External Email - Use Caution
Dear freesurfer team,
I am dealing with PET scans that were acquired at different sites. They do not have uniform voxel size and dimensions. I was wondering if this would be an issue for the sGTM and MG PETSurfer-PVC and/or for the "vol2surf --projfrac 0.5" and vertex-wise PET group-analyses. Should I resample to a uniform voxelsize prior to these steps or does freesurfer take care of this issue internally?
Thank you for the information. Best regards Julie
No, not a problem.
On 12/21/2020 12:52 PM, Julie Ottoy wrote:
External Email - Use Caution
Dear freesurfer team,
I am dealing with PET scans that were acquired at different sites. They do not have uniform voxel size and dimensions. I was wondering if this would be an issue for the sGTM and MG PETSurfer-PVC and/or for the "vol2surf --projfrac 0.5" and vertex-wise PET group-analyses. Should I resample to a uniform voxelsize prior to these steps or does freesurfer take care of this issue internally?
Thank you for the information. Best regards Julie
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
External Email - Use Caution
Thank you Doug! I have another question related to voxel size.
In the GTM PVC pipeline, the gtm.stats.dat file also outputs the NVoxels. However, is there a way to easily retrieve the volume (instead of NVoxels) for each ROI within the gtm.stats file? I know that you should rescale by the pet voxel size; however, I have a multi-site study with all different voxel sizes. Or is there perhaps a way to apply the "aparcstats2table -meas volume" command but get the same ROIs outputted as those in the gtm.stats file?
Thank you for the info! Julie
On Wed, 23 Dec 2020 at 13:11, Greve, Douglas N.,Ph.D. < DGREVE@mgh.harvard.edu> wrote:
No, not a problem.
On 12/21/2020 12:52 PM, Julie Ottoy wrote:
External Email - Use CautionDear freesurfer team,
I am dealing with PET scans that were acquired at different sites. They do not have uniform voxel size and dimensions. I was wondering if this would be an issue for the sGTM and MG PETSurfer-PVC and/or for the "vol2surf --projfrac 0.5" and vertex-wise PET group-analyses. Should I resample to a uniform voxelsize prior to these steps or does freesurfer take care of this issue internally?
Thank you for the information. Best regards Julie
Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://secure-web.cisco.com/1u58coWJ8-AkXrLWwU5c4kWgRB7z9zS2zw0Ra9eO1hjd6ge...
I've just created a new version of gtmstats2table (attached). This will take a --volume flag to report the volume of the ROIs instead of the uptake
On 1/6/2021 6:00 PM, Julie Ottoy wrote:
External Email - Use Caution
Thank you Doug! I have another question related to voxel size.
In the GTM PVC pipeline, the gtm.stats.dat file also outputs the NVoxels. However, is there a way to easily retrieve the volume (instead of NVoxels) for each ROI within the gtm.stats file? I know that you should rescale by the pet voxel size; however, I have a multi-site study with all different voxel sizes. Or is there perhaps a way to apply the "aparcstats2table -meas volume" command but get the same ROIs outputted as those in the gtm.stats file?
Thank you for the info! Julie
On Wed, 23 Dec 2020 at 13:11, Greve, Douglas N.,Ph.D. <DGREVE@mgh.harvard.edumailto:DGREVE@mgh.harvard.edu> wrote: No, not a problem.
On 12/21/2020 12:52 PM, Julie Ottoy wrote:
External Email - Use Caution
Dear freesurfer team,
I am dealing with PET scans that were acquired at different sites. They do not have uniform voxel size and dimensions. I was wondering if this would be an issue for the sGTM and MG PETSurfer-PVC and/or for the "vol2surf --projfrac 0.5" and vertex-wise PET group-analyses. Should I resample to a uniform voxelsize prior to these steps or does freesurfer take care of this issue internally?
Thank you for the information. Best regards Julie
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurferhttps://secure-web.cisco.com/1u58coWJ8-AkXrLWwU5c4kWgRB7z9zS2zw0Ra9eO1hjd6ge84eAzD3evbeGVj3jBjXy4ArObGAjd58Dq_pR2m2k57kT3YbH3f4Mo8TvicIp4ue7R-V2PUJgX3B1WHTduN1YbmPbDTE9BfxryTwhni-VIFrCceTc5SGkKCGMVIywW4syAzAjn2elnyQnQn7r2NnZNpoKpcaQpSMFgkHmxtrOx1Y4rrC7qjzOLKROb5oYuusaCd4C4hkEIGAnRrHNRUS2CFUjsvxoDnJFFaRU02uQ/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer
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Thank you Doug, this is great!
On Wed, 13 Jan 2021 at 10:41, Greve, Douglas N.,Ph.D. < DGREVE@mgh.harvard.edu> wrote:
I've just created a new version of gtmstats2table (attached). This will take a --volume flag to report the volume of the ROIs instead of the uptake
On 1/6/2021 6:00 PM, Julie Ottoy wrote:
External Email - Use CautionThank you Doug! I have another question related to voxel size.
In the GTM PVC pipeline, the gtm.stats.dat file also outputs the NVoxels. However, is there a way to easily retrieve the volume (instead of NVoxels) for each ROI within the gtm.stats file? I know that you should rescale by the pet voxel size; however, I have a multi-site study with all different voxel sizes. Or is there perhaps a way to apply the "aparcstats2table -meas volume" command but get the same ROIs outputted as those in the gtm.stats file?
Thank you for the info! Julie
On Wed, 23 Dec 2020 at 13:11, Greve, Douglas N.,Ph.D. < DGREVE@mgh.harvard.edu> wrote:
No, not a problem.
On 12/21/2020 12:52 PM, Julie Ottoy wrote:
External Email - Use CautionDear freesurfer team,
I am dealing with PET scans that were acquired at different sites. They do not have uniform voxel size and dimensions. I was wondering if this would be an issue for the sGTM and MG PETSurfer-PVC and/or for the "vol2surf --projfrac 0.5" and vertex-wise PET group-analyses. Should I resample to a uniform voxelsize prior to these steps or does freesurfer take care of this issue internally?
Thank you for the information. Best regards Julie
Freesurfer mailing listFreesurfer@nmr.mgh.harvard.edu*MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* https://secure-web.cisco.com/1Sr2dyYPrnapj6D6lY_IdXuqjUsoAqOqqqOuK7DCKcIqNvw... https://secure-web.cisco.com/1u58coWJ8-AkXrLWwU5c4kWgRB7z9zS2zw0Ra9eO1hjd6ge84eAzD3evbeGVj3jBjXy4ArObGAjd58Dq_pR2m2k57kT3YbH3f4Mo8TvicIp4ue7R-V2PUJgX3B1WHTduN1YbmPbDTE9BfxryTwhni-VIFrCceTc5SGkKCGMVIywW4syAzAjn2elnyQnQn7r2NnZNpoKpcaQpSMFgkHmxtrOx1Y4rrC7qjzOLKROb5oYuusaCd4C4hkEIGAnRrHNRUS2CFUjsvxoDnJFFaRU02uQ/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer
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Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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freesurfer@nmr.mgh.harvard.edu
-
Greve, Douglas N.,Ph.D. -
Julie Ottoy