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Published 20 hours ago • verified publisher icon nipy

runing error

Open tanjia123456 opened this issue 4 years ago • 13 comments

Hello, The first four commands can be run, but the last four will report errors. Do you know where the error is？ recon-all -i t1weighted_brain.MNI152.nii.gz -s bert1 -all recon-all -i t1weighted_brain.nii.gz -s bert2 -all recon-all -i t1weighted.nii.gz -s bert3 -all recon-all -i t1weighted.MNI152.nii.gz -s bert4 -all

recon-all -i labels.DKT31.manual.nii.gz -s bert5 -all recon-all -i labels.DKT31.manual.MNI152.nii.gz -s bert6 -all recon-all -i labels.DKT31.manual+aseg.nii.gz -s bert7 -all recon-all -i labels.DKT31.manual+aseg.MNI152.nii.gz -s bert8 -all

tanjia123456 avatar Dec 22 '20 03:12 tanjia123456

Have you tried to run the mindboggle command from the command line?

binarybottle avatar Dec 22 '20 06:12 binarybottle

No, I just need to process 6 subjects. What does it mean to run the mindbogle command from the command line？

tanjia123456 avatar Dec 22 '20 06:12 tanjia123456

Please read the documentation on the mindboggle.info software site.

binarybottle avatar Dec 22 '20 06:12 binarybottle

I have read it, but i haven't found it. could you please tell me? I just want to get lh.labels.DKT31.manual.annot file

tanjia123456 avatar Dec 22 '20 12:12 tanjia123456

Wait, I am confused. Please tell me exactly what you want to do here. Do you want to convert manually labeled Mindboggle-101 surface labels to FreeSurfer .annot files, since you specify "manual" files in the commands above, or do you want to use the mindboggle software to automatically label your own brain images?

binarybottle avatar Dec 22 '20 23:12 binarybottle

Yes, I want to convert manually labeled Mindboggle-101 surface labels to FreeSurfer .annot files. I found out that the MMRR-3T7T-1 subjects lacked the lh.labels.DKT31.manual.annot file, so I wanted to use labels.DKT31.manual.nii.gz or other files to get the above file.

tanjia123456 avatar Dec 23 '20 01:12 tanjia123456

I was going to convert lh.labels.DKT31.manual.vtk to lh.labels.DKT31.manual.annot, but I don’t know how to convert it.

tanjia123456 avatar Dec 23 '20 01:12 tanjia123456

I know how to convert .annot files to .vtk files, and FS .label to .annot files, but I don't know how to convert .vtk to .annot files. I tried to find out 8 years ago but didn't receive a response: https://www.mail-archive.com/[email protected]/msg24431.html

binarybottle avatar Dec 23 '20 04:12 binarybottle

I see your questions in freesurfer maillist，So how do you make your lh.manalDTK31.annot file？maybe this will be a solution. ------------------ 原始邮件 ------------------ 发件人: "Arno&nbsp;Klein"<[email protected]> 发送时间: 2020年12月23日(星期三) 中午12:56 收件人: "nipy/mindboggle"<[email protected]>; 抄送: "tanjia123456"<[email protected]>;"Author"<[email protected]>; 主题: Re: [nipy/mindboggle] runing error (#204)

tanjia123456 avatar Dec 23 '20 05:12 tanjia123456

I hired the company Neuromorphometrics to manually edit FreeSurfer surface labels.

binarybottle avatar Dec 23 '20 05:12 binarybottle

Then I want to know, how long do you plan to add the missing label files in the data set? I am also doing cortex segmentation, thank you very much for the public data set.

tanjia123456 avatar Dec 23 '20 05:12 tanjia123456

I'm sorry, but I don't understand your question. Please clarify.

binarybottle avatar Dec 24 '20 05:12 binarybottle

I found the freesurfer_output/MMRR-3T7T-1 missing the lh.manalDTK31.annot file, I don’t know how long you can make up.

tanjia123456 avatar Dec 24 '20 06:12 tanjia123456