Hello,
I am looking at cortical thickness and surface area using Freesurfer. I have transferred label V1 from freesurfer onto the brains of my participants and when I view them on the inflated brains in tksurfer , I notice that there are holes in the label. Is this an issue when calculating mean cortical thickness and total surface area estimations? Should I fill these in somehow?
I've attached a picture to show as an example. Please let me know if the picture cannot be viewed.
Thanks! Krista
How did you do the transfer? What was your cmd line? doug
On 09/10/2013 05:31 PM, krista kelly wrote:
Hello,
I am looking at cortical thickness and surface area using Freesurfer. I have transferred label V1 from freesurfer onto the brains of my participants and when I view them on the inflated brains in tksurfer , I notice that there are holes in the label. Is this an issue when calculating mean cortical thickness and total surface area estimations? Should I fill these in somehow?
I've attached a picture to show as an example. Please let me know if the picture cannot be viewed.
Thanks! Krista
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hi Doug,
Sorry it's been a while since I've ran the initial codes, but I think these are the labels automatically generated by Freesurfer v5.0 during recon-all (correct me if I'm wrong). Here's what I ran below:
recon-all -all -notal-check -cw256 -force -subjid MB18 -i ~/Desktop/New_CT_niis/MB18.nii.gz
then
recon-all -force -s MB18 -qcache -i ~/Desktop/New_CT_niis/MB18.nii.gz
I've checked a few more brains and noticed the same problem. I've also noticed that the left hemisphere is always worse than the right. When opening the brains in tkmedit, the labels are not continuous on the surface. Could this be the problem? Is this label the same as the Hinds label and if not, should I run that instead?
Is possible to edit the label, and if so, how often does one have to edit the labels automatically created by freesurfer? I know that too much editing can take away from the standardization of the process and I wouldn't want to mess with that too much.
Thanks!
On Tue, Sep 10, 2013 at 6:35 PM, Douglas N Greve greve@nmr.mgh.harvard.edu wrote:
How did you do the transfer? What was your cmd line? doug
On 09/10/2013 05:31 PM, krista kelly wrote:
Hello,
I am looking at cortical thickness and surface area using Freesurfer. I have transferred label V1 from freesurfer onto the brains of my participants and when I view them on the inflated brains in tksurfer , I notice that there are holes in the label. Is this an issue when calculating mean cortical thickness and total surface area estimations? Should I fill these in somehow?
I've attached a picture to show as an example. Please let me know if the picture cannot be viewed.
Thanks! Krista
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
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 all,
I'm having trouble with V1 labels that are mapped automatically in freesurfer. I've noticed that there are holes in the label when I load it onto a 3d brain in tksurfer. This happens more often for the left hemisphere and not so much for the right. I've found the problem persists even after doing manual edits of the borders and fixing the brain extraction. I was just wondering if anyone has had the same problem or knows how to fix it (see message previously posted below).
Thanks!
Hi Doug,
Sorry it's been a while since I've ran the initial codes, but I think these are the labels automatically generated by Freesurfer v5.0 during recon-all (correct me if I'm wrong). Here's what I ran below:
recon-all -all -notal-check -cw256 -force -subjid MB18 -i ~/Desktop/New_CT_niis/MB18.nii.gz
then
recon-all -force -s MB18 -qcache -i ~/Desktop/New_CT_niis/MB18.nii.gz
I've checked a few more brains and noticed the same problem. I've also noticed that the left hemisphere is always worse than the right. When opening the brains in tkmedit, the labels are not continuous on the surface. Could this be the problem? Is this label the same as the Hinds label and if not, should I run that instead?
Is possible to edit the label, and if so, how often does one have to edit the labels automatically created by freesurfer? I know that too much editing can take away from the standardization of the process and I wouldn't want to mess with that too much.
Thanks!
On Tue, Sep 10, 2013 at 6:35 PM, Douglas N Greve greve@nmr.mgh.harvard.edu wrote:
How did you do the transfer? What was your cmd line? doug
On 09/10/2013 05:31 PM, krista kelly wrote:
Hello,
I am looking at cortical thickness and surface area using Freesurfer. I have transferred label V1 from freesurfer onto the brains of my participants and when I view them on the inflated brains in tksurfer , I notice that there are holes in the label. Is this an issue when calculating mean cortical thickness and total surface area estimations? Should I fill these in somehow?
