Hi FreeSurfer community,
I am working on elderly subjects and have had this kind of surface error quite often in different locations. Usually, it's over about 3-4 slices (in one view) and can be fixed, but I am finding multiple in almost every subject and therefore taking a lot of time to edit (and then once reprocessed new ones sometimes come up in different locations). I was wondering if these are normal to have, minor surface errors that do not necessarily need to be fixed. I have added images of an example below. Here are some of the values I get from aparc.stats for caudal middle frontal lh after manually editing:
Surface area: Original - 2500 mm^2 Edited - 2532 mm^2
Grey volume: Original - 1710 mm^3 Edited - 1727 mm^3
Thickness avg Original - 4455 mm std: 2.371 Edited - 4445 mm std: 2.365
Although the thickness values only differ by 10 mm, we are a little concerned because the difference is not within the standard deviation.
Please let me know if all of these errors should be edited or if it may be okay to keep the smaller segmentation/topological errors as they are.
Thank you,
Emily
sorry, what kind of errors? I could not really tell from the images what the problem was
On 02/20/2018 10:22 AM, Emily Schwartz wrote:
Hi FreeSurfer community,
I am working on elderly subjects and have had this kind of surface error quite often in different locations. Usually, it's over about 3-4 slices (in one view) and can be fixed, but I am finding multiple in almost every subject and therefore taking a lot of time to edit (and then once reprocessed new ones sometimes come up in different locations). I was wondering if these are normal to have, minor surface errors that do not necessarily need to be fixed. I have added images of an example below. Here are some of the values I get from aparc.stats for caudal middle frontal lh after manually editing:
Surface area: Original - 2500 mm^2 Edited - 2532 mm^2
Grey volume: Original - 1710 mm^3 Edited - 1727 mm^3
Thickness avg Original - 4455 mm std: 2.371 Edited - 4445 mm std: 2.365
Although the thickness values only differ by 10 mm, we are a little concerned because the difference is not within the standard deviation.
Please let me know if all of these errors should be edited or if it may be okay to keep the smaller segmentation/topological errors as they are.
Thank you,
Emily
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hi Doug,
Thank you for getting back to me. I've attached two images (Slice165 and Slice166) with an arrow pointing to the location. I am new at this, so maybe I am wrong and it is not a segmentation error.
I've also attached an additional image (Slice185) of what I think is a type of topological error that I often see multiple times in a subject. Is this a topological defect? If so, if it is only over 3 slices does it need to be corrected?
Thanks again,
Emily ________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Douglas N Greve [greve@nmr.mgh.harvard.edu] Sent: Tuesday, February 20, 2018 4:59 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Surface Errors
sorry, what kind of errors? I could not really tell from the images what the problem was
On 02/20/2018 10:22 AM, Emily Schwartz wrote:
Hi FreeSurfer community,
I am working on elderly subjects and have had this kind of surface error quite often in different locations. Usually, it's over about 3-4 slices (in one view) and can be fixed, but I am finding multiple in almost every subject and therefore taking a lot of time to edit (and then once reprocessed new ones sometimes come up in different locations). I was wondering if these are normal to have, minor surface errors that do not necessarily need to be fixed. I have added images of an example below. Here are some of the values I get from aparc.stats for caudal middle frontal lh after manually editing:
Surface area: Original - 2500 mm^2 Edited - 2532 mm^2
Grey volume: Original - 1710 mm^3 Edited - 1727 mm^3
Thickness avg Original - 4455 mm std: 2.371 Edited - 4445 mm std: 2.365
Although the thickness values only differ by 10 mm, we are a little concerned because the difference is not within the standard deviation.
Please let me know if all of these errors should be edited or if it may be okay to keep the smaller segmentation/topological errors as they are.
Thank you,
Emily
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
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.
Hi Emily
it is a segmentation error, but it's a pretty small one. It will mess up the thickness in a region a few mm^2. You could fix it by editing the wm.mgz if you really care about that spot
cheers Bruce
On Wed, 21 Feb 2018, Emily Schwartz wrote:
Hi Doug,
Thank you for getting back to me. I've attached two images (Slice165 and Slice166) with an arrow pointing to the location. I am new at this, so maybe I am wrong and it is not a segmentation error.
I've also attached an additional image (Slice185) of what I think is a type of topological error that I often see multiple times in a subject. Is this a topological defect? If so, if it is only over 3 slices does it need to be corrected?
Thanks again,
Emily ________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Douglas N Greve [greve@nmr.mgh.harvard.edu] Sent: Tuesday, February 20, 2018 4:59 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Surface Errors
sorry, what kind of errors? I could not really tell from the images what the problem was
On 02/20/2018 10:22 AM, Emily Schwartz wrote:
Hi FreeSurfer community,
I am working on elderly subjects and have had this kind of surface error quite often in different locations. Usually, it's over about 3-4 slices (in one view) and can be fixed, but I am finding multiple in almost every subject and therefore taking a lot of time to edit (and then once reprocessed new ones sometimes come up in different locations). I was wondering if these are normal to have, minor surface errors that do not necessarily need to be fixed. I have added images of an example below. Here are some of the values I get from aparc.stats for caudal middle frontal lh after manually editing:
Surface area: Original - 2500 mm^2 Edited - 2532 mm^2
Grey volume: Original - 1710 mm^3 Edited - 1727 mm^3
Thickness avg Original - 4455 mm std: 2.371 Edited - 4445 mm std: 2.365
Although the thickness values only differ by 10 mm, we are a little concerned because the difference is not within the standard deviation.
