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 hemisphere 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/subjects/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
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 when loaded in the AFNI. Is there any code to volume-based conversion from mgh 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 cannot be created. So I want to view it in other formats, such as nii. So how to convert it into nii format. Thanks. All the best. Rujing Zha 2014-03-11
?? ?> charujing123
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it i s addressed. If you believe this e-mail was sent to you in error and the e-ma il contains patient information, please contact the Partners Compliance HelpLi ne at http://www.partners.org/complianceline . If the e-mail was sent to you in e rror but does not contain patient information, please contact the sender and pro perly dispose of the e-mail.
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hi Rujing
1. No, you can always combine the hemispheres into a volume later (e.g. by adding them).
2. 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 hemisphere 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/subjects/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
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 whe
n
loaded in the AFNI. Is there any code to volume-based conversion from mgh
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 cannot
?? ?
> be created. So I want to view it in other formats, such as nii. So how
?? ?
> to convert it into nii format. > Thanks. > All the best. > Rujing Zha > 2014-03-11 > -----------------------------------------------------------------------
- ?? ?> charujing123
> > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer%C2%A0%C2%A0 -- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2%C2%A0%C2%A0 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
?? ?
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer%C2%A0%C2%A0 The information in this e-mail is intended only for the person to whom it
i
s addressed. If you believe this e-mail was sent to you in error and the e-
ma
il contains patient information, please contact the Partners Compliance Help
Li
ne at http://www.partners.org/complianceline%C2%A0.%C2%A0If%C2%A0the%C2%A0e-mail%C...
e
rror but does not contain patient information, please contact the sender and p
ro
perly dispose of the e-mail.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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
1. No, you can always combine the hemispheres into a volume later (e.g. by adding them).
2. 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 hemisphere 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/subjects/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
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 whe
n
loaded in the AFNI. Is there any code to volume-based conversion from mgh
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 cannot
?? ?
be created. So I want to view it in other formats, such as nii. So how
?? ?
to convert it into nii format. Thanks. All the best. Rujing Zha 2014-03-11
?? ?> charujing123
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
?? ?
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it
i
s addressed. If you believe this e-mail was sent to you in error and the e-
ma
il contains patient information, please contact the Partners Compliance Help
Li
ne at http://www.partners.org/complianceline . If the e-mail was sent to you in
e
rror but does not contain patient information, please contact the sender and p
ro
perly dispose of the e-mail.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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 1. No, you can always combine the hemispheres into a volume later (e.g. by
?? ?
adding them). 2. 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
?? ?>
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 > > > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer%C2%A0%C2%A0%C2%... > > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > greve@nmr.mgh.harvard.edu > Phone Number: 617-724-2358 > Fax: 617-726-7422 > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2%C2%A0%C2%A0%C2%A0 > www.nmr.mgh.harvard.edu/facility/filedrop/index.html > Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve
/ ?? ?
> > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer%C2%A0%C2%A0%C2%... > > > The information in this e-mail is intended only for the person to whom
?? ?it
i > s > addressed. If you believe this e-mail was sent to you in error and the
?? ?e-
ma > il > contains patient information, please contact the Partners Compliance He
lp
Li > ne at > http://www.partners.org/complianceline%C2%A0.%C2%A0If%C2%A0the%C2%A0e-mail%C...
?? ?in
e > rror > but does not contain patient information, please contact the sender and
p
ro > perly > dispose of the e-mail. > > > _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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
?? ?>
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
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?? ?> charujing123
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On 03/15/2014 01:33 AM, 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 hemisphere I can see in the AFNI?
You have to run mri_surf2vol for each hemisphere, but you can merge them together. See the --help for surf2vol
2,After typing this code: "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." the command window echo this error message: "gdiagno = -1 A volume registration file must be supplied"
Have you looked at the help? Run mri_surf2vol with --help doug
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
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 when
loaded in the AFNI. Is there any code to volume-based conversion
from mgh 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
cannot
be created. So I want to view it in other formats, such as nii.
So how
to convert it into nii format. Thanks. All the best. Rujing Zha 2014-03-11
?? ?> charujing123
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing:
ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to
whom it i
s addressed. If you believe this e-mail was sent to you in error and
the e-ma
il contains patient information, please contact the Partners
Compliance HelpLi
ne at http://www.partners.org/complianceline . If the e-mail was sent to
you in e
rror but does not contain patient information, please contact the sender
and pro
perly dispose of the e-mail.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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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Bruce Fischl -
charujing123 -
Douglas N Greve