Hello freesurfer,
I received this odd inflated surface image. I am not sure if this is something that can be fixed via a registration step or should be fixed in another step. Your input as to how to correct this image would be greatly appreciated. Also, I noticed that this participant's hippocampal volume is half the amount compared to the rest of my participants. Is it possible these two problems are related or am I possibly dealing with two separate issues? I have attached a screen shot of both problems.
Thank you very much, Jasmin
Hi Jasmin,
nothing looks wrong with the inflated brain images to me. Remember, the inflated brain doesn't have the same space as the T1 or white matter surface, so they are just centered. And overlap one another as the slice views showed. I'm afraid I can't help with the hippocampal question, though you may want to try adding some details.
hth d
On Wed, Feb 10, 2016 at 5:30 PM, Jasmin Alves jalves@usc.edu wrote:
Hello freesurfer,
I received this odd inflated surface image. I am not sure if this is something that can be fixed via a registration step or should be fixed in another step. Your input as to how to correct this image would be greatly appreciated. Also, I noticed that this participant's hippocampal volume is half the amount compared to the rest of my participants. Is it possible these two problems are related or am I possibly dealing with two separate issues? I have attached a screen shot of both problems.
Thank you very much, Jasmin
-- Jasmin Alves Predoctoral Student Medical Biology Graduate Program University of Southern California jalves@usc.edu
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Hello,
Thank you for the speedy reply. I ran recon-all and the process occurred without error. I have quality checked the various steps and have found no issues. But this participant's hippocampal volume is approximately 2000 while all the others in my cohort are about 4000. Is it possible for there to be such a large discrepancy? The participants are all the same age. Is this sufficient information?
Thanks again, Jasmin
On Wed, Feb 10, 2016 at 2:37 PM, dgw dgwakeman@gmail.com wrote:
Hi Jasmin,
nothing looks wrong with the inflated brain images to me. Remember, the inflated brain doesn't have the same space as the T1 or white matter surface, so they are just centered. And overlap one another as the slice views showed. I'm afraid I can't help with the hippocampal question, though you may want to try adding some details.
hth d
On Wed, Feb 10, 2016 at 5:30 PM, Jasmin Alves jalves@usc.edu wrote:
Hello freesurfer,
I received this odd inflated surface image. I am not sure if this is something that can be fixed via a registration step or should be fixed in another step. Your input as to how to correct this image would be greatly appreciated. Also, I noticed that this participant's hippocampal volume
is
half the amount compared to the rest of my participants. Is it possible these two problems are related or am I possibly dealing with two separate issues? I have attached a screen shot of both problems.
Thank you very much, Jasmin
-- Jasmin Alves Predoctoral Student Medical Biology Graduate Program University of Southern California jalves@usc.edu
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it is
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I agree that the inflated is fine. It doesn't live in any particularly interesting volumetric coordinate system, so displaying it that way doesn't really make sense.
As for the hippocampus, it looks fine on the slices you sent. If you upload the dataset I'll take a look cheers Bruce On Wed, 10 Feb 2016, dgw wrote:
Hi Jasmin,
nothing looks wrong with the inflated brain images to me. Remember, the inflated brain doesn't have the same space as the T1 or white matter surface, so they are just centered. And overlap one another as the slice views showed. I'm afraid I can't help with the hippocampal question, though you may want to try adding some details.
hth d
On Wed, Feb 10, 2016 at 5:30 PM, Jasmin Alves jalves@usc.edu wrote:
Hello freesurfer,
I received this odd inflated surface image. I am not sure if this is something that can be fixed via a registration step or should be fixed in another step. Your input as to how to correct this image would be greatly appreciated. Also, I noticed that this participant's hippocampal volume is half the amount compared to the rest of my participants. Is it possible these two problems are related or am I possibly dealing with two separate issues? I have attached a screen shot of both problems.
Thank you very much, Jasmin
-- Jasmin Alves Predoctoral Student Medical Biology Graduate Program University of Southern California jalves@usc.edu
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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dgw -
Jasmin Alves