Please let me know if all of these errors should be edited or if it may be okay to keep the smaller segmentation/topological errors as they are.
Thank you,
Emily
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
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.
Got it, thank you so much!
Best,
Emily ________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Bruce Fischl [fischl@nmr.mgh.harvard.edu] Sent: Wednesday, February 21, 2018 10:23 AM To: Freesurfer support list Subject: Re: [Freesurfer] Surface Errors
Hi Emily
it is a segmentation error, but it's a pretty small one. It will mess up the thickness in a region a few mm^2. You could fix it by editing the wm.mgz if you really care about that spot
cheers Bruce
On Wed, 21 Feb 2018, Emily Schwartz wrote:
Hi Doug,
Thank you for getting back to me. I've attached two images (Slice165 and Slice166) with an arrow pointing to the location. I am new at this, so maybe I am wrong and it is not a segmentation error.
I've also attached an additional image (Slice185) of what I think is a type of topological error that I often see multiple times in a subject. Is this a topological defect? If so, if it is only over 3 slices does it need to be corrected?
Thanks again,
Emily ________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Douglas N Greve [greve@nmr.mgh.harvard.edu] Sent: Tuesday, February 20, 2018 4:59 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Surface Errors
sorry, what kind of errors? I could not really tell from the images what the problem was
On 02/20/2018 10:22 AM, Emily Schwartz wrote:
Hi FreeSurfer community,
I am working on elderly subjects and have had this kind of surface error quite often in different locations. Usually, it's over about 3-4 slices (in one view) and can be fixed, but I am finding multiple in almost every subject and therefore taking a lot of time to edit (and then once reprocessed new ones sometimes come up in different locations). I was wondering if these are normal to have, minor surface errors that do not necessarily need to be fixed. I have added images of an example below. Here are some of the values I get from aparc.stats for caudal middle frontal lh after manually editing:
Surface area: Original - 2500 mm^2 Edited - 2532 mm^2
Grey volume: Original - 1710 mm^3 Edited - 1727 mm^3
Thickness avg Original - 4455 mm std: 2.371 Edited - 4445 mm std: 2.365
Although the thickness values only differ by 10 mm, we are a little concerned because the difference is not within the standard deviation.
Please let me know if all of these errors should be edited or if it may be okay to keep the smaller segmentation/topological errors as they are.
Thank you,
Emily
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
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
btw, what verions of FS are you using?
On 02/21/2018 01:25 PM, Emily Schwartz wrote:
Got it, thank you so much!
Best,
Emily ________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Bruce Fischl [fischl@nmr.mgh.harvard.edu] Sent: Wednesday, February 21, 2018 10:23 AM To: Freesurfer support list Subject: Re: [Freesurfer] Surface Errors
Hi Emily
it is a segmentation error, but it's a pretty small one. It will mess up the thickness in a region a few mm^2. You could fix it by editing the wm.mgz if you really care about that spot
cheers Bruce
On Wed, 21 Feb 2018, Emily Schwartz wrote:
Hi Doug,
Thank you for getting back to me. I've attached two images (Slice165 and Slice166) with an arrow pointing to the location. I am new at this, so maybe I am wrong and it is not a segmentation error.
I've also attached an additional image (Slice185) of what I think is a type of topological error that I often see multiple times in a subject. Is this a topological defect? If so, if it is only over 3 slices does it need to be corrected?
Thanks again,
Emily ________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Douglas N Greve [greve@nmr.mgh.harvard.edu] Sent: Tuesday, February 20, 2018 4:59 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Surface Errors
sorry, what kind of errors? I could not really tell from the images what the problem was
On 02/20/2018 10:22 AM, Emily Schwartz wrote:
Hi FreeSurfer community,
I am working on elderly subjects and have had this kind of surface error quite often in different locations. Usually, it's over about 3-4 slices (in one view) and can be fixed, but I am finding multiple in almost every subject and therefore taking a lot of time to edit (and then once reprocessed new ones sometimes come up in different locations). I was wondering if these are normal to have, minor surface errors that do not necessarily need to be fixed. I have added images of an example below. Here are some of the values I get from aparc.stats for caudal middle frontal lh after manually editing:
Surface area: Original - 2500 mm^2 Edited - 2532 mm^2
Grey volume: Original - 1710 mm^3 Edited - 1727 mm^3
Thickness avg Original - 4455 mm std: 2.371 Edited - 4445 mm std: 2.365
Although the thickness values only differ by 10 mm, we are a little concerned because the difference is not within the standard deviation.
Please let me know if all of these errors should be edited or if it may be okay to keep the smaller segmentation/topological errors as they are.
Thank you,
Emily
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
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
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hi Doug,
I am using V6.0.0 (x86_64) on Ubuntu. Should I not be getting these errors so often?
Best,
Emily ________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Douglas N Greve [greve@nmr.mgh.harvard.edu] Sent: Wednesday, February 21, 2018 2:18 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Surface Errors
btw, what verions of FS are you using?
On 02/21/2018 01:25 PM, Emily Schwartz wrote:
Got it, thank you so much!
