Hi doug, Thanks doug. I cannot see my last e-mail file in the https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/index.html#35468. However I can receive it in my box, and none reply it. Maybe pitfalls in the network so that you cannot read my last e-mail file. So I send my last e-mail file to the freesurfer list again. Also I send to you. Looking forward to your new reply. Thanks again. All the best. Rujing Zha
2014-04-26
charujing123
发件人："charujing123"charujing123@163.com 发送时间：2014-04-25 19:22 主题：Re: [Freesurfer] convert volume-based mni152 space into fsaverage surface space(MNI305) 收件人："Freesurfer support list"freesurfer@nmr.mgh.harvard.edu 抄送：
Hi FS experts and users, Is there anyone can help me? Any reply will be highly appreaciated. Thanks. All the best. Rujing Zha
2014-04-25
charujing123
发件人："charujing123"charujing123@163.com 发送时间：2014-04-24 09:43 主题：Re: [Freesurfer] convert volume-based mni152 space into fsaverage surface space(MNI305) 收件人："Freesurfer support list"freesurfer@nmr.mgh.harvard.edu 抄送：
Hi doug, Thanks doug. I used this DAT file,and the command termination without any problem.However the mask file dosenot overlay the rIPL area but frontal area when the mask file and fsaverage file were loaded in the freeview. Here are my scripts for creating the mask. mri_vol2surf --hemi rh --reg $FREESURFER_HOME/average/mni152.register.dat --mov ./rIPL.nii --o ./rIPL_mask.mgh --trgsubject fsaverage Source file volume-based mask ROI "rIPL.nii" is in the MNI152 space, and two snapshot can be got in the attachment. Also registrated surface ROI mask rIPL_mask.mgh snapshot can be got in the attachment. Here is its output in the command window. ========================================================================================= srcvol = ./rIPL.nii srcreg = /mnt/sdb1/psylab16/BACKUP/freesurfer/freesurfer/average/mni152.register.dat srcregold = 0 srcwarp unspecified surf = white hemi = rh trgsubject = fsaverage surfreg = sphere.reg reshape = 0 interp = nearest float2int = round GetProjMax = 0 INFO: float2int code = 0 INFO: changing type to float Done loading volume WARNING: the voxel resolution in the source volume (2,2,2) differs from that listed in the registration file (1,1,1) Reading surface /mnt/sdb1/psylab16/BACKUP/freesurfer/freesurfer/subjects/fsaverage/surf/rh.white Done reading source surface Mapping Source Volume onto Source Subject Surface 1 0 0 0 using old Done mapping volume to surface Number of source voxels hit = 21146 Writing to ./rIPL_mask.mgh Dim: 163842 1 1 ================================================================================================= Thanks All the best Rujing Zha 2014-04-24
charujing123
发件人：Douglas N Greve greve@nmr.mgh.harvard.edu 发送时间：2014-04-22 23:53 主题：Re: [Freesurfer] convert volume-based mni152 space into fsaverage surface space(MNI305) 收件人："freesurfer"freesurfer@nmr.mgh.harvard.edu 抄送：
Use mri_vol2surf with $FREESURFER_HOME/average/mni152.register.dat On 04/21/2014 10:20 PM, charujing123 wrote:
Hi FS experts and users, I created a mask volume, whose space is in MNI152 space. And I want to convert this volume into surface-based in fsaverage. How can I realize this? Thanks All the best. Rujing Zha 2014-04-22
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 is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Try running
tkmedit fsaverage orig.mgz -reg $FREESURFER_HOME/average/mni152.register.dat -overlay rIPL.nii -fminmax .1 1
to see if they mask lands in the right place. If it does not, then your input data are not in mni152 space
On 04/25/2014 10:38 PM, charujing123 wrote:
Hi doug, Thanks doug. I cannot see my last e-mail file in the https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/index.html#35468. However I can receive it in my box, and none reply it. Maybe pitfalls in the network so that you cannot read my last e-mail file. So I send my last e-mail file to the freesurfer list again. Also I send to you. Looking forward to your new reply. Thanks again. All the best. Rujing Zha 2014-04-26
charujing123
*发件人：*"charujing123"charujing123@163.com *发送时间：*2014-04-25 19:22 *主题：*Re: [Freesurfer] convert volume-based mni152 space into fsaverage surface space(MNI305) *收件人：*"Freesurfer support list"freesurfer@nmr.mgh.harvard.edu *抄送：* Hi FS experts and users, Is there anyone can help me? Any reply will be highly appreaciated. Thanks. All the best. Rujing Zha 2014-04-25
charujing123
*发件人：*"charujing123"charujing123@163.com *发送时间：*2014-04-24 09:43 *主题：*Re: [Freesurfer] convert volume-based mni152 space into fsaverage surface space(MNI305) *收件人：*"Freesurfer support list"freesurfer@nmr.mgh.harvard.edu *抄送：* Hi doug, Thanks doug. I used this DAT file,and the command termination without any problem.However the mask file dosenot overlay the rIPL area but frontal area when the mask file and fsaverage file were loaded in the freeview. Here are my scripts for creating the mask. mri_vol2surf --hemi rh --reg $FREESURFER_HOME/average/mni152.register.dat --mov ./rIPL.nii --o ./rIPL_mask.mgh --trgsubject fsaverage Source file volume-based mask ROI "rIPL.nii" is in the MNI152 space, and two snapshot can be got in the attachment. Also registrated surface ROI mask rIPL_mask.mgh snapshot can be got in the attachment. Here is its output in the command window. ========================================================================================= srcvol = ./rIPL.nii srcreg = /mnt/sdb1/psylab16/BACKUP/freesurfer/freesurfer/average/mni152.register.dat srcregold = 0 srcwarp unspecified surf = white hemi = rh trgsubject = fsaverage surfreg = sphere.reg reshape = 0 interp = nearest float2int = round GetProjMax = 0 INFO: float2int code = 0 INFO: changing type to float Done loading volume WARNING: the voxel resolution in the source volume (2,2,2) differs from that listed in the registration file (1,1,1) Reading surface /mnt/sdb1/psylab16/BACKUP/freesurfer/freesurfer/subjects/fsaverage/surf/rh.white Done reading source surface Mapping Source Volume onto Source Subject Surface 1 0 0 0 using old Done mapping volume to surface Number of source voxels hit = 21146 Writing to ./rIPL_mask.mgh Dim: 163842 1 1 ================================================================================================= Thanks All the best Rujing Zha 2014-04-24
charujing123
*发件人：*Douglas N Greve greve@nmr.mgh.harvard.edu *发送时间：*2014-04-22 23:53 *主题：*Re: [Freesurfer] convert volume-based mni152 space into fsaverage surface space(MNI305) *收件人：*"freesurfer"freesurfer@nmr.mgh.harvard.edu *抄送：* Use mri_vol2surf with $FREESURFER_HOME/average/mni152.register.dat On 04/21/2014 10:20 PM, charujing123 wrote:
Hi FS experts and users, I created a mask volume, whose space is in MNI152 space. And I want to convert this volume into surface-based in fsaverage. How can I realize this? Thanks All the best. Rujing Zha 2014-04-22
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 is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.
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freesurfer@nmr.mgh.harvard.edu
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charujing123 -
Douglas N Greve