Hi,
I’ve been having trouble on a few of our subjects with getting the white matter and pial surface files to “line up” correctly with the volume files. I’ve attached a screenshot of what is happening: the pial surface is in red and the white matter surface file is in yellow. I have also attached an example of a “good” subject for comparison.
I’ve tried looking through the tutorials online but didn’t see anything that was really related to my issue and I was wondering what the best way to correct this. We have T2 weighted images for several subjects is well if that helps. Not sure if Freesurfer can use T2 images instead of T1 in the –reconall script but I thought I would mention it. Thank you very much in advance!
Best,
Michael S.
Hi Michael
sure, the T2 can help if you have it (although you'll need to download some updated binaries), but it is impossible to tell from these images what is going on. Looks either the intensity normalization, mri_segment or mris_make_surfaces failed. You can try the expert options for each one to prespecify the range of allowable intensities for gray and white matter. If you upload the subject to our ftp site (the whole subject directory tarred and gzipped) we will take a look
cheers Bruce
On Mon, 6 Oct 2014, Smith, Michael wrote:
Hi,
I’ve been having trouble on a few of our subjects with getting the white matter and pial surface files to “line up” correctly with the volume files. I’ve attached a screenshot of what is happening: the pial surface is in red and the white matter surface file is in yellow. I have also attached an example of a “good” subject for comparison.
I’ve tried looking through the tutorials online but didn’t see anything that was really related to my issue and I was wondering what the best way to correct this. We have T2 weighted images for several subjects is well if that helps. Not sure if Freesurfer can use T2 images instead of T1 in the –reconall script but I thought I would mention it. Thank you very much in advance!
Best,
Michael S.
Hi Bruce,
Do I not have permission to transfer files to the remote machine? I can login fine as an anonymous user but when I attempt to use the put command it says it could not create the file.
On 10/7/14, 7:33 PM, "Bruce Fischl" fischl@nmr.mgh.harvard.edu wrote:
Hi Michael
sure, the T2 can help if you have it (although you'll need to download some updated binaries), but it is impossible to tell from these images what is going on. Looks either the intensity normalization, mri_segment or mris_make_surfaces failed. You can try the expert options for each one to prespecify the range of allowable intensities for gray and white matter. If you upload the subject to our ftp site (the whole subject directory tarred and gzipped) we will take a look
cheers Bruce
On Mon, 6 Oct 2014, Smith, Michael wrote:
Hi,
I¹ve been having trouble on a few of our subjects with getting the white matter and pial surface files to ³line up² correctly with the volume files. I¹ve attached a screenshot of what is happening: the pial surface is in red and the white matter surface file is in yellow. I have also attached an example of a ³good² subject for comparison.
I¹ve tried looking through the tutorials online but didn¹t see anything that was really related to my issue and I was wondering what the best way to correct this. We have T2 weighted images for several subjects is well if that helps. Not sure if Freesurfer can use T2 images instead of T1 in the reconall script but I thought I would mention it. Thank you very much in advance!
Best,
Michael S.
can you send us the details of your ftp command? On Wed, 8 Oct 2014, Smith, Michael wrote:
Hi Bruce,
Do I not have permission to transfer files to the remote machine? I can login fine as an anonymous user but when I attempt to use the put command it says it could not create the file.
On 10/7/14, 7:33 PM, "Bruce Fischl" fischl@nmr.mgh.harvard.edu wrote:
Hi Michael
sure, the T2 can help if you have it (although you'll need to download some updated binaries), but it is impossible to tell from these images what is going on. Looks either the intensity normalization, mri_segment or mris_make_surfaces failed. You can try the expert options for each one to prespecify the range of allowable intensities for gray and white matter. If you upload the subject to our ftp site (the whole subject directory tarred and gzipped) we will take a look
cheers Bruce
On Mon, 6 Oct 2014, Smith, Michael wrote:
Hi,
I¹ve been having trouble on a few of our subjects with getting the white matter and pial surface files to ³line up² correctly with the volume files. I¹ve attached a screenshot of what is happening: the pial surface is in red and the white matter surface file is in yellow. I have also attached an example of a ³good² subject for comparison.
I¹ve tried looking through the tutorials online but didn¹t see anything that was really related to my issue and I was wondering what the best way to correct this. We have T2 weighted images for several subjects is well if that helps. Not sure if Freesurfer can use T2 images instead of T1 in the reconall script but I thought I would mention it. Thank you very much in advance!
Best,
Michael S.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
See attached
On 10/8/14, 10:46 AM, "Bruce Fischl" fischl@nmr.mgh.harvard.edu wrote:
can you send us the details of your ftp command? On Wed, 8 Oct 2014, Smith, Michael wrote:
Hi Bruce,
Do I not have permission to transfer files to the remote machine? I can login fine as an anonymous user but when I attempt to use the put command it says it could not create the file.