Best,
Emily ________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Bruce Fischl [fischl@nmr.mgh.harvard.edu] Sent: Wednesday, February 21, 2018 10:23 AM To: Freesurfer support list Subject: Re: [Freesurfer] Surface Errors
Hi Emily
it is a segmentation error, but it's a pretty small one. It will mess up the thickness in a region a few mm^2. You could fix it by editing the wm.mgz if you really care about that spot
cheers Bruce
On Wed, 21 Feb 2018, Emily Schwartz wrote:
Hi Doug,
Thank you for getting back to me. I've attached two images (Slice165 and Slice166) with an arrow pointing to the location. I am new at this, so maybe I am wrong and it is not a segmentation error.
I've also attached an additional image (Slice185) of what I think is a type of topological error that I often see multiple times in a subject. Is this a topological defect? If so, if it is only over 3 slices does it need to be corrected?
Thanks again,
Emily ________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Douglas N Greve [greve@nmr.mgh.harvard.edu] Sent: Tuesday, February 20, 2018 4:59 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Surface Errors
sorry, what kind of errors? I could not really tell from the images what the problem was
On 02/20/2018 10:22 AM, Emily Schwartz wrote:
Hi FreeSurfer community,
I am working on elderly subjects and have had this kind of surface error quite often in different locations. Usually, it's over about 3-4 slices (in one view) and can be fixed, but I am finding multiple in almost every subject and therefore taking a lot of time to edit (and then once reprocessed new ones sometimes come up in different locations). I was wondering if these are normal to have, minor surface errors that do not necessarily need to be fixed. I have added images of an example below. Here are some of the values I get from aparc.stats for caudal middle frontal lh after manually editing:
Surface area: Original - 2500 mm^2 Edited - 2532 mm^2
Grey volume: Original - 1710 mm^3 Edited - 1727 mm^3
Thickness avg Original - 4455 mm std: 2.371 Edited - 4445 mm std: 2.365
Although the thickness values only differ by 10 mm, we are a little concerned because the difference is not within the standard deviation.
Please let me know if all of these errors should be edited or if it may be okay to keep the smaller segmentation/topological errors as they are.
Thank you,
Emily
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
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
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
I'm a little surprised you are getting them so frequently. Can you upload a couple of subjects so I can take a look?
On 02/21/2018 02:52 PM, Emily Schwartz wrote:
Hi Doug,
I am using V6.0.0 (x86_64) on Ubuntu. Should I not be getting these errors so often?
Best,
Emily ________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Douglas N Greve [greve@nmr.mgh.harvard.edu] Sent: Wednesday, February 21, 2018 2:18 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Surface Errors
btw, what verions of FS are you using?
On 02/21/2018 01:25 PM, Emily Schwartz wrote:
Got it, thank you so much!
Best,
Emily ________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Bruce Fischl [fischl@nmr.mgh.harvard.edu] Sent: Wednesday, February 21, 2018 10:23 AM To: Freesurfer support list Subject: Re: [Freesurfer] Surface Errors
Hi Emily
it is a segmentation error, but it's a pretty small one. It will mess up the thickness in a region a few mm^2. You could fix it by editing the wm.mgz if you really care about that spot
cheers Bruce
On Wed, 21 Feb 2018, Emily Schwartz wrote:
Hi Doug,
Thank you for getting back to me. I've attached two images (Slice165 and Slice166) with an arrow pointing to the location. I am new at this, so maybe I am wrong and it is not a segmentation error.
I've also attached an additional image (Slice185) of what I think is a type of topological error that I often see multiple times in a subject. Is this a topological defect? If so, if it is only over 3 slices does it need to be corrected?
Thanks again,
Emily ________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Douglas N Greve [greve@nmr.mgh.harvard.edu] Sent: Tuesday, February 20, 2018 4:59 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Surface Errors
sorry, what kind of errors? I could not really tell from the images what the problem was
On 02/20/2018 10:22 AM, Emily Schwartz wrote:
Hi FreeSurfer community,
I am working on elderly subjects and have had this kind of surface error quite often in different locations. Usually, it's over about 3-4 slices (in one view) and can be fixed, but I am finding multiple in almost every subject and therefore taking a lot of time to edit (and then once reprocessed new ones sometimes come up in different locations). I was wondering if these are normal to have, minor surface errors that do not necessarily need to be fixed. I have added images of an example below. Here are some of the values I get from aparc.stats for caudal middle frontal lh after manually editing:
Surface area: Original - 2500 mm^2 Edited - 2532 mm^2
Grey volume: Original - 1710 mm^3 Edited - 1727 mm^3
Thickness avg Original - 4455 mm std: 2.371 Edited - 4445 mm std: 2.365
Although the thickness values only differ by 10 mm, we are a little concerned because the difference is not within the standard deviation.
Please let me know if all of these errors should be edited or if it may be okay to keep the smaller segmentation/topological errors as they are.
Thank you,
Emily
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
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
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
Hi Doug,
I definitely can. I cannot use FTP from this computer for some reason. Can I upload it via filedrop and should I send it to your email?
Thanks,
Emily
________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Douglas N Greve [greve@nmr.mgh.harvard.edu] Sent: Wednesday, February 21, 2018 4:29 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Surface Errors
I'm a little surprised you are getting them so frequently. Can you upload a couple of subjects so I can take a look?
On 02/21/2018 02:52 PM, Emily Schwartz wrote:
Hi Doug,
I am using V6.0.0 (x86_64) on Ubuntu. Should I not be getting these errors so often?
