[Freesurfer] dilating labels within a parcellation
Hi all, Is there a tool to surface-dilate all the labels contained within an annotation file simultaneously, while preserving the non-overlapping nature of the labels? I saw there is a development version of mri_label2label that works for individual label files separately, but that gets me into the problem of overlap and arbitrary starting points. Thanks very much, 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] generating new FREESURFER directory from linear transform
Hey Bruce, Thanks for your response - is it in principle possible to achieve what I want by applying the transform to the segmentations and surface files and then running the latter stages of recon-all to regenerate the parcellations and stats? Or is there a reason you might foresee that this simply won't work in a piecemeal fashion either? Wondering if it's even worth going down this rabbit hole... Thanks again, David -Original Message- From: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Bruce Fischl Sent: Friday, September 04, 2015 5:25 PM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] generating new FREESURFER directory from linear transform Hi David I don't think there's an easy way to do it all at once unless you apply the transform to the orig.mgz then rerun recon-all (which will not be the same as applying it to the outputs) sorry Bruce On Fri, 4 Sep 2015, David Grayson wrote: > > Hi all, > > > > I would like to take a single subject’s freesurfer directory and apply > a single linear transform (I already have the .dat file I would like > to use) to all of the recon-all output (volumes, surfaces, label files, etc). > Essentially I would like to apply the transform and make a new > freesurfer directory that keeps as much of the same contents as > possible. The transform is not just rigid-body, it includes scaling and > skewing. > > > > Is there a suggested way to do this, either all-at-once or piece-by-piece? > > > > Thank you very much, > > > > 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.
[Freesurfer] generating new FREESURFER directory from linear transform
Hi all, I would like to take a single subject's freesurfer directory and apply a single linear transform (I already have the .dat file I would like to use) to all of the recon-all output (volumes, surfaces, label files, etc). Essentially I would like to apply the transform and make a new freesurfer directory that keeps as much of the same contents as possible. The transform is not just rigid-body, it includes scaling and skewing. Is there a suggested way to do this, either all-at-once or piece-by-piece? Thank you very much, 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] warping segmentations onto unprocessed brain
ok, great. so let's say I have a linear transformation or a full warp field to go between the freesurfer processed image and the unprocessed brain. is there a way that I can propagate onto the unprocessed image the entire freesurfer contents including the mri and label and everything else, using the warp? The processed image has extensive manual edits, so I basically just want to transfer everything over. Thanks Bruce! -David On Thu, Feb 26, 2015 at 6:05 AM, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: Hi David yes, you can use bbregister to do the rigid alignment, then use it as initialization for mri_nl_align. I would think you are better off doing the surface recons and using cvs though. It's only computer time cheers Bruce On Wed, 25 Feb 2015, David Grayson wrote: Hey Bruce, Thanks for responding. I would actually prefer nonlinear. I did not mention it, but the aseg data that I have is on a distortion-corrected T1 image, whereas the unprocessed image I want to warp onto is the same scan but not corrected for distortion. The distortions are nonlinear. I was hoping there might be a way to get a warp field to go between the two images without running both images through the recon-all pipeline. Are there any other possible tools? Thanks! -David On Wed, Feb 25, 2015 at 8:29 PM, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: Is there any reason you need it to be nonlinear? I would think bbregister and mri_vol2vol would do the trick Cheers Bruce On Feb 25, 2015, at 11:18 PM, David Grayson dgray...@ucdavis.edu wrote: Hi freesurfers, I am hoping to warp an aparc+aseg.mgh file from a subject's freesurfer-processed image to a separate (unprocessed) T1 image on the same subject. I would like to use a purely intensity-based nonlinear volumetric registration to do this, to save time and complication. I understand I can do this if I have a .m3z warp file. My question is, how can I get this warp file? I have tried using mri_cvs_register with the --step3 option, but that appears to only work after the surface-based registrations have been carried out. I haven't found another tool to do this yet. Are there any ideas? Thank you very much for your time. -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. ___ 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] warping segmentations onto unprocessed brain
