Hi Freesurfer Developers,
I'm trying to map the vertices of caudal middle frontal in one subject into the space of another subject by using mri_label2label. And I used the method mentioned in this https://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/2015-November/042298.h...
We are using freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0, and I noticed the mri_label2label in v5.1 has the bug of getting holes in the mapped labels( http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg42600.html). So I am using the /usr/local/freesurfer/freesurfer_dev/bin/mri_label2label.bin from freesurfer-x86_64-unknown-linux-gnu-dev5-20160513.
For example, we have source Labels(aparc-lh-003_5thCol.label), which are all in SurfaceRAS coordinates: #!ascii label , from subject FreeSurfer vox2ras=TkReg 8 104996 -35.679 16.281 25.156 1 104997 -36.480 16.439 25.362 2 104998 -37.443 16.702 25.369 3 105705 -41.554 16.840 28.930 4 105716 -40.445 17.153 28.046 5 105720 -39.570 17.200 26.959 6 131017 -29.315 12.915 45.422 7 131030 -31.304 12.514 46.455 8
By running this: /usr/local/freesurfer/freesurfer_dev/bin/mri_label2label.bin --srclabel aparc-lh-003_5thCol.label --srcsubject FreeSurfer --trglabel aparc-lh-003_5thCol_Reg2MNI.label --trgsubject FreeSurferMNI152 --regmethod surface --hemi lh
We got mapped Labels(aparc-lh-003_5thCol_Reg2MNI.label), which are all in SurfaceRAS coordinates: 119096 -39.670 37.222 12.833 3.0000000000 117433 -44.642 35.253 14.575 4.0000000000 118250 -43.206 35.844 14.273 5.0000000000 119091 -42.114 36.692 14.044 6.0000000000 120517 -26.436 38.614 21.780 7.0000000000 121236 -25.959 39.757 24.739 8.0000000000 1321 -22.346 -82.436 -9.530 0.0000000000 121253 -26.213 39.504 23.711 8.0000000000
But the mapped labels I got from the mri_label2label in v5.1 and that from using mri_label2label.bin in dev are quite similar to each other when applying the method to around 3500 labels.
So I am wondering if the bug of getting holes was fixed by providing morphological operations in the updated mri_label2label like close operation. If it is true, I am confused about the mapped labels from mri_label2label with close operation.
For example, with the same source labels above, I ran
/usr/local/freesurfer/freesurfer_dev/bin/mri_label2label.bin --srclabel aparc-lh-003_5thCol.label --srcsubject FreeSurfer --trglabel aparc-lh-003_5thCol_Reg2MNI_close2.label --trgsubject FreeSurferMNI152 --regmethod surface --hemi lh --close 2
And we got mapped Labels(aparc-lh-003_5thCol_Reg2MNI_close2.label): 119096 -39.670 37.222 12.833 3.0000000000 117433 -44.642 35.253 14.575 4.0000000000 118250 -43.206 35.844 14.273 5.0000000000 119091 -42.114 36.692 14.044 6.0000000000 120517 -26.436 38.614 21.780 7.0000000000 121236 -25.959 39.757 24.739 8.0000000000 1321 -22.346 -82.436 -9.530 0.0000000000 121253 -26.213 39.504 23.711 8.0000000000 1045 -1.690 -91.572 -40.145 0.0000000000 118251 -18.413 75.394 63.061 0.0000000000 118258 -21.026 75.715 61.847 0.0000000000 119092 -19.797 75.786 62.165 0.0000000000
The problem is that four additional labels 1045, 118251, 118258 and 119092 are not actually on the white matter surface but seem to be right on a sphere(ex. label 1045, 1.690^2+91.572^2+40.145^2=100^2). But I checked all other mapped labels like 119096, they are on the WM surface in the SurfaceRAS coordinates.
I am using CentOS release 6.9.
Thanks!
All the Best, Hengda
Is it just those few vertices that are appear to be on the sphere? Can you send me the terminal output from the mri_label2label with the --close operation?