Best,
Emily ________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Douglas N Greve [greve@nmr.mgh.harvard.edu] Sent: Wednesday, February 21, 2018 2:18 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Surface Errors
btw, what verions of FS are you using?
On 02/21/2018 01:25 PM, Emily Schwartz wrote:
Got it, thank you so much!
Best,
Emily ________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Bruce Fischl [fischl@nmr.mgh.harvard.edu] Sent: Wednesday, February 21, 2018 10:23 AM To: Freesurfer support list Subject: Re: [Freesurfer] Surface Errors
Hi Emily
it is a segmentation error, but it's a pretty small one. It will mess up the thickness in a region a few mm^2. You could fix it by editing the wm.mgz if you really care about that spot
cheers Bruce
On Wed, 21 Feb 2018, Emily Schwartz wrote:
Hi Doug,
Thank you for getting back to me. I've attached two images (Slice165 and Slice166) with an arrow pointing to the location. I am new at this, so maybe I am wrong and it is not a segmentation error.
I've also attached an additional image (Slice185) of what I think is a type of topological error that I often see multiple times in a subject. Is this a topological defect? If so, if it is only over 3 slices does it need to be corrected?
Thanks again,
Emily ________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Douglas N Greve [greve@nmr.mgh.harvard.edu] Sent: Tuesday, February 20, 2018 4:59 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Surface Errors
sorry, what kind of errors? I could not really tell from the images what the problem was
On 02/20/2018 10:22 AM, Emily Schwartz wrote:
Hi FreeSurfer community,
I am working on elderly subjects and have had this kind of surface error quite often in different locations. Usually, it's over about 3-4 slices (in one view) and can be fixed, but I am finding multiple in almost every subject and therefore taking a lot of time to edit (and then once reprocessed new ones sometimes come up in different locations). I was wondering if these are normal to have, minor surface errors that do not necessarily need to be fixed. I have added images of an example below. Here are some of the values I get from aparc.stats for caudal middle frontal lh after manually editing:
Surface area: Original - 2500 mm^2 Edited - 2532 mm^2
Grey volume: Original - 1710 mm^3 Edited - 1727 mm^3
Thickness avg Original - 4455 mm std: 2.371 Edited - 4445 mm std: 2.365
Although the thickness values only differ by 10 mm, we are a little concerned because the difference is not within the standard deviation.
Please let me know if all of these errors should be edited or if it may be okay to keep the smaller segmentation/topological errors as they are.
Thank you,
Emily
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
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
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
yes, filedrop should be find
thanks
On 02/21/2018 04:44 PM, Emily Schwartz wrote:
Hi Doug,
I definitely can. I cannot use FTP from this computer for some reason. Can I upload it via filedrop and should I send it to your email?
Thanks,
Emily
From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Douglas N Greve [greve@nmr.mgh.harvard.edu] Sent: Wednesday, February 21, 2018 4:29 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Surface Errors
I'm a little surprised you are getting them so frequently. Can you upload a couple of subjects so I can take a look?
On 02/21/2018 02:52 PM, Emily Schwartz wrote:
Hi Doug,
I am using V6.0.0 (x86_64) on Ubuntu. Should I not be getting these errors so often?
Best,
Emily ________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Douglas N Greve [greve@nmr.mgh.harvard.edu] Sent: Wednesday, February 21, 2018 2:18 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Surface Errors
btw, what verions of FS are you using?
On 02/21/2018 01:25 PM, Emily Schwartz wrote:
Got it, thank you so much!
Best,
Emily ________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Bruce Fischl [fischl@nmr.mgh.harvard.edu] Sent: Wednesday, February 21, 2018 10:23 AM To: Freesurfer support list Subject: Re: [Freesurfer] Surface Errors
Hi Emily
it is a segmentation error, but it's a pretty small one. It will mess up the thickness in a region a few mm^2. You could fix it by editing the wm.mgz if you really care about that spot
cheers Bruce
On Wed, 21 Feb 2018, Emily Schwartz wrote:
Hi Doug,
Thank you for getting back to me. I've attached two images (Slice165 and Slice166) with an arrow pointing to the location. I am new at this, so maybe I am wrong and it is not a segmentation error.
I've also attached an additional image (Slice185) of what I think is a type of topological error that I often see multiple times in a subject. Is this a topological defect? If so, if it is only over 3 slices does it need to be corrected?
Thanks again,
Emily ________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Douglas N Greve [greve@nmr.mgh.harvard.edu] Sent: Tuesday, February 20, 2018 4:59 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Surface Errors
sorry, what kind of errors? I could not really tell from the images what the problem was
On 02/20/2018 10:22 AM, Emily Schwartz wrote:
Hi FreeSurfer community,
I am working on elderly subjects and have had this kind of surface error quite often in different locations. Usually, it's over about 3-4 slices (in one view) and can be fixed, but I am finding multiple in almost every subject and therefore taking a lot of time to edit (and then once reprocessed new ones sometimes come up in different locations). I was wondering if these are normal to have, minor surface errors that do not necessarily need to be fixed. I have added images of an example below. Here are some of the values I get from aparc.stats for caudal middle frontal lh after manually editing:
Surface area: Original - 2500 mm^2 Edited - 2532 mm^2
Grey volume: Original - 1710 mm^3 Edited - 1727 mm^3
Thickness avg Original - 4455 mm std: 2.371 Edited - 4445 mm std: 2.365
Although the thickness values only differ by 10 mm, we are a little concerned because the difference is not within the standard deviation.
