It seems like it getting darker messes up the normalization later on; could this be the case? Here's what it looks like in AFNI (1029-afni.jpg), and here's what it looks like after we run motioncor (1029-orig.jpg).
On Mon, Jun 3, 2013 at 1:33 PM, Douglas N Greve greve@nmr.mgh.harvard.eduwrote:
that will not change the intensities at all. It is probably just a display issue. Try changing the brightness/contrast. The artifact might cause problems later on, but this is not an issue I think doug
On 06/03/2013 02:20 PM, Erin Browning wrote:
We use:
mri_convert N1029-anat+orig.BRIK freesurfer/mri/orig/001.mgz
where freesurfer is our freesurfer subject folder.
On Mon, Jun 3, 2013 at 1:18 PM, Douglas N Greve < greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.**edugreve@nmr.mgh.harvard.edu>> wrote:
what is your mri_convert command line? On 06/03/2013 02:11 PM, Erin Browning wrote: > Hi everyone-- > > We have a series of scans with an hyperintense artifact cutting > through the temporal and frontal lobe. When we run mri_convert to > convert from AFNI .BRIK files to .mgz fles, the results look like the > attached image. > > How can I correct for this? We tried skullstripping in AFNI first to > remove some of the artifact, but that didn't seem to help very much. > > Thank you, > Erin Browning > > > > ______________________________**_________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.**harvard.edu<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 <mailto:greve@nmr.mgh.harvard.**edu<greve@nmr.mgh.harvard.edu>Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/**fswiki/BugReporting<http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> <http://surfer.nmr.mgh.**harvard.edu/fswiki/**BugReporting<http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting>FileDrop: https://gate.nmr.mgh.harvard.**edu/filedrop2<https://gate.nmr.mgh.harvard.edu/filedrop2> www.nmr.mgh.harvard.edu/**facility/filedrop/index.html<http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> <http://www.nmr.mgh.harvard.**edu/facility/filedrop/index.**html<http://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 <mailto:Freesurfer@nmr.mgh.**harvard.edu 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/**complianceline<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.-- 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/
Hi Erin
that can happen if you lose too much dynamic range when "conforming". What does the orig.mgz look like? What voxel format is the afni file in (uchar? float?) mri_convert has a -ns 1 flag to turn off intensity scaling ("no scale"). If the brik was in float you could use something like (from the mri dir)
mri_convert file.BRIK orig/001.mgz -odt uchar -rl orig.mgz --out-scale <N> -ns
this will turn off auto scaling (-ns) then use the scale factor you supply isntead (<N>), which you should estimate to bring white matter intensities to around 110.
cheers Bruce
On Mon, 3 Jun 2013, Erin Browning wrote:
It seems like it getting darker messes up the normalization later on; could this be the case? Here's what it looks like in AFNI (1029-afni.jpg), and here's what it looks like after we run motioncor (1029-orig.jpg).
On Mon, Jun 3, 2013 at 1:33 PM, Douglas N Greve greve@nmr.mgh.harvard.edu wrote:
that will not change the intensities at all. It is probably just a display issue. Try changing the brightness/contrast. The artifact might cause problems later on, but this is not an issue I think doug On 06/03/2013 02:20 PM, Erin Browning wrote: We use: mri_convert N1029-anat+orig.BRIK freesurfer/mri/orig/001.mgz where freesurfer is our freesurfer subject folder.On Mon, Jun 3, 2013 at 1:18 PM, Douglas N Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:
what is your mri_convert command line?
On 06/03/2013 02:11 PM, Erin Browning wrote: > Hi everyone-- > > We have a series of scans with an hyperintense artifact cutting > through the temporal and frontal lobe. When we run mri_convert to > convert from AFNI .BRIK files to .mgz fles, the results look like the > attached image. > > How can I correct for this? We tried skullstripping in AFNI first to > remove some of the artifact, but that didn't seem to help very much. > > Thank you, > Erin Browning > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu mailto: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 mailto:greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html http://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 mailto: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.
