Hi Bruce, Thanks Bruce. When I run this command:mri_surf2vol --surfval rh.36sb.10.mgh --hemi rh --fillribbon --subject fsaverage --template /mnt/sdb1/psylab16/BACKUP/freesurfer/freesurfer/subjects/fsaverage/mri/orig --o test.nii; it echo this error message: ==================================== gdiagno = -1 Using identity matrix for registration Overriding reg subject fsaverage with fsaverage corRead(): can't open file ../fsaverage/mri/orig/COR-.info mri_surf2vol ERROR: reading ../fsaverage/mri/orig header ================================================ I have no idea about that. Would you please help me? All the best. Rujing Zha 2014-03-15
charujing123
发件人：Bruce Fischl fischl@nmr.mgh.harvard.edu 发送时间：2014-03-15 21:41 主题：Re: [Freesurfer] Fw: Re: convert sig.mgh into *.nii 收件人："charujing123"charujing123@163.com 抄送："freesurfer@nmr.mgh.harvard.edu"freesurfer@nmr.mgh.harvard.edu
Hi Rujing
1. whatever subject's surface the data is mapped to (probably fsaverage in this case, but I haven't been following the conversation).
2. mri_or should do the trick:
mri_or left_hemi.mgz right_hemi.mgz both_hemis.mgz
cheers Bruce
On Sat, 15 Mar 2014, charujing123 wrote:
Hi Bruce and other FS experts, Thanks Bruce. 1,How can I adding them? 2,--identity option need to applied one subject's name. Which subject should I supply? or can it be anyone? Thanks again. All the best. Rujing Zha
2014-03-15
charujing123
发件人：Bruce Fischl fischl@nmr.mgh.harvard.edu 发送时间：2014-03-15 21:30 主题：Re: [Freesurfer] Fw: Re: convert sig.mgh into *.nii 收件人："charujing123"charujing123@163.com 抄送："freesurfer@nmr.mgh.harvard.edu"freesurfer@nmr.mgh.harvard.edu
Hi Rujing
- No, you can always combine the hemispheres into a volume later (e.g. by
?? ?
adding them).
- Try --identity <subject name>
cheers Bruce
On Sat, 15 Mar 2014, charujing123 wrote:
Hi doug and other FS experts, Thanks doug. I have 2 new questions: 1,What you told me is generate a hemisphere. So there is only one hemisph
ere
I can see in the AFNI? 2,After typing this code: "mri_surf2vol --surfval rh.36sb.10.mgh --hemi rh --fillribbon --subject fsaverage --template/mnt/sdb1/psylab16/BACKUP/freesurfer/freesurfer/subje
cts/fsaverage/mri/orig
--o test.nii." the command window echo this error message: "gdiagno = -1 A volume registration file must be supplied" Thanks. All the best. Rujing Zha
2014-03-13
charujing123
发件人：Douglas Greve greve@nmr.mgh.harvard.edu 发送时间：2014-03-12 23:00 主题：Re: [Freesurfer] convert sig.mgh into *.nii 收件人："freesurfer"freesurfer@nmr.mgh.harvard.edu 抄送：
Use mri_surf2vol to do this. Soemthing like
mri_surf2vol --surfval rh.36...mgh --hemi rh --fillribbon --subject fsaverage --template $SUBJECTS_DIR/fsaverage/mri/orig --o yourvolume.nii
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doug
On 3/11/14 10:10 PM, charujing123 wrote: Hi Bruce, Thanks Bruce. I knew that code, but I have no idea to deal with my problem after reading the help. Would you please tell me how to use mri_surf2vol after I describe my problem details? I have a file named rh.36sb.score.thickness.10.mgh which is created from the "mris_preproc --fsgd $FSGDFILE --target fsaverage --hemi $style --meas thickness --out ${style}.${FSGDFILE%_*}.00.mgh". I want to convert this file into nii format volume-based, so I can read it by AFNI. Thanks. All the best. Rujing Zha
2014-03-12
charujing123
发件人：Bruce Fischl fischl@nmr.mgh.harvard.edu 发送时间：2014-03-12 09:44 主题：Re: [Freesurfer] convert sig.mgh into *.nii 收件人："charujing123"charujing123@163.com 抄送："freesurfer@nmr.mgh.harvard.edu"freesurfer@nmr.mgh.harvard.edu
try mri_surf2vol with the output volume named .nii
cheers Bruce On Wed, 12 Mar 2014, charujing123 wrote:
Hi doug, Thanks doug. I try this code, but it represent two dimension for each subject data w
he
n
loaded in the AFNI. Is there any code to volume-based conversion from m
gh
to
nii? All the best. Rujing Zha
2014-03-12
__
charujing123
__
发件 人：Douglas N Greve greve@nmr.mgh.harvard.edu 发送时间：2014-03-12 00:16 主题：Re: [Freesurfer] convert sig.mgh into *.nii 收件 人："freesurfer"freesurfer@nmr.mgh.harvard.edu 抄送：
mri_convert file.mgh file.nii
doug
On 03/11/2014 05:55 AM, charujing123 wrote:
Hi FS experts, I want to extract time course from sig.mgh. But the *.y.ocn.mgh canno
t ?? ?
be created. So I want to view it in other formats, such as nii. So ho
w ?? ?
to convert it into nii format. Thanks. All the best. Rujing Zha 2014-03-11
--
?? ?> charujing123
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