Hello,
I'm a complete newbie to FreeSurfer, so I appreciate any and all help you can provide. I am trying to use FreeSurfer to automatically create some masks of subcortical structures, but am having trouble getting the whole process started.
When I run "recon-all -autorecon1 -noskullstrip -s FAD" (where FAD is my subject name) it quits with the error
"ERROR: talairach_afd: Talairach Transform: transforms/talairach.xfm ***FAILED*** (p=0.0000, pval=0.0000 < threshold=0.0050)"
I am trying to do this to a skull-stripped brain originally in Analyze format (there are no DICOMs since it's actually an average of many skull-stripped scans), to which I've already registered all of the scans I want to study. I used mri_convert to convert the .img file into a .mgz file, but compared to the bert example, the background (non-brain area) is a light gray instead of black. I don't know if this is where the error is occuring, and if it is, how to correct it. If it helps, the scan I'm trying to create masks from has been registered to the ICBM brain template.
Let me know what other information you need and thanks for the help, -- Andrew
add the flag -notal-check to the end of recon-all command to skip the check.
if you can make your average using nifti format you're better off as analyze doesnt retain orientation (l/r) info.
you may have to manually register the brain following this: http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Talairach
n.
On Wed, 2011-02-23 at 13:38 -0800, andrewkrause@ucla.edu wrote:
Hello,
I'm a complete newbie to FreeSurfer, so I appreciate any and all help you can provide. I am trying to use FreeSurfer to automatically create some masks of subcortical structures, but am having trouble getting the whole process started.
When I run "recon-all -autorecon1 -noskullstrip -s FAD" (where FAD is my subject name) it quits with the error
"ERROR: talairach_afd: Talairach Transform: transforms/talairach.xfm ***FAILED*** (p=0.0000, pval=0.0000 < threshold=0.0050)"
I am trying to do this to a skull-stripped brain originally in Analyze format (there are no DICOMs since it's actually an average of many skull-stripped scans), to which I've already registered all of the scans I want to study. I used mri_convert to convert the .img file into a .mgz file, but compared to the bert example, the background (non-brain area) is a light gray instead of black. I don't know if this is where the error is occuring, and if it is, how to correct it. If it helps, the scan I'm trying to create masks from has been registered to the ICBM brain template.
Let me know what other information you need and thanks for the help, -- Andrew _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
does the orig.mgz show up properly in tkmedit? On Wed, 23 Feb 2011, Nick Schmansky wrote:
add the flag -notal-check to the end of recon-all command to skip the check.
if you can make your average using nifti format you're better off as analyze doesnt retain orientation (l/r) info.
you may have to manually register the brain following this: http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Talairach
n.
On Wed, 2011-02-23 at 13:38 -0800, andrewkrause@ucla.edu wrote:
Hello,
I'm a complete newbie to FreeSurfer, so I appreciate any and all help you can provide. I am trying to use FreeSurfer to automatically create some masks of subcortical structures, but am having trouble getting the whole process started.
When I run "recon-all -autorecon1 -noskullstrip -s FAD" (where FAD is my subject name) it quits with the error
"ERROR: talairach_afd: Talairach Transform: transforms/talairach.xfm ***FAILED*** (p=0.0000, pval=0.0000 < threshold=0.0050)"
I am trying to do this to a skull-stripped brain originally in Analyze format (there are no DICOMs since it's actually an average of many skull-stripped scans), to which I've already registered all of the scans I want to study. I used mri_convert to convert the .img file into a .mgz file, but compared to the bert example, the background (non-brain area) is a light gray instead of black. I don't know if this is where the error is occuring, and if it is, how to correct it. If it helps, the scan I'm trying to create masks from has been registered to the ICBM brain template.
Let me know what other information you need and thanks for the help, -- Andrew _______________________________________________ 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 orig.mgz shows up with weird colors (the grey matter is black, the background is light gray, and there's a white halo around the brain and in the ventricles/CSF).
Another possibility I just thought of is that the original ANALYZE image is 16-bit, and is 230 x 230 x 230 voxels. Does mri_convert (or any of the downstream programs) expect the scan to be 8-bit and/or a different size?
Again, like I said, I'm completely new to Free Surfer (just started trying to figure it out today), so sorry if this is an obvious first thing to check.
-- Andrew
Quoting Bruce Fischl fischl@nmr.mgh.harvard.edu:
does the orig.mgz show up properly in tkmedit? On Wed, 23 Feb 2011, Nick Schmansky wrote:
add the flag -notal-check to the end of recon-all command to skip the check.
if you can make your average using nifti format you're better off as analyze doesnt retain orientation (l/r) info.
you may have to manually register the brain following this: http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Talairach
n.
On Wed, 2011-02-23 at 13:38 -0800, andrewkrause@ucla.edu wrote:
Hello,
I'm a complete newbie to FreeSurfer, so I appreciate any and all help you can provide. I am trying to use FreeSurfer to automatically create some masks of subcortical structures, but am having trouble getting the whole process started.