Please let me know if all of these errors should be edited or if it may be okay to keep the smaller segmentation/topological errors as they are.
Thank you,
Emily
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
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
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 mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hi Doug,
Great, thank you. I sent it to you via filedrop.
Best,
Emily ________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Douglas N Greve [greve@nmr.mgh.harvard.edu] Sent: Wednesday, February 21, 2018 4:52 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Surface Errors
yes, filedrop should be find
thanks
On 02/21/2018 04:44 PM, Emily Schwartz wrote:
Hi Doug,
I definitely can. I cannot use FTP from this computer for some reason. Can I upload it via filedrop and should I send it to your email?
Thanks,
Emily
From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Douglas N Greve [greve@nmr.mgh.harvard.edu] Sent: Wednesday, February 21, 2018 4:29 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Surface Errors
I'm a little surprised you are getting them so frequently. Can you upload a couple of subjects so I can take a look?
On 02/21/2018 02:52 PM, Emily Schwartz wrote:
Hi Doug,
I am using V6.0.0 (x86_64) on Ubuntu. Should I not be getting these errors so often?
Best,
Emily ________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Douglas N Greve [greve@nmr.mgh.harvard.edu] Sent: Wednesday, February 21, 2018 2:18 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Surface Errors
btw, what verions of FS are you using?
On 02/21/2018 01:25 PM, Emily Schwartz wrote:
Got it, thank you so much!
Best,
Emily ________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Bruce Fischl [fischl@nmr.mgh.harvard.edu] Sent: Wednesday, February 21, 2018 10:23 AM To: Freesurfer support list Subject: Re: [Freesurfer] Surface Errors
Hi Emily
it is a segmentation error, but it's a pretty small one. It will mess up the thickness in a region a few mm^2. You could fix it by editing the wm.mgz if you really care about that spot
cheers Bruce
On Wed, 21 Feb 2018, Emily Schwartz wrote:
Hi Doug,
Thank you for getting back to me. I've attached two images (Slice165 and Slice166) with an arrow pointing to the location. I am new at this, so maybe I am wrong and it is not a segmentation error.
I've also attached an additional image (Slice185) of what I think is a type of topological error that I often see multiple times in a subject. Is this a topological defect? If so, if it is only over 3 slices does it need to be corrected?
Thanks again,
Emily ________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Douglas N Greve [greve@nmr.mgh.harvard.edu] Sent: Tuesday, February 20, 2018 4:59 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Surface Errors
sorry, what kind of errors? I could not really tell from the images what the problem was
On 02/20/2018 10:22 AM, Emily Schwartz wrote:
Hi FreeSurfer community,
I am working on elderly subjects and have had this kind of surface error quite often in different locations. Usually, it's over about 3-4 slices (in one view) and can be fixed, but I am finding multiple in almost every subject and therefore taking a lot of time to edit (and then once reprocessed new ones sometimes come up in different locations). I was wondering if these are normal to have, minor surface errors that do not necessarily need to be fixed. I have added images of an example below. Here are some of the values I get from aparc.stats for caudal middle frontal lh after manually editing:
Surface area: Original - 2500 mm^2 Edited - 2532 mm^2
Grey volume: Original - 1710 mm^3 Edited - 1727 mm^3
Thickness avg Original - 4455 mm std: 2.371 Edited - 4445 mm std: 2.365
Although the thickness values only differ by 10 mm, we are a little concerned because the difference is not within the standard deviation.
Please let me know if all of these errors should be edited or if it may be okay to keep the smaller segmentation/topological errors as they are.
Thank you,
Emily
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
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
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 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
got em. can you send me coordinates (col, row,slice) where you are seeing the errors? You can also create a point set in FreeView (under File->New PointSet)
On 02/22/2018 08:48 AM, Emily Schwartz wrote:
Hi Doug,
Great, thank you. I sent it to you via filedrop.
Best,
Emily ________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Douglas N Greve [greve@nmr.mgh.harvard.edu] Sent: Wednesday, February 21, 2018 4:52 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Surface Errors
yes, filedrop should be find
thanks
On 02/21/2018 04:44 PM, Emily Schwartz wrote:
Hi Doug,
I definitely can. I cannot use FTP from this computer for some reason. Can I upload it via filedrop and should I send it to your email?
Thanks,
Emily
From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Douglas N Greve [greve@nmr.mgh.harvard.edu] Sent: Wednesday, February 21, 2018 4:29 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Surface Errors
I'm a little surprised you are getting them so frequently. Can you upload a couple of subjects so I can take a look?
On 02/21/2018 02:52 PM, Emily Schwartz wrote:
Hi Doug,
I am using V6.0.0 (x86_64) on Ubuntu. Should I not be getting these errors so often?
Best,
Emily ________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Douglas N Greve [greve@nmr.mgh.harvard.edu] Sent: Wednesday, February 21, 2018 2:18 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Surface Errors
btw, what verions of FS are you using?
On 02/21/2018 01:25 PM, Emily Schwartz wrote:
Got it, thank you so much!