On 05/10/2017 12:16 PM, Hengda He wrote:
Hi Freesurfer Developers,
I'm trying to map the vertices of caudal middle frontal in one subject into the space of another subject by using mri_label2label. And I used the method mentioned in this https://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/2015-November/042298.h...
We are using freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0, and I noticed the mri_label2label in v5.1 has the bug of getting holes in the mapped labels(http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg42600.html). So I am using the /usr/local/freesurfer/freesurfer_dev/bin/mri_label2label.bin from freesurfer-x86_64-unknown-linux-gnu-dev5-20160513.
For example, we have source Labels(aparc-lh-003_5thCol.label), which are all in SurfaceRAS coordinates: #!ascii label , from subject FreeSurfer vox2ras=TkReg 8 104996 -35.679 16.281 25.156 1 104997 -36.480 16.439 25.362 2 104998 -37.443 16.702 25.369 3 105705 -41.554 16.840 28.930 4 105716 -40.445 17.153 28.046 5 105720 -39.570 17.200 26.959 6 131017 -29.315 12.915 45.422 7 131030 -31.304 12.514 46.455 8
By running this: /usr/local/freesurfer/freesurfer_dev/bin/mri_label2label.bin --srclabel aparc-lh-003_5thCol.label --srcsubject FreeSurfer --trglabel aparc-lh-003_5thCol_Reg2MNI.label --trgsubject FreeSurferMNI152 --regmethod surface --hemi lh
We got mapped Labels(aparc-lh-003_5thCol_Reg2MNI.label), which are all in SurfaceRAS coordinates: 119096 -39.670 37.222 12.833 3.0000000000 117433 -44.642 35.253 14.575 4.0000000000 118250 -43.206 35.844 14.273 5.0000000000 119091 -42.114 36.692 14.044 6.0000000000 120517 -26.436 38.614 21.780 7.0000000000 121236 -25.959 39.757 24.739 8.0000000000 1321 -22.346 -82.436 -9.530 0.0000000000 121253 -26.213 39.504 23.711 8.0000000000
But the mapped labels I got from the mri_label2label in v5.1 and that from using mri_label2label.bin in dev are quite similar to each other when applying the method to around 3500 labels.
So I am wondering if the bug of getting holes was fixed by providing morphological operations in the updated mri_label2label like close operation. If it is true, I am confused about the mapped labels from mri_label2label with close operation.
For example, with the same source labels above, I ran
/usr/local/freesurfer/freesurfer_dev/bin/mri_label2label.bin --srclabel aparc-lh-003_5thCol.label --srcsubject FreeSurfer --trglabel aparc-lh-003_5thCol_Reg2MNI_close2.label --trgsubject FreeSurferMNI152 --regmethod surface --hemi lh --close 2
And we got mapped Labels(aparc-lh-003_5thCol_Reg2MNI_close2.label): 119096 -39.670 37.222 12.833 3.0000000000 117433 -44.642 35.253 14.575 4.0000000000 118250 -43.206 35.844 14.273 5.0000000000 119091 -42.114 36.692 14.044 6.0000000000 120517 -26.436 38.614 21.780 7.0000000000 121236 -25.959 39.757 24.739 8.0000000000 1321 -22.346 -82.436 -9.530 0.0000000000 121253 -26.213 39.504 23.711 8.0000000000 1045 -1.690 -91.572 -40.145 0.0000000000 118251 -18.413 75.394 63.061 0.0000000000 118258 -21.026 75.715 61.847 0.0000000000 119092 -19.797 75.786 62.165 0.0000000000
The problem is that four additional labels 1045, 118251, 118258 and 119092 are not actually on the white matter surface but seem to be right on a sphere(ex. label 1045, 1.690^2+91.572^2+40.145^2=100^2). But I checked all other mapped labels like 119096, they are on the WM surface in the SurfaceRAS coordinates.
I am using CentOS release 6.9.
Thanks!
All the Best, Hengda
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Douglas N Greve -
Hengda He