Hi freesurfers, I am hoping to warp an aparc+aseg.mgh file from a subject's freesurfer-processed image to a separate (unprocessed) T1 image on the same subject. I would like to use a purely intensity-based nonlinear volumetric registration to do this, to save time and complication. I understand I can do this if I have a .m3z warp file. My question is, how can I get this warp file? I have tried using mri_cvs_register with the --step3 option, but that appears to only work after the surface-based registrations have been carried out. I haven't found another tool to do this yet. Are there any ideas? Thank you very much for your time. -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] warping segmentations onto unprocessed brain
Hey Bruce, Thanks for responding. I would actually prefer nonlinear. I did not mention it, but the aseg data that I have is on a distortion-corrected T1 image, whereas the unprocessed image I want to warp onto is the same scan but not corrected for distortion. The distortions are nonlinear. I was hoping there might be a way to get a warp field to go between the two images without running both images through the recon-all pipeline. Are there any other possible tools? Thanks! -David On Wed, Feb 25, 2015 at 8:29 PM, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: Is there any reason you need it to be nonlinear? I would think bbregister and mri_vol2vol would do the trick Cheers Bruce On Feb 25, 2015, at 11:18 PM, David Grayson dgray...@ucdavis.edu wrote: Hi freesurfers, I am hoping to warp an aparc+aseg.mgh file from a subject's freesurfer-processed image to a separate (unprocessed) T1 image on the same subject. I would like to use a purely intensity-based nonlinear volumetric registration to do this, to save time and complication. I understand I can do this if I have a .m3z warp file. My question is, how can I get this warp file? I have tried using mri_cvs_register with the --step3 option, but that appears to only work after the surface-based registrations have been carried out. I haven't found another tool to do this yet. Are there any ideas? Thank you very much for your time. -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. ___ 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] applying manual freesurfer edits to warped brain image
Thanks Bruce, So I just need a warp field in .m3z format. Cool. As this distortion correction is proprietary, we don't actually get the warp fields, which is silly. But I was thinking since scanner distortions are subtle and coarse, it should be sufficient to nonlinearly register the two unsegmented images using a simple intensity-based volumetric registration at a coarse warp resolution. Would the mri_cvs_register tool be suitable for this if I supply the --step3 flag? Otherwise I am stuck with trying to go between Freesurfer and another set of tools. Thanks! -David Date: Sun, 2 Nov 2014 21:44:23 -0500 From: Bruce Fischl fis...@nmr.mgh.harvard.edu javascript:; Subject: Re: [Freesurfer] applying manual freesurfer edits to warped brain image To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu javascript:; Message-ID: 35417931-ce03-4cb8-a30e-c1f34c174...@nmr.mgh.harvard.edu javascript:; Content-Type: text/plain; charset=us-ascii What format is the distortion field stored in? If you can get it into .m3z I believe we have tools to do what you want On Nov 2, 2014, at 9:37 PM, David Grayson dgray...@ucdavis.edu javascript:; wrote: Hi freesurfer experts, I have two T1 images from the same subject acquired at the same time point. One of the images is distortion corrected using a calibration phantom, put through the full freesurfer pipeline and then extensively manually edited. The uncorrected image has had zero processing. What I would like now is to have the freesurfer segmentations on the uncorrected image and preserve as much as possible the manual edits. In other words, I would like to warp the surface meshes already obtained on the distortion corrected image to the uncorrected image. Is there already a suggested method that is optimal for this purpose? Thanks in advance for any advice! -David ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu javascript:; https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- next part -- An HTML attachment was scrubbed... URL: http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20141102/65628850/attachment-0001.html ___ 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] applying manual freesurfer edits to warped brain image
Hi freesurfer experts, I have two T1 images from the same subject acquired at the same time point. One of the images is distortion corrected using a calibration phantom, put through the full freesurfer pipeline and then extensively manually edited. The uncorrected image has had zero processing. What I would like now is to have the freesurfer segmentations on the uncorrected image and preserve as much as possible the manual edits. In other words, I would like to warp the surface meshes already obtained on the distortion corrected image to the uncorrected image. Is there already a suggested method that is optimal for this purpose? Thanks in advance for any advice! -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.
