Hi Koen,

Thanks for such a prompt reply.

I visualized it in freeview with:

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

Thanks,

Joana

2014-06-13 15:23 GMT+02:00 Koen Van Leemput koen@nmr.mgh.harvard.edu:

Hi Joana,

This looks like a visualization issue rather than a segmentation error to me. How did you visualize this?

Koen On Jun 13, 2014 2:59 PM, "Joana Braga Pereira" jbragapereira@gmail.com wrote:

...

Dear all,

I'm running the GEMS tool in Freesurfer 5.3 to measure the volumes of hippocampal subfields in subjects between 9 and 14 years of age with 3T T1-weighted MRI scans.

I noticed that a blackline is consistently drawn around the surface of the subfields (see attached figure) and was wondering whether this is normal.

Since the tool has not been validated in young subjects I would like to know if the black line observed in the figure shows that the segmentation has not been carried out correctly.

Any help will be greatly appreciated.

Many thanks,

Joana

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Hi Joana,

Sorry for the delayed response. I'm a bit puzzled because it really looks like a visualization issue in freeview. Could you please send me the original *.mgz files, so I can try the visualization myself?

Thanks,

Koen

On Mon, Jun 23, 2014 at 9:38 PM, Joana Braga Pereira jbragapereira@gmail.com wrote:

Dear Koen and Freesurfers,

I haven't receive any further replies regarding the black lines surrounding the subfields I found in the sample of subjects I am analyzing.

As I said the subjects are quite young (9-14 years of age) and I visualized the subfields with Freeview.

Do you have any idea why this is happening? This does mean the GEMS tool should not be applied in such young subjects?

Any help would be greatly appreciated!

Many thanks,

joana

2014-06-13 15:40 GMT+02:00 Joana Braga Pereira jbragapereira@gmail.com:

...

Hi Koen,

Thanks for such a prompt reply.

I visualized it in freeview with:

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

Thanks,

Joana

2014-06-13 15:23 GMT+02:00 Koen Van Leemput koen@nmr.mgh.harvard.edu:

...

Hi Joana,

This looks like a visualization issue rather than a segmentation error to me. How did you visualize this?

Koen

On Jun 13, 2014 2:59 PM, "Joana Braga Pereira" jbragapereira@gmail.com wrote:

...

Dear all,

I'm running the GEMS tool in Freesurfer 5.3 to measure the volumes of hippocampal subfields in subjects between 9 and 14 years of age with 3T T1-weighted MRI scans.

I noticed that a blackline is consistently drawn around the surface of the subfields (see attached figure) and was wondering whether this is normal.

Since the tool has not been validated in young subjects I would like to know if the black line observed in the figure shows that the segmentation has not been carried out correctly.

Any help will be greatly appreciated.

Many thanks,

Joana

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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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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.