Best,
Emily ________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Bruce Fischl [fischl@nmr.mgh.harvard.edu] Sent: Wednesday, February 21, 2018 10:23 AM To: Freesurfer support list Subject: Re: [Freesurfer] Surface Errors
Hi Emily
it is a segmentation error, but it's a pretty small one. It will mess up the thickness in a region a few mm^2. You could fix it by editing the wm.mgz if you really care about that spot
cheers Bruce
On Wed, 21 Feb 2018, Emily Schwartz wrote:
Hi Doug,
Thank you for getting back to me. I've attached two images (Slice165 and Slice166) with an arrow pointing to the location. I am new at this, so maybe I am wrong and it is not a segmentation error.
I've also attached an additional image (Slice185) of what I think is a type of topological error that I often see multiple times in a subject. Is this a topological defect? If so, if it is only over 3 slices does it need to be corrected?
Thanks again,
Emily ________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Douglas N Greve [greve@nmr.mgh.harvard.edu] Sent: Tuesday, February 20, 2018 4:59 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Surface Errors
sorry, what kind of errors? I could not really tell from the images what the problem was
On 02/20/2018 10:22 AM, Emily Schwartz wrote:
Hi FreeSurfer community,
I am working on elderly subjects and have had this kind of surface error quite often in different locations. Usually, it's over about 3-4 slices (in one view) and can be fixed, but I am finding multiple in almost every subject and therefore taking a lot of time to edit (and then once reprocessed new ones sometimes come up in different locations). I was wondering if these are normal to have, minor surface errors that do not necessarily need to be fixed. I have added images of an example below. Here are some of the values I get from aparc.stats for caudal middle frontal lh after manually editing:
Surface area: Original - 2500 mm^2 Edited - 2532 mm^2
Grey volume: Original - 1710 mm^3 Edited - 1727 mm^3
Thickness avg Original - 4455 mm std: 2.371 Edited - 4445 mm std: 2.365
Although the thickness values only differ by 10 mm, we are a little concerned because the difference is not within the standard deviation.
Please let me know if all of these errors should be edited or if it may be okay to keep the smaller segmentation/topological errors as they are.
Thank you,
Emily
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
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
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 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
Hi Doug,
Attached are the point sets for the 3 subjects. For some issues, I put a range of coordinate points. Let me know if you need anything else.
Thanks!
Emily ________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Douglas N Greve [greve@nmr.mgh.harvard.edu] Sent: Thursday, February 22, 2018 11:55 AM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Surface Errors
got em. can you send me coordinates (col, row,slice) where you are seeing the errors? You can also create a point set in FreeView (under File->New PointSet)
On 02/22/2018 08:48 AM, Emily Schwartz wrote:
Hi Doug,
Great, thank you. I sent it to you via filedrop.
Best,
Emily ________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Douglas N Greve [greve@nmr.mgh.harvard.edu] Sent: Wednesday, February 21, 2018 4:52 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Surface Errors
yes, filedrop should be find
thanks
On 02/21/2018 04:44 PM, Emily Schwartz wrote:
Hi Doug,
I definitely can. I cannot use FTP from this computer for some reason. Can I upload it via filedrop and should I send it to your email?
Thanks,
Emily
From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Douglas N Greve [greve@nmr.mgh.harvard.edu] Sent: Wednesday, February 21, 2018 4:29 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Surface Errors
I'm a little surprised you are getting them so frequently. Can you upload a couple of subjects so I can take a look?
On 02/21/2018 02:52 PM, Emily Schwartz wrote:
Hi Doug,
I am using V6.0.0 (x86_64) on Ubuntu. Should I not be getting these errors so often?
Best,
Emily ________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Douglas N Greve [greve@nmr.mgh.harvard.edu] Sent: Wednesday, February 21, 2018 2:18 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Surface Errors
btw, what verions of FS are you using?
On 02/21/2018 01:25 PM, Emily Schwartz wrote:
Got it, thank you so much!
Best,
Emily ________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Bruce Fischl [fischl@nmr.mgh.harvard.edu] Sent: Wednesday, February 21, 2018 10:23 AM To: Freesurfer support list Subject: Re: [Freesurfer] Surface Errors
Hi Emily
it is a segmentation error, but it's a pretty small one. It will mess up the thickness in a region a few mm^2. You could fix it by editing the wm.mgz if you really care about that spot
cheers Bruce
On Wed, 21 Feb 2018, Emily Schwartz wrote:
Hi Doug,
Thank you for getting back to me. I've attached two images (Slice165 and Slice166) with an arrow pointing to the location. I am new at this, so maybe I am wrong and it is not a segmentation error.
I've also attached an additional image (Slice185) of what I think is a type of topological error that I often see multiple times in a subject. Is this a topological defect? If so, if it is only over 3 slices does it need to be corrected?
Thanks again,
Emily ________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Douglas N Greve [greve@nmr.mgh.harvard.edu] Sent: Tuesday, February 20, 2018 4:59 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Surface Errors
sorry, what kind of errors? I could not really tell from the images what the problem was
On 02/20/2018 10:22 AM, Emily Schwartz wrote:
Hi FreeSurfer community,
I am working on elderly subjects and have had this kind of surface error quite often in different locations. Usually, it's over about 3-4 slices (in one view) and can be fixed, but I am finding multiple in almost every subject and therefore taking a lot of time to edit (and then once reprocessed new ones sometimes come up in different locations). I was wondering if these are normal to have, minor surface errors that do not necessarily need to be fixed. I have added images of an example below. Here are some of the values I get from aparc.stats for caudal middle frontal lh after manually editing:
Surface area: Original - 2500 mm^2 Edited - 2532 mm^2
Grey volume: Original - 1710 mm^3 Edited - 1727 mm^3
Thickness avg Original - 4455 mm std: 2.371 Edited - 4445 mm std: 2.365
Although the thickness values only differ by 10 mm, we are a little concerned because the difference is not within the standard deviation.