When I run "recon-all -autorecon1 -noskullstrip -s FAD" (where FAD is my subject name) it quits with the error
"ERROR: talairach_afd: Talairach Transform: transforms/talairach.xfm ***FAILED*** (p=0.0000, pval=0.0000 < threshold=0.0050)"
I am trying to do this to a skull-stripped brain originally in Analyze format (there are no DICOMs since it's actually an average of many skull-stripped scans), to which I've already registered all of the scans I want to study. I used mri_convert to convert the .img file into a .mgz file, but compared to the bert example, the background (non-brain area) is a light gray instead of black. I don't know if this is where the error is occuring, and if it is, how to correct it. If it helps, the scan I'm trying to create masks from has been registered to the ICBM brain template.
Let me know what other information you need and thanks for the help, -- Andrew _______________________________________________ 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.
Can you send us an image? The 16 bit shouldn't be a problem Bruce
On Feb 23, 2011, at 7:28 PM, andrewkrause@ucla.edu wrote:
The orig.mgz shows up with weird colors (the grey matter is black, the background is light gray, and there's a white halo around the brain and in the ventricles/CSF).
Another possibility I just thought of is that the original ANALYZE image is 16-bit, and is 230 x 230 x 230 voxels. Does mri_convert (or any of the downstream programs) expect the scan to be 8-bit and/or a different size?
Again, like I said, I'm completely new to Free Surfer (just started trying to figure it out today), so sorry if this is an obvious first thing to check.
-- Andrew
Quoting Bruce Fischl fischl@nmr.mgh.harvard.edu:
does the orig.mgz show up properly in tkmedit? On Wed, 23 Feb 2011, Nick Schmansky wrote:
add the flag -notal-check to the end of recon-all command to skip the check.
if you can make your average using nifti format you're better off as analyze doesnt retain orientation (l/r) info.
you may have to manually register the brain following this: http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Talairach
n.
On Wed, 2011-02-23 at 13:38 -0800, andrewkrause@ucla.edu wrote:
Hello,
I'm a complete newbie to FreeSurfer, so I appreciate any and all help you can provide. I am trying to use FreeSurfer to automatically create some masks of subcortical structures, but am having trouble getting the whole process started.
When I run "recon-all -autorecon1 -noskullstrip -s FAD" (where FAD is my subject name) it quits with the error
"ERROR: talairach_afd: Talairach Transform: transforms/talairach.xfm ***FAILED*** (p=0.0000, pval=0.0000 < threshold=0.0050)"
I am trying to do this to a skull-stripped brain originally in Analyze format (there are no DICOMs since it's actually an average of many skull-stripped scans), to which I've already registered all of the scans I want to study. I used mri_convert to convert the .img file into a .mgz file, but compared to the bert example, the background (non-brain area) is a light gray instead of black. I don't know if this is where the error is occuring, and if it is, how to correct it. If it helps, the scan I'm trying to create masks from has been registered to the ICBM brain template.
Let me know what other information you need and thanks for the help, -- Andrew _______________________________________________ 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.
Sure. Here's a screenshot of the orig.mgz.
Quoting Bruce Fischl fischl@nmr.mgh.harvard.edu:
Can you send us an image? The 16 bit shouldn't be a problem Bruce
On Feb 23, 2011, at 7:28 PM, andrewkrause@ucla.edu wrote:
The orig.mgz shows up with weird colors (the grey matter is black, the background is light gray, and there's a white halo around the brain and in the ventricles/CSF).
Another possibility I just thought of is that the original ANALYZE image is 16-bit, and is 230 x 230 x 230 voxels. Does mri_convert (or any of the downstream programs) expect the scan to be 8-bit and/or a different size?
Again, like I said, I'm completely new to Free Surfer (just started trying to figure it out today), so sorry if this is an obvious first thing to check.
-- Andrew
Quoting Bruce Fischl fischl@nmr.mgh.harvard.edu:
does the orig.mgz show up properly in tkmedit? On Wed, 23 Feb 2011, Nick Schmansky wrote:
add the flag -notal-check to the end of recon-all command to skip the check.
if you can make your average using nifti format you're better off as analyze doesnt retain orientation (l/r) info.
you may have to manually register the brain following this: http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Talairach
n.
On Wed, 2011-02-23 at 13:38 -0800, andrewkrause@ucla.edu wrote:
Hello,
I'm a complete newbie to FreeSurfer, so I appreciate any and all help you can provide. I am trying to use FreeSurfer to automatically create some masks of subcortical structures, but am having trouble getting the whole process started.
When I run "recon-all -autorecon1 -noskullstrip -s FAD" (where FAD is my subject name) it quits with the error
"ERROR: talairach_afd: Talairach Transform: transforms/talairach.xfm ***FAILED*** (p=0.0000, pval=0.0000 < threshold=0.0050)"
I am trying to do this to a skull-stripped brain originally in Analyze format (there are no DICOMs since it's actually an average of many skull-stripped scans), to which I've already registered all of the scans I want to study. I used mri_convert to convert the .img file into a .mgz file, but compared to the bert example, the background (non-brain area) is a light gray instead of black. I don't know if this is where the error is occuring, and if it is, how to correct it. If it helps, the scan I'm trying to create masks from has been registered to the ICBM brain template.
Let me know what other information you need and thanks for the help, -- Andrew _______________________________________________ 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
Does it look like that when you load the original analyze into tkmedit?
andrewkrause@ucla.edu wrote:
Sure. Here's a screenshot of the orig.mgz.