I've attached a picture to show as an example. Please let me know if the picture cannot be viewed.
Thanks! Krista
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
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 Krista,
which V1 label are you talking about? And when you say holes when you load it onto the 3D brain with tksurfer, what exactly do you mean? Can you send us a snapshot? Bruce
On Mon, 23 Sep 2013, krista kelly wrote:
Hi all, I'm having trouble with V1 labels that are mapped automatically in freesurfer. I've noticed that there are holes in the label when I load it onto a 3d brain in tksurfer. This happens more often for the left hemisphere and not so much for the right. I've found the problem persists even after doing manual edits of the borders and fixing the brain extraction. I was just wondering if anyone has had the same problem or knows how to fix it (see message previously posted below).
Thanks!
Hi Doug,
Sorry it's been a while since I've ran the initial codes, but I think these are the labels automatically generated by Freesurfer v5.0 during recon-all (correct me if I'm wrong). Here's what I ran below:
recon-all -all -notal-check -cw256 -force -subjid MB18 -i ~/Desktop/New_CT_niis/MB18.nii.gz
then
recon-all -force -s MB18 -qcache -i ~/Desktop/New_CT_niis/MB18.nii.gz
I've checked a few more brains and noticed the same problem. I've also noticed that the left hemisphere is always worse than the right. When opening the brains in tkmedit, the labels are not continuous on the surface. Could this be the problem? Is this label the same as the Hinds label and if not, should I run that instead?
Is possible to edit the label, and if so, how often does one have to edit the labels automatically created by freesurfer? I know that too much editing can take away from the standardization of the process and I wouldn't want to mess with that too much.
Thanks!
On Tue, Sep 10, 2013 at 6:35 PM, Douglas N Greve greve@nmr.mgh.harvard.edu wrote:
How did you do the transfer? What was your cmd line? doug
On 09/10/2013 05:31 PM, krista kelly wrote:
Hello,
I am looking at cortical thickness and surface area using Freesurfer. I have transferred label V1 from freesurfer onto the brains of my participants and when I view them on the inflated brains in tksurfer , I notice that there are holes in the label. Is this an issue when calculating mean cortical thickness and total surface area estimations? Should I fill these in somehow?
I've attached a picture to show as an example. Please let me know if the picture cannot be viewed.
Thanks! Krista
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 Bruce,
I'm using the V1 labels that are automatically generated during recon-all (I think at autorecon step 28??). There are also V2 and MT labels that get generated. Are they the Hinds ones? I'm using freesurfer version 5.0 and have tried in 5.1 as well.
Here are the commands I ran:
recon-all -all -notal-check -cw256 -force -subjid BV20 -i ~/Desktop/New_CT_niis/BV20.**nii.gz
By holes, I mean that when I look at the label on the 3d brain in tksurfer, there are areas on the surface that are coloured in by the label. I've attached a photograph of the left and right hemispheres with the V1 label overlaid. It's even worse, and in both hemispheres, when I look at the cuneus label automatically generated with freesurfer (see attached file). Is there something I'm doing wrong? Please let me know you're not able to see the snapshots.
Thanks! Krista
On Mon, Sep 23, 2013 at 5:10 PM, Bruce Fischl fischl@nmr.mgh.harvard.eduwrote:
Hi Krista,
which V1 label are you talking about? And when you say holes when you load it onto the 3D brain with tksurfer, what exactly do you mean? Can you send us a snapshot? Bruce
On Mon, 23 Sep 2013, krista kelly wrote:
Hi all,
I'm having trouble with V1 labels that are mapped automatically in freesurfer. I've noticed that there are holes in the label when I load it onto a 3d brain in tksurfer. This happens more often for the left hemisphere and not so much for the right. I've found the problem persists even after doing manual edits of the borders and fixing the brain extraction. I was just wondering if anyone has had the same problem or knows how to fix it (see message previously posted below).
Thanks!