Please let me know if all of these errors should be edited or if it may be okay to keep the smaller segmentation/topological errors as they are.
Thank you,
Emily
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
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
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 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 Emily, I looked over these subjects. While a few of the flagged spots are not really problems, most of them are true inaccuracies. I think the underlying problem is that your data is pretty noisy and have some ringing. What kind of acq was it? Scanner, field strength, pulse seq? Was it acquired at 1mm resolution or was it resampled? It looks a little blurry to me. What are the subject characteristics? I don't think there is an easy way to fix it. This might not be fatal as the errors are probably randomly distributed across space. If you have a good number of subjects, then there might not be much of an effect on group maps.
On 02/22/2018 02:50 PM, Emily Schwartz wrote:
Hi Doug,
Attached are the point sets for the 3 subjects. For some issues, I put a range of coordinate points. Let me know if you need anything else.
Thanks!
Emily ________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Douglas N Greve [greve@nmr.mgh.harvard.edu] Sent: Thursday, February 22, 2018 11:55 AM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Surface Errors
got em. can you send me coordinates (col, row,slice) where you are seeing the errors? You can also create a point set in FreeView (under File->New PointSet)
On 02/22/2018 08:48 AM, Emily Schwartz wrote:
Hi Doug,
Great, thank you. I sent it to you via filedrop.
Best,
Emily ________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Douglas N Greve [greve@nmr.mgh.harvard.edu] Sent: Wednesday, February 21, 2018 4:52 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Surface Errors
yes, filedrop should be find
thanks
On 02/21/2018 04:44 PM, Emily Schwartz wrote:
Hi Doug,
I definitely can. I cannot use FTP from this computer for some reason. Can I upload it via filedrop and should I send it to your email?
Thanks,
Emily
From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Douglas N Greve [greve@nmr.mgh.harvard.edu] Sent: Wednesday, February 21, 2018 4:29 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Surface Errors
I'm a little surprised you are getting them so frequently. Can you upload a couple of subjects so I can take a look?
On 02/21/2018 02:52 PM, Emily Schwartz wrote:
Hi Doug,
I am using V6.0.0 (x86_64) on Ubuntu. Should I not be getting these errors so often?
Best,
Emily ________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Douglas N Greve [greve@nmr.mgh.harvard.edu] Sent: Wednesday, February 21, 2018 2:18 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Surface Errors
btw, what verions of FS are you using?
On 02/21/2018 01:25 PM, Emily Schwartz wrote:
Got it, thank you so much!
Best,
Emily ________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Bruce Fischl [fischl@nmr.mgh.harvard.edu] Sent: Wednesday, February 21, 2018 10:23 AM To: Freesurfer support list Subject: Re: [Freesurfer] Surface Errors
Hi Emily
it is a segmentation error, but it's a pretty small one. It will mess up the thickness in a region a few mm^2. You could fix it by editing the wm.mgz if you really care about that spot
cheers Bruce
On Wed, 21 Feb 2018, Emily Schwartz wrote:
Hi Doug,
Thank you for getting back to me. I've attached two images (Slice165 and Slice166) with an arrow pointing to the location. I am new at this, so maybe I am wrong and it is not a segmentation error.
I've also attached an additional image (Slice185) of what I think is a type of topological error that I often see multiple times in a subject. Is this a topological defect? If so, if it is only over 3 slices does it need to be corrected?
Thanks again,
Emily ________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Douglas N Greve [greve@nmr.mgh.harvard.edu] Sent: Tuesday, February 20, 2018 4:59 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Surface Errors
sorry, what kind of errors? I could not really tell from the images what the problem was
On 02/20/2018 10:22 AM, Emily Schwartz wrote: > Hi FreeSurfer community, > > I am working on elderly subjects and have had this kind of surface error quite often in different locations. Usually, it's over about 3-4 slices (in one view) and can be fixed, but I am finding multiple in almost every subject and therefore taking a lot of time to edit (and then once reprocessed new ones sometimes come up in different locations). I was wondering if these are normal to have, minor surface errors that do not necessarily need to be fixed. I have added images of an example below. Here are some of the values I get from aparc.stats for caudal middle frontal lh after manually editing: > > Surface area: > Original - 2500 mm^2 > Edited - 2532 mm^2 > > Grey volume: > Original - 1710 mm^3 > Edited - 1727 mm^3 > > Thickness avg > Original - 4455 mm std: 2.371 > Edited - 4445 mm std: 2.365 > > Although the thickness values only differ by 10 mm, we are a little concerned because the difference is not within the standard deviation. > > Please let me know if all of these errors should be edited or if it may be okay to keep the smaller segmentation/topological errors as they are. > > Thank you, > > Emily > > > > > _______________________________________________ > 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
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
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 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 mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hi Doug,
They were initially reoriented for VBM analysis, but nothing else was changed (comparing original versus reoriented, there does not seem to be differences). The subjects are elderly (mean age = 74.08). We are investigating a new pre-dementia syndrome so there may be greater atrophy in some subjects, but the majority of the participants processed so far should be cognitively healthy.