On 10/7/14, 7:33 PM, "Bruce Fischl" fischl@nmr.mgh.harvard.edu wrote:
Hi Michael
sure, the T2 can help if you have it (although you'll need to download some updated binaries), but it is impossible to tell from these images what is going on. Looks either the intensity normalization, mri_segment or mris_make_surfaces failed. You can try the expert options for each one to prespecify the range of allowable intensities for gray and white matter. If you upload the subject to our ftp site (the whole subject directory tarred and gzipped) we will take a look
cheers Bruce
On Mon, 6 Oct 2014, Smith, Michael wrote:
Hi,
I¹ve been having trouble on a few of our subjects with getting the white matter and pial surface files to ³line up² correctly with the volume files. I¹ve attached a screenshot of what is happening: the pial surface is in red and the white matter surface file is in yellow. I have also attached an example of a ³good² subject for comparison.
I¹ve tried looking through the tutorials online but didn¹t see anything that was really related to my issue and I was wondering what the best way to correct this. We have T2 weighted images for several subjects is well if that helps. Not sure if Freesurfer can use T2 images instead of T1 in the reconall script but I thought I would mention it. Thank you very much in advance!
Best,
Michael S.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hi Michael
you need to follow the directions on this page:
http://surfer.nmr.mgh.harvard.edu/fswiki/FtpFileExchange
in particular, make sure you change directories before trying to put
cheers Bruce
On Wed, 8 Oct 2014, Smith, Michael wrote:
See attached
On 10/8/14, 10:46 AM, "Bruce Fischl" fischl@nmr.mgh.harvard.edu wrote:
can you send us the details of your ftp command? On Wed, 8 Oct 2014, Smith, Michael wrote:
Hi Bruce,
Do I not have permission to transfer files to the remote machine? I can login fine as an anonymous user but when I attempt to use the put command it says it could not create the file.
On 10/7/14, 7:33 PM, "Bruce Fischl" fischl@nmr.mgh.harvard.edu wrote:
Hi Michael
sure, the T2 can help if you have it (although you'll need to download some updated binaries), but it is impossible to tell from these images what is going on. Looks either the intensity normalization, mri_segment or mris_make_surfaces failed. You can try the expert options for each one to prespecify the range of allowable intensities for gray and white matter. If you upload the subject to our ftp site (the whole subject directory tarred and gzipped) we will take a look
cheers Bruce
On Mon, 6 Oct 2014, Smith, Michael wrote:
Hi,
I¹ve been having trouble on a few of our subjects with getting the white matter and pial surface files to ³line up² correctly with the volume files. I¹ve attached a screenshot of what is happening: the pial surface is in red and the white matter surface file is in yellow. I have also attached an example of a ³good² subject for comparison.
I¹ve tried looking through the tutorials online but didn¹t see anything that was really related to my issue and I was wondering what the best way to correct this. We have T2 weighted images for several subjects is well if that helps. Not sure if Freesurfer can use T2 images instead of T1 in the reconall script but I thought I would mention it. Thank you very much in advance!
Best,
Michael S.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Ah, sorry for some reason it just wasn’t clicking before. I was able to upload a dataset. Thanks!
On 10/8/14, 10:59 AM, "Bruce Fischl" fischl@nmr.mgh.harvard.edu wrote:
Hi Michael
you need to follow the directions on this page:
http://surfer.nmr.mgh.harvard.edu/fswiki/FtpFileExchange
in particular, make sure you change directories before trying to put
cheers Bruce
On Wed, 8 Oct 2014, Smith, Michael wrote:
See attached
On 10/8/14, 10:46 AM, "Bruce Fischl" fischl@nmr.mgh.harvard.edu wrote:
can you send us the details of your ftp command? On Wed, 8 Oct 2014, Smith, Michael wrote:
Hi Bruce,
Do I not have permission to transfer files to the remote machine? I can login fine as an anonymous user but when I attempt to use the put command it says it could not create the file.
On 10/7/14, 7:33 PM, "Bruce Fischl" fischl@nmr.mgh.harvard.edu wrote:
Hi Michael
sure, the T2 can help if you have it (although you'll need to download some updated binaries), but it is impossible to tell from these images what is going on. Looks either the intensity normalization, mri_segment or mris_make_surfaces failed. You can try the expert options for each one to prespecify the range of allowable intensities for gray and white matter. If you upload the subject to our ftp site (the whole subject directory tarred and gzipped) we will take a look
cheers Bruce
On Mon, 6 Oct 2014, Smith, Michael wrote:
Hi,
I¹ve been having trouble on a few of our subjects with getting the white matter and pial surface files to ³line up² correctly with the volume files. I¹ve attached a screenshot of what is happening: the pial surface is in red and the white matter surface file is in yellow. I have also attached an example of a ³good² subject for comparison.
