Dear FreeSurfer community,
I'm using the mri_label2vol, the output is in .mgz. I then use mri_convert to convert it to .nii.gz. When I do so, the output is corrupted (see attached images). Some colleagues told me that it was because my FreeSurfer had a bug so I uninstalled and installed it back again but nothing changed. I then tried to run it on some other colleague's machine and it worked fine (on one subject just to test).
Any ideas what could be the problem ? I tried to flip the image 90 degrees but it won't flip, nothing changes.
Here are the commands I'm launching :
mri_label2vol --seg ~/Documents/freesurfer/subjects/pre_al_t1/mri/aparc+aseg.mgz --temp ~/Documents/freesurfer/subjects/pre_al_t1/mri/rawavg.mgz --o ~/Documents/freesurfer/subjects/pre_al_t1/mri/aparc+aseg_t1ref.mgz --regheader ~/Documents/freesurfer/subjects/pre_al_t1/mri/aparc+aseg.mgz
mri_convert aparc+aseg_t1ref.mgz aparc+aseg_t1ref.nii.gz
The data looks fine when I open it with tkmedit but it's inverted and cut when opened with fslview.
I cannot continue my analyses even if the data looks fine on tkmedit. When I apply a flirt transformation on the data I get the same cut and inverted brain than on fslview (see flirt attached image).
Is it a problem with my FreeSurfer or a command I'm running the wrong way ? Is there another software to convert .mgz to .nii.gz ?
Thank you very much !
Jimmy
Hi Jimmy, I think the problem, if you can call it that, is with fslview. Below is from our FAQ. See if that makes sense.
doug
Q. Why would the orientation of my scans look wrong after processing my DICOM files with 'mri_convert'?
A: It can be misleading to check orientation using FSLVIEW because it orients volumes based on the way they are on disk so you often get things looking pretty strange (e.g., upside-down). FSLVIEW does display little letters along the side of the image to indicate what it thinks the orientation is, so if you stick to those, then you can properly judge whether the orientation is correct.
Jimmy Ghaziri wrote:
Dear FreeSurfer community,
I'm using the mri_label2vol, the output is in .mgz. I then use mri_convert to convert it to .nii.gz. When I do so, the output is corrupted (see attached images). Some colleagues told me that it was because my FreeSurfer had a bug so I uninstalled and installed it back again but nothing changed. I then tried to run it on some other colleague's machine and it worked fine (on one subject just to test).
Any ideas what could be the problem ? I tried to flip the image 90 degrees but it won't flip, nothing changes.
Here are the commands I'm launching :
mri_label2vol --seg ~/Documents/freesurfer/subjects/pre_al_t1/mri/aparc+aseg.mgz --temp ~/Documents/freesurfer/subjects/pre_al_t1/mri/rawavg.mgz --o ~/Documents/freesurfer/subjects/pre_al_t1/mri/aparc+aseg_t1ref.mgz --regheader ~/Documents/freesurfer/subjects/pre_al_t1/mri/aparc+aseg.mgz
mri_convert aparc+aseg_t1ref.mgz aparc+aseg_t1ref.nii.gz
The data looks fine when I open it with tkmedit but it's inverted and cut when opened with fslview.
I cannot continue my analyses even if the data looks fine on tkmedit. When I apply a flirt transformation on the data I get the same cut and inverted brain than on fslview (see flirt attached image).
Is it a problem with my FreeSurfer or a command I'm running the wrong way ? Is there another software to convert .mgz to .nii.gz ?
Thank you very much !
Jimmy
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Yes, since it appears fine when I open it with tkmedit. But once I apply a flirt transformation I get the same image on tkmedit than the one on fslview. I tried to flip the image but it won't change anything since the brain is cut. Also, I followed the same steps on my colleagues machine and it worked fine on his...
Thank you
Jimmy
On Fri, Feb 24, 2012 at 14:27, Douglas N Greve greve@nmr.mgh.harvard.eduwrote:
Hi Jimmy, I think the problem, if you can call it that, is with fslview. Below is from our FAQ. See if that makes sense.doug
Q. Why would the orientation of my scans look wrong after processing my DICOM files with 'mri_convert'?A: It can be misleading to check orientation using FSLVIEW because it orients volumes based on the way they are on disk so you often get things looking pretty strange (e.g., upside-down). FSLVIEW does display little letters along the side of the image to indicate what it thinks the orientation is, so if you stick to those, then you can properly judge whether the orientation is correct.
