External Email - Use Caution        

An update:

I tried to change the shell into tcsh (exec /bin/tcsh) temporarily but
other errors appeared. I added "setenv MY_MORPHS_DO_NOT_CONFORM_DEAL_WITH_IT"
at the beginning of the $FREESURFER_HOME/bin/trac-preproc and the problem
is now solved.

Cheers!
Amir

On Thu, Jul 22, 2021 at 11:52 PM AmirHussein Abdolalizadeh <
amirhussei...@gmail.com> wrote:

> You're welcome 😀
> But the problem still remains.
>
> I am using ubuntu (bash shell) thus I added "export
> MY_MORPHS_DO_NOT_CONFORM_DEAL_WITH_IT" to the first line of the "jobs"
> file but the issue remained. Should I add value after it? Maybe "export
> MY_MORPHS_DO_NOT_CONFORM_DEAL_WITH_IT=1"? I am using parallel like this:
> cat jobs_prep | parallel -j 10 (to allocate 10 cores).
>
> On Thu, Jul 22, 2021 at 9:09 PM Yendiki, Anastasia <
> ayend...@mgh.harvard.edu> wrote:
>
>> Ah, I see. Please add this at the top of your job:
>>     setenv MY_MORPHS_DO_NOT_CONFORM_DEAL_WITH_IT
>>
>> Although trac-all takes care of this when you use ANTs morphs, when you
>> submit jobs separately these jobs don't call trac-all. I'll fix this too in
>> the next version, but for now you have to setenv for every job.
>>
>> Thanks again for catching these things!
>>
>> Anastasia.
>> ------------------------------
>> *From:* freesurfer-boun...@nmr.mgh.harvard.edu <
>> freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of AmirHussein
>> Abdolalizadeh <amirhussei...@gmail.com>
>> *Sent:* Thursday, July 22, 2021 12:11 PM
>> *To:* Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
>> *Subject:* Re: [Freesurfer] dwi_orig_las issue trac-all -prep
>>
>>
>>         External Email - Use Caution
>>
>> Thanks! I also encountered an error while running -prep using
>> parallel tool (-jobs) on a batch of my subjects in mri_vol2vol part and I
>> couldn't find any relevant information searching the forum nor I couldn't
>> solve it after a few tries. I didn't encountered this error while running
>> it on my pilot subject (the protocols are same):
>>
>> In the subjects:
>> mri_vol2vol --gcam
>> /media/inrp/Data/Amir/SoldierSleep/AnalyzeDWI/1049/dlabel/anatorig/aparc+aseg.nii.gz
>> /media/inrp/Data/Amir/SoldierSleep/AnalyzeDWI/1049/dmri/xfms/anatorig2syn.bbr.lta
>> /media/inrp/Data/Amir/SoldierSleep/AnalyzeDWI/1049/dmri/xfms/syn_warp.m3z
>> /media/inrp/Data/Amir/SoldierSleep/AnalyzeDWI/1049/dmri/xfms/syn2syn.lta 0
>> 0
>> /media/inrp/Data/Amir/SoldierSleep/AnalyzeDWI/1049/dlabel/syn/aparc+aseg.nii.gz
>> Loading mov
>> /media/inrp/Data/Amir/SoldierSleep/AnalyzeDWI/1049/dlabel/anatorig/aparc+aseg.nii.gz
>> Loading source LTA
>> /media/inrp/Data/Amir/SoldierSleep/AnalyzeDWI/1049/dmri/xfms/anatorig2syn.bbr.lta
>> Loading GCAM
>> /media/inrp/Data/Amir/SoldierSleep/AnalyzeDWI/1049/dmri/xfms/syn_warp.m3z
>> setting orig areas to linear transform determinant scaled 1.00
>> Loading destination LTA
>> /media/inrp/Data/Amir/SoldierSleep/AnalyzeDWI/1049/dmri/xfms/syn2syn.lta
>> MRIvol2volGCAM(): VSM not used
>> MRIvol2volGCAM(): interpolation type is 0 nearest
>> MRIvol2volGCAM(): Inverting Source LTA
>> ERROR: MRIvol2volGCAM(): neither src nor dst VG of Dest LTA is conformed
>> Linux INRPAzhdar 5.4.0-80-generic #90~18.04.1-Ubuntu SMP Tue Jul 13
>> 19:40:02 UTC 2021 x86_64 x86_64 x86_64 GNU/Linux
>>
>> trac-preproc exited with ERRORS at Thu Jul 22 20:09:08 +0430 2021
>>
>>
>> However, for the pilot subject it was:
>> mri_vol2vol --gcam
>> /media/inrp/Data/Amir/SoldierSleep/AnalyzeDWI/pilot/dlabel/anatorig/aparc+aseg.nii.gz
>> /media/inrp/Data/Amir/SoldierSleep/AnalyzeDWI/pilot/dmri/xfms/anatorig2syn.bbr.lta
>> /media/inrp/Data/Amir/SoldierSleep/AnalyzeDWI/pilot/dmri/xfms/syn_warp.m3z
>> /media/inrp/Data/Amir/SoldierSleep/AnalyzeDWI/pilot/dmri/xfms/syn2syn.lta 0
>> 0
>> /media/inrp/Data/Amir/SoldierSleep/AnalyzeDWI/pilot/dlabel/syn/aparc+aseg.nii.gz
>> Loading mov
>> /media/inrp/Data/Amir/SoldierSleep/AnalyzeDWI