Quoting Bruce Fischl fischl@nmr.mgh.harvard.edu:
Can you send us an image? The 16 bit shouldn't be a problem Bruce
On Feb 23, 2011, at 7:28 PM, andrewkrause@ucla.edu wrote:
The orig.mgz shows up with weird colors (the grey matter is black, the background is light gray, and there's a white halo around the brain and in the ventricles/CSF).
Another possibility I just thought of is that the original ANALYZE image is 16-bit, and is 230 x 230 x 230 voxels. Does mri_convert (or any of the downstream programs) expect the scan to be 8-bit and/or a different size?
Again, like I said, I'm completely new to Free Surfer (just started trying to figure it out today), so sorry if this is an obvious first thing to check.
-- Andrew
Quoting Bruce Fischl fischl@nmr.mgh.harvard.edu:
does the orig.mgz show up properly in tkmedit? On Wed, 23 Feb 2011, Nick Schmansky wrote:
add the flag -notal-check to the end of recon-all command to skip the check.
if you can make your average using nifti format you're better off as analyze doesnt retain orientation (l/r) info.
you may have to manually register the brain following this: http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Talairach
n.
On Wed, 2011-02-23 at 13:38 -0800, andrewkrause@ucla.edu wrote:
Hello,
I'm a complete newbie to FreeSurfer, so I appreciate any and all help you can provide. I am trying to use FreeSurfer to automatically create some masks of subcortical structures, but am having trouble getting the whole process started.
When I run "recon-all -autorecon1 -noskullstrip -s FAD" (where FAD is my subject name) it quits with the error
"ERROR: talairach_afd: Talairach Transform: transforms/talairach.xfm ***FAILED*** (p=0.0000, pval=0.0000 < threshold=0.0050)"
I am trying to do this to a skull-stripped brain originally in Analyze format (there are no DICOMs since it's actually an average of many skull-stripped scans), to which I've already registered all of the scans I want to study. I used mri_convert to convert the .img file into a .mgz file, but compared to the bert example, the background (non-brain area) is a light gray instead of black. I don't know if this is where the error is occuring, and if it is, how to correct it. If it helps, the scan I'm trying to create masks from has been registered to the ICBM brain template.
Let me know what other information you need and thanks for the help, -- Andrew _______________________________________________ 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 mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
I actually didn't know you could load analyze into tkmedit, but now that I have, it does look like that too (just without the direction arrows). It doesn't look like that when I look at it in other viewing programs, though (it looks like you'd expect).
-- Andrew
Quoting Douglas N Greve greve@nmr.mgh.harvard.edu:
Does it look like that when you load the original analyze into tkmedit?
andrewkrause@ucla.edu wrote:
Sure. Here's a screenshot of the orig.mgz.
Quoting Bruce Fischl fischl@nmr.mgh.harvard.edu:
Can you send us an image? The 16 bit shouldn't be a problem Bruce
On Feb 23, 2011, at 7:28 PM, andrewkrause@ucla.edu wrote:
The orig.mgz shows up with weird colors (the grey matter is black, the background is light gray, and there's a white halo around the brain and in the ventricles/CSF).
Another possibility I just thought of is that the original ANALYZE image is 16-bit, and is 230 x 230 x 230 voxels. Does mri_convert (or any of the downstream programs) expect the scan to be 8-bit and/or a different size?
Again, like I said, I'm completely new to Free Surfer (just started trying to figure it out today), so sorry if this is an obvious first thing to check.
-- Andrew
Quoting Bruce Fischl fischl@nmr.mgh.harvard.edu:
does the orig.mgz show up properly in tkmedit? On Wed, 23 Feb 2011, Nick Schmansky wrote:
add the flag -notal-check to the end of recon-all command to skip the check.
if you can make your average using nifti format you're better off as analyze doesnt retain orientation (l/r) info.
you may have to manually register the brain following this: http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Talairach
n.
On Wed, 2011-02-23 at 13:38 -0800, andrewkrause@ucla.edu wrote: > Hello, > > I'm a complete newbie to FreeSurfer, so I appreciate any and all help > you can provide. I am trying to use FreeSurfer to automatically create > some masks of subcortical structures, but am having trouble getting > the whole process started. > > When I run "recon-all -autorecon1 -noskullstrip -s FAD" (where FAD is > my subject name) it quits with the error > > "ERROR: talairach_afd: Talairach Transform: transforms/talairach.xfm > ***FAILED*** (p=0.0000, pval=0.0000 < threshold=0.0050)" > > > I am trying to do this to a skull-stripped brain originally in Analyze > format (there are no DICOMs since it's actually an average of many > skull-stripped scans), to which I've already registered all of the > scans I want to study. I used mri_convert to convert the .img file > into a .mgz file, but compared to the bert example, the background > (non-brain area) is a light gray instead of black. I don't know if > this is where the error is occuring, and if it is, how to correct it. > If it helps, the scan I'm trying to create masks from has been > registered to the ICBM brain template. > > Let me know what other information you need and thanks for the help, > -- Andrew > _______________________________________________ > 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 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: www.nmr.mgh.harvard.edu/facility/filedrop/index.html
Can you send us the analyze files?
On Feb 24, 2011, at 12:37 PM, andrewkrause@ucla.edu wrote:
I actually didn't know you could load analyze into tkmedit, but now that I have, it does look like that too (just without the direction arrows). It doesn't look like that when I look at it in other viewing programs, though (it looks like you'd expect).