Hi Doug,
Sorry it's been a while since I've ran the initial codes, but I think these are the labels automatically generated by Freesurfer v5.0 during recon-all (correct me if I'm wrong). Here's what I ran below:
recon-all -all -notal-check -cw256 -force -subjid MB18 -i ~/Desktop/New_CT_niis/MB18.**nii.gz
then
recon-all -force -s MB18 -qcache -i ~/Desktop/New_CT_niis/MB18.**nii.gz
I've checked a few more brains and noticed the same problem. I've also noticed that the left hemisphere is always worse than the right. When opening the brains in tkmedit, the labels are not continuous on the surface. Could this be the problem? Is this label the same as the Hinds label and if not, should I run that instead?
Is possible to edit the label, and if so, how often does one have to edit the labels automatically created by freesurfer? I know that too much editing can take away from the standardization of the process and I wouldn't want to mess with that too much.
Thanks!
On Tue, Sep 10, 2013 at 6:35 PM, Douglas N Greve < greve@nmr.mgh.harvard.edu> wrote:
How did you do the transfer? What was your cmd line? doug
On 09/10/2013 05:31 PM, krista kelly wrote:
Hello,
I am looking at cortical thickness and surface area using Freesurfer. I have transferred label V1 from freesurfer onto the brains of my participants and when I view them on the inflated brains in tksurfer , I notice that there are holes in the label. Is this an issue when calculating mean cortical thickness and total surface area estimations? Should I fill these in somehow?
I've attached a picture to show as an example. Please let me know if the picture cannot be viewed.
Thanks! Krista
______________________________**_________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.**edu/mailman/listinfo/**freesurferhttps://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/BugReportinghttp://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.**edu/filedrop2https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/**facility/filedrop/index.htmlhttp://www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.**edu/transfer/outgoing/flat/**
greve/ 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/**freesurferhttps://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
contains patient information, please contact the Partners Compliance
HelpLine at
http://www.partners.org/**compliancelinehttp://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 Bruce,
I'm using the V1 labels that are automatically generated during recon-all (I think at autorecon step 28??). There are also V2 and MT labels that get generated. Are they the Hinds ones? I'm using freesurfer version 5.0 and have tried in 5.1 as well.
Here are the commands I ran:
recon-all -all -notal-check -cw256 -force -subjid BV20 -i ~/Desktop/New_CT_niis/BV20.**nii.gz
By holes, I mean that when I look at the label on the 3d brain in tksurfer, there are areas on the surface that are coloured in by the label. I've attached a photograph of the left and right hemispheres with the V1 label overlaid. It's even worse, and in both hemispheres, when I look at the cuneus label automatically generated with freesurfer (see attached file). Is there something I'm doing wrong? Please let me know you're not able to see the snapshots.
Thanks! Krista
On Mon, Sep 23, 2013 at 5:10 PM, Bruce Fischl fischl@nmr.mgh.harvard.eduwrote:
Hi Krista,
which V1 label are you talking about? And when you say holes when you load it onto the 3D brain with tksurfer, what exactly do you mean? Can you send us a snapshot? Bruce
On Mon, 23 Sep 2013, krista kelly wrote:
Hi all,
I'm having trouble with V1 labels that are mapped automatically in freesurfer. I've noticed that there are holes in the label when I load it onto a 3d brain in tksurfer. This happens more often for the left hemisphere and not so much for the right. I've found the problem persists even after doing manual edits of the borders and fixing the brain extraction. I was just wondering if anyone has had the same problem or knows how to fix it (see message previously posted below).
Thanks!
Hi Doug,
Sorry it's been a while since I've ran the initial codes, but I think these are the labels automatically generated by Freesurfer v5.0 during recon-all (correct me if I'm wrong). Here's what I ran below:
recon-all -all -notal-check -cw256 -force -subjid MB18 -i ~/Desktop/New_CT_niis/MB18.**nii.gz
then
recon-all -force -s MB18 -qcache -i ~/Desktop/New_CT_niis/MB18.**nii.gz
I've checked a few more brains and noticed the same problem. I've also noticed that the left hemisphere is always worse than the right. When opening the brains in tkmedit, the labels are not continuous on the surface. Could this be the problem? Is this label the same as the Hinds label and if not, should I run that instead?
Is possible to edit the label, and if so, how often does one have to edit the labels automatically created by freesurfer? I know that too much editing can take away from the standardization of the process and I wouldn't want to mess with that too much.
