_* posterior_Left-Hippocampus.mgz \ -p-labels posterior_right_* posterior_Right-Hippocampus.mgz \ -p-prefix posterior_ -p-lut $FREESURFER_HOME/FreeSurferColorLUT.txt
Wayne
On 12/07/11 5:33 AM, "Bruce Fischl" fischl@nmr.mgh.harvard.edu wrote:
Or you could use freeview to display them as an overlay without any resampling. What is it you are trying to do?
On Jul 12, 2011, at 5:56 AM, Koen Van Leemput koen@nmr.mgh.harvard.edu wrote:
Hi Wayne,
You're right: It will be difficult to somehow shoehorn the probability images with voxel size 0.5mm isotropic into the orginal 1mm isotropic FreeSurfer volumes. The other way around, by resampling the 1mm input image onto the correct 0.5mm grid is easy, though:
kvlUpsample nu.mgz 2 kvlResample posterior_left_presubiculum.mgz nu_upsampled_2_2_2.mgz 0 0 0
will result in the files nu_upsampled_2_2_2.mgz and posterior_left_presubiculum_resampled.mgz that are both in the same space and contain 2^3 = 8 times more voxels than the original 1mm voxels.
Hope this helps - please let me know if you need more information.
Koen
On Wed, Jul 6, 2011 at 1:48 PM, Wayne Su wsu@interchange.ubc.ca wrote:
Hi Koen, Look like the outputs (posterior_*.mgz) are probability kind of images. How can I transfer them back into 1x1x1 mm^3 FS space? Maybe merge them into one image without overlapping? Or maybe transfer my own image into this 0.5x0.5x0.5 mm^3 space. How can I achieve this? Thanks, Wayne
On 06/07/11 5:59 AM, "Koen Van Leemput" koen@nmr.mgh.harvard.edu wrote:
Hi Tricia,
Yes, that summarizes it neatly. :-)
Koen
On Mon, Jul 4, 2011 at 10:44 PM, Tricia Merkley tmerkle22@yahoo.com wrote:
Hi,
I understand that the models for the hippocampal subfield segmentation were created using high resolution MRI scans. But it sounds like this procedure can be used for scans with 1mm ^3 resolution, right? The resulting values would just need to be divided by 8 in order to get the subfield volumes in 1mm^3 though, since the resulting volumes are reported as 0.5x0.5x0.5mm^3. Is that correct?
Thanks, Tricia Merkley
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
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Bruce Fischl -
Koen Van Leemput -
Tricia Merkley -
Wayne Su