[Freesurfer] overlapping labels
Hi freesurfers, Can a .annot file include labels with overlapping vertices? If not, then when using mris_label2annot, how does freesurfer decide which label to assign the vertices to? Thanks, 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.
[Freesurfer] method for detecting neighboring labels?
Is there a way to output a list of all the labels within a given annotation file which share a border with another specified label? Thank you very much, 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.
[Freesurfer] last index missing when using mri_label2vol
Hi, I am noticing that when I use ‘mri_label2vol --annot’ it is not creating the final label from the color table file. I tried using the --thresh 1 option, but that didn't work either. i.e... mri_label2vol --annot lh.custom.annot --temp ../mri/orig.mgz --o custom_lh.nii.gz --subject FREESURFER --hemi lh --identity The last index is no where to be found in the custom_lh.nii.gz. But the other indices look OK. Has anyone encountered this before, and know what to do? Thanks very much! 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
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 gray...@ohsu.edumailto: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.edumailto: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 gray...@ohsu.edumailto: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.edumailto: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.
[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.
[Freesurfer] applying new cortical parcellations
Hi Freesurfer experts, I would like to apply a novel cortical parcellation from an average surface (http://surfer.nmr.mgh.harvard.edu/fswiki/CorticalParcellation_Yeo2011) to subjects that I have previously ran through recon-all. I have found a number of tools that seem related to this – can anyone tell me the precise steps that need to be taken? Thank you very much, 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] propagating labels to gray matter
One more thing I noticed... When I run mri_anatomical_stats on the annot file, it tells me this: reading colortable from annotation file... colortable with 207 entries read (originally /home/leila/freesurfer/mycolortables/original_color_P1_16_R.txt) I don't find this txt file anywhere though. Is this important? Thanks, David -Original Message- From: Douglas Greve [mailto:gr...@nmr.mgh.harvard.edu] Sent: Monday, October 31, 2011 7:40 PM To: David Grayson Cc: 'freesurfer@nmr.mgh.harvard.edu' Subject: Re: [Freesurfer] propagating labels to gray matter Hi David, you can use mri_label2vol with the --proj option. This works ok, but it is often not great. Another way (the way that aparc+aseg) is created is to convert your label into an annotation, then use mri_aparc2aseg. doug On 10/31/11 7:22 PM, David Grayson wrote: Hi Doug, Although in principle, yes this is the idea, we have a set of labels that aren't actually in the aparc+aseg file (basically a set of high-density subdivisions of those regions). The only problem is that the labels I have are just in surface-land. I am wondering, once I have the surface labels, is there a way to re-propagate them back into the gray matter? Thanks again, David -Original Message- From: Douglas N Greve [mailto:gr...@nmr.mgh.harvard.edu] Sent: Monday, October 31, 2011 2:38 PM To: David Grayson Cc: 'freesurfer@nmr.mgh.harvard.edu' Subject: Re: [Freesurfer] propagating labels to gray matter Do you just want the label in the orig volume space? If so, just use the labels in aparc+aseg.mgz doug David Grayson wrote: Hi Doug, /path/to/FREESURFER/label/regenerated_lh_36$ mri_label2vol --label lh.bankssts.label --temp ../../mri/orig.mgz --identity --o TEST.nii.gz Thanks, David -Original Message- From: Douglas N Greve [mailto:gr...@nmr.mgh.harvard.edu] Sent: Monday, October 31, 2011 2:04 PM To: David Grayson Cc: 'freesurfer@nmr.mgh.harvard.edu' Subject: Re: [Freesurfer] propagating labels to gray matter what was your label2vol command line? doug David Grayson wrote: Hi freesurfer experts, I currently have a set of cortical labels that are the result of a high-resolution parcellation of the standard aparc.annot labels (via the ‘connectomemapper’ software). I would like to extract the gray matter ROIs that correspond to these labels, and I understand that this requires a method to ‘propagate’ these labels through the gray matter. I have so far been unsuccessful – ‘mri_label2vol’ seems to only give me that pial or white surfaces, as opposed to the gray matter bodies. Does anyone know how to accomplish this? Thank you very much, David Grayson ___ 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] converting annotation values to label codes
Hi, I have converted a custom-made annotation file to a volume, and now I am trying to find a table with the labels and their corresponding label codes (index values which are created when the annotation file is converted to a volume). I only have the “annotation values” or color codes for each region, which I found with the read_annotation() function in matlab. The online wiki states that this color code then has to be used to look up the label code, but it’s unclear to me how to do this. Is there be a table somewhere so that I can cross-reference the color codes to the label codes? Thank you, 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.
