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Greetings,
I am trying to convert a surface label (e.g., lh.V1_exvivo.thresh.label) into a volume to use as an ROI mask.
I have played around with the mri_label2vol command, but I can't seem to get it to work. Here is the command I am using:
mri_label2vol --label lh.V1_exvivo.thresh.label --temp T1.mgz --reg register.dat --fillthresh .3 --proj frac 0 1 .1 --subject sub1 --hemi lh --o V1Test.nii.gz
The issue I believe is that I don't have seem to have a register.dat file. However, I'm not sure how to generate the relevant registration file since the surface label I'm using is already in subject space. The label that I need was created when I used recon-all to generate surfaces from my anatomical image. If it is relevant, my original anatomical image is a skull stripped T1 generated using FSL which I then converted to .mgz.
Does anyone have any insight? Thank you! Vlad
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since you are mapping back into the conformed anatomical space, you should be able to use --identity instead of specifing a registration matrix
On 7/26/18 8:25 PM, Ayzenberg, Vladislav wrote:
External Email - Use Caution
Greetings,
I am trying to convert a surface label (e.g., lh.V1_exvivo.thresh.label) into a volume to use as an ROI mask.
I have played around with the mri_label2vol command, but I can’t seem to get it to work. Here is the command I am using:
mri_label2vol --label lh.V1_exvivo.thresh.label --temp T1.mgz --reg register.dat --fillthresh .3 --proj frac 0 1 .1 --subject sub1 --hemi lh --o V1Test.nii.gz
The issue I believe is that I don’t have seem to have a register.dat file. However, I’m not sure how to generate the relevant registration file since the surface label I’m using is already in subject space. The label that I need was created when I used recon-all to generate surfaces from my anatomical image. If it is relevant, my original anatomical image is a skull stripped T1 generated using FSL which I then converted to .mgz.
Does anyone have any insight? Thank you!
Vlad
This e-mail message (including any attachments) is for the sole use of the intended recipient(s) and may contain confidential and privileged information. If the reader of this message is not the intended recipient, you are hereby notified that any dissemination, distribution or copying of this message (including any attachments) is strictly prohibited.
If you have received this message in error, please contact the sender by reply e-mail message and destroy all copies of the original message (including attachments).
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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Swapping in --identity let's the code run but it doesn't register the overlay the label correctly (see attached image).
mri_label2vol --label ./sub1/label/lh.V1_exvivo.thresh.label --temp ./sub1/mri/orig/001.mgz --identity --fillthresh .3 --proj frac 0 1 .1 --subject sub1 --hemi lh --o ./sub1/label/V1Test.nii.gz
Essentially, the original surface label floats below the brain.
________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Douglas Greve dgreve@mgh.harvard.edu Sent: Friday, July 27, 2018 11:36 AM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] no register.dat file for mri_label2vol
since you are mapping back into the conformed anatomical space, you should be able to use --identity instead of specifing a registration matrix
On 7/26/18 8:25 PM, Ayzenberg, Vladislav wrote:
External Email - Use Caution
Greetings,
I am trying to convert a surface label (e.g., lh.V1_exvivo.thresh.label) into a volume to use as an ROI mask.
I have played around with the mri_label2vol command, but I can’t seem to get it to work. Here is the command I am using:
mri_label2vol --label lh.V1_exvivo.thresh.label --temp T1.mgz --reg register.dat --fillthresh .3 --proj frac 0 1 .1 --subject sub1 --hemi lh --o V1Test.nii.gz
The issue I believe is that I don’t have seem to have a register.dat file. However, I’m not sure how to generate the relevant registration file since the surface label I’m using is already in subject space. The label that I need was created when I used recon-all to generate surfaces from my anatomical image. If it is relevant, my original anatomical image is a skull stripped T1 generated using FSL which I then converted to .mgz.
Does anyone have any insight? Thank you!
Vlad
________________________________
This e-mail message (including any attachments) is for the sole use of the intended recipient(s) and may contain confidential and privileged information. If the reader of this message is not the intended recipient, you are hereby notified that any dissemination, distribution or copying of this message (including any attachments) is strictly prohibited.
If you have received this message in error, please contact the sender by reply e-mail message and destroy all copies of the original message (including attachments).
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
freesurfer@nmr.mgh.harvard.edu
-
Ayzenberg, Vladislav -
Douglas Greve