External Email - Use Caution Hi Andrew
Thanks fro your response. I have soruced the Freesurfer. Attached is the recon-all log. Best, Jie > -----Original Messages----- > From: "Hoopes, Andrew" <ahoo...@mgh.harvard.edu> > Sent Time: 2020-08-24 22:22:28 (Monday) > To: "Freesurfer support list" <freesurfer@nmr.mgh.harvard.edu> > Cc: > Subject: Re: [Freesurfer] recon-all error > > Hi Jie, > > Can you send the subject's full recon-all.log file to provide some more > context for this failure? Usually this error is due to a poor registration, > but there might be something else going wrong here based on those p values. > Have you sourced freesurfer in your environment? Adding the freesurfer bin > dir to your PATH will provide access to binaries, but there are a few other > PATH variables and settings that get configured by running `source > $FREESURFER_HOME/SetUpFreeSurfer.sh`. > > best > Andrew > > On 8/24/20, 10:12 AM, "freesurfer-boun...@nmr.mgh.harvard.edu on behalf of > Jie Zhao" <freesurfer-boun...@nmr.mgh.harvard.edu on behalf of > zjuzhao...@zju.edu.cn> wrote: > > External Email - Use Caution > > Hi, Tim > > Thanks for your quick response. > I set the PATH environment varible to include Freesurfer binary directory. > > I have the new problem when using recon-all , the error is like this: > ERROR: talairach_afd: Talairach Transform: transforms/talairach.xfm > ***FAILED*** (p=0.0000, pval=0.0000 < threshold=0.0050 > > How can solve this error? > > Regards, > Jie > > > -----原始邮件----- > > 发件人: "Tim Schäfer" <ts...@rcmd.org> > > 发送时间: 2020-08-23 16:24:28 (星期日) > > 收件人: "Freesurfer support list" <freesurfer@nmr.mgh.harvard.edu> > > 抄送: > > 主题: Re: [Freesurfer] recon-all error > > > > External Email - Use Caution > > > > What happems if you type 'mri_ca_label' in your shell? > > > > Did you setup your PATH environment variable to include the Freesurfer > binary directory? > > > > Tim > > > > > On August 23, 2020 at 9:34 AM Jie Zhao <zjuzhao...@zju.edu.cn> wrote: > > > > > > > > > External Email - Use Caution > > > > > > Dear freesurfer developer: > > > > > > I am using Freesurfer 7.1.1 and encounter an error like this when > using recon-all : > > > > > > zhao@zhao-VirtualBox:~$ export > SUBJECTS_DIR=/usr/local/freesurfer/subjects > > > zhao@zhao-VirtualBox:~$ recon-all -s test4 -i sample-002.nii.gz > -autorecon1 > > > Subject Stamp: freesurfer-linux-centos6_x86_64-7.1.1-20200723-8b40551 > > > Current Stamp: freesurfer-linux-centos6_x86_64-7.1.1-20200723-8b40551 > > > INFO: SUBJECTS_DIR is /usr/local/freesurfer/subjects > > > Actual FREESURFER_HOME /usr/local/freesurfer > > > Linux zhao-VirtualBox 4.15.0-20-generic #21-Ubuntu SMP Tue Apr 24 > 06:16:15 UTC 2018 x86_64 x86_64 x86_64 GNU/Linux > > > Segmentation fault > > > ERROR: Executable 'mri_ca_label -all-info failed! Is it missing from > the distribution?' > > > > > > What can I do to fix this? Thanks > > > > > > > > > > > > > > > Best regards > > > > > > Jie Zhao > > > > > > > > > _______________________________________________ > > > Freesurfer mailing list > > > Freesurfer@nmr.mgh.harvard.edu > > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > -- > > Tim Schäfer > > > > _______________________________________________ > > 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 mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
recon-all log.odt
Description: application/vnd.oasis.opendocument.text
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
