Hi, Freesurfers. I need to create some labels from binary masks. Sometime ago I read a post (https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2013-October/033783.h... ) and, unless I am wrong, it seemed to me that mri_label2vol could be the tool to get it. If so, could you please explain how? I read documentation on wiki and help from the command itself and could not see how to accomplish that. I could only find how to create a volume from a label. What I need to do is to get a mask like the binLeftHippoHead.mgz (attached) and create a label. Assuming it is possible, I could also make labels for Hippocampal body and head, merge the 3 labels into an annot file. This way i can use Freeview to load the whole hippocampal surface and discriminate the 3 segments by colors with the annot file. Thanks in advance for any help. Cheers, Marcos.
I think you need to use mri_cor2label (not very well named:) doug
On 10/16/13 4:24 PM, Marcos Martins da Silva wrote:
Hi, Freesurfers. I need to create some labels from binary masks. Sometime ago I read a post (https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2013-October/033783.h... ) and, unless I am wrong, it seemed to me that mri_label2vol could be the tool to get it. If so, could you please explain how? I read documentation on wiki and help from the command itself and could not see how to accomplish that. I could only find how to create a volume from a label. What I need to do is to get a mask like the binLeftHippoHead.mgz (attached) and create a label. Assuming it is possible, I could also make labels for Hippocampal body and head, merge the 3 labels into an annot file. This way i can use Freeview to load the whole hippocampal surface and discriminate the 3 segments by colors with the annot file. Thanks in advance for any help. Cheers, Marcos.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hi, Doug Thank you for your answer.
I am trying cor2label as you suggested. First of all I am afraid to say that website documentation and help from the own command are a bit different so I got a little confused. But the following command worked: mri_cor2label --i binLeftHippoBody.mgz --id 1 --l 2.leftBody
Using freeview I could load the hippocampus volume and 2.leftBody as a ROI. I attached a screenshot that also included 1.leftHead and 3.leftTail, generated in the same way. When I tried to concatenate the 3 labels into an annot file I got an error:
mris_label2annot --s bert --h lh --ctab HippoColorLUT.txt --l 1.leftHead.label --l 2.leftBody.label --l 3.leftTail.label --a lefthippo Loading /home/marcos/freesurfer/subjects/bert/surf/lh.orig 1 16711680 leftHead ERROR: 1.leftHead.label, n=0, vertex -1 out of range
When I checked label file generated by mri_cor2label the first collumn (vertex number) contains only -1 as value. It seems that when you use mri_cor2label it does not preserve or even recover the vertex number. It also seems I need the correct vertex number in label file to use mris_label2annot Just to rule out a problem with the hippocampal subfield files I tried the example command (extracted from command help): mri_cor2label --i aseg.mgz --id 12 --l left-putamen.label This label also shows only -1 as vertex number.
Could you please explain me what do I need to do to get the vertex numbers in the label file as output of mri_cor2label?
Cheers, Marcos
Em Qua, 2013-10-16 às 20:34 -0400, Douglas Greve escreveu:
I think you need to use mri_cor2label (not very well named:) doug
On 10/16/13 4:24 PM, Marcos Martins da Silva wrote:
Hi, Freesurfers. I need to create some labels from binary masks. Sometime ago I read a post (https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2013-October/033783.h... ) and, unless I am wrong, it seemed to me that mri_label2vol could be the tool to get it. If so, could you please explain how? I read documentation on wiki and help from the command itself and could not see how to accomplish that. I could only find how to create a volume from a label. What I need to do is to get a mask like the binLeftHippoHead.mgz (attached) and create a label. Assuming it is possible, I could also make labels for Hippocampal body and head, merge the 3 labels into an annot file. This way i can use Freeview to load the whole hippocampal surface and discriminate the 3 segments by colors with the annot file. Thanks in advance for any help. Cheers, Marcos.
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.
Is *binLeftHippoBody.mgz a volume label or a surface label? If a volume label, map it onto the surface with mri_vol2surf, the run mri_cor2label *specifying --surf
doug
On 10/17/13 5:00 PM, Marcos Martins da Silva wrote:
Hi, Doug Thank you for your answer.