Thanks!
On Tue, Sep 10, 2013 at 6:35 PM, Douglas N Greve < greve@nmr.mgh.harvard.edu> wrote:
How did you do the transfer? What was your cmd line? doug
On 09/10/2013 05:31 PM, krista kelly wrote:
Hello,
I am looking at cortical thickness and surface area using Freesurfer. I have transferred label V1 from freesurfer onto the brains of my participants and when I view them on the inflated brains in tksurfer , I notice that there are holes in the label. Is this an issue when calculating mean cortical thickness and total surface area estimations? Should I fill these in somehow?
I've attached a picture to show as an example. Please let me know if the picture cannot be viewed.
Thanks! Krista
______________________________**_________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.**edu/mailman/listinfo/**freesurferhttps://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/BugReportinghttp://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.**edu/filedrop2https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/**facility/filedrop/index.htmlhttp://www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.**edu/transfer/outgoing/flat/**
greve/ 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/**freesurferhttps://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
contains patient information, please contact the Partners Compliance
HelpLine at
http://www.partners.org/**compliancelinehttp://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 Bruce,
I've tried twice to post this to the freesurfer mail list but it hasn't worked, I'm assuming because of the attached pictures. I'm going to try this again with only one picture and see if it works.
I'm using the V1 labels that are automatically generated during recon-all (I think at autorecon step 28??). There are also V2 and MT labels that get generated. Are they the Hinds ones? I'm using freesurfer version 5.0 and have tried in 5.1 as well.
Here are the commands I ran:
recon-all -all -notal-check -cw256 -force -subjid BV20 -i ~/Desktop/New_CT_niis/BV20.**nii.gz
By holes, I mean that when I look at the label on the 3d brain in tksurfer, there are areas on the surface that are coloured in by the label. I've attached a photograph of the left hemisphere with the V1 label overlaid. It's even worse, and in both hemispheres, when I look at the cuneus label automatically generated with freesurfer. Is there something I'm doing wrong? Please let me know you're not able to see the snapshots.
Thanks! Krista
On Mon, Sep 23, 2013 at 5:10 PM, Bruce Fischl fischl@nmr.mgh.harvard.eduwrote:
Hi Krista,
which V1 label are you talking about? And when you say holes when you load it onto the 3D brain with tksurfer, what exactly do you mean? Can you send us a snapshot? Bruce
On Mon, 23 Sep 2013, krista kelly wrote:
Hi all,
I'm having trouble with V1 labels that are mapped automatically in freesurfer. I've noticed that there are holes in the label when I load it onto a 3d brain in tksurfer. This happens more often for the left hemisphere and not so much for the right. I've found the problem persists even after doing manual edits of the borders and fixing the brain extraction. I was just wondering if anyone has had the same problem or knows how to fix it (see message previously posted below).
Thanks!
Hi Doug,
Sorry it's been a while since I've ran the initial codes, but I think these are the labels automatically generated by Freesurfer v5.0 during recon-all (correct me if I'm wrong). Here's what I ran below:
recon-all -all -notal-check -cw256 -force -subjid MB18 -i ~/Desktop/New_CT_niis/MB18.**nii.gz
then
recon-all -force -s MB18 -qcache -i ~/Desktop/New_CT_niis/MB18.**nii.gz
I've checked a few more brains and noticed the same problem. I've also noticed that the left hemisphere is always worse than the right. When opening the brains in tkmedit, the labels are not continuous on the surface. Could this be the problem? Is this label the same as the Hinds label and if not, should I run that instead?
Is possible to edit the label, and if so, how often does one have to edit the labels automatically created by freesurfer? I know that too much editing can take away from the standardization of the process and I wouldn't want to mess with that too much.
Thanks!
On Tue, Sep 10, 2013 at 6:35 PM, Douglas N Greve < greve@nmr.mgh.harvard.edu> wrote:
How did you do the transfer? What was your cmd line? doug
On 09/10/2013 05:31 PM, krista kelly wrote:
Hello,
I am looking at cortical thickness and surface area using Freesurfer. I have transferred label V1 from freesurfer onto the brains of my participants and when I view them on the inflated brains in tksurfer , I notice that there are holes in the label. Is this an issue when calculating mean cortical thickness and total surface area estimations? Should I fill these in somehow?