-- 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/
Here is an example of what AR2 looks like (without playing with niterations or anything like that to reduce the overall hypterintensity). The white matter line is much closer to the pial line than it should be.
On Mon, Jun 3, 2013 at 2:00 PM, Bruce Fischl fischl@nmr.mgh.harvard.eduwrote:
Hi Erin
that can happen if you lose too much dynamic range when "conforming". What does the orig.mgz look like? What voxel format is the afni file in (uchar? float?) mri_convert has a -ns 1 flag to turn off intensity scaling ("no scale"). If the brik was in float you could use something like (from the mri dir)
mri_convert file.BRIK orig/001.mgz -odt uchar -rl orig.mgz --out-scale <N> -ns
this will turn off auto scaling (-ns) then use the scale factor you supply isntead (<N>), which you should estimate to bring white matter intensities to around 110.
cheers Bruce
On Mon, 3 Jun 2013, Erin Browning wrote:
It seems like it getting darker messes up the normalization later on; could this be the case? Here's what it looks like in AFNI (1029-afni.jpg), and here's what it looks like after we run motioncor (1029-orig.jpg).
On Mon, Jun 3, 2013 at 1:33 PM, Douglas N Greve < greve@nmr.mgh.harvard.edu> wrote:
that will not change the intensities at all. It is probably just a display issue. Try changing the brightness/contrast. The artifact might cause problems later on, but this is not an issue I think doug On 06/03/2013 02:20 PM, Erin Browning wrote: We use: mri_convert N1029-anat+orig.BRIK freesurfer/mri/orig/001.mgz where freesurfer is our freesurfer subject folder.On Mon, Jun 3, 2013 at 1:18 PM, Douglas N Greve <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.**edugreve@nmr.mgh.harvard.edu
wrote:
what is your mri_convert command line? On 06/03/2013 02:11 PM, Erin Browning wrote: > Hi everyone-- > > We have a series of scans with an hyperintense artifactcutting > through the temporal and frontal lobe. When we run mri_convert to > convert from AFNI .BRIK files to .mgz fles, the results look like the > attached image. > > How can I correct for this? We tried skullstripping in AFNI first to > remove some of the artifact, but that didn't seem to help very much. > > Thank you, > Erin Browning > > > > ______________________________**_________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.**harvard.eduFreesurfer@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 <mailto:greve@nmr.mgh.harvard.**edu<greve@nmr.mgh.harvard.edu>Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/**fswiki/BugReporting<http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> <http://surfer.nmr.mgh.**harvard.edu/fswiki/**BugReporting<http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting>FileDrop: https://gate.nmr.mgh.harvard.**edu/filedrop2<https://gate.nmr.mgh.harvard.edu/filedrop2> www.nmr.mgh.harvard.edu/**facility/filedrop/index.html<http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html><http://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<mailto:Freesurfer@nmr.mgh.**harvard.edu 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 theperson 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.
-- 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/
try what I suggested and see if that helps On Mon, 3 Jun 2013, Erin Browning wrote:
Here is an example of what AR2 looks like (without playing with niterations or anything like that to reduce the overall hypterintensity). The white matter line is much closer to the pial line than it should be.