Jimmy Ghaziri wrote:
Dear FreeSurfer community,
I'm using the mri_label2vol, the output is in .mgz. I then use mri_convert to convert it to .nii.gz. When I do so, the output is corrupted (see attached images). Some colleagues told me that it was because my FreeSurfer had a bug so I uninstalled and installed it back again but nothing changed. I then tried to run it on some other colleague's machine and it worked fine (on one subject just to test).
Any ideas what could be the problem ? I tried to flip the image 90 degrees but it won't flip, nothing changes.
Here are the commands I'm launching :
mri_label2vol --seg ~/Documents/freesurfer/** subjects/pre_al_t1/mri/aparc+**aseg.mgz --temp ~/Documents/freesurfer/** subjects/pre_al_t1/mri/rawavg.**mgz --o ~/Documents/freesurfer/** subjects/pre_al_t1/mri/aparc+**aseg_t1ref.mgz --regheader ~/Documents/freesurfer/**subjects/pre_al_t1/mri/aparc+**aseg.mgz
mri_convert aparc+aseg_t1ref.mgz aparc+aseg_t1ref.nii.gz
The data looks fine when I open it with tkmedit but it's inverted and cut when opened with fslview.
I cannot continue my analyses even if the data looks fine on tkmedit. When I apply a flirt transformation on the data I get the same cut and inverted brain than on fslview (see flirt attached image).
Is it a problem with my FreeSurfer or a command I'm running the wrong way ? Is there another software to convert .mgz to .nii.gz ?
Thank you very much !
Jimmy
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______________________________**_________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.**edu/mailman/listinfo/**freesurferhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/**fswiki/BugReportinghttp://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/**facility/filedrop/index.htmlhttp://www.nmr.mgh.harvard.edu/facility/filedrop/index.html
The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/**compliancelinehttp://www.partners.org/complianceline. If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Oh, the problem may be in your label2vol cmd. Try this one
mri_label2vol --seg ~/Documents/freesurfer/subjects/pre_al_t1/mri/aparc+aseg.mgz --temp ~/Documents/freesurfer/subjects/pre_al_t1/mri/aparc+aseg.mgz --o ~/Documents/freesurfer/subjects/pre_al_t1/mri/aparc+aseg_t1ref.mgz --regheader ~/Documents/freesurfer/subjects/pre_al_t1/mri/aparc+aseg.mgz
Jimmy Ghaziri wrote:
Yes, since it appears fine when I open it with tkmedit. But once I apply a flirt transformation I get the same image on tkmedit than the one on fslview. I tried to flip the image but it won't change anything since the brain is cut. Also, I followed the same steps on my colleagues machine and it worked fine on his...
Thank you
Jimmy
On Fri, Feb 24, 2012 at 14:27, Douglas N Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:
Hi Jimmy, I think the problem, if you can call it that, is with fslview. Below is from our FAQ. See if that makes sense. doug Q. Why would the orientation of my scans look wrong after processing my DICOM files with 'mri_convert'? A: It can be misleading to check orientation using FSLVIEW because it orients volumes based on the way they are on disk so you often get things looking pretty strange (e.g., upside-down). FSLVIEW does display little letters along the side of the image to indicate what it thinks the orientation is, so if you stick to those, then you can properly judge whether the orientation is correct. Jimmy Ghaziri wrote: Dear FreeSurfer community, I'm using the mri_label2vol, the output is in .mgz. I then use mri_convert to convert it to .nii.gz. When I do so, the output is corrupted (see attached images). Some colleagues told me that it was because my FreeSurfer had a bug so I uninstalled and installed it back again but nothing changed. I then tried to run it on some other colleague's machine and it worked fine (on one subject just to test). Any ideas what could be the problem ? I tried to flip the image 90 degrees but it won't flip, nothing changes. Here are the commands I'm launching : mri_label2vol --seg ~/Documents/freesurfer/subjects/pre_al_t1/mri/aparc+aseg.mgz --temp ~/Documents/freesurfer/subjects/pre_al_t1/mri/rawavg.mgz --o ~/Documents/freesurfer/subjects/pre_al_t1/mri/aparc+aseg_t1ref.mgz --regheader ~/Documents/freesurfer/subjects/pre_al_t1/mri/aparc+aseg.mgz mri_convert aparc+aseg_t1ref.mgz aparc+aseg_t1ref.nii.gz The data looks fine when I open it with tkmedit but it's inverted and cut when opened with fslview. I cannot continue my analyses even if the data looks fine on tkmedit. When I apply a flirt transformation on the data I get the same cut and inverted brain than on fslview (see flirt