Dear FreeSurfer experts,
I've been using FreeSurfer for 2 months now, and I have a question on how to proceed to do the following thing:
My goal is to obtain the CRS coordinates of the corpus callossum.
Here is what I was thinking to do, based on what I read:
1. Annotation to segmentation: mri_annotation2label --seg --hemi ?? --subject bert volume_annot.mgh
=> I need to provide an hemisphere, which one should I use, should I do this for both ?
2. Binarize the volume, keeping the label we want: mri_binarize --i volume_annot.mgh --match 86 --o corpusCallossum.mgh
=> I use the number 86 based on the LUT table...
3. Execute: mri_surfcluster --in corpusCallossum.mgh --thmin 0.5 --subject bert --hemi ?? --o outputfile.mgh
Am I on the right path? I am not sure on how to use the outputfile.mgh after. Did I miss any arguments in the command line?
Thank you in advance for your help
Thomas Paul.
Hi Thomas
you are probably better off getting it right out of the aseg.mgz. The cc labels in it are:
#define CC_Posterior 251 #define CC_Mid_Posterior 252 #define CC_Central 253 #define CC_Mid_Anterior 254 #define CC_Anterior 255
so you should just be able to run mri_extrac_label directly
set mdir=$SUBJECTS_DIR/$s/mri mri_extract_label $mdir/aseg.mgz 251 252 253 254 255 $mdir/cc.mgz
then go from there cheers Bruce
On Fri, 14 Mar 2014, Thomas PAUL wrote:
Dear FreeSurfer experts, I've been using FreeSurfer for 2 months now, and I have a question on how to proceed to do the following thing:
My goal is to obtain the CRS coordinates of the corpus callossum.
Here is what I was thinking to do, based on what I read:
- Annotation to segmentation:
mri_annotation2label --seg --hemi ?? --subject bert volume_annot.mgh
=> I need to provide an hemisphere, which one should I use, should I do this for both ?
- Binarize the volume, keeping the label we want:
mri_binarize --i volume_annot.mgh --match 86 --o corpusCallossum.mgh
=> I use the number 86 based on the LUT table...
- Execute:
mri_surfcluster --in corpusCallossum.mgh --thmin 0.5 --subject bert --hemi ?? --o outputfile.mgh
Am I on the right path? I am not sure on how to use the outputfile.mgh after. Did I miss any arguments in the command line?
Thank you in advance for your help
Thomas Paul.
Thank you Bruce for your help, it works. I didn't noticed that mri_extract_label existed. So just to be sure, the output volume is not a mask, right? If I want to convert it to a mask, I use mri_binarize ?
Thomas Paul.
On Fri, Mar 14, 2014 at 2:51 PM, Bruce Fischl fischl@nmr.mgh.harvard.eduwrote:
Hi Thomas
you are probably better off getting it right out of the aseg.mgz. The cc labels in it are:
#define CC_Posterior 251 #define CC_Mid_Posterior 252 #define CC_Central 253 #define CC_Mid_Anterior 254 #define CC_Anterior 255
so you should just be able to run mri_extrac_label directly
set mdir=$SUBJECTS_DIR/$s/mri mri_extract_label $mdir/aseg.mgz 251 252 253 254 255 $mdir/cc.mgz
then go from there cheers Bruce
On Fri, 14 Mar 2014, Thomas PAUL wrote:
Dear FreeSurfer experts,
I've been using FreeSurfer for 2 months now, and I have a question on how to proceed to do the following thing:
My goal is to obtain the CRS coordinates of the corpus callossum.
Here is what I was thinking to do, based on what I read:
- Annotation to segmentation: mri_annotation2label --seg --hemi ?? --subject bert volume_annot.mgh
=> I need to provide an hemisphere, which one should I use, should I do this for both ?
- Binarize the volume, keeping the label we want: mri_binarize --i volume_annot.mgh --match 86 --o corpusCallossum.mgh
=> I use the number 86 based on the LUT table...
- Execute: mri_surfcluster --in corpusCallossum.mgh --thmin 0.5 --subject bert
--hemi ?? --o outputfile.mgh
Am I on the right path? I am not sure on how to use the outputfile.mgh after. Did I miss any arguments in the command line?
Thank you in advance for your help
Thomas Paul.
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.
yes On Sat, 15 Mar 2014, Thomas PAUL wrote:
Thank you Bruce for your help, it works. I didn't noticed that mri_extract_label existed. So just to be sure, the output volume is not a mask, right? If I want to convert it to a mask, I use mri_binarize ? Thomas Paul.
On Fri, Mar 14, 2014 at 2:51 PM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote: Hi Thomas
you are probably better off getting it right out of the aseg.mgz. The cc labels in it are: #define CC_Posterior 251 #define CC_Mid_Posterior 252 #define CC_Central 253 #define CC_Mid_Anterior 254 #define CC_Anterior 255 so you should just be able to run mri_extrac_label directly set mdir=$SUBJECTS_DIR/$s/mri mri_extract_label $mdir/aseg.mgz 251 252 253 254 255 $mdir/cc.mgz then go from there cheers Bruce On Fri, 14 Mar 2014, Thomas PAUL wrote: Dear FreeSurfer experts, I've been using FreeSurfer for 2 months now, and I have a question on how to proceed to do the following thing: My goal is to obtain the CRS coordinates of the corpus callossum. Here is what I was thinking to do, based on what I read: 1. Annotation to segmentation: mri_annotation2label --seg --hemi ?? --subject bert volume_annot.mgh => I need to provide an hemisphere, which one should I use, should I do this for both ? 2. Binarize the volume, keeping the label we want: mri_binarize --i volume_annot.mgh --match 86 --o corpusCallossum.mgh => I use the number 86 based on the LUT table... 3. Execute: mri_surfcluster --in corpusCallossum.mgh --thmin 0.5 --subject bert --hemi ?? --o outputfile.mgh Am I on the right path? I am not sure on how to use the outputfile.mgh after. Did I miss any arguments in the command line? Thank you in advance for your help Thomas Paul.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.