I've attached a picture to show as an example. Please let me know if the picture cannot be viewed.
Thanks! Krista
______________________________**_________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.**edu/mailman/listinfo/**freesurferhttps://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/BugReportinghttp://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.**edu/filedrop2https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/**facility/filedrop/index.htmlhttp://www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.**edu/transfer/outgoing/flat/**
greve/ 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/**freesurferhttps://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
contains patient information, please contact the Partners Compliance
HelpLine at
http://www.partners.org/**compliancelinehttp://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 Krista
I've never seen that happen before. Can you upload this subject and we will take a look?
thanks Bruce On Wed, 2 Oct 2013, krista kelly wrote:
Hi Bruce, I've tried twice to post this to the freesurfer mail list but it hasn't worked, I'm assuming because of the attached pictures. I'm going to try this again with only one picture and see if it works.
I'm using the V1 labels that are automatically generated during recon-all (I think at autorecon step 28??). There are also V2 and MT labels that get generated. Are they the Hinds ones? I'm using freesurfer version 5.0 and have tried in 5.1 as well.
Here are the commands I ran:
recon-all -all -notal-check -cw256 -force -subjid BV20 -i ~/Desktop/New_CT_niis/BV20.nii.gz
By holes, I mean that when I look at the label on the 3d brain in tksurfer, there are areas on the surface that are coloured in by the label. I've attached a photograph of the left hemisphere with the V1 label overlaid. It's even worse, and in both hemispheres, when I look at the cuneus label automatically generated with freesurfer. Is there something I'm doing wrong? Please let me know you're not able to see the snapshots.
Thanks! Krista
On Mon, Sep 23, 2013 at 5:10 PM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote: Hi Krista,
which V1 label are you talking about? And when you say holes when you load it onto the 3D brain with tksurfer, what exactly do you mean? Can you send us a snapshot? Bruce On Mon, 23 Sep 2013, krista kelly wrote: Hi all, I'm having trouble with V1 labels that are mapped automatically in freesurfer. I've noticed that there are holes in the label when I load it onto a 3d brain in tksurfer. This happens more often for the left hemisphere and not so much for the right. I've found the problem persists even after doing manual edits of the borders and fixing the brain extraction. I was just wondering if anyone has had the same problem or knows how to fix it (see message previously posted below). Thanks! Hi Doug, Sorry it's been a while since I've ran the initial codes, but I think these are the labels automatically generated by Freesurfer v5.0 during recon-all (correct me if I'm wrong). Here's what I ran below: recon-all -all -notal-check -cw256 -force -subjid MB18 -i ~/Desktop/New_CT_niis/MB18.nii.gz then recon-all -force -s MB18 -qcache -i ~/Desktop/New_CT_niis/MB18.nii.gz I've checked a few more brains and noticed the same problem. I've also noticed that the left hemisphere is always worse than the right. When opening the brains in tkmedit, the labels are not continuous on the surface. Could this be the problem? Is this label the same as the Hinds label and if not, should I run that instead? Is possible to edit the label, and if so, how often does one have to edit the labels automatically created by freesurfer? I know that too much editing can take away from the standardization of the process and I wouldn't want to mess with that too much. Thanks! On Tue, Sep 10, 2013 at 6:35 PM, Douglas N Greve <greve@nmr.mgh.harvard.edu> wrote: > > How did you do the transfer? What was your cmd line? > doug > > On 09/10/2013 05:31 PM, krista kelly wrote: > > Hello, > > > > I am looking at cortical thickness and surface area using Freesurfer. > > I have transferred label V1 from freesurfer onto the brains of my > > participants and when I view them on the inflated brains in tksurfer , > > I notice that there are holes in the label. Is this an issue when > > calculating mean cortical thickness and total surface area > > estimations? Should I fill these in somehow? > > > > I've attached a picture to show as an example. Please let me know if > > the picture cannot be viewed. > > > > Thanks! > > Krista > > > > > > _______________________________________________ > > 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. >
Sure! Where/how do I upload the subject's folder? I've tried attaching a zipped copy to my email but it exceeds the size limit.
