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Hi Bruce, I drawed a 3D ROI on the original image using freeview,and saved it as an label file. Then I wanted to sample it to my subject and to found the closest surface vertices so that I can extract the cortical thickness of ROI. I used the command line: mri_label2label --srclabel 4gt.label --s PT1_4 --trglabel 4reg.on-pial.label --hemi rh --paint 30 pial --trgsurf pial. But it reported error: Line 3:4445 Segmentation fault(core dumped), mri_label2label.bin "$@". Can you tell me how to solve this problem?Is it wrong to use the mri_label2label? Thanks. Best wishes， Kan Deng
Can you send the full terminal output?
On 3/12/19 10:36 AM, 310913949 wrote:
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Hi Bruce, I drawed a 3D ROI on the original image using freeview,and saved it as an label file. Then I wanted to sample it to my subject and to found the closest surface vertices so that I can extract the cortical thickness of ROI. I used the command line: mri_label2label --srclabel 4gt.label --s PT1_4 --trglabel 4reg.on-pial.label --hemi rh --paint 30 pial --trgsurf pial. But it reported error: Line 3:4445 Segmentation fault(core dumped), mri_label2label.bin "$@". Can you tell me how to solve this problem?Is it wrong to use the mri_label2label? Thanks. Best wishes， Kan Deng
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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Sure.This is the full terminal output:
root@zourushi-All-Series:/usr/local/freesurfer/subjects/PT1_4# mri_label2label --srclabel label/4gt.label --s PT1_4 --trglabel 4gtreg.label --hemi rh --paint 30 pial --trgsurf pial
Could not set locale No such file or directory Could not set locale srclabel = label/4gt.label srcsubject = PT1_4 trgsubject = PT1_4 trglabel = 4gtreg.label regmethod = surface
srchemi = rh trghemi = rh trgsurface = pial srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 1 PaintMax 30.000000
SUBJECTS_DIR /usr/local/freesurfer/subjects FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 59455 points in source label. Starting surface-based mapping Reading source registration /usr/local/freesurfer/subjects/PT1_4/surf/rh.sphere.reg 59455 unassigned vertices in label - building spatial LUT... assigning vertex numbers to label... /usr/local/freesurfer/bin/mri_label2label: line 3: 4446 Segmentation fault (core dumped) mri_label2label.bin "$@"
------------------ 原始邮件 ------------------ 发件人: "Greve, Douglas N.,Ph.D."DGREVE@mgh.harvard.edu; 发送时间: 2019年3月13日(星期三) 凌晨0:06 收件人: "freesurfer@nmr.mgh.harvard.edu"freesurfer@nmr.mgh.harvard.edu;
主题: Re: [Freesurfer] Error with mri_label2label(Segmentation fault(coredumped))
Can you send the full terminal output?
On 3/12/19 10:36 AM, 310913949 wrote:
External Email - Use Caution Hi Bruce, I drawed a 3D ROI on the original image using freeview,and saved it as an label file. Then I wanted to sample it to my subject and to found the closest surface vertices so that I can extract the cortical thickness of ROI. I used the command line: mri_label2label --srclabel 4gt.label --s PT1_4 --trglabel 4reg.on-pial.label --hemi rh --paint 30 pial --trgsurf pial. But it reported error: Line 3:4445 Segmentation fault(core dumped), mri_label2label.bin "$@". Can you tell me how to solve this problem?Is it wrong to use the mri_label2label? Thanks. Best wishes， Kan Deng