I am trying cor2label as you suggested. First of all I am afraid to say that website documentation and help from the own command are a bit different so I got a little confused. But the following command worked: *mri_cor2label --i binLeftHippoBody.mgz --id 1 --l 2.leftBody*
Using freeview I could load the hippocampus volume and 2.leftBody as a ROI. I attached a screenshot that also included 1.leftHead and 3.leftTail, generated in the same way. When I tried to concatenate the 3 labels into an annot file I got an error:
*mris_label2annot --s bert --h lh --ctab HippoColorLUT.txt --l 1.leftHead.label --l 2.leftBody.label --l 3.leftTail.label --a lefthippo* *Loading /home/marcos/freesurfer/subjects/bert/surf/lh.orig* *1 16711680 leftHead* *ERROR: 1.leftHead.label, n=0, vertex -1 out of range*
When I checked label file generated by mri_cor2label the first collumn (vertex number) contains only *-1* as value. It seems that when you use mri_cor2label it does not preserve or even recover the vertex number. It also seems I need the correct vertex number in label file to use mris_label2annot Just to rule out a problem with the hippocampal subfield files I tried the example command (extracted from command help): mri_cor2label --i aseg.mgz --id 12 --l left-putamen.label This label also shows only -1 as vertex number.
Could you please explain me what do I need to do to get the vertex numbers in the label file as output of mri_cor2label?
Cheers, Marcos
Em Qua, 2013-10-16 às 20:34 -0400, Douglas Greve escreveu:
I think you need to use mri_cor2label (not very well named:) doug
On 10/16/13 4:24 PM, Marcos Martins da Silva wrote:
Hi, Freesurfers. I need to create some labels from binary masks. Sometime ago I read a post (https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2013-October/033783.h... ) and, unless I am wrong, it seemed to me that mri_label2vol could be the tool to get it. If so, could you please explain how? I read documentation on wiki and help from the command itself and could not see how to accomplish that. I could only find how to create a volume from a label. What I need to do is to get a mask like the binLeftHippoHead.mgz (attached) and create a label. Assuming it is possible, I could also make labels for Hippocampal body and head, merge the 3 labels into an annot file. This way i can use Freeview to load the whole hippocampal surface and discriminate the 3 segments by colors with the annot file. Thanks in advance for any help. Cheers, Marcos.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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.
Hi, Doug Sorry for this late feedback. Just so you can understand what is binLeftHippoBody.mgz I will explain its origin. 1) recon-all --hippo-subfields 2) mri_concat the posterior*.mgz to get the whole hippocampus 3) a custom octave routine to segment the whole hippocampus into head, body and tail. This routine preserves the probability values of the original posterior*.mgz 4) mri_binarize the whole hippocampus and its segments. So binLeftHippoBody.mgz is the binary mask of left hippocampal body. 5) mri-tesselate and mris_smooth the whole hippocampus binary mask to create a surface (lh.surfHippo)
Now that is the reason I would like to get the surface labels for head, body and tail. I would like to build a annot in order to display the colored segments over the whole hippocampus surface. Your last tip was great and now I have vertex numbers at the labels files and mris_label2annot works. It follows the commands I used to process the hippocampal body: mri_vol2surf --src binLeftHippoBody.mgz --out LeftHippoBody_surf.mgh --out_type mgh --hemi lh --regheader suj1 --surf surfHippo mri_cor2label --i LeftHippoBody_surf.mgh --surf suj1 lh surfHippo --id 1 --l lh.HippoBody.label
I put the --surf parameter pointing to lh.surfHippo because, if not, it would use lh.white (default). As I said it works but the results are not visually correct (see attached file). The surface loads on freeview with no problem but if I try to load the label representing the body or the annot with the 3 segments they do not appear. It seems only a small part of the vertices appears in blue. I also get the following output at the terminal window I used to start freeview:
MRISreadAnnotationIntoArray: vertex index out of range: 122882 i=00000000, in_array_size=11627 annot file: ../label/lh.Hippo.annot MRISreadAnnotationIntoArray: vertex index out of range: 122883 i=00000000, in_array_size=11627 annot file: ../label/lh.Hippo.annot MRISreadAnnotationIntoArray: vertex index out of range: 122884 i=00000000, in_array_size=11627 annot file: ../label/lh.Hippo.annot MRISreadAnnotationIntoArray: vertex index out of range: 122885 i=00000000, in_array_size=11627 annot file: ../label/lh.Hippo.annot reading colortable from annotation file... colortable with 4 entries read (originally ../label/Hippo.ctab) colortable with 4 entries read (originally ../label/Hippo.ctab) =00000000, in_array_size=11627
Since the posterior*.mgz files are 0.5 x 0.5 x 0.5 mm I also tried to use mri_convert --vs 1 1 1, but it did not worked too. I guess, or at least, I hope I am closer the image I want but I guess some more steps are necessary. Thank you for any help. Marcos
Em Qui, 2013-10-17 às 22:19 -0400, Douglas Greve escreveu:
Is binLeftHippoBody.mgz a volume label or a surface label? If a volume label, map it onto the surface with mri_vol2surf, the run mri_cor2label specifying --surf
doug
On 10/17/13 5:00 PM, Marcos Martins da Silva wrote:
Hi, Doug Thank you for your answer.