On Mon, Jun 3, 2013 at 2:00 PM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote: Hi Erin
that can happen if you lose too much dynamic range when "conforming". What does the orig.mgz look like? What voxel format is the afni file in (uchar? float?) mri_convert has a -ns 1 flag to turn off intensity scaling ("no scale"). If the brik was in float you could use something like (from the mri dir) mri_convert file.BRIK orig/001.mgz -odt uchar -rl orig.mgz --out-scale <N> -ns this will turn off auto scaling (-ns) then use the scale factor you supply isntead (<N>), which you should estimate to bring white matter intensities to around 110. cheers Bruce On Mon, 3 Jun 2013, Erin Browning wrote: It seems like it getting darker messes up the normalization later on; could this be the case? Here's what it looks like in AFNI (1029-afni.jpg), and here's what it looks like after we run motioncor (1029-orig.jpg). On Mon, Jun 3, 2013 at 1:33 PM, Douglas N Greve <greve@nmr.mgh.harvard.edu> wrote: that will not change the intensities at all. It is probably just a display issue. Try changing the brightness/contrast. The artifact might cause problems later on, but this is not an issue I think doug On 06/03/2013 02:20 PM, Erin Browning wrote: We use: mri_convert N1029-anat+orig.BRIK freesurfer/mri/orig/001.mgz where freesurfer is our freesurfer subject folder. On Mon, Jun 3, 2013 at 1:18 PM, Douglas N Greve <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> wrote: what is your mri_convert command line? On 06/03/2013 02:11 PM, Erin Browning wrote: > Hi everyone-- > > We have a series of scans with an hyperintense artifact cutting > through the temporal and frontal lobe. When we run mri_convert to > convert from AFNI .BRIK files to .mgz fles, the results look like the > attached image. > > How can I correct for this? We tried skullstripping in AFNI first to > remove some of the artifact, but that didn't seem to help very much. > > Thank you, > Erin Browning > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu <mailto: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 <mailto:greve@nmr.mgh.harvard.edu> Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html <http://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 <mailto: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. -- 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/
The orig.mgz is hyerintense (there's a screenshot of it in another post now). The AFNI file is in float.
I ran:
mri_convert N1029-anat+orig.BRIK freesurfer/mri/orig/001.mgz -odt float --out-scale 1.5 -ns 1
and then I ran motioncor:
recon-all -subjid freesurfer -motioncor
Attached is what the scan looks like after each step; it's still coming out hyperintense like before. I'm concerned it will segment poorly again.
On Mon, Jun 3, 2013 at 2:00 PM, Bruce Fischl fischl@nmr.mgh.harvard.eduwrote:
Hi Erin
that can happen if you lose too much dynamic range when "conforming". What does the orig.mgz look like? What voxel format is the afni file in (uchar? float?) mri_convert has a -ns 1 flag to turn off intensity scaling ("no scale"). If the brik was in float you could use something like (from the mri dir)
mri_convert file.BRIK orig/001.mgz -odt uchar -rl orig.mgz --out-scale <N> -ns
this will turn off auto scaling (-ns) then use the scale factor you supply isntead (<N>), which you should estimate to bring white matter intensities to around 110.
cheers Bruce
On Mon, 3 Jun 2013, Erin Browning wrote:
It seems like it getting darker messes up the normalization later on; could this be the case? Here's what it looks like in AFNI (1029-afni.jpg), and here's what it looks like after we run motioncor (1029-orig.jpg).
On Mon, Jun 3, 2013 at 1:33 PM, Douglas N Greve < greve@nmr.mgh.harvard.edu> wrote:
that will not change the intensities at all. It is probably just a display issue. Try changing the brightness/contrast. The artifact might cause problems later on, but this is not an issue I think doug On 06/03/2013 02:20 PM, Erin Browning wrote: We use: mri_convert N1029-anat+orig.BRIK freesurfer/mri/orig/001.mgz where freesurfer is our freesurfer subject folder.On Mon, Jun 3, 2013 at 1:18 PM, Douglas N Greve <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.**edugreve@nmr.mgh.harvard.edu
wrote:
what is your mri_convert command line? On 06/03/2013 02:11 PM, Erin Browning wrote: > Hi everyone-- > > We have a series of scans with an hyperintense artifactcutting > through the temporal and frontal lobe. When we run mri_convert to > convert from AFNI .BRIK files to .mgz fles, the results look like the > attached image. > > How can I correct for this? We tried skullstripping in AFNI first to > remove some of the artifact, but that didn't seem to help very much. > > Thank you, > Erin Browning > > > > ______________________________**_________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.**harvard.eduFreesurfer@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 <mailto:greve@nmr.mgh.harvard.**edu<greve@nmr.mgh.harvard.edu>Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/**fswiki/BugReporting<http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> <http://surfer.nmr.mgh.**harvard.edu/fswiki/**BugReporting<http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting>FileDrop: https://gate.nmr.mgh.harvard.**edu/filedrop2<https://gate.nmr.mgh.harvard.edu/filedrop2> www.nmr.mgh.harvard.edu/**facility/filedrop/index.html<http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html><http://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<mailto:Freesurfer@nmr.mgh.**harvard.edu 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 theperson 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.
