Hello Freesurfer,
I have 3 PET images per individual. I am learning PetSurfer based on the Greve et al., 2014 paper.
On the PetSurfer link, there are 2 methods.
mri_convert pet.nii.gz —frame frameno template.nii.gz or mri_concat pet.nii.gz --mean —0 template.nii.gz
What are the differences? My files are listed as subject123_a.nii.gz, subject123_b.nii.gz, subject123_c.nii.gz
Is "mri_concat subject123_a.nii.gz, subject123_b.nii.gz, subject123_c.nii.gz —mean —o template.nii.gz” correct?
Thank you for helping.
Best Wishes,
S -- Shane Schofield
No, the template is a within subject template used for registration. If your pet data only has one frame (eg, FDG SUV), then you don't need to run mri_convert or mri_concat, just use your pet image as the template
On 3/8/17 11:11 AM, Shane S wrote:
Hello Freesurfer,
I have 3 PET images per individual. I am learning PetSurfer based on the Greve et al., 2014 paper.
On the PetSurfer link, there are 2 methods.
mri_convert pet.nii.gz —frame frameno template.nii.gz or mri_concat pet.nii.gz --mean —0 template.nii.gz
What are the differences? My files are listed as subject123_a.nii.gz, subject123_b.nii.gz, subject123_c.nii.gz
Is "mri_concat subject123_a.nii.gz, subject123_b.nii.gz, subject123_c.nii.gz —mean —o template.nii.gz” correct?
Thank you for helping.
Best Wishes,
S
Shane Schofield
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Dear Doug,
My PET data is 3 x 5 minute acquisitions. Each subject has subject123_a.nii.gz, subject123_b.nii.gz, subject123_c.nii.gz and I am supposed to align and average them.
Please advise.
Thanks!
-- Shane Schofield
On 8 March 2017 at 22:31:06, Douglas Greve (greve@nmr.mgh.harvard.edu) wrote:
No, the template is a within subject template used for registration. If your pet data only has one frame (eg, FDG SUV), then you don't need to run mri_convert or mri_concat, just use your pet image as the template
On 3/8/17 11:11 AM, Shane S wrote: Hello Freesurfer,
I have 3 PET images per individual. I am learning PetSurfer based on the Greve et al., 2014 paper.
On the PetSurfer link, there are 2 methods.
mri_convert pet.nii.gz —frame frameno template.nii.gz or mri_concat pet.nii.gz --mean —0 template.nii.gz
What are the differences? My files are listed as subject123_a.nii.gz, subject123_b.nii.gz, subject123_c.nii.gz
Is "mri_concat subject123_a.nii.gz, subject123_b.nii.gz, subject123_c.nii.gz —mean —o template.nii.gz” correct?
Thank you for helping.
Best Wishes,
S -- Shane Schofield
_______________________________________________ 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.
How are you planning on analyzing the different time points?
On 03/08/2017 05:33 PM, Shane S wrote:
Dear Doug,
My PET data is 3 x 5 minute acquisitions. Each subject has subject123_a.nii.gz, subject123_b.nii.gz, subject123_c.nii.gz and I am supposed to align and average them.
Please advise.
Thanks!
-- Shane Schofield
On 8 March 2017 at 22:31:06, Douglas Greve (greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu) wrote:
No, the template is a within subject template used for registration. If your pet data only has one frame (eg, FDG SUV), then you don't need to run mri_convert or mri_concat, just use your pet image as the template
On 3/8/17 11:11 AM, Shane S wrote:
Hello Freesurfer,
I have 3 PET images per individual. I am learning PetSurfer based on the Greve et al., 2014 paper.
On the PetSurfer link, there are 2 methods.
mri_convert pet.nii.gz —frame frameno template.nii.gz or mri_concat pet.nii.gz --mean —0 template.nii.gz
What are the differences? My files are listed as subject123_a.nii.gz, subject123_b.nii.gz, subject123_c.nii.gz
Is "mri_concat subject123_a.nii.gz, subject123_b.nii.gz, subject123_c.nii.gz —mean —o template.nii.gz” correct?
Thank you for helping.