I am trying cor2label as you suggested. First of all I am afraid to say that website documentation and help from the own command are a bit different so I got a little confused. But the following command worked: mri_cor2label --i binLeftHippoBody.mgz --id 1 --l 2.leftBody
Using freeview I could load the hippocampus volume and 2.leftBody as a ROI. I attached a screenshot that also included 1.leftHead and 3.leftTail, generated in the same way. When I tried to concatenate the 3 labels into an annot file I got an error:
mris_label2annot --s bert --h lh --ctab HippoColorLUT.txt --l 1.leftHead.label --l 2.leftBody.label --l 3.leftTail.label --a lefthippo Loading /home/marcos/freesurfer/subjects/bert/surf/lh.orig 1 16711680 leftHead ERROR: 1.leftHead.label, n=0, vertex -1 out of range
When I checked label file generated by mri_cor2label the first collumn (vertex number) contains only -1 as value. It seems that when you use mri_cor2label it does not preserve or even recover the vertex number. It also seems I need the correct vertex number in label file to use mris_label2annot Just to rule out a problem with the hippocampal subfield files I tried the example command (extracted from command help): mri_cor2label --i aseg.mgz --id 12 --l left-putamen.label This label also shows only -1 as vertex number.
Could you please explain me what do I need to do to get the vertex numbers in the label file as output of mri_cor2label?
Cheers, Marcos
Em Qua, 2013-10-16 às 20:34 -0400, Douglas Greve escreveu:
I think you need to use mri_cor2label (not very well named:) doug
On 10/16/13 4:24 PM, Marcos Martins da Silva wrote:
Hi, Freesurfers. I need to create some labels from binary masks. Sometime ago I read a post (https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2013-October/033783.h... ) and, unless I am wrong, it seemed to me that mri_label2vol could be the tool to get it. If so, could you please explain how? I read documentation on wiki and help from the command itself and could not see how to accomplish that. I could only find how to create a volume from a label. What I need to do is to get a mask like the binLeftHippoHead.mgz (attached) and create a label. Assuming it is possible, I could also make labels for Hippocampal body and head, merge the 3 labels into an annot file. This way i can use Freeview to load the whole hippocampal surface and discriminate the 3 segments by colors with the annot file. Thanks in advance for any help. Cheers, Marcos.
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.
Can you load it properly in tksurfer?
On 10/23/2013 12:44 AM, Marcos Martins da Silva wrote:
Hi, Doug Sorry for this late feedback. Just so you can understand what is binLeftHippoBody.mgz I will explain its origin.