Thanks! Krista
On Thu, Oct 3, 2013 at 8:23 AM, Bruce Fischl fischl@nmr.mgh.harvard.eduwrote:
Hi Krista
I've never seen that happen before. Can you upload this subject and we will take a look?
thanks Bruce
On Wed, 2 Oct 2013, krista kelly wrote:
Hi Bruce, I've tried twice to post this to the freesurfer mail list but it hasn't worked, I'm assuming because of the attached pictures. I'm going to try this again with only one picture and see if it works.
I'm using the V1 labels that are automatically generated during recon-all (I think at autorecon step 28??). There are also V2 and MT labels that get generated. Are they the Hinds ones? I'm using freesurfer version 5.0 and have tried in 5.1 as well.
Here are the commands I ran:
recon-all -all -notal-check -cw256 -force -subjid BV20 -i ~/Desktop/New_CT_niis/BV20.**nii.gz
By holes, I mean that when I look at the label on the 3d brain in tksurfer, there are areas on the surface that are coloured in by the label. I've attached a photograph of the left hemisphere with the V1 label overlaid. It's even worse, and in both hemispheres, when I look at the cuneus label automatically generated with freesurfer. Is there something I'm doing wrong? Please let me know you're not able to see the snapshots.
Thanks! Krista
On Mon, Sep 23, 2013 at 5:10 PM, Bruce Fischl <fischl@nmr.mgh.harvard.edu
wrote: Hi Krista,
which V1 label are you talking about? And when you say holes when you load it onto the 3D brain with tksurfer, what exactly do you mean? Can you send us a snapshot? Bruce On Mon, 23 Sep 2013, krista kelly wrote: Hi all, I'm having trouble with V1 labels that are mapped automatically in freesurfer. I've noticed that there are holes in the label when I load it onto a 3d brain in tksurfer. This happens more often for the left hemisphere and not so much for the right. I've found the problem persists even after doing manual edits of the borders and fixing the brain extraction. I was just wondering if anyone has had the same problem or knows how to fix it (see message previously posted below). Thanks! Hi Doug, Sorry it's been a while since I've ran the initial codes, but I think these are the labels automatically generated by Freesurfer v5.0 during recon-all (correct me if I'm wrong). Here's what I ran below: recon-all -all -notal-check -cw256 -force -subjid MB18 -i ~/Desktop/New_CT_niis/MB18.**nii.gz then recon-all -force -s MB18 -qcache -i ~/Desktop/New_CT_niis/MB18.**nii.gz I've checked a few more brains and noticed the same problem. I've also noticed that the left hemisphere is always worse than the right. When opening the brains in tkmedit, the labels are not continuous on the surface. Could this be the problem? Is this label the same as the Hinds label and if not, should I run that instead? Is possible to edit the label, and if so, how often does one have to edit the labels automatically created by freesurfer? I know that too much editing can take away from the standardization of the process and I wouldn't want to mess with that too much. Thanks! On Tue, Sep 10, 2013 at 6:35 PM, Douglas N Greve <greve@nmr.mgh.harvard.edu> wrote: > > How did you do the transfer? What was your cmd line? > doug > > On 09/10/2013 05:31 PM, krista kelly wrote: > > Hello, > > > > I am looking at cortical thickness and surface area using Freesurfer. > > I have transferred label V1 from freesurfer onto the brains of my > > participants and when I view them on the inflated brains in tksurfer , > > I notice that there are holes in the label. Is this an issue when > > calculating mean cortical thickness and total surface area > > estimations? Should I fill these in somehow? > > > > I've attached a picture to show as an example. Please let me know if > > the picture cannot be viewed. > > > > Thanks! > > Krista > > > > > > ______________________________**_________________ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu > > https://mail.nmr.mgh.harvard.**edu/mailman/listinfo/**freesurfer 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/BugReportinghttp://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > FileDrop: https://gate.nmr.mgh.harvard.**edu/filedrop2https://gate.nmr.mgh.harvard.edu/filedrop2 > www.nmr.mgh.harvard.edu/**facility/filedrop/index.htmlhttp://www.nmr.mgh.harvard.edu/facility/filedrop/index.html > Outgoing: ftp://surfer.nmr.mgh.harvard.**edu/transfer/outgoing/flat/** greve/ 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 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/**compliancelinehttp://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. >