-- Andrew
Quoting Douglas N Greve greve@nmr.mgh.harvard.edu:
Does it look like that when you load the original analyze into tkmedit?
andrewkrause@ucla.edu wrote:
Sure. Here's a screenshot of the orig.mgz.
Quoting Bruce Fischl fischl@nmr.mgh.harvard.edu:
Can you send us an image? The 16 bit shouldn't be a problem Bruce
On Feb 23, 2011, at 7:28 PM, andrewkrause@ucla.edu wrote:
The orig.mgz shows up with weird colors (the grey matter is black, the background is light gray, and there's a white halo around the brain and in the ventricles/CSF).
Another possibility I just thought of is that the original ANALYZE image is 16-bit, and is 230 x 230 x 230 voxels. Does mri_convert (or any of the downstream programs) expect the scan to be 8-bit and/or a different size?
Again, like I said, I'm completely new to Free Surfer (just started trying to figure it out today), so sorry if this is an obvious first thing to check.
-- Andrew
Quoting Bruce Fischl fischl@nmr.mgh.harvard.edu:
does the orig.mgz show up properly in tkmedit? On Wed, 23 Feb 2011, Nick Schmansky wrote:
> add the flag -notal-check to the end of recon-all command to skip the > check. > > if you can make your average using nifti format you're better off as > analyze doesnt retain orientation (l/r) info. > > you may have to manually register the brain following this: > http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Talairach > > n. > > > On Wed, 2011-02-23 at 13:38 -0800, andrewkrause@ucla.edu wrote: >> Hello, >> >> I'm a complete newbie to FreeSurfer, so I appreciate any and all help >> you can provide. I am trying to use FreeSurfer to automatically create >> some masks of subcortical structures, but am having trouble getting >> the whole process started. >> >> When I run "recon-all -autorecon1 -noskullstrip -s FAD" (where FAD is >> my subject name) it quits with the error >> >> "ERROR: talairach_afd: Talairach Transform: transforms/talairach.xfm >> ***FAILED*** (p=0.0000, pval=0.0000 < threshold=0.0050)" >> >> >> I am trying to do this to a skull-stripped brain originally in Analyze >> format (there are no DICOMs since it's actually an average of many >> skull-stripped scans), to which I've already registered all of the >> scans I want to study. I used mri_convert to convert the .img file >> into a .mgz file, but compared to the bert example, the background >> (non-brain area) is a light gray instead of black. I don't know if >> this is where the error is occuring, and if it is, how to correct it. >> If it helps, the scan I'm trying to create masks from has been >> registered to the ICBM brain template. >> >> Let me know what other information you need and thanks for the help, >> -- Andrew >> _______________________________________________ >> 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 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: www.nmr.mgh.harvard.edu/facility/filedrop/index.html
Sure. Since it's probably a bit big for email, I uploaded it to http://dl.dropbox.com/u/432093/ANALYZE.zip
-- Andrew
Quoting Bruce Fischl fischl@nmr.mgh.harvard.edu:
Can you send us the analyze files?
On Feb 24, 2011, at 12:37 PM, andrewkrause@ucla.edu wrote:
I actually didn't know you could load analyze into tkmedit, but now that I have, it does look like that too (just without the direction arrows). It doesn't look like that when I look at it in other viewing programs, though (it looks like you'd expect).
-- Andrew
Quoting Douglas N Greve greve@nmr.mgh.harvard.edu:
Does it look like that when you load the original analyze into tkmedit?
andrewkrause@ucla.edu wrote:
Sure. Here's a screenshot of the orig.mgz.
Quoting Bruce Fischl fischl@nmr.mgh.harvard.edu:
Can you send us an image? The 16 bit shouldn't be a problem Bruce
On Feb 23, 2011, at 7:28 PM, andrewkrause@ucla.edu wrote:
The orig.mgz shows up with weird colors (the grey matter is black, the background is light gray, and there's a white halo around the brain and in the ventricles/CSF).
Another possibility I just thought of is that the original ANALYZE image is 16-bit, and is 230 x 230 x 230 voxels. Does mri_convert (or any of the downstream programs) expect the scan to be 8-bit and/or a different size?
Again, like I said, I'm completely new to Free Surfer (just started trying to figure it out today), so sorry if this is an obvious first thing to check.
-- Andrew
Quoting Bruce Fischl fischl@nmr.mgh.harvard.edu:
> does the orig.mgz show up properly in tkmedit? > On Wed, 23 Feb 2011, Nick > Schmansky wrote: > >> add the flag -notal-check to the end of recon-all command to skip the >> check. >> >> if you can make your average using nifti format you're better off as >> analyze doesnt retain orientation (l/r) info. >> >> you may have to manually register the brain following this: >> http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Talairach >> >> n. >> >> >> On Wed, 2011-02-23 at 13:38 -0800, andrewkrause@ucla.edu wrote: >>> Hello, >>> >>> I'm a complete newbie to FreeSurfer, so I appreciate any and all help >>> you can provide. I am trying to use FreeSurfer to >>> automatically create >>> some masks of subcortical structures, but am having trouble getting >>> the whole process started. >>> >>> When I run "recon-all -autorecon1 -noskullstrip -s FAD" (where FAD is >>> my subject name) it quits with the error >>> >>> "ERROR: talairach_afd: Talairach Transform: transforms/talairach.xfm >>> ***FAILED*** (p=0.0000, pval=0.0000 < threshold=0.0050)" >>> >>> >>> I am trying to do this to a skull-stripped brain originally >>> in Analyze >>> format (there are no DICOMs since it's actually an average of many >>> skull-stripped scans), to which I've already registered all of the >>> scans I want to study. I used mri_convert to convert the .img file >>> into a .mgz file, but compared to the bert example, the background >>> (non-brain area) is a light gray instead of black. I don't know if >>> this is where the error is occuring, and if it is, how to correct it. >>> If it helps, the scan I'm trying to create masks from has been >>> registered to the ICBM brain template. >>> >>> Let me know what other information you need and thanks for the help, >>> -- Andrew >>> _______________________________________________ >>> 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 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: www.nmr.mgh.harvard.edu/facility/filedrop/index.html
It looks the same to me in fslview. I'm guessing that there is a byte-swapping problem. Any chance the .img file was created under linux and the .hdr created under windows (or vice versa)?
