[Freesurfer] weird relabeling with mri_convert
Hi freesurfer folks, I am using mri_convert to reorient my custom cortical parcellation (a nifti file generated from an annotation file), and I have run into some unexpected blips with some seemingly errant reindexing. Here is the command I am using: mri_convert -rl FREESURFER/mri/orig/001.mgz -rt nearest FREESURFER/label/ROIs_custom.nii.gz -nc reorient/ROIs_custom_reorient.nii.gz For the most part, this works well for most of the indices. The biggest problem is that the highest value index (2063) is being completely relabeled in ‘ROIs_custom_reorient.nii.gz’ with several smaller values in the 20’s range. But this occurs to a smaller extent with many of the other regions as well, where small parts of those regions are being relabeled with values anywhere from 1 to 20. Can anyone give me some insight as to what’s up with this and what I might be able to do to fix it? Thank you very much for any help. -David ___ 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.
Re: [Freesurfer] weird relabeling with mri_convert
Try -odt short to stop it from changing the data type to uchar On Feb 21, 2012, at 12:04 AM, David Grayson wrote: > Hi freesurfer folks, > > I am using mri_convert to reorient my custom cortical parcellation (a nifti > file generated from an annotation file), and I have run into some unexpected > blips with some seemingly errant reindexing. Here is the command I am using: > > mri_convert -rl FREESURFER/mri/orig/001.mgz -rt nearest > FREESURFER/label/ROIs_custom.nii.gz -nc reorient/ROIs_custom_reorient.nii.gz > > For the most part, this works well for most of the indices. The biggest > problem is that the highest value index (2063) is being completely relabeled > in ‘ROIs_custom_reorient.nii.gz’ with several smaller values in the 20’s > range. But this occurs to a smaller extent with many of the other regions as > well, where small parts of those regions are being relabeled with values > anywhere from 1 to 20. > > Can anyone give me some insight as to what’s up with this and what I might be > able to do to fix it? Thank you very much for any help. > > -David > ___ > 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.
Re: [Freesurfer] weird relabeling with mri_convert
Hi, Thanks for your response. When I tried that option I got the same results, and I looked at the output header file and it still said ‘float32.’ I tried removing the -nc option, but that messed it up worse. None of my other attempts at tweaking the command are working thus far. Is there anything else I can try? Thank you, David From: Bruce Fischl [mailto:fis...@nmr.mgh.harvard.edu] Sent: Tuesday, February 21, 2012 12:58 AM To: David Grayson Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] weird relabeling with mri_convert Try -odt short to stop it from changing the data type to uchar On Feb 21, 2012, at 12:04 AM, David Grayson mailto:gray...@ohsu.edu>> wrote: Hi freesurfer folks, I am using mri_convert to reorient my custom cortical parcellation (a nifti file generated from an annotation file), and I have run into some unexpected blips with some seemingly errant reindexing. Here is the command I am using: mri_convert -rl FREESURFER/mri/orig/001.mgz -rt nearest FREESURFER/label/ROIs_custom.nii.gz -nc reorient/ROIs_custom_reorient.nii.gz For the most part, this works well for most of the indices. The biggest problem is that the highest value index (2063) is being completely relabeled in ‘ROIs_custom_reorient.nii.gz’ with several smaller values in the 20’s range. But this occurs to a smaller extent with many of the other regions as well, where small parts of those regions are being relabeled with values anywhere from 1 to 20. Can anyone give me some insight as to what’s up with this and what I might be able to do to fix it? Thank you very much for any help. -David ___ 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. ___ 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.
Re: [Freesurfer] weird relabeling with mri_convert
Hi folks, Sorry, I messed up – mri_convert is working fine. The error is actually occurring prior to that when I use ‘mri_label2vol’ to convert the annotation file to a volume. Here’s where it happens mri_label2vol --annot lh.Yeo_singles.annot --temp ../mri/orig.mgz --o Yeo_WMGM_lh.nii.gz --subject FREESURFER --hemi lh --identity Has anyone encountered something like this before, where some of the label assignments in the resulting nifti file, and for some reason the last one in particular, are screwy? Interestingly, I don’t have this issue at all when I use mri_aparc2aseg with the --annot option, but then that gives me the parcellations in the gray matter, whereas I want them on the WM/GM boundary. Any ideas? Thanks if you’re still reading! David From: David Grayson Sent: Tuesday, February 21, 2012 7:04 PM To: 'Bruce Fischl' Cc: freesurfer@nmr.mgh.harvard.edu Subject: RE: [Freesurfer] weird relabeling with mri_convert Hi, Thanks for your response. When I tried that option I got the same results, and I looked at the output header file and it still said ‘float32.’ I tried removing the -nc option, but that messed it up worse. None of my other attempts at tweaking the command are working thus far. Is there anything else I can try? Thank you, David From: Bruce Fischl [mailto:fis...@nmr.mgh.harvard.edu] Sent: Tuesday, February 21, 2012 12:58 AM To: David Grayson Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] weird relabeling with mri_convert Try -odt short to stop it from changing the data type to uchar On Feb 21, 2012, at 12:04 AM, David Grayson mailto:gray...@ohsu.edu>> wrote: Hi freesurfer folks, I am using mri_convert to reorient my custom cortical parcellation (a nifti file generated from an annotation file), and I have run into some unexpected blips with some seemingly errant reindexing. Here is the command I am using: mri_convert -rl FREESURFER/mri/orig/001.mgz -rt nearest FREESURFER/label/ROIs_custom.nii.gz -nc reorient/ROIs_custom_reorient.nii.gz For the most part, this works well for most of the indices. The biggest problem is that the highest value index (2063) is being completely relabeled in ‘ROIs_custom_reorient.nii.gz’ with several smaller values in the 20’s range. But this occurs to a smaller extent with many of the other regions as well, where small parts of those regions are being relabeled with values anywhere from 1 to 20. Can anyone give me some insight as to what’s up with this and what I might be able to do to fix it? Thank you very much for any help. -David ___ 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. ___ 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.