MRI scanning was performed with a Philips 3T Achieva Quasar TX multinuclear MRI/MRS system equipped with a Dual Quasar High Performance Gradient System, 32-channel broadband digital RF system, Quadrature T/R Head Coil, Rapid View reconstructor, Intera Achieva Scan-Tools Pro R2.5 Package, NetForum and ExamCards, and SENSE parallel imaging capability.
The T1-weighted whole head structural image was acquired using axial 3D-MP-RAGE parameters over a 240 mm FOV and 1.0 mm isotropic resolution, TE: 54.6 ms, TR: 59.9 ms, with SENSE factor 2.5.
We really appreciate your help. Please let me know if you need any more info.
Best,
Emily ________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Douglas N Greve [greve@nmr.mgh.harvard.edu] Sent: Monday, February 26, 2018 1:27 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Surface Errors
Hi Emily, I looked over these subjects. While a few of the flagged spots are not really problems, most of them are true inaccuracies. I think the underlying problem is that your data is pretty noisy and have some ringing. What kind of acq was it? Scanner, field strength, pulse seq? Was it acquired at 1mm resolution or was it resampled? It looks a little blurry to me. What are the subject characteristics? I don't think there is an easy way to fix it. This might not be fatal as the errors are probably randomly distributed across space. If you have a good number of subjects, then there might not be much of an effect on group maps.
On 02/22/2018 02:50 PM, Emily Schwartz wrote:
Hi Doug,
Attached are the point sets for the 3 subjects. For some issues, I put a range of coordinate points. Let me know if you need anything else.
Thanks!
Emily ________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Douglas N Greve [greve@nmr.mgh.harvard.edu] Sent: Thursday, February 22, 2018 11:55 AM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Surface Errors
got em. can you send me coordinates (col, row,slice) where you are seeing the errors? You can also create a point set in FreeView (under File->New PointSet)
On 02/22/2018 08:48 AM, Emily Schwartz wrote:
Hi Doug,
Great, thank you. I sent it to you via filedrop.
Best,
Emily ________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Douglas N Greve [greve@nmr.mgh.harvard.edu] Sent: Wednesday, February 21, 2018 4:52 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Surface Errors
yes, filedrop should be find
thanks
On 02/21/2018 04:44 PM, Emily Schwartz wrote:
Hi Doug,
I definitely can. I cannot use FTP from this computer for some reason. Can I upload it via filedrop and should I send it to your email?
Thanks,
Emily
From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Douglas N Greve [greve@nmr.mgh.harvard.edu] Sent: Wednesday, February 21, 2018 4:29 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Surface Errors
I'm a little surprised you are getting them so frequently. Can you upload a couple of subjects so I can take a look?
On 02/21/2018 02:52 PM, Emily Schwartz wrote:
Hi Doug,
I am using V6.0.0 (x86_64) on Ubuntu. Should I not be getting these errors so often?
Best,
Emily ________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Douglas N Greve [greve@nmr.mgh.harvard.edu] Sent: Wednesday, February 21, 2018 2:18 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Surface Errors
btw, what verions of FS are you using?
On 02/21/2018 01:25 PM, Emily Schwartz wrote:
Got it, thank you so much!
Best,
Emily ________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Bruce Fischl [fischl@nmr.mgh.harvard.edu] Sent: Wednesday, February 21, 2018 10:23 AM To: Freesurfer support list Subject: Re: [Freesurfer] Surface Errors
Hi Emily
it is a segmentation error, but it's a pretty small one. It will mess up the thickness in a region a few mm^2. You could fix it by editing the wm.mgz if you really care about that spot
cheers Bruce
On Wed, 21 Feb 2018, Emily Schwartz wrote:
Hi Doug,
Thank you for getting back to me. I've attached two images (Slice165 and Slice166) with an arrow pointing to the location. I am new at this, so maybe I am wrong and it is not a segmentation error.
I've also attached an additional image (Slice185) of what I think is a type of topological error that I often see multiple times in a subject. Is this a topological defect? If so, if it is only over 3 slices does it need to be corrected?
Thanks again,
Emily ________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Douglas N Greve [greve@nmr.mgh.harvard.edu] Sent: Tuesday, February 20, 2018 4:59 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Surface Errors
sorry, what kind of errors? I could not really tell from the images what the problem was
On 02/20/2018 10:22 AM, Emily Schwartz wrote: > Hi FreeSurfer community, > > I am working on elderly subjects and have had this kind of surface error quite often in different locations. Usually, it's over about 3-4 slices (in one view) and can be fixed, but I am finding multiple in almost every subject and therefore taking a lot of time to edit (and then once reprocessed new ones sometimes come up in different locations). I was wondering if these are normal to have, minor surface errors that do not necessarily need to be fixed. I have added images of an example below. Here are some of the values I get from aparc.stats for caudal middle frontal lh after manually editing: > > Surface area: > Original - 2500 mm^2 > Edited - 2532 mm^2 > > Grey volume: > Original - 1710 mm^3 > Edited - 1727 mm^3 > > Thickness avg > Original - 4455 mm std: 2.371 > Edited - 4445 mm std: 2.365 > > Although the thickness values only differ by 10 mm, we are a little concerned because the difference is not within the standard deviation. > > Please let me know if all of these errors should be edited or if it may be okay to keep the smaller segmentation/topological errors as they are. > > Thank you, > > Emily > > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu
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-- 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/
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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/
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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/
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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/
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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/
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