attached image). Is it a problem with my FreeSurfer or a command I'm running the wrong way ? Is there another software to convert .mgz to .nii.gz ? Thank you very much ! Jimmy ------------------------------------------------------------------------ ------------------------------------------------------------------------ ------------------------------------------------------------------------ ------------------------------------------------------------------------ _______________________________________________ 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 <tel:617-724-2358> Fax: 617-726-7422 <tel:617-726-7422> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> 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
Could you explain why please ? I'm following this : http://surfer.nmr.mgh.harvard.edu/fswiki/FsAnat-to-NativeAnat
On Fri, Feb 24, 2012 at 18:51, Douglas N Greve greve@nmr.mgh.harvard.eduwrote:
Oh, the problem may be in your label2vol cmd. Try this one
mri_label2vol --seg ~/Documents/freesurfer/**subjects/pre_al_t1/mri/aparc+ **aseg.mgz --temp ~/Documents/freesurfer/**subjects/pre_al_t1/mri/aparc+* *aseg.mgz --o ~/Documents/freesurfer/**subjects/pre_al_t1/mri/aparc+**aseg_t1ref.mgz --regheader ~/Documents/freesurfer/**subjects/pre_al_t1/mri/aparc+** aseg.mgz
Jimmy Ghaziri wrote:
Yes, since it appears fine when I open it with tkmedit. But once I apply a flirt transformation I get the same image on tkmedit than the one on fslview. I tried to flip the image but it won't change anything since the brain is cut. Also, I followed the same steps on my colleagues machine and it worked fine on his...
Thank you
Jimmy
On Fri, Feb 24, 2012 at 14:27, Douglas N Greve <greve@nmr.mgh.harvard.edu<mailto: greve@nmr.mgh.harvard.**edu greve@nmr.mgh.harvard.edu>> wrote:
Hi Jimmy, I think the problem, if you can call it that, is with fslview. Below is from our FAQ. See if that makes sense.doug
Q. Why would the orientation of my scans look wrong after processing my DICOM files with 'mri_convert'?A: It can be misleading to check orientation using FSLVIEW because it orients volumes based on the way they are on disk so you often get things looking pretty strange (e.g., upside-down). FSLVIEW does display little letters along the side of the image to indicate what it thinks the orientation is, so if you stick to those, then you can properly judge whether the orientation is correct.
Jimmy Ghaziri wrote:
Dear FreeSurfer community, I'm using the mri_label2vol, the output is in .mgz. I then use mri_convert to convert it to .nii.gz. When I do so, the output is corrupted (see attached images). Some colleagues told me that it was because my FreeSurfer had a bug so I uninstalled and installed it back again but nothing changed. I then tried to run it on some other colleague's machine and it worked fine (on one subject just to test). Any ideas what could be the problem ? I tried to flip the image 90 degrees but it won't flip, nothing changes. Here are the commands I'm launching : mri_label2vol --seg ~/Documents/freesurfer/**subjects/pre_al_t1/mri/aparc+**aseg.mgz --temp ~/Documents/freesurfer/**subjects/pre_al_t1/mri/rawavg.**mgz --o ~/Documents/freesurfer/**subjects/pre_al_t1/mri/aparc+**aseg_t1ref.mgz --regheader ~/Documents/freesurfer/**subjects/pre_al_t1/mri/aparc+**aseg.mgz
mri_convert aparc+aseg_t1ref.mgz aparc+aseg_t1ref.nii.gz The data looks fine when I open it with tkmedit but it's inverted and cut when opened with fslview. I cannot continue my analyses even if the data looks fine on tkmedit. When I apply a flirt transformation on the data I get the same cut and inverted brain than on fslview (see flirt attached image). Is it a problem with my FreeSurfer or a command I'm running the wrong way ? Is there another software to convert .mgz to .nii.gz ? Thank you very much ! Jimmy ------------------------------**------------------------------**
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______________________________**_________________ 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.**edugreve@nmr.mgh.harvard.edu
Phone Number: 617-724-2358 tel:617-724-2358 Fax: 617-726-7422 tel:617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/**fswiki/BugReportinghttp://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://surfer.nmr.mgh.**harvard.edu/fswiki/**BugReportinghttp://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: www.nmr.mgh.harvard.edu/**facility/filedrop/index.htmlhttp://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
The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/**compliancelinehttp://www.partners.org/complianceline. If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
