Hi all, I'm trying to obtain skull stripped images using freesurfer.
Unfortunately, I couldn't perform the skull stripping function for 7_8 data within IBSR dataset (http://www.cma.mgh.harvard.edu/ibsr/). I used following command.
mri_watershed -T1 7_8.img f7_8.img
The error message was --- mri_watershed error: w=White Matter =Intensity too high (>240)... valid input? ---
How can I deal with this kind of error?
regards, Jinyoung
Hi Jinyoung ,
those images have labels - why not just zero out everything with a zero label? And make sure you are trying to srip the intensity image, not the label one. You probably don't want to use a -T1 flag unless you used our intensity normalization.
cheers Bruce On Sat, 5 Jun 2010, Jinyoung Hwang wrote:
Hi all, I'm trying to obtain skull stripped images using freesurfer.
Unfortunately, I couldn't perform the skull stripping function for 7_8 data within IBSR dataset (http://www.cma.mgh.harvard.edu/ibsr/). I used following command.
mri_watershed -T1 7_8.img f7_8.img
The error message was
mri_watershed error: w=White Matter =Intensity too high (>240)... valid input?
How can I deal with this kind of error?
regards, Jinyoung
hi bruce, In fact, I'm trying to test the skull stripping method of freesurfer.
Other images showed good skull stripped results, but 7_8 data couldn't be segmented as the previous e-mail.
I also tested mri_watershed without -T1 option, and I met same error message.
How can I treat the error?
regards, Jinyoung
2010/6/6, Bruce Fischl fischl@nmr.mgh.harvard.edu:
Hi Jinyoung ,
those images have labels - why not just zero out everything with a zero label? And make sure you are trying to srip the intensity image, not the label one. You probably don't want to use a -T1 flag unless you used our intensity normalization.
cheers Bruce On Sat, 5 Jun 2010, Jinyoung Hwang wrote:
Hi all, I'm trying to obtain skull stripped images using freesurfer.
Unfortunately, I couldn't perform the skull stripping function for 7_8 data within IBSR dataset (http://www.cma.mgh.harvard.edu/ibsr/). I used following command.
mri_watershed -T1 7_8.img f7_8.img
The error message was
mri_watershed error: w=White Matter =Intensity too high (>240)... valid input?
How can I deal with this kind of error?
regards, Jinyoung
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.
try without the atlas (-noatlas? Check the help, can't remember) On Sun, 6 Jun 2010, Jinyoung Hwang wrote:
hi bruce, In fact, I'm trying to test the skull stripping method of freesurfer.
Other images showed good skull stripped results, but 7_8 data couldn't be segmented as the previous e-mail.
I also tested mri_watershed without -T1 option, and I met same error message.
How can I treat the error?
regards, Jinyoung
2010/6/6, Bruce Fischl fischl@nmr.mgh.harvard.edu:
Hi Jinyoung ,
those images have labels - why not just zero out everything with a zero label? And make sure you are trying to srip the intensity image, not the label one. You probably don't want to use a -T1 flag unless you used our intensity normalization.
cheers Bruce On Sat, 5 Jun 2010, Jinyoung Hwang wrote:
Hi all, I'm trying to obtain skull stripped images using freesurfer.
Unfortunately, I couldn't perform the skull stripping function for 7_8 data within IBSR dataset (http://www.cma.mgh.harvard.edu/ibsr/). I used following command.
mri_watershed -T1 7_8.img f7_8.img
The error message was
mri_watershed error: w=White Matter =Intensity too high (>240)... valid input?
How can I deal with this kind of error?
regards, Jinyoung
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
-
Bruce Fischl -
Jinyoung Hwang