-- 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/
what does the 001.mgz look like? Do you have more than one input (otherwise you wouldn't need motion correction)? If so, you'll need to do this for each one On Mon, 3 Jun 2013, Erin Browning wrote:
The orig.mgz is hyerintense (there's a screenshot of it in another post now). The AFNI file is in float. I ran:
mri_convert N1029-anat+orig.BRIK freesurfer/mri/orig/001.mgz -odt float --out-scale 1.5 -ns 1
and then I ran motioncor:
recon-all -subjid freesurfer -motioncor
Attached is what the scan looks like after each step; it's still coming out hyperintense like before. I'm concerned it will segment poorly again.
On Mon, Jun 3, 2013 at 2:00 PM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote: Hi Erin
that can happen if you lose too much dynamic range when "conforming". What does the orig.mgz look like? What voxel format is the afni file in (uchar? float?) mri_convert has a -ns 1 flag to turn off intensity scaling ("no scale"). If the brik was in float you could use something like (from the mri dir) mri_convert file.BRIK orig/001.mgz -odt uchar -rl orig.mgz --out-scale <N> -ns this will turn off auto scaling (-ns) then use the scale factor you supply isntead (<N>), which you should estimate to bring white matter intensities to around 110. cheers Bruce On Mon, 3 Jun 2013, Erin Browning wrote: It seems like it getting darker messes up the normalization later on; could this be the case? Here's what it looks like in AFNI (1029-afni.jpg), and here's what it looks like after we run motioncor (1029-orig.jpg). On Mon, Jun 3, 2013 at 1:33 PM, Douglas N Greve <greve@nmr.mgh.harvard.edu> wrote: that will not change the intensities at all. It is probably just a display issue. Try changing the brightness/contrast. The artifact might cause problems later on, but this is not an issue I think doug On 06/03/2013 02:20 PM, Erin Browning wrote: We use: mri_convert N1029-anat+orig.BRIK freesurfer/mri/orig/001.mgz where freesurfer is our freesurfer subject folder. On Mon, Jun 3, 2013 at 1:18 PM, Douglas N Greve <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> wrote: what is your mri_convert command line? On 06/03/2013 02:11 PM, Erin Browning wrote: > Hi everyone-- > > We have a series of scans with an hyperintense artifact cutting > through the temporal and frontal lobe. When we run mri_convert to > convert from AFNI .BRIK files to .mgz fles, the results look like the > attached image. > > How can I correct for this? We tried skullstripping in AFNI first to > remove some of the artifact, but that didn't seem to help very much. > > Thank you, > Erin Browning > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu <mailto: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 <mailto:greve@nmr.mgh.harvard.edu> Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html <http://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 <mailto: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. -- 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/
I only have one input. The last posting's orig.jpg was 001.mgz, and motioncor.jpg is orig.mgz. We usually run motioncor because it produces the orig.mgz which has been conformed.
On Mon, Jun 3, 2013 at 2:41 PM, Bruce Fischl fischl@nmr.mgh.harvard.eduwrote:
what does the 001.mgz look like? Do you have more than one input (otherwise you wouldn't need motion correction)? If so, you'll need to do this for each one
On Mon, 3 Jun 2013, Erin Browning wrote:
The orig.mgz is hyerintense (there's a screenshot of it in another post
now). The AFNI file is in float. I ran:
mri_convert N1029-anat+orig.BRIK freesurfer/mri/orig/001.mgz -odt float --out-scale 1.5 -ns 1
and then I ran motioncor:
recon-all -subjid freesurfer -motioncor
Attached is what the scan looks like after each step; it's still coming out hyperintense like before. I'm concerned it will segment poorly again.