andrewkrause@ucla.edu wrote:
Sure. Since it's probably a bit big for email, I uploaded it to http://dl.dropbox.com/u/432093/ANALYZE.zip
-- Andrew
Quoting Bruce Fischl fischl@nmr.mgh.harvard.edu:
Can you send us the analyze files?
On Feb 24, 2011, at 12:37 PM, andrewkrause@ucla.edu wrote:
I actually didn't know you could load analyze into tkmedit, but now that I have, it does look like that too (just without the direction arrows). It doesn't look like that when I look at it in other viewing programs, though (it looks like you'd expect).
-- Andrew
Quoting Douglas N Greve greve@nmr.mgh.harvard.edu:
Does it look like that when you load the original analyze into tkmedit?
andrewkrause@ucla.edu wrote:
Sure. Here's a screenshot of the orig.mgz.
Quoting Bruce Fischl fischl@nmr.mgh.harvard.edu:
Can you send us an image? The 16 bit shouldn't be a problem Bruce
On Feb 23, 2011, at 7:28 PM, andrewkrause@ucla.edu wrote:
> The orig.mgz shows up with weird colors (the grey matter is > black, the background is light gray, and there's a white halo > around the brain and in the ventricles/CSF). > > Another possibility I just thought of is that the original > ANALYZE image is 16-bit, and is 230 x 230 x 230 voxels. Does > mri_convert (or any of the downstream programs) expect the scan > to be 8-bit and/or a different size? > > Again, like I said, I'm completely new to Free Surfer (just > started trying to figure it out today), so sorry if this is an > obvious first thing to check. > > -- Andrew > > Quoting Bruce Fischl fischl@nmr.mgh.harvard.edu: > >> does the orig.mgz show up properly in tkmedit? >> On Wed, 23 Feb 2011, Nick >> Schmansky wrote: >> >>> add the flag -notal-check to the end of recon-all command to >>> skip the >>> check. >>> >>> if you can make your average using nifti format you're better >>> off as >>> analyze doesnt retain orientation (l/r) info. >>> >>> you may have to manually register the brain following this: >>> http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Talairach >>> >>> n. >>> >>> >>> On Wed, 2011-02-23 at 13:38 -0800, andrewkrause@ucla.edu wrote: >>>> Hello, >>>> >>>> I'm a complete newbie to FreeSurfer, so I appreciate any and >>>> all help >>>> you can provide. I am trying to use FreeSurfer to >>>> automatically create >>>> some masks of subcortical structures, but am having trouble >>>> getting >>>> the whole process started. >>>> >>>> When I run "recon-all -autorecon1 -noskullstrip -s FAD" >>>> (where FAD is >>>> my subject name) it quits with the error >>>> >>>> "ERROR: talairach_afd: Talairach Transform: >>>> transforms/talairach.xfm >>>> ***FAILED*** (p=0.0000, pval=0.0000 < threshold=0.0050)" >>>> >>>> >>>> I am trying to do this to a skull-stripped brain originally >>>> in Analyze >>>> format (there are no DICOMs since it's actually an average of >>>> many >>>> skull-stripped scans), to which I've already registered all >>>> of the >>>> scans I want to study. I used mri_convert to convert the .img >>>> file >>>> into a .mgz file, but compared to the bert example, the >>>> background >>>> (non-brain area) is a light gray instead of black. I don't >>>> know if >>>> this is where the error is occuring, and if it is, how to >>>> correct it. >>>> If it helps, the scan I'm trying to create masks from has been >>>> registered to the ICBM brain template. >>>> >>>> Let me know what other information you need and thanks for >>>> the help, >>>> -- Andrew >>>> _______________________________________________ >>>> 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 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: www.nmr.mgh.harvard.edu/facility/filedrop/index.html
There's actually quite a large chance for that, as we convert the DICOMs to ANALYZE on iMacs; skull-strip mostly on PCs; register and do other processing on remote machines running OpenBSD, IRIX, and Linux (some of which are little-endian and some of which are big-endian); and then check everything and do stats locally on the Macs.
When I look at the ANALYZE image in BrainSuite and Shiva (two programs from LONI), they look fine, but I don't know if they're treating the headers differently than other viewers. Is there a way to check besides just how it looks?
