External Email - Use Caution Hi All
I tryed the tkregister2 to change the postion for Talairach Registration,but some error occured in the tkregister, so some button were not functioning well. I can not find useful info. on the internet, could you tell me how to correct it.Thanks. Please check the error log file attached. King regards, Jie > -----Original Messages----- > From: "Douglas N. Greve" <dgr...@mgh.harvard.edu> > Sent Time: 2020-08-28 00:06:31 (Friday) > To: freesurfer@nmr.mgh.harvard.edu > Cc: > Subject: Re: [Freesurfer] recon-all error > > This is the automatic failure detection raising a warning flag. Did you > notice that the output suggested that you take some action? > > On 8/27/2020 11:39 AM, Fischl, Bruce wrote: > > Hi Jie > > > > I would start by looking at your input volume in freeview: > > > > freeview -v /usr/local/freesurfer/subjects/2018MPRAGE_p4iso.nii > > > > and make sure that the orientation it displays in is correct (that is, that > > what freeview thinks is anterior/superior/left are indeed those > > directions). Usually when we see this type of failure it is because the > > direction cosines in the input volume are incorrect (typically because the > > volume was at some point converted to analyze format). Not always, but > > usually. > > > > Cheers > > Bruce > > > > > > -----Original Message----- > > From: freesurfer-boun...@nmr.mgh.harvard.edu > > <freesurfer-boun...@nmr.mgh.harvard.edu> On Behalf Of Jie Zhao > > Sent: Thursday, August 27, 2020 11:21 AM > > To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu> > > Subject: Re: [Freesurfer] recon-all error > > > > External Email - Use Caution > > > > Hi, Andrew > > > > Attached is the right recon-all.log file, please check it. > > I am new to the freesurfer, so really need you advice, Thanks > > > > Kind Regards, > > Jie > > > > > >> -----Original Messages----- > >> From: "Hoopes, Andrew" <ahoo...@mgh.harvard.edu> Sent Time: 2020-08-26 > >> 10:17:00 (Wednesday) > >> To: "Freesurfer support list" <freesurfer@nmr.mgh.harvard.edu> > >> Cc: > >> Subject: Re: [Freesurfer] recon-all error > >> > >> Hi Jie, this appears to be the log for your original issue, and not the > >> talairach registration failure. > >> Andrew > >> > >> On 8/25/20, 9:23 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 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 > >> > >> > >> > >> _______________________________________________ > >> 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
tkregister error
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_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