you can do it here:
https://gate.nmr.mgh.harvard.edu/filedrop2/ On Thu, 3 Oct 2013, krista kelly wrote:
Sure! Where/how do I upload the subject's folder? I've tried attaching a zipped copy to my email but it exceeds the size limit. Thanks! Krista
On Thu, Oct 3, 2013 at 8:23 AM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote: Hi Krista
I've never seen that happen before. Can you upload this subject and we will take a look? thanks Bruce On Wed, 2 Oct 2013, krista kelly wrote: Hi Bruce, I've tried twice to post this to the freesurfer mail list but it hasn't worked, I'm assuming because of the attached pictures. I'm going to try this again with only one picture and see if it works. I'm using the V1 labels that are automatically generated during recon-all (I think at autorecon step 28??). There are also V2 and MT labels that get generated. Are they the Hinds ones? I'm using freesurfer version 5.0 and have tried in 5.1 as well. Here are the commands I ran: recon-all -all -notal-check -cw256 -force -subjid BV20 -i ~/Desktop/New_CT_niis/BV20.nii.gz By holes, I mean that when I look at the label on the 3d brain in tksurfer, there are areas on the surface that are coloured in by the label. I've attached a photograph of the left hemisphere with the V1 label overlaid. It's even worse, and in both hemispheres, when I look at the cuneus label automatically generated with freesurfer. Is there something I'm doing wrong? Please let me know you're not able to see the snapshots. Thanks! Krista On Mon, Sep 23, 2013 at 5:10 PM, Bruce Fischl <fischl@nmr.mgh.harvard.edu> wrote: Hi Krista, which V1 label are you talking about? And when you say holes when you load it onto the 3D brain with tksurfer, what exactly do you mean? Can you send us a snapshot? Bruce On Mon, 23 Sep 2013, krista kelly wrote: Hi all, I'm having trouble with V1 labels that are mapped automatically in freesurfer. I've noticed that there are holes in the label when I load it onto a 3d brain in tksurfer. This happens more often for the left hemisphere and not so much for the right. I've found the problem persists even after doing manual edits of the borders and fixing the brain extraction. I was just wondering if anyone has had the same problem or knows how to fix it (see message previously posted below). Thanks! Hi Doug, Sorry it's been a while since I've ran the initial codes, but I think these are the labels automatically generated by Freesurfer v5.0 during recon-all (correct me if I'm wrong). Here's what I ran below: recon-all -all -notal-check -cw256 -force -subjid MB18 -i ~/Desktop/New_CT_niis/MB18.nii.gz then recon-all -force -s MB18 -qcache -i ~/Desktop/New_CT_niis/MB18.nii.gz I've checked a few more brains and noticed the same problem. I've also noticed that the left hemisphere is always worse than the right. When opening the brains in tkmedit, the labels are not continuous on the surface. Could this be the problem? Is this label the same as the Hinds label and if not, should I run that instead? Is possible to edit the label, and if so, how often does one have to edit the labels automatically created by freesurfer? I know that too much editing can take away from the standardization of the process and I wouldn't want to mess with that too much. Thanks! On Tue, Sep 10, 2013 at 6:35 PM, Douglas N Greve <greve@nmr.mgh.harvard.edu> wrote: > > How did you do the transfer? What was your cmd line? > doug > > On 09/10/2013 05:31 PM, krista kelly wrote: > > Hello, > > > > I am looking at cortical thickness and surface area using Freesurfer. > > I have transferred label V1 from freesurfer onto the brains of my > > participants and when I view them on the inflated brains in tksurfer , > > I notice that there are holes in the label. Is this an issue when > > calculating mean cortical thickness and total surface area > > estimations? Should I fill these in somehow? > > > > I've attached a picture to show as an example. Please let me know if > > the picture cannot be viewed. > > > > Thanks! > > Krista > > > > > > _______________________________________________ > > 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 all,
I'm having a problem similar to Krista's, where I'm getting holes in a few labels (e.g. V1.label, MT.label, BA44.label, BA45.label) produced by the recon-all pipeline. Did you ever discover the solution to this issue?