Best Wishes,
S
Shane Schofield
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.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hi Doug,
I want to derive a single averaged PET volume from the three reconstructed 5 min acquisitions, expressed in detected counts. Then we will divide the counts based on the cerebellum. Following that, I want to use PetSurfer for partial volume correction and GLM comparisons. May I upload the 3 images per subject?
Thank you.
-- Shane S
On 9 March 2017 at 16:18:33, Douglas N Greve (greve@nmr.mgh.harvard.edu) wrote:
How are you planning on analyzing the different time points?
On 03/08/2017 05:33 PM, Shane S wrote:
Dear Doug,
My PET data is 3 x 5 minute acquisitions. Each subject has subject123_a.nii.gz, subject123_b.nii.gz, subject123_c.nii.gz and I am supposed to align and average them.
Please advise.
Thanks!
-- Shane Schofield
On 8 March 2017 at 22:31:06, Douglas Greve (greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu) wrote:
No, the template is a within subject template used for registration. If your pet data only has one frame (eg, FDG SUV), then you don't need to run mri_convert or mri_concat, just use your pet image as the template
On 3/8/17 11:11 AM, Shane S wrote:
Hello Freesurfer,
I have 3 PET images per individual. I am learning PetSurfer based on the Greve et al., 2014 paper.
On the PetSurfer link, there are 2 methods.
mri_convert pet.nii.gz —frame frameno template.nii.gz or mri_concat pet.nii.gz --mean —0 template.nii.gz
What are the differences? My files are listed as subject123_a.nii.gz, subject123_b.nii.gz, subject123_c.nii.gz
Is "mri_concat subject123_a.nii.gz, subject123_b.nii.gz, subject123_c.nii.gz —mean —o template.nii.gz” correct?
Thank you for helping.
Best Wishes,
S
Shane Schofield
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.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
If the 3 volumes are in register (ie, no motion between them), then I would just run the mri_concat command to create a single volume which is the average of the 3, then proceed as described.
On 03/09/2017 11:58 AM, Shane S wrote:
Hi Doug,
I want to derive a single averaged PET volume from the three reconstructed 5 min acquisitions, expressed in detected counts. Then we will divide the counts based on the cerebellum. Following that, I want to use PetSurfer for partial volume correction and GLM comparisons. May I upload the 3 images per subject?
Thank you.
-- Shane S
On 9 March 2017 at 16:18:33, Douglas N Greve (greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu) wrote:
How are you planning on analyzing the different time points?
On 03/08/2017 05:33 PM, Shane S wrote:
Dear Doug,
My PET data is 3 x 5 minute acquisitions. Each subject has subject123_a.nii.gz, subject123_b.nii.gz, subject123_c.nii.gz and I am supposed to align and average them.
Please advise.
Thanks!
-- Shane Schofield
On 8 March 2017 at 22:31:06, Douglas Greve (greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu) wrote:
No, the template is a within subject template used for registration. If your pet data only has one frame (eg, FDG SUV), then you don't need to run mri_convert or mri_concat, just use your pet image as the template
On 3/8/17 11:11 AM, Shane S wrote:
Hello Freesurfer,
I have 3 PET images per individual. I am learning PetSurfer based on the Greve et al., 2014 paper.
On the PetSurfer link, there are 2 methods.
mri_convert pet.nii.gz —frame frameno template.nii.gz or mri_concat pet.nii.gz --mean —0 template.nii.gz
What are the differences? My files are listed as subject123_a.nii.gz, subject123_b.nii.gz, subject123_c.nii.gz
Is "mri_concat subject123_a.nii.gz, subject123_b.nii.gz, subject123_c.nii.gz —mean —o template.nii.gz” correct?
Thank you for helping.
Best Wishes,
S
Shane Schofield
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.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
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
Thank you very much!!
-- Shane S
On 9 March 2017 at 17:01:28, Douglas N Greve (greve@nmr.mgh.harvard.edu) wrote:
If the 3 volumes are in register (ie, no motion between them), then I would just run the mri_concat command to create a single volume which is the average of the 3, then proceed as described.