I¹ve tried looking through the tutorials online but didn¹t see anything that was really related to my issue and I was wondering what the best way to correct this. We have T2 weighted images for several subjects is well if that helps. Not sure if Freesurfer can use T2 images instead of T1 in the reconall script but I thought I would mention it. Thank you very much in advance!
Best,
Michael S.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hi Michael,
I took a look at your data and it seems that you paired a T2 image with a T1 image when you submitted to recon all. Recon-all will try to average these together, and since they have such different contrasts, you will end up with a poor template for surfaces later on.
Try running recon-all again without the T2 and see if that helps.
-Ani
On Wed, 2014-10-08 at 17:21 +0000, Smith, Michael wrote:
Ah, sorry for some reason it just wasn’t clicking before. I was able to upload a dataset. Thanks!
On 10/8/14, 10:59 AM, "Bruce Fischl" fischl@nmr.mgh.harvard.edu wrote:
Hi Michael
you need to follow the directions on this page:
http://surfer.nmr.mgh.harvard.edu/fswiki/FtpFileExchange
in particular, make sure you change directories before trying to put
cheers Bruce
On Wed, 8 Oct 2014, Smith, Michael wrote:
See attached
On 10/8/14, 10:46 AM, "Bruce Fischl" fischl@nmr.mgh.harvard.edu wrote:
can you send us the details of your ftp command? On Wed, 8 Oct 2014, Smith, Michael wrote:
Hi Bruce,
Do I not have permission to transfer files to the remote machine? I can login fine as an anonymous user but when I attempt to use the put command it says it could not create the file.
On 10/7/14, 7:33 PM, "Bruce Fischl" fischl@nmr.mgh.harvard.edu wrote:
Hi Michael
sure, the T2 can help if you have it (although you'll need to download some updated binaries), but it is impossible to tell from these images what is going on. Looks either the intensity normalization, mri_segment or mris_make_surfaces failed. You can try the expert options for each one to prespecify the range of allowable intensities for gray and white matter. If you upload the subject to our ftp site (the whole subject directory tarred and gzipped) we will take a look
cheers Bruce
On Mon, 6 Oct 2014, Smith, Michael wrote:
> Hi, > > I¹ve been having trouble on a few of our subjects with getting the > white > matter and pial surface files to ³line up² correctly with the volume > files. > I¹ve attached a screenshot of what is happening: the pial surface >is > in red > and the white matter surface file is in yellow. I have also attached > an > example of a ³good² subject for comparison. > > I¹ve tried looking through the tutorials online but didn¹t see > anything > that > was really related to my issue and I was wondering what the best way > to > correct this. We have T2 weighted images for several subjects is >well > if > that helps. Not sure if Freesurfer can use T2 images instead of T1 >in > the > reconall script but I thought I would mention it. Thank you very > much > in > advance! > > Best, > > Michael S. >
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
We re-ran that subject and it seemed to fix the problem, thanks! We will test it out on the other subjects with the same issue and see how that goes, but it looks like everything is good. Thanks again!
-----Original Message----- From: freesurfer-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] On Behalf Of Varjabedian, Ani Sent: Thursday, October 09, 2014 10:02 AM To: Freesurfer support list Subject: Re: [Freesurfer] WM & Pial Segmentation Errors
Hi Michael,
I took a look at your data and it seems that you paired a T2 image with a T1 image when you submitted to recon all. Recon-all will try to average these together, and since they have such different contrasts, you will end up with a poor template for surfaces later on.
Try running recon-all again without the T2 and see if that helps.
-Ani
On Wed, 2014-10-08 at 17:21 +0000, Smith, Michael wrote:
Ah, sorry for some reason it just wasn’t clicking before. I was able to upload a dataset. Thanks!
On 10/8/14, 10:59 AM, "Bruce Fischl" fischl@nmr.mgh.harvard.edu wrote:
Hi Michael
you need to follow the directions on this page:
http://surfer.nmr.mgh.harvard.edu/fswiki/FtpFileExchange
in particular, make sure you change directories before trying to put
cheers Bruce
On Wed, 8 Oct 2014, Smith, Michael wrote:
See attached
On 10/8/14, 10:46 AM, "Bruce Fischl" fischl@nmr.mgh.harvard.edu wrote:
can you send us the details of your ftp command? On Wed, 8 Oct 2014, Smith, Michael wrote:
Hi Bruce,
Do I not have permission to transfer files to the remote machine? I can login fine as an anonymous user but when I attempt to use the put command it says it could not create the file.