I'm running Freesurfer v5.3.0.
Andrew
On Thu, Oct 3, 2013 at 6:49 PM, Bruce Fischl fischl@nmr.mgh.harvard.eduwrote:
you can do it here:
https://gate.nmr.mgh.harvard.edu/filedrop2/
On Thu, 3 Oct 2013, krista kelly wrote:
Sure! Where/how do I upload the subject's folder? I've tried attaching a
zipped copy to my email but it exceeds the size limit. Thanks! Krista
On Thu, Oct 3, 2013 at 8:23 AM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote: Hi Krista
I've never seen that happen before. Can you upload this subject and we will take a look? thanks Bruce On Wed, 2 Oct 2013, krista kelly wrote: Hi Bruce, I've tried twice to post this to the freesurfer mail list but it hasn't worked, I'm assuming because of the attached pictures. I'm going to try this again with only one picture and see if it works. I'm using the V1 labels that are automatically generated during recon-all (I think at autorecon step 28??). There are also V2 and MT labels that get generated. Are they the Hinds ones? I'm using freesurfer version 5.0 and have tried in 5.1 as well. Here are the commands I ran: recon-all -all -notal-check -cw256 -force -subjid BV20 -i ~/Desktop/New_CT_niis/BV20.nii.gz By holes, I mean that when I look at the label on the 3d brain in tksurfer, there are areas on the surface that are coloured in by the label. I've attached a photograph of the left hemisphere with the V1 label overlaid. It's even worse, and in both hemispheres, when I look at the cuneus label automatically generated with freesurfer. Is there something I'm doing wrong? Please let me know you're not able to see the snapshots. Thanks! Krista On Mon, Sep 23, 2013 at 5:10 PM, Bruce Fischl <fischl@nmr.mgh.harvard.edu> wrote: Hi Krista, which V1 label are you talking about? And when you say holes when you load it onto the 3D brain with tksurfer, what exactly do you mean? Can you send us a snapshot? Bruce On Mon, 23 Sep 2013, krista kelly wrote: Hi all, I'm having trouble with V1 labels that are mapped automatically in freesurfer. I've noticed that there are holes in the label when I load it onto a 3d brain in tksurfer. This happens more often for the left hemisphere and not so much for the right. I've found the problem persists even after doing manual edits of the borders and fixing the brain extraction. I was just wondering if anyone has had the same problem or knows how to fix it (see message previously posted below). Thanks! Hi Doug, Sorry it's been a while since I've ran the initial codes, but I think these are the labels automatically generated by Freesurfer v5.0 during recon-all (correct me if I'm wrong). Here's what I ran below: recon-all -all -notal-check -cw256 -force -subjid MB18 -i ~/Desktop/New_CT_niis/MB18.nii.gz then recon-all -force -s MB18 -qcache -i ~/Desktop/New_CT_niis/MB18.nii.gz I've checked a few more brains and noticed the same problem. I've also noticed that the left hemisphere is always worse than the right. When opening the brains in tkmedit, the labels are not continuous on the surface. Could this be the problem? Is this label the same as the Hinds label and if not, should I run that instead? Is possible to edit the label, and if so, how often does one have to edit the labels automatically created by freesurfer? I know that too much editing can take away from the standardization of the process and I wouldn't want to mess with that too much. Thanks! On Tue, Sep 10, 2013 at 6:35 PM, Douglas N Greve <greve@nmr.mgh.harvard.edu> wrote: > > How did you do the transfer? What was your cmd line? > doug > > On 09/10/2013 05:31 PM, krista kelly wrote: > > Hello, > > > > I am looking at cortical thickness and surface area using Freesurfer. > > I have transferred label V1 from freesurfer onto the brains of my > > participants and when I view them on the inflated brains in tksurfer , > > I notice that there are holes in the label. Is this an issue when > > calculating mean cortical thickness and total surface area > > estimations? Should I fill these in somehow? > > > > I've attached a picture to show as an example. Please let me know if > > the picture cannot be viewed. > > > > Thanks! > > Krista > > > > > > _______________________________________________ > > 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
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@nmr.mgh.harvard.edu
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Andrew Bock -
Bruce Fischl -
Douglas N Greve -
krista kelly