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Dear freesurfer experts： I want to know how to register feature maps to an average space (fsaverage6) so that I can get an identical number of vertices(40962) for each hemisphere. Can you tell me what is the command line? I am looking forward to your reply!Thanks.
------------------
邓刊 Kan Deng
E-mail：310913949@qq.com
TEL：13728774014
are you feature maps already on individual subject surfaces? If so, you an use mri_surf2surf with fsaverage6 as the target
cheers Bruce
On Tue, 22 Jan 2019, 310913949 wrote:
External Email - Use Caution
Dear freesurfer experts?? I want to know how to register feature maps to an average space (fsaverage6) so that I can get an identical number of vertices(40962) for each hemisphere. Can you tell me what is the command line? I am looking forward to your reply!Thanks.
???? Kan Deng
E-mail??310913949@qq.com
TEL??13728774014
External Email - Use Caution
Thanks for your reply! Actually, i first use "recon-all -s PT1_13 -i PT1_13.nii -all -qcache -target fsaverage6 " to process the subject, but i think i make some mistakes as i find there are about 110,000 vertex values in the"lh.thickness"file. and I also find that it generates a file named"recon-all.error",the context is as follows:
Linux zhangjianing-Precision-Tower-7910 4.4.0-83-generic #106~14.04.1-Ubuntu SMP Mon Jun 26 18:10:19 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux $Id: recon-all,v 1.601 2017/02/08 21:17:33 greve Exp $ /media/root/533b526f-751c-4a6a-a3da-11856d602f84/usr/local/freesurfer/bin/recon-all PWD /media/root/533b526f-751c-4a6a-a3da-11856d602f84/usr/local/freesurfer/subjects/PT1_1302/surf CMD mris_preproc --s PT1_1302 --hemi lh --meas thickness --target fsaverage6 --out lh.thickness.fsaverage6.mgh" I am not sure whether i misused this command and how to correct that.
Besides,i tried to use these two commands after recon-all, "mris_register -curv surf/lh.sphere $SUBJECTS_DIR/fsaverage6/lh.reg.template.tif surf/lh.sphere.reg.newtemplate" and"mris_preproc --s PT1_13--hemi lh --meas thickness --target $SUBJECTS_DIR/fsaverage6 --out lh.thickness.fsaverage6.mgh",but it didn't work.
I also tried to use"mris_preproc --s PT1_1302 --hemi lh --meas thickness --target fsaverage6 --out lh.thickness.fsaverage6.mgh",but it didn't work too.
So do you mean that i need to use"mris_surf2surf" after recon-all ?And am i wrong that i used above command lines to register subjects to fsaverage6?
Thanks for any info! ------------------
邓刊 Kan Deng
E-mail：310913949@qq.com
TEL：13728774014
------------------ 原始邮件 ------------------ 发件人: "Bruce Fischl"fischl@nmr.mgh.harvard.edu; 发送时间: 2019年1月22日(星期二) 上午10:37 收件人: "Freesurfer support list"freesurfer@nmr.mgh.harvard.edu;
主题: Re: [Freesurfer] how to register feature maps to fsaverage6?
are you feature maps already on individual subject surfaces? If so, you an use mri_surf2surf with fsaverage6 as the target
cheers Bruce
On Tue, 22 Jan 2019, 310913949 wrote:
External Email - Use CautionDear freesurfer experts?? I want to know how to register feature maps to an average space (fsaverage6) so that I can get an identical number of vertices(40962) for each hemisphere. Can you tell me what is the command line? I am looking forward to your reply!Thanks.
???? Kan Deng
E-mail??310913949@qq.com
TEL??13728774014
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
can we take a step back. What feature maps are you trying to map? recon-all will create individual subject thickness maps by default (lh.thickness/rh.thickness) and will also map them to fsaverage if you specify -qcache. If you want to further map those to fsaverage6 you should use mri_surf2surf. You don't need to run mris_register (it is run by recon-all).
If you try using mri_surf2surf and fail please send us the entire command line and screen output.
cheers Bruce
On Tue, 22 Jan 2019, 310913949 wrote:
External Email - Use Caution
Thanks for your reply! Actually, i first use "recon-all -s PT1_13 -i PT1_13.nii -all -qcache -target fsaverage6 " to process the subject, but i think i make some mistakes as i find there are about 110,000 vertex values in the"lh.thickness"file. and I also find that it generates a file named"recon-all.error",the context is as follows:
Linux zhangjianing-Precision-Tower-7910 4.4.0-83-generic #106~14.04.1-Ubuntu SMP Mon Jun 26 18:10:19 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux $Id: recon-all,v 1.601 2017/02/08 21:17:33 greve Exp $ /media/root/533b526f-751c-4a6a-a3da-11856d602f84/usr/local/freesurfer/bin/recon-all PWD /media/root/533b526f-751c-4a6a-a3da-11856d602f84/usr/local/freesurfer/subjects/PT1_1302/surf CMD mris_preproc --s PT1_1302 --hemi lh --meas thickness --target fsaverage6 --out lh.thickness.fsaverage6.mgh" I am not sure whether i misused this command and how to correct that.
Besides,i tried to use these two commands after recon-all, "mris_register -curv surf/lh.sphere $SUBJECTS_DIR/fsaverage6/lh.reg.template.tif surf/lh.sphere.reg.newtemplate" and"mris_preproc --s PT1_13--hemi lh --meas thickness --target $SUBJECTS_DIR/fsaverage6 --out lh.thickness.fsaverage6.mgh",but it didn't work.
I also tried to use"mris_preproc --s PT1_1302 --hemi lh --meas thickness --target fsaverage6 --out lh.thickness.fsaverage6.mgh",but it didn't work too.
So do you mean that i need to use"mris_surf2surf" after recon-all ?And am i wrong that i used above command lines to register subjects to fsaverage6?
Thanks for any info!
???? Kan Deng
E-mail??310913949@qq.com
TEL??13728774014
------------------ ???????? ------------------ ??????: "Bruce Fischl"fischl@nmr.mgh.harvard.edu; ????????: 2019??1??22??(??????) ????10:37 ??????: "Freesurfer support list"freesurfer@nmr.mgh.harvard.edu; ????: Re: [Freesurfer] how to register feature maps to fsaverage6?
are you feature maps already on individual subject surfaces? If so, you an use mri_surf2surf with fsaverage6 as the target
cheers Bruce
On Tue, 22 Jan 2019, 310913949 wrote:
External Email - Use Caution
Dear freesurfer experts?? I want to know how to register feature maps to an average space (fsaverage6) so that I can get an
identical
number of vertices(40962) for each hemisphere. Can you tell me what is the command line? I am looking forward to your reply!Thanks.
???? Kan Deng
E-mail??310913949@qq.com
TEL??13728774014
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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310913949 -
Bruce Fischl