Thank you, doug, I will try xfm!
On Thu, Mar 7, 2013 at 7:03 PM, Douglas N Greve <gr...@nmr.mgh.harvard.edu>wrote: > The xform has to be linear in the xfm format. The m3z cannot be used. > doug > > On 03/07/2013 06:44 PM, Xiaowei Song wrote: > > Thanks for your help. > > > > My command line is > > make_average_subject --out avgGrp139 --subjects `cat > > script/subjects.id <http://subjects.id>` --xform talairach.m3z > > > > > > On Thu, Mar 7, 2013 at 6:15 PM, Bruce Fischl > > <fis...@nmr.mgh.harvard.edu <mailto:fis...@nmr.mgh.harvard.edu>> wrote: > > > > what was your command line? > > > > On Thu, 7 Mar 2013, Xiaowei Song wrote: > > > > Sorry, I did not make it clear. > > In make_average_volume.log, the error message is: > > > > 1/139 1173622 aseg Sat Feb 23 02:26:02 EST 2013 > > mri_vol2vol --mov /data/lis9/fs/x/1173622/mri/aseg.mgz --targ > > /usr/local/freesurfer/average/mni305.cor.mgz --xfm > > /data/lis9/fs/x/1173622/mri/transforms/talairach.m3z --o > > > /data/lis9/fs/x/avgGrp139/tmp/make_average_vol-tmp-55832/seg-1173622.mgh > > --interp nearest > > ERROR: /data/lis9/fs/x/1173622/mri/transforms/talairach.m3z > > does not start > > as 'MNI Transform File'/spin1/users/lis9/fs/dcm.mprage.mgz > > ERROR: mri_vol2vol failed. > > > > > > On Thu, Mar 7, 2013 at 5:49 PM, Bruce Fischl > > <fis...@nmr.mgh.harvard.edu <mailto:fis...@nmr.mgh.harvard.edu>> > > wrote: > > sorry, I don't understand. What was the error? I don't > > see one > > in this email. Can you send us the actual screen output? > > > > cheers > > Bruce > > On Thu, 7 Mar 2013, Xiaowei Song wrote: > > > > This error may come from regio_read_mincxfm function > > in registerio.c.Does > > this mean something wrong in recon-all? > > > > I forgot to mention that FreeSurfer version is > > freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0 > > > > > > On Thu, Mar 7, 2013 at 5:34 PM, Xiaowei Song > > <dawnwei.s...@gmail.com > > <mailto:dawnwei.s...@gmail.com>> wrote: > > Hi all, > > > > Did you encounter the error message talairach.m3z > > does not start as > > 'MNI Transform File' when making average of > > subjects? > > > > I checked all the recon-all.log file and did not > > find error, but when > > running make_average_subject after recon-all, then > > this error shoot. > > > > To repeat the error message, I tried the following > > command which is > > called by make_average_subject and found all my > > subjects shoot this > > error. > > > > mri_vol2vol --mov 1173622/mri/aseg.mgz --targ > > /usr/local/freesurfer/average/mni305.cor.mgz --xfm > > 1173622/mri/transforms/talairach.m3z --o > > /tmp/make_average_vol-tmp-164320_seg-1173622.mgh > > --interp nearest > > > > I found another same question asked before, > > butnoanswer. > > > https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2012-May/0 > > 24 > > 064.html > > > > Any hint or help will be appreciated. Thank you. > > > > -- > > Xiaowei Song > > > > > > > > > > -- > > Xiaowei Song > > > > > > > > > > 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. > > > > > > > > > > -- > > Xiaowei Song > > > > > > > > > > -- > > Xiaowei Song > > > > > > _______________________________________________ > > 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 > gr...@nmr.mgh.harvard.edu > Phone Number: 617-724-2358 > Fax: 617-726-7422 > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > FileDrop: 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 > -- Xiaowei Song
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