On 03/09/2017 11:58 AM, Shane S wrote:
Hi Doug,
I want to derive a single averaged PET volume from the three reconstructed 5 min acquisitions, expressed in detected counts. Then we will divide the counts based on the cerebellum. Following that, I want to use PetSurfer for partial volume correction and GLM comparisons. May I upload the 3 images per subject?
Thank you.
-- Shane S
On 9 March 2017 at 16:18:33, Douglas N Greve (greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu) wrote:
How are you planning on analyzing the different time points?
On 03/08/2017 05:33 PM, Shane S wrote:
Dear Doug,
My PET data is 3 x 5 minute acquisitions. Each subject has subject123_a.nii.gz, subject123_b.nii.gz, subject123_c.nii.gz and I am supposed to align and average them.
Please advise.
Thanks!
-- Shane Schofield
On 8 March 2017 at 22:31:06, Douglas Greve (greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu) wrote:
No, the template is a within subject template used for registration. If your pet data only has one frame (eg, FDG SUV), then you don't need to run mri_convert or mri_concat, just use your pet image as the template
On 3/8/17 11:11 AM, Shane S wrote:
Hello Freesurfer,
I have 3 PET images per individual. I am learning PetSurfer based on the Greve et al., 2014 paper.
On the PetSurfer link, there are 2 methods.
mri_convert pet.nii.gz —frame frameno template.nii.gz or mri_concat pet.nii.gz --mean —0 template.nii.gz
What are the differences? My files are listed as subject123_a.nii.gz, subject123_b.nii.gz, subject123_c.nii.gz
Is "mri_concat subject123_a.nii.gz, subject123_b.nii.gz, subject123_c.nii.gz —mean —o template.nii.gz” correct?
Thank you for helping.
Best Wishes,
S
Shane Schofield
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.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
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
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hi Doug,
There is a bit of movement across the 3 acquisitions. How may I align everything together before running mri_concat?
1. Run bbregister or mri_coreg to register 1 acquisition to T1 2. Use the reg file to move the remaining 2 acquisitions ?
Is there a quicker way?
Thank you.
-- Shane Schofield
On 9 March 2017 at 17:01:28, Douglas N Greve (greve@nmr.mgh.harvard.edu) wrote:
If the 3 volumes are in register (ie, no motion between them), then I would just run the mri_concat command to create a single volume which is the average of the 3, then proceed as described.
On 03/09/2017 11:58 AM, Shane S wrote:
Hi Doug,
I want to derive a single averaged PET volume from the three reconstructed 5 min acquisitions, expressed in detected counts. Then we will divide the counts based on the cerebellum. Following that, I want to use PetSurfer for partial volume correction and GLM comparisons. May I upload the 3 images per subject?
Thank you.
-- Shane S
On 9 March 2017 at 16:18:33, Douglas N Greve (greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu) wrote:
How are you planning on analyzing the different time points?
On 03/08/2017 05:33 PM, Shane S wrote:
Dear Doug,
My PET data is 3 x 5 minute acquisitions. Each subject has subject123_a.nii.gz, subject123_b.nii.gz, subject123_c.nii.gz and I am supposed to align and average them.
Please advise.
Thanks!
-- Shane Schofield
On 8 March 2017 at 22:31:06, Douglas Greve (greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu) wrote:
No, the template is a within subject template used for registration. If your pet data only has one frame (eg, FDG SUV), then you don't need to run mri_convert or mri_concat, just use your pet image as the template
On 3/8/17 11:11 AM, Shane S wrote:
Hello Freesurfer,
I have 3 PET images per individual. I am learning PetSurfer based on the Greve et al., 2014 paper.
On the PetSurfer link, there are 2 methods.
mri_convert pet.nii.gz —frame frameno template.nii.gz or mri_concat pet.nii.gz --mean —0 template.nii.gz
What are the differences? My files are listed as subject123_a.nii.gz, subject123_b.nii.gz, subject123_c.nii.gz
Is "mri_concat subject123_a.nii.gz, subject123_b.nii.gz, subject123_c.nii.gz —mean —o template.nii.gz” correct?
Thank you for helping.
Best Wishes,
S
Shane Schofield
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.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
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
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
freesurfer@nmr.mgh.harvard.edu
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Douglas Greve -
Douglas N Greve
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Shane S