On 10/7/14, 7:33 PM, "Bruce Fischl" fischl@nmr.mgh.harvard.edu wrote:
Hi Michael
sure, the T2 can help if you have it (although you'll need to download some updated binaries), but it is impossible to tell from these images what is going on. Looks either the intensity normalization, mri_segment or mris_make_surfaces failed. You can try the expert options for each one to prespecify the range of allowable intensities for gray and white matter. If you upload the subject to our ftp site (the whole subject directory tarred and gzipped) we will take a look
cheers Bruce
On Mon, 6 Oct 2014, Smith, Michael wrote:
> Hi, > > I¹ve been having trouble on a few of our subjects with getting >the white matter and pial surface files to ³line up² correctly >with the volume files. > I¹ve attached a screenshot of what is happening: the pial >surface is in red and the white matter surface file is in >yellow. I have also attached an example of a ³good² subject >for comparison. > > I¹ve tried looking through the tutorials online but didn¹t see >anything that was really related to my issue and I was >wondering what the best way to correct this. We have T2 >weighted images for several subjects is well if that helps. >Not sure if Freesurfer can use T2 images instead of T1 in the >reconall script but I thought I would mention it. Thank you >very much in advance! > > Best, > > Michael S. >
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
_______________________________________________ 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.
glad to hear it Bruce On Fri, 10 Oct 2014, Smith, Michael wrote:
We re-ran that subject and it seemed to fix the problem, thanks! We will test it out on the other subjects with the same issue and see how that goes, but it looks like everything is good. Thanks again!
-----Original Message----- From: freesurfer-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] On Behalf Of Varjabedian, Ani Sent: Thursday, October 09, 2014 10:02 AM To: Freesurfer support list Subject: Re: [Freesurfer] WM & Pial Segmentation Errors
Hi Michael,
I took a look at your data and it seems that you paired a T2 image with a T1 image when you submitted to recon all. Recon-all will try to average these together, and since they have such different contrasts, you will end up with a poor template for surfaces later on.
Try running recon-all again without the T2 and see if that helps.
-Ani
On Wed, 2014-10-08 at 17:21 +0000, Smith, Michael wrote:
Ah, sorry for some reason it just wasn’t clicking before. I was able to upload a dataset. Thanks!
On 10/8/14, 10:59 AM, "Bruce Fischl" fischl@nmr.mgh.harvard.edu wrote:
Hi Michael
you need to follow the directions on this page:
http://surfer.nmr.mgh.harvard.edu/fswiki/FtpFileExchange
in particular, make sure you change directories before trying to put
cheers Bruce
On Wed, 8 Oct 2014, Smith, Michael wrote:
See attached
On 10/8/14, 10:46 AM, "Bruce Fischl" fischl@nmr.mgh.harvard.edu wrote:
can you send us the details of your ftp command? On Wed, 8 Oct 2014, Smith, Michael wrote:
Hi Bruce,
Do I not have permission to transfer files to the remote machine? I can login fine as an anonymous user but when I attempt to use the put command it says it could not create the file.
On 10/7/14, 7:33 PM, "Bruce Fischl" fischl@nmr.mgh.harvard.edu wrote:
> Hi Michael > > sure, the T2 can help if you have it (although you'll need to > download some updated binaries), but it is impossible to tell > from these images what is going on. Looks either the intensity > normalization, mri_segment or mris_make_surfaces failed. You can > try the expert options for each one to prespecify the range of > allowable intensities for gray and white matter. > If > you upload the subject to our ftp site (the whole subject > directory tarred and gzipped) we will take a look > > cheers > Bruce > > On Mon, 6 Oct 2014, Smith, Michael wrote: > >> Hi, >> >> I¹ve been having trouble on a few of our subjects with getting >> the white matter and pial surface files to ³line up² correctly >> with the volume files. >> I¹ve attached a screenshot of what is happening: the pial >> surface is in red and the white matter surface file is in >> yellow. I have also attached an example of a ³good² subject >> for comparison. >> >> I¹ve tried looking through the tutorials online but didn¹t see >> anything that was really related to my issue and I was >> wondering what the best way to correct this. We have T2 >> weighted images for several subjects is well if that helps. >> Not sure if Freesurfer can use T2 images instead of T1 in the >> reconall script but I thought I would mention it. Thank you >> very much in advance! >> >> Best, >> >> Michael S. >>
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
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@nmr.mgh.harvard.edu
-
Bruce Fischl -
Smith, Michael -
Varjabedian, Ani