-- Andrew
Quoting Douglas N Greve greve@nmr.mgh.harvard.edu:
It looks the same to me in fslview. I'm guessing that there is a byte-swapping problem. Any chance the .img file was created under linux and the .hdr created under windows (or vice versa)?
andrewkrause@ucla.edu wrote:
Sure. Since it's probably a bit big for email, I uploaded it to http://dl.dropbox.com/u/432093/ANALYZE.zip
-- Andrew
Quoting Bruce Fischl fischl@nmr.mgh.harvard.edu:
Can you send us the analyze files?
On Feb 24, 2011, at 12:37 PM, andrewkrause@ucla.edu wrote:
I actually didn't know you could load analyze into tkmedit, but now that I have, it does look like that too (just without the direction arrows). It doesn't look like that when I look at it in other viewing programs, though (it looks like you'd expect).
-- Andrew
Quoting Douglas N Greve greve@nmr.mgh.harvard.edu:
Does it look like that when you load the original analyze into tkmedit?
andrewkrause@ucla.edu wrote:
Sure. Here's a screenshot of the orig.mgz.
Quoting Bruce Fischl fischl@nmr.mgh.harvard.edu:
> Can you send us an image? The 16 bit shouldn't be a problem > Bruce > > > > On Feb 23, 2011, at 7:28 PM, andrewkrause@ucla.edu wrote: > >> The orig.mgz shows up with weird colors (the grey matter is >> black, the background is light gray, and there's a white halo >> around the brain and in the ventricles/CSF). >> >> Another possibility I just thought of is that the original >> ANALYZE image is 16-bit, and is 230 x 230 x 230 voxels. Does >> mri_convert (or any of the downstream programs) expect the scan >> to be 8-bit and/or a different size? >> >> Again, like I said, I'm completely new to Free Surfer (just >> started trying to figure it out today), so sorry if this is an >> obvious first thing to check. >> >> -- Andrew >> >> Quoting Bruce Fischl fischl@nmr.mgh.harvard.edu: >> >>> does the orig.mgz show up properly in tkmedit? >>> On Wed, 23 Feb 2011, Nick >>> Schmansky wrote: >>> >>>> add the flag -notal-check to the end of recon-all command to >>>> skip the >>>> check. >>>> >>>> if you can make your average using nifti format you're better >>>> off as >>>> analyze doesnt retain orientation (l/r) info. >>>> >>>> you may have to manually register the brain following this: >>>> http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Talairach >>>> >>>> n. >>>> >>>> >>>> On Wed, 2011-02-23 at 13:38 -0800, andrewkrause@ucla.edu wrote: >>>>> Hello, >>>>> >>>>> I'm a complete newbie to FreeSurfer, so I appreciate any and >>>>> all help >>>>> you can provide. I am trying to use FreeSurfer to >>>>> automatically create >>>>> some masks of subcortical structures, but am having trouble >>>>> getting >>>>> the whole process started. >>>>> >>>>> When I run "recon-all -autorecon1 -noskullstrip -s FAD" >>>>> (where FAD is >>>>> my subject name) it quits with the error >>>>> >>>>> "ERROR: talairach_afd: Talairach Transform: >>>>> transforms/talairach.xfm >>>>> ***FAILED*** (p=0.0000, pval=0.0000 < threshold=0.0050)" >>>>> >>>>> >>>>> I am trying to do this to a skull-stripped brain originally >>>>> in Analyze >>>>> format (there are no DICOMs since it's actually an average of >>>>> many >>>>> skull-stripped scans), to which I've already registered all >>>>> of the >>>>> scans I want to study. I used mri_convert to convert the .img >>>>> file >>>>> into a .mgz file, but compared to the bert example, the >>>>> background >>>>> (non-brain area) is a light gray instead of black. I don't >>>>> know if >>>>> this is where the error is occuring, and if it is, how to >>>>> correct it. >>>>> If it helps, the scan I'm trying to create masks from has been >>>>> registered to the ICBM brain template. >>>>> >>>>> Let me know what other information you need and thanks for >>>>> the help, >>>>> -- Andrew >>>>> _______________________________________________ >>>>> 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 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: www.nmr.mgh.harvard.edu/facility/filedrop/index.html
-- 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: www.nmr.mgh.harvard.edu/facility/filedrop/index.html
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
not an easy way. You'd have to find out what the byte swapping is in each file (or verify that the byteswapping is different). The other programs may check that the voxel values are "reasonable" and byteswap them if they are not.
andrewkrause@ucla.edu wrote:
There's actually quite a large chance for that, as we convert the DICOMs to ANALYZE on iMacs; skull-strip mostly on PCs; register and do other processing on remote machines running OpenBSD, IRIX, and Linux (some of which are little-endian and some of which are big-endian); and then check everything and do stats locally on the Macs.
When I look at the ANALYZE image in BrainSuite and Shiva (two programs from LONI), they look fine, but I don't know if they're treating the headers differently than other viewers. Is there a way to check besides just how it looks?
-- Andrew
Quoting Douglas N Greve greve@nmr.mgh.harvard.edu:
It looks the same to me in fslview. I'm guessing that there is a byte-swapping problem. Any chance the .img file was created under linux and the .hdr created under windows (or vice versa)?
andrewkrause@ucla.edu wrote:
Sure. Since it's probably a bit big for email, I uploaded it to http://dl.dropbox.com/u/432093/ANALYZE.zip
-- Andrew
Quoting Bruce Fischl fischl@nmr.mgh.harvard.edu:
Can you send us the analyze files?