- recon-all --hippo-subfields
- mri_concat the posterior*.mgz to get the whole hippocampus
- a custom octave routine to segment the whole hippocampus into head,
body and tail. This routine preserves the probability values of the original posterior*.mgz 4) mri_binarize the whole hippocampus and its segments. So binLeftHippoBody.mgz is the binary mask of left hippocampal body. 5) mri-tesselate and mris_smooth the whole hippocampus binary mask to create a surface (lh.surfHippo)
Now that is the reason I would like to get the surface labels for head, body and tail. I would like to build a annot in order to display the colored segments over the whole hippocampus surface. Your last tip was great and now I have vertex numbers at the labels files and mris_label2annot works. It follows the commands I used to process the hippocampal body: mri_vol2surf --src binLeftHippoBody.mgz --out LeftHippoBody_surf.mgh --out_type mgh --hemi lh --regheader suj1 --surf surfHippo mri_cor2label --i LeftHippoBody_surf.mgh --surf suj1 lh surfHippo --id 1 --l lh.HippoBody.label
I put the --surf parameter pointing to lh.surfHippo because, if not, it would use lh.white (default). As I said it works but the results are not visually correct (see attached file). The surface loads on freeview with no problem but if I try to load the label representing the body or the annot with the 3 segments they do not appear. It seems only a small part of the vertices appears in blue. I also get the following output at the terminal window I used to start freeview:
MRISreadAnnotationIntoArray: vertex index out of range: 122882 i=00000000, in_array_size=11627 annot file: ../label/lh.Hippo.annot MRISreadAnnotationIntoArray: vertex index out of range: 122883 i=00000000, in_array_size=11627 annot file: ../label/lh.Hippo.annot MRISreadAnnotationIntoArray: vertex index out of range: 122884 i=00000000, in_array_size=11627 annot file: ../label/lh.Hippo.annot MRISreadAnnotationIntoArray: vertex index out of range: 122885 i=00000000, in_array_size=11627 annot file: ../label/lh.Hippo.annot reading colortable from annotation file... colortable with 4 entries read (originally ../label/Hippo.ctab) colortable with 4 entries read (originally ../label/Hippo.ctab) =00000000, in_array_size=11627
Since the posterior*.mgz files are 0.5 x 0.5 x 0.5 mm I also tried to use mri_convert --vs 1 1 1, but it did not worked too. I guess, or at least, I hope I am closer the image I want but I guess some more steps are necessary. Thank you for any help. Marcos
Em Qui, 2013-10-17 às 22:19 -0400, Douglas Greve escreveu:
Is *binLeftHippoBody.mgz a volume label or a surface label? If a volume label, map it onto the surface with mri_vol2surf, the run mri_cor2label *specifying --surf
doug
On 10/17/13 5:00 PM, Marcos Martins da Silva wrote:
Hi, Doug Thank you for your answer.
I am trying cor2label as you suggested. First of all I am afraid to say that website documentation and help from the own command are a bit different so I got a little confused. But the following command worked: *mri_cor2label --i binLeftHippoBody.mgz --id 1 --l 2.leftBody*
Using freeview I could load the hippocampus volume and 2.leftBody as a ROI. I attached a screenshot that also included 1.leftHead and 3.leftTail, generated in the same way. When I tried to concatenate the 3 labels into an annot file I got an error:
*mris_label2annot --s bert --h lh --ctab HippoColorLUT.txt --l 1.leftHead.label --l 2.leftBody.label --l 3.leftTail.label --a lefthippo* *Loading /home/marcos/freesurfer/subjects/bert/surf/lh.orig* *1 16711680 leftHead* *ERROR: 1.leftHead.label, n=0, vertex -1 out of range*
When I checked label file generated by mri_cor2label the first collumn (vertex number) contains only *-1* as value. It seems that when you use mri_cor2label it does not preserve or even recover the vertex number. It also seems I need the correct vertex number in label file to use mris_label2annot Just to rule out a problem with the hippocampal subfield files I tried the example command (extracted from command help): mri_cor2label --i aseg.mgz --id 12 --l left-putamen.label This label also shows only -1 as vertex number.
Could you please explain me what do I need to do to get the vertex numbers in the label file as output of mri_cor2label?
Cheers, Marcos
Em Qua, 2013-10-16 às 20:34 -0400, Douglas Greve escreveu:
I think you need to use mri_cor2label (not very well named:) doug
On 10/16/13 4:24 PM, Marcos Martins da Silva wrote:
Hi, Freesurfers. I need to create some labels from binary masks. Sometime ago I read a post (https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2013-October/033783.h... ) and, unless I am wrong, it seemed to me that mri_label2vol could be the tool to get it. If so, could you please explain how? I read documentation on wiki and help from the command itself and could not see how to accomplish that. I could only find how to create a volume from a label. What I need to do is to get a mask like the binLeftHippoHead.mgz (attached) and create a label. Assuming it is possible, I could also make labels for Hippocampal body and head, merge the 3 labels into an annot file. This way i can use Freeview to load the whole hippocampal surface and discriminate the 3 segments by colors with the annot file. Thanks in advance for any help. Cheers, Marcos.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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@nmr.mgh.harvard.edu
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Douglas Greve -
Douglas N Greve
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Marcos Martins da Silva