------------------------------**------------------------------**
______________________________**_________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.**edu/mailman/listinfo/**freesurferhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/**fswiki/BugReportinghttp://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/**facility/filedrop/index.htmlhttp://www.nmr.mgh.harvard.edu/facility/filedrop/index.html
Sorry, I think you did have the right command originally. If everything looks good in tkmedit but bad in fslview, then I think you'll need to talk to the FSL people (or at least tell us exactly what FSL commands you are running on the data). doug
Jimmy Ghaziri wrote:
Could you explain why please ? I'm following this : http://surfer.nmr.mgh.harvard.edu/fswiki/FsAnat-to-NativeAnat
On Fri, Feb 24, 2012 at 18:51, Douglas N Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:
Oh, the problem may be in your label2vol cmd. Try this one mri_label2vol --seg ~/Documents/freesurfer/subjects/pre_al_t1/mri/aparc+aseg.mgz --temp ~/Documents/freesurfer/subjects/pre_al_t1/mri/aparc+aseg.mgz --o ~/Documents/freesurfer/subjects/pre_al_t1/mri/aparc+aseg_t1ref.mgz --regheader ~/Documents/freesurfer/subjects/pre_al_t1/mri/aparc+aseg.mgz Jimmy Ghaziri wrote: Yes, since it appears fine when I open it with tkmedit. But once I apply a flirt transformation I get the same image on tkmedit than the one on fslview. I tried to flip the image but it won't change anything since the brain is cut. Also, I followed the same steps on my colleagues machine and it worked fine on his... Thank you Jimmy On Fri, Feb 24, 2012 at 14:27, 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: Hi Jimmy, I think the problem, if you can call it that, is with fslview. Below is from our FAQ. See if that makes sense. doug Q. Why would the orientation of my scans look wrong after processing my DICOM files with 'mri_convert'? A: It can be misleading to check orientation using FSLVIEW because it orients volumes based on the way they are on disk so you often get things looking pretty strange (e.g., upside-down). FSLVIEW does display little letters along the side of the image to indicate what it thinks the orientation is, so if you stick to those, then you can properly judge whether the orientation is correct. Jimmy Ghaziri wrote: Dear FreeSurfer community, I'm using the mri_label2vol, the output is in .mgz. I then use mri_convert to convert it to .nii.gz. When I do so, the output is corrupted (see attached images). Some colleagues told me that it was because my FreeSurfer had a bug so I uninstalled and installed it back again but nothing changed. I then tried to run it on some other colleague's machine and it worked fine (on one subject just to test). Any ideas what could be the problem ? I tried to flip the image 90 degrees but it won't flip, nothing changes. Here are the commands I'm launching : mri_label2vol --seg ~/Documents/freesurfer/subjects/pre_al_t1/mri/aparc+aseg.mgz --temp ~/Documents/freesurfer/subjects/pre_al_t1/mri/rawavg.mgz --o ~/Documents/freesurfer/subjects/pre_al_t1/mri/aparc+aseg_t1ref.mgz --regheader ~/Documents/freesurfer/subjects/pre_al_t1/mri/aparc+aseg.mgz mri_convert aparc+aseg_t1ref.mgz aparc+aseg_t1ref.nii.gz The data looks fine when I open it with tkmedit but it's inverted and cut when opened with fslview. I cannot continue my analyses even if the data looks fine on tkmedit. When I apply a flirt transformation on the data I get the same cut and inverted brain than on fslview (see flirt attached image). Is it a problem with my FreeSurfer or a command I'm running the wrong way ? Is there another software to convert .mgz to .nii.gz ? Thank you very much ! Jimmy ------------------------------------------------------------------------ ------------------------------------------------------------------------ ------------------------------------------------------------------------ ------------------------------------------------------------------------ _______________________________________________ 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 <tel:617-724-2358> <tel:617-724-2358 <tel:617-724-2358>> Fax: 617-726-7422 <tel:617-726-7422> <tel:617-726-7422 <tel: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: 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> 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 <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 <tel:617-724-2358> Fax: 617-726-7422 <tel:617-726-7422> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html>
freesurfer@nmr.mgh.harvard.edu
-
Douglas N Greve -
Jimmy Ghaziri