On Mon, Jun 3, 2013 at 2:00 PM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote: Hi Erin
that can happen if you lose too much dynamic range when "conforming". What does the orig.mgz look like? What voxel format is the afni file in (uchar? float?) mri_convert has a -ns 1 flag to turn off intensity scaling ("no scale"). If the brik was in float you could use something like (from the mri dir) mri_convert file.BRIK orig/001.mgz -odt uchar -rl orig.mgz --out-scale <N> -ns this will turn off auto scaling (-ns) then use the scale factor you supply isntead (<N>), which you should estimate to bring white matter intensities to around 110. cheers Bruce On Mon, 3 Jun 2013, Erin Browning wrote: It seems like it getting darker messes up the normalization later on; could this be the case? Here's what it looks like in AFNI (1029-afni.jpg), and here's what it looks like after we run motioncor (1029-orig.jpg). On Mon, Jun 3, 2013 at 1:33 PM, Douglas N Greve <greve@nmr.mgh.harvard.edu> wrote: that will not change the intensities at all. It is probably just a display issue. Try changing the brightness/contrast. The artifact might cause problems later on, but this is not an issue I think doug On 06/03/2013 02:20 PM, Erin Browning wrote: We use: mri_convert N1029-anat+orig.BRIK freesurfer/mri/orig/001.mgz where freesurfer is our freesurfer subject folder. On Mon, Jun 3, 2013 at 1:18 PM, Douglas N Greve <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.**edu<greve@nmr.mgh.harvard.edu>wrote: what is your mri_convert command line? On 06/03/2013 02:11 PM, Erin Browning wrote: > Hi everyone-- > > We have a series of scans with an hyperintense artifact cutting > through the temporal and frontal lobe. When we run mri_convert to > convert from AFNI .BRIK files to .mgz fles, the results look like the > attached image. > > How can I correct for this? We tried skullstripping in AFNI first to > remove some of the artifact, but that didn't seem to help very much. > > Thank you, > Erin Browning > > > > ______________________________**_________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.**harvard.edu<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 <mailto:greve@nmr.mgh.harvard.**edu<greve@nmr.mgh.harvard.edu>Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/**fswiki/BugReporting<http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> <http://surfer.nmr.mgh.**harvard.edu/fswiki/**BugReporting<http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting>FileDrop: https://gate.nmr.mgh.harvard.**edu/filedrop2<https://gate.nmr.mgh.harvard.edu/filedrop2> www.nmr.mgh.harvard.edu/**facility/filedrop/index.html<http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> <http://www.nmr.mgh.harvard.**edu/facility/filedrop/index.**html http://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/
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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<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. -- 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<http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> FileDrop: https://gate.nmr.mgh.harvard.**edu/filedrop2<https://gate.nmr.mgh.harvard.edu/filedrop2> www.nmr.mgh.harvard.edu/**facility/filedrop/index.html<http://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/
what is the problemexactly? how do the surfaces look? doug
On 06/03/2013 02:54 PM, Erin Browning wrote:
It seems like it getting darker messes up the normalization later on; could this be the case? Here's what it looks like in AFNI (1029-afni.jpg), and here's what it looks like after we run motioncor (1029-orig.jpg).
On Mon, Jun 3, 2013 at 1:33 PM, Douglas N Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:
that will not change the intensities at all. It is probably just a display issue. Try changing the brightness/contrast. The artifact might cause problems later on, but this is not an issue I think doug On 06/03/2013 02:20 PM, Erin Browning wrote: We use: mri_convert N1029-anat+orig.BRIK freesurfer/mri/orig/001.mgz where freesurfer is our freesurfer subject folder. On Mon, Jun 3, 2013 at 1:18 PM, Douglas N Greve <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>> wrote: what is your mri_convert command line? On 06/03/2013 02:11 PM, Erin Browning wrote: > Hi everyone-- > > We have a series of scans with an hyperintense artifact cutting > through the temporal and frontal lobe. When we run mri_convert to > convert from AFNI .BRIK files to .mgz fles, the results look like the > attached image. > > How can I correct for this? We tried skullstripping in AFNI first to > remove some of the artifact, but that didn't seem to help very much. > > Thank you, > Erin Browning > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto: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 <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> <http://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 <mailto:Freesurfer@nmr.mgh.harvard.edu> <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto: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. -- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
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Erin Browning