On Feb 24, 2011, at 12:37 PM, andrewkrause@ucla.edu wrote:
I actually didn't know you could load analyze into tkmedit, but now that I have, it does look like that too (just without the direction arrows). It doesn't look like that when I look at it in other viewing programs, though (it looks like you'd expect).
-- Andrew
Quoting Douglas N Greve greve@nmr.mgh.harvard.edu:
Does it look like that when you load the original analyze into tkmedit?
andrewkrause@ucla.edu wrote:
> Sure. Here's a screenshot of the orig.mgz. > > Quoting Bruce Fischl fischl@nmr.mgh.harvard.edu: > > >> Can you send us an image? The 16 bit shouldn't be a problem >> Bruce >> >> >> >> On Feb 23, 2011, at 7:28 PM, andrewkrause@ucla.edu wrote: >> >> >>> The orig.mgz shows up with weird colors (the grey matter is >>> black, the background is light gray, and there's a white halo >>> around the brain and in the ventricles/CSF). >>> >>> Another possibility I just thought of is that the original >>> ANALYZE image is 16-bit, and is 230 x 230 x 230 voxels. Does >>> mri_convert (or any of the downstream programs) expect the scan >>> to be 8-bit and/or a different size? >>> >>> Again, like I said, I'm completely new to Free Surfer (just >>> started trying to figure it out today), so sorry if this is an >>> obvious first thing to check. >>> >>> -- Andrew >>> >>> Quoting Bruce Fischl fischl@nmr.mgh.harvard.edu: >>> >>> >>>> does the orig.mgz show up properly in tkmedit? >>>> On Wed, 23 Feb 2011, Nick >>>> Schmansky wrote: >>>> >>>> >>>>> add the flag -notal-check to the end of recon-all command to >>>>> skip the >>>>> check. >>>>> >>>>> if you can make your average using nifti format you're better >>>>> off as >>>>> analyze doesnt retain orientation (l/r) info. >>>>> >>>>> you may have to manually register the brain following this: >>>>> http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Talairach >>>>> >>>>> n. >>>>> >>>>> >>>>> On Wed, 2011-02-23 at 13:38 -0800, andrewkrause@ucla.edu wrote: >>>>> >>>>>> Hello, >>>>>> >>>>>> I'm a complete newbie to FreeSurfer, so I appreciate any and >>>>>> all help >>>>>> you can provide. I am trying to use FreeSurfer to >>>>>> automatically create >>>>>> some masks of subcortical structures, but am having trouble >>>>>> getting >>>>>> the whole process started. >>>>>> >>>>>> When I run "recon-all -autorecon1 -noskullstrip -s FAD" >>>>>> (where FAD is >>>>>> my subject name) it quits with the error >>>>>> >>>>>> "ERROR: talairach_afd: Talairach Transform: >>>>>> transforms/talairach.xfm >>>>>> ***FAILED*** (p=0.0000, pval=0.0000 < threshold=0.0050)" >>>>>> >>>>>> >>>>>> I am trying to do this to a skull-stripped brain originally >>>>>> in Analyze >>>>>> format (there are no DICOMs since it's actually an average of >>>>>> many >>>>>> skull-stripped scans), to which I've already registered all >>>>>> of the >>>>>> scans I want to study. I used mri_convert to convert the .img >>>>>> file >>>>>> into a .mgz file, but compared to the bert example, the >>>>>> background >>>>>> (non-brain area) is a light gray instead of black. I don't >>>>>> know if >>>>>> this is where the error is occuring, and if it is, how to >>>>>> correct it. >>>>>> If it helps, the scan I'm trying to create masks from has been >>>>>> registered to the ICBM brain template. >>>>>> >>>>>> Let me know what other information you need and thanks for >>>>>> the help, >>>>>> -- Andrew >>>>>> _______________________________________________ >>>>>> 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 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: www.nmr.mgh.harvard.edu/facility/filedrop/index.html
-- 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: www.nmr.mgh.harvard.edu/facility/filedrop/index.html
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
I've played around with byteswaping, but alas it doesn't seem to be the issue. The original ANALYZE file is 16-bit little endian (or at least says it is), but when I swap just the .img to big endian and use the original header, or give the original .img a 16-bit big-endian header, the result is a brain filled with static like the attached image. Byteswapping both the .img and the .hdr does nothing (it still looks like the first screenshot I sent). I also just double-checked, and the header and image were both created by the same program on the same computer at the same time, so they should be the same endian.
Someone else in the lab pointed out that we've had scans look like this before in Shiva, which we fix by clicking the "big volume" option when loading it. I'm trying to figure out what this does, in the hopes that we can replicate it and it'd solve this problem too, but I thought I'd toss this out to the mailing list in case someone has an idea.
Thanks so much, by the way, for all of the help you've been giving.
-- Andrew
Quoting Douglas N Greve greve@nmr.mgh.harvard.edu:
not an easy way. You'd have to find out what the byte swapping is in each file (or verify that the byteswapping is different). The other programs may check that the voxel values are "reasonable" and byteswap them if they are not.
andrewkrause@ucla.edu wrote:
There's actually quite a large chance for that, as we convert the DICOMs to ANALYZE on iMacs; skull-strip mostly on PCs; register and do other processing on remote machines running OpenBSD, IRIX, and Linux (some of which are little-endian and some of which are big-endian); and then check everything and do stats locally on the Macs.