Okay thank you Bruce for your quick answer. I have one more question. I went through the whole ReconAllTable, and I can't find the answer:
Based on what I read, I think that all the volumes created by freesurfer (all the outputs) have had the Tailarach transform applied to them? So when I have extracted the label I want from aseg.mgz, how can I go back easily to the original space and apply my mask to the original scan?
Thank you again for your help.
Thomas PAUL.
On Sat, Mar 15, 2014 at 3:05 PM, Bruce Fischl fischl@nmr.mgh.harvard.eduwrote:
yes
On Sat, 15 Mar 2014, Thomas PAUL wrote:
Thank you Bruce for your help, it works. I didn't noticed that
mri_extract_label existed. So just to be sure, the output volume is not a mask, right? If I want to convert it to a mask, I use mri_binarize ? Thomas Paul.
On Fri, Mar 14, 2014 at 2:51 PM, Bruce Fischl <fischl@nmr.mgh.harvard.edu
wrote: Hi Thomas
you are probably better off getting it right out of the aseg.mgz. The cc labels in it are: #define CC_Posterior 251 #define CC_Mid_Posterior 252 #define CC_Central 253 #define CC_Mid_Anterior 254 #define CC_Anterior 255 so you should just be able to run mri_extrac_label directly set mdir=$SUBJECTS_DIR/$s/mri mri_extract_label $mdir/aseg.mgz 251 252 253 254 255 $mdir/cc.mgz then go from there cheers Bruce On Fri, 14 Mar 2014, Thomas PAUL wrote: Dear FreeSurfer experts, I've been using FreeSurfer for 2 months now, and I have a question on how to proceed to do the following thing: My goal is to obtain the CRS coordinates of the corpus callossum. Here is what I was thinking to do, based on what I read: 1. Annotation to segmentation: mri_annotation2label --seg --hemi ?? --subject bert volume_annot.mgh => I need to provide an hemisphere, which one should I use, should I do this for both ? 2. Binarize the volume, keeping the label we want: mri_binarize --i volume_annot.mgh --match 86 --o corpusCallossum.mgh => I use the number 86 based on the LUT table... 3. Execute: mri_surfcluster --in corpusCallossum.mgh --thmin 0.5 --subject bert --hemi ?? --o outputfile.mgh Am I on the right path? I am not sure on how to use the outputfile.mgh after. Did I miss any arguments in the command line? Thank you in advance for your help Thomas Paul.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.
Hi Thomas,
no, all the values are in individual subject space.
cheers Bruce On Mon, 17 Mar 2014, Thomas PAUL wrote:
Okay thank you Bruce for your quick answer. I have one more question. I went through the whole ReconAllTable, and I can't find the answer:
Based on what I read, I think that all the volumes created by freesurfer (all the outputs) have had the Tailarach transform applied to them? So when I have extracted the label I want from aseg.mgz, how can I go back easily to the original space and apply my mask to the original scan?
Thank you again for your help.
Thomas PAUL.
On Sat, Mar 15, 2014 at 3:05 PM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote: yes On Sat, 15 Mar 2014, Thomas PAUL wrote:
Thank you Bruce for your help, it works. I didn't noticed that mri_extract_label existed. So just to be sure, the output volume is not a mask, right? If I want to convert it to a mask, I use mri_binarize ? Thomas Paul. On Fri, Mar 14, 2014 at 2:51 PM, Bruce Fischl <fischl@nmr.mgh.harvard.edu> wrote: Hi Thomas you are probably better off getting it right out of the aseg.mgz. The cc labels in it are: #define CC_Posterior 251 #define CC_Mid_Posterior 252 #define CC_Central 253 #define CC_Mid_Anterior 254 #define CC_Anterior 255 so you should just be able to run mri_extrac_label directly set mdir=$SUBJECTS_DIR/$s/mri mri_extract_label $mdir/aseg.mgz 251 252 253 254 255 $mdir/cc.mgz then go from there cheers Bruce On Fri, 14 Mar 2014, Thomas PAUL wrote: Dear FreeSurfer experts, I've been using FreeSurfer for 2 months now, and I have a question on how to proceed to do the following thing: My goal is to obtain the CRS coordinates of the corpus callossum. Here is what I was thinking to do, based on what I read: 1. Annotation to segmentation: mri_annotation2label --seg --hemi ?? --subject bert volume_annot.mgh => I need to provide an hemisphere, which one should I use, should I do this for both ? 2. Binarize the volume, keeping the label we want: mri_binarize --i volume_annot.mgh --match 86 --o corpusCallossum.mgh => I use the number 86 based on the LUT table... 3. Execute: mri_surfcluster --in corpusCallossum.mgh --thmin 0.5 --subject bert --hemi ?? --o outputfile.mgh Am I on the right path? I am not sure on how to use the outputfile.mgh after. Did I miss any arguments in the command line? Thank you in advance for your help Thomas Paul. 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@nmr.mgh.harvard.edu
-
Bruce Fischl -
Thomas PAUL