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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Hi,I think I need to send you the information of my ROI,i am not sure whether it is something wrong. This is the part of the 4gt.label I drew.And the attachment is the picture of the 4gt.label. Thanks again #!ascii label , from subject vox2ras=scanner 59455 -1 43.255 58.553 -24.301 0.0000000000 -1 43.255 58.553 -24.301 0.0000000000 -1 42.058 58.629 -24.306 0.0000000000 -1 40.860 58.704 -24.310 0.0000000000 -1 40.860 58.704 -24.310 0.0000000000 -1 40.799 57.729 -24.310 0.0000000000 -1 40.799 57.729 -24.310 0.0000000000 -1 39.601 57.805 -24.314 0.0000000000 -1 39.601 57.805 -24.314 0.0000000000 -1 38.404 57.880 -24.318 0.0000000000 -1 38.404 57.880 -24.318 0.0000000000 -1 37.206 57.955 -24.322 0.0000000000 -1 37.206 57.955 -24.322 0.0000000000 -1 35.947 57.056 -24.326 0.0000000000 -1 35.947 57.056 -24.326 0.0000000000 -1 34.749 57.131 -24.330 0.0000000000 -1 34.749 57.131 -24.330 0.0000000000 -1 33.552 57.207 -24.334 0.0000000000 -1 33.552 57.207 -24.334 0.0000000000 -1 32.293 56.307 -24.338 0.0000000000 -1 32.293 56.307 -24.338 0.0000000000 -1 32.293 56.307 -24.338 0.0000000000 -1 32.232 55.333 -24.338 0.0000000000 -1 32.232 55.333 -24.338 0.0000000000 -1 31.034 55.408 -24.342 0.0000000000 -1 29.836 55.483 -24.346 0.0000000000 -1 29.836 55.483 -24.346 0.0000000000 -1 29.836 55.483 -24.346 0.0000000000 -1 28.639 55.558 -24.350 0.0000000000 -1 28.639 55.558 -24.350 0.0000000000 -1 28.577 54.584 -24.350 0.0000000000 -1 27.318 53.685 -24.354 0.0000000000 -1 27.318 53.685 -24.354 0.0000000000 -1 27.257 52.710 -24.354 0.0000000000 -1 27.257 52.710 -24.354 0.0000000000 -1 27.257 52.710 -24.354 0.0000000000 -1 27.196 51.735 -24.354 0.0000000000 -1 27.196 51.735 -24.354 0.0000000000 -1 27.135 50.761 -24.354 0.0000000000 -1 27.135 50.761 -24.354 0.0000000000
------------------ 原始邮件 ------------------ 发件人: "邓刊"310913949@qq.com; 发送时间: 2019年3月14日(星期四) 上午10:03 收件人: "Freesurfer support list"freesurfer@nmr.mgh.harvard.edu;
主题: [Freesurfer] 回复： Error with mri_label2label(Segmentation fault(coredumped))
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Sure.This is the full terminal output:
root@zourushi-All-Series:/usr/local/freesurfer/subjects/PT1_4# mri_label2label --srclabel label/4gt.label --s PT1_4 --trglabel 4gtreg.label --hemi rh --paint 30 pial --trgsurf pial
Could not set locale No such file or directory Could not set locale srclabel = label/4gt.label srcsubject = PT1_4 trgsubject = PT1_4 trglabel = 4gtreg.label regmethod = surface
srchemi = rh trghemi = rh trgsurface = pial srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 1 PaintMax 30.000000
SUBJECTS_DIR /usr/local/freesurfer/subjects FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 59455 points in source label. Starting surface-based mapping Reading source registration /usr/local/freesurfer/subjects/PT1_4/surf/rh.sphere.reg 59455 unassigned vertices in label - building spatial LUT... assigning vertex numbers to label... /usr/local/freesurfer/bin/mri_label2label: line 3: 4446 Segmentation fault (core dumped) mri_label2label.bin "$@"
------------------ 原始邮件 ------------------ 发件人: "Greve, Douglas N.,Ph.D."DGREVE@mgh.harvard.edu; 发送时间: 2019年3月13日(星期三) 凌晨0:06 收件人: "freesurfer@nmr.mgh.harvard.edu"freesurfer@nmr.mgh.harvard.edu;
主题: Re: [Freesurfer] Error with mri_label2label(Segmentation fault(coredumped))
Can you send the full terminal output?
On 3/12/19 10:36 AM, 310913949 wrote:
External Email - Use Caution Hi Bruce, I drawed a 3D ROI on the original image using freeview,and saved it as an label file. Then I wanted to sample it to my subject and to found the closest surface vertices so that I can extract the cortical thickness of ROI. I used the command line: mri_label2label --srclabel 4gt.label --s PT1_4 --trglabel 4reg.on-pial.label --hemi rh --paint 30 pial --trgsurf pial. But it reported error: Line 3:4445 Segmentation fault(core dumped), mri_label2label.bin "$@". Can you tell me how to solve this problem?Is it wrong to use the mri_label2label? Thanks. Best wishes， Kan Deng
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
freesurfer@nmr.mgh.harvard.edu
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310913949 -
Greve, Douglas N.,Ph.D.