When I look at the ANALYZE image in BrainSuite and Shiva (two programs from LONI), they look fine, but I don't know if they're treating the headers differently than other viewers. Is there a way to check besides just how it looks?
-- Andrew
Quoting Douglas N Greve greve@nmr.mgh.harvard.edu:
It looks the same to me in fslview. I'm guessing that there is a byte-swapping problem. Any chance the .img file was created under linux and the .hdr created under windows (or vice versa)?
andrewkrause@ucla.edu wrote:
Sure. Since it's probably a bit big for email, I uploaded it to http://dl.dropbox.com/u/432093/ANALYZE.zip
-- Andrew
Quoting Bruce Fischl fischl@nmr.mgh.harvard.edu:
Can you send us the analyze files?
On Feb 24, 2011, at 12:37 PM, andrewkrause@ucla.edu wrote:
I actually didn't know you could load analyze into tkmedit, but now that I have, it does look like that too (just without the direction arrows). It doesn't look like that when I look at it in other viewing programs, though (it looks like you'd expect).
-- Andrew
Quoting Douglas N Greve greve@nmr.mgh.harvard.edu:
> Does it look like that when you load the original analyze into > tkmedit? > > andrewkrause@ucla.edu wrote: > >> Sure. Here's a screenshot of the orig.mgz. >> >> Quoting Bruce Fischl fischl@nmr.mgh.harvard.edu: >> >> >>> Can you send us an image? The 16 bit shouldn't be a problem >>> Bruce >>> >>> >>> >>> On Feb 23, 2011, at 7:28 PM, andrewkrause@ucla.edu wrote: >>> >>> >>>> The orig.mgz shows up with weird colors (the grey matter is >>>> black, the background is light gray, and there's a white halo >>>> around the brain and in the ventricles/CSF). >>>> >>>> Another possibility I just thought of is that the original >>>> ANALYZE image is 16-bit, and is 230 x 230 x 230 voxels. Does >>>> mri_convert (or any of the downstream programs) expect the scan >>>> to be 8-bit and/or a different size? >>>> >>>> Again, like I said, I'm completely new to Free Surfer (just >>>> started trying to figure it out today), so sorry if this is an >>>> obvious first thing to check. >>>> >>>> -- Andrew >>>> >>>> Quoting Bruce Fischl fischl@nmr.mgh.harvard.edu: >>>> >>>> >>>>> does the orig.mgz show up properly in tkmedit? >>>>> On Wed, 23 Feb 2011, Nick >>>>> Schmansky wrote: >>>>> >>>>> >>>>>> add the flag -notal-check to the end of recon-all command to >>>>>> skip the >>>>>> check. >>>>>> >>>>>> if you can make your average using nifti format you're better >>>>>> off as >>>>>> analyze doesnt retain orientation (l/r) info. >>>>>> >>>>>> you may have to manually register the brain following this: >>>>>> http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Talairach >>>>>> >>>>>> n. >>>>>> >>>>>> >>>>>> On Wed, 2011-02-23 at 13:38 -0800, andrewkrause@ucla.edu wrote: >>>>>> >>>>>>> Hello, >>>>>>> >>>>>>> I'm a complete newbie to FreeSurfer, so I appreciate any and >>>>>>> all help >>>>>>> you can provide. I am trying to use FreeSurfer to >>>>>>> automatically create >>>>>>> some masks of subcortical structures, but am having trouble >>>>>>> getting >>>>>>> the whole process started. >>>>>>> >>>>>>> When I run "recon-all -autorecon1 -noskullstrip -s FAD" >>>>>>> (where FAD is >>>>>>> my subject name) it quits with the error >>>>>>> >>>>>>> "ERROR: talairach_afd: Talairach Transform: >>>>>>> transforms/talairach.xfm >>>>>>> ***FAILED*** (p=0.0000, pval=0.0000 < threshold=0.0050)" >>>>>>> >>>>>>> >>>>>>> I am trying to do this to a skull-stripped brain originally >>>>>>> in Analyze >>>>>>> format (there are no DICOMs since it's actually an average of >>>>>>> many >>>>>>> skull-stripped scans), to which I've already registered all >>>>>>> of the >>>>>>> scans I want to study. I used mri_convert to convert the .img >>>>>>> file >>>>>>> into a .mgz file, but compared to the bert example, the >>>>>>> background >>>>>>> (non-brain area) is a light gray instead of black. I don't >>>>>>> know if >>>>>>> this is where the error is occuring, and if it is, how to >>>>>>> correct it. >>>>>>> If it helps, the scan I'm trying to create masks from has been >>>>>>> registered to the ICBM brain template. >>>>>>> >>>>>>> Let me know what other information you need and thanks for >>>>>>> the help, >>>>>>> -- Andrew >>>>>>> _______________________________________________ >>>>>>> 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 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: www.nmr.mgh.harvard.edu/facility/filedrop/index.html > > >
-- 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: www.nmr.mgh.harvard.edu/facility/filedrop/index.html
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: www.nmr.mgh.harvard.edu/facility/filedrop/index.html
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
freesurfer@nmr.mgh.harvard.edu
-
andrewkrause＠ucla.edu -
Bruce Fischl -
Douglas N Greve -
Nick Schmansky