[Freesurfer] propagating labels to gray matter
Hi freesurfer experts, I currently have a set of cortical labels that are the result of a high-resolution parcellation of the standard aparc.annot labels (via the ‘connectomemapper’ software). I would like to extract the gray matter ROIs that correspond to these labels, and I understand that this requires a method to ‘propagate’ these labels through the gray matter. I have so far been unsuccessful – ‘mri_label2vol’ seems to only give me that pial or white surfaces, as opposed to the gray matter bodies. Does anyone know how to accomplish this? Thank you very much, David Grayson ___ 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] propagating labels to gray matter
Hi Doug, /path/to/FREESURFER/label/regenerated_lh_36$ mri_label2vol --label lh.bankssts.label --temp ../../mri/orig.mgz --identity --o TEST.nii.gz Thanks, David -Original Message- From: Douglas N Greve [mailto:gr...@nmr.mgh.harvard.edu] Sent: Monday, October 31, 2011 2:04 PM To: David Grayson Cc: 'freesurfer@nmr.mgh.harvard.edu' Subject: Re: [Freesurfer] propagating labels to gray matter what was your label2vol command line? doug David Grayson wrote: Hi freesurfer experts, I currently have a set of cortical labels that are the result of a high-resolution parcellation of the standard aparc.annot labels (via the ‘connectomemapper’ software). I would like to extract the gray matter ROIs that correspond to these labels, and I understand that this requires a method to ‘propagate’ these labels through the gray matter. I have so far been unsuccessful – ‘mri_label2vol’ seems to only give me that pial or white surfaces, as opposed to the gray matter bodies. Does anyone know how to accomplish this? Thank you very much, David Grayson ___ 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 gr...@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 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
Re: [Freesurfer] propagating labels to gray matter
Hi Doug, Although in principle, yes this is the idea, we have a set of labels that aren't actually in the aparc+aseg file (basically a set of high-density subdivisions of those regions). The only problem is that the labels I have are just in surface-land. I am wondering, once I have the surface labels, is there a way to re-propagate them back into the gray matter? Thanks again, David -Original Message- From: Douglas N Greve [mailto:gr...@nmr.mgh.harvard.edu] Sent: Monday, October 31, 2011 2:38 PM To: David Grayson Cc: 'freesurfer@nmr.mgh.harvard.edu' Subject: Re: [Freesurfer] propagating labels to gray matter Do you just want the label in the orig volume space? If so, just use the labels in aparc+aseg.mgz doug David Grayson wrote: Hi Doug, /path/to/FREESURFER/label/regenerated_lh_36$ mri_label2vol --label lh.bankssts.label --temp ../../mri/orig.mgz --identity --o TEST.nii.gz Thanks, David -Original Message- From: Douglas N Greve [mailto:gr...@nmr.mgh.harvard.edu] Sent: Monday, October 31, 2011 2:04 PM To: David Grayson Cc: 'freesurfer@nmr.mgh.harvard.edu' Subject: Re: [Freesurfer] propagating labels to gray matter what was your label2vol command line? doug David Grayson wrote: Hi freesurfer experts, I currently have a set of cortical labels that are the result of a high-resolution parcellation of the standard aparc.annot labels (via the ‘connectomemapper’ software). I would like to extract the gray matter ROIs that correspond to these labels, and I understand that this requires a method to ‘propagate’ these labels through the gray matter. I have so far been unsuccessful – ‘mri_label2vol’ seems to only give me that pial or white surfaces, as opposed to the gray matter bodies. Does anyone know how to accomplish this? Thank you very much, David Grayson ___ 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 gr...@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 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
