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nipy / mindboggle

Automated anatomical brain label/shape analysis software (+ website)
http://mindboggle.info
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datasets update #206

Open tanjia123456 opened 3 years ago

tanjia123456 commented 3 years ago

Hello, I'm sorry to have come to disturb you again The six files (twins-2, mmrr-3t7t, hln-12-2, oasis-20-1) mentioned to you in mindboggle dataset have been damaged. Would you mind sending me the intact files? My email address: 1248742467@qq.com

sgiavasis commented 3 years ago

Hi @tanjia123456,

I can try to help you with this issue, but I may need some more info from you before I contact the team that originally curated/labelled the dataset.

I assume this is a continuation of this thread: https://github.com/nipy/mindboggle/issues/202

Hope to hear from you soon.

Best, Steve

tanjia123456 commented 3 years ago

Hello, For the first question, I used the mri_surf2surf command to register, specifically:  mri_surf2surf --srcsubject OASIS-TRT-20--1 --trgsubject fsaverage5 --hemi lh --sval-annot /home/tj/application/freesurfer/subjects/OASIS-TRT-20-1/label/lh.labels.DKT31.manual.annot  --tval   /home/tj/application/freesurfer/subjects/min_template/OASIS-TRT-20-1-target/lh.labels.DKT31.manual.annot.

For the second question, I guess it's because the number of vertices is inconsistent, display surface can't match. Specific error information: (base) @.***:~/Freesurfer/freesurfer/subjects/autoseg/Users/arno.klein/Data/Mindboggle101/subjects$ mri_surf2surf --srcsubject /autoseg/HLN-12-2 --sval area --src_type curv --trgsubject fsaverage5 --trgsurfval /home/lxw/Freesurfer/freesurfer/subjects/autoseg/HLN-12-2-template/area --trg_type curv --hemi lh  $Id: mri_surf2surf.c,v 1.103 2015/11/05 22:07:33 greve Exp $

setenv SUBJECTS_DIR /home/lxw/Freesurfer/freesurfer/subjects cd /home/lxw/Freesurfer/freesurfer/subjects/autoseg/Users/arno.klein/Data/Mindboggle101/subjects mri_surf2surf --srcsubject /autoseg/HLN-12-2 --sval area --src_type curv --trgsubject fsaverage5 --trgsurfval /home/lxw/Freesurfer/freesurfer/subjects/autoseg/HLN-12-2-template/area --trg_type curv --hemi lh 

sysname  Linux hostname acer machine  x86_64 user     lxw srcsubject = /autoseg/HLN-12-2 srcval     = area srctype    = curv trgsubject = fsaverage5 trgval     = /home/lxw/Freesurfer/freesurfer/subjects/autoseg/HLN-12-2-template/area trgtype    = curv srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi    = lh trghemi    = lh frame      = 0 fwhm-in    = 0 fwhm-out   = 0 label-src  = (null) label-trg  = (null) OKToRevFaceOrder  = 1 UseDualHemi = 0 Reading source surface reg /home/lxw/Freesurfer/freesurfer/subjects//autoseg/HLN-12-2/surf/lh.sphere.reg

Loading source data Reading curvature file /home/lxw/Freesurfer/freesurfer/subjects//autoseg/HLN-12-2/surf/lh.area ERROR: number of vertices in /home/lxw/Freesurfer/freesurfer/subjects//autoseg/HLN-12-2/surf/lh.area does not match surface (148208,146833) ERROR: reading curvature file

For the third question, yes, the feature file is missing. After recon all, I directly mapped the generated feature files into the fsaverage5 space, and then gradually mapped your.manual.annot files into the fsaverage5 space as well. Is this operation feasible?

------------------ 原始邮件 ------------------ 发件人: "nipy/mindboggle" @.>; 发送时间: 2021年4月2日(星期五) 凌晨5:35 @.>; @.**@.>; 主题: Re: [nipy/mindboggle] datasets update (#206)

Hi @tanjia123456,

I can try to help you with this issue, but I may need some more info from you before I contact the team that originally curated/labelled the dataset.

I assume this is a continuation of this thread: #202

How did you perform the mapping of lh.labels.DKT25.manual.annot to the fsaverage5 template space? I'd like to try to reproduce the memory allocation error you reported.

Can you post a snapshot of the mismatch of HLN-12-1 lh.area lh.volume lh.jac_white ?

The rest of the issues were simply missing files that were expected, correct?

Hope to hear from you soon.

Best, Steve

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