External Email - Use Caution tkregister2 --s mprage --fstal , below is the error:
Determinant 26.9764 subject = mprage Zoom Factor = 2, SQR() = 4 FOV = 256 Opening window mprage Opening mprage, xnum = 256, xdim = 512 Setting scale Tcl_Init failed: Can't find a usable init.tcl in the following directories: /usr/pubsw/packages/tcltktixblt/current/lib/tcl8.4 This probably means that Tcl wasn't installed properly. Tk_Init failed: invalid command name "tcl_findLibrary" tkregister2: interface: /usr/local/freesurfer/tktools/tkregister2.tcl tkregister.tcl: startup done tkregister.tcl: default macro interface (to change: macro,mini,micro) tkregister.tcl: or: setenv tkregisterinterface {macro,mini,micro} % invalid command name "tk::ScreenChanged" while executing "tk::ScreenChanged :0.0" (changing screen in event binding) -----Original Messages----- From:"Douglas N. Greve" <dgr...@mgh.harvard.edu> Sent Time:2020-08-29 23:31:44 (Saturday) To: freesurfer@nmr.mgh.harvard.edu Cc: Subject: Re: [Freesurfer] recon-all error What is the error? tkregister2 is an old program, and it might not work on all systems. You can try using tkregisterfv instead, available here https://gate.nmr.mgh.harvard.edu/safelinks/greve/tkregisterfv On 8/29/2020 11:26 AM, Jie Zhao wrote: 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 freesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer _______________________________________________ Freesurfer mailing list freesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer _______________________________________________ Freesurfer mailing list freesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer _______________________________________________ Freesurfer mailing list freesur...@nmr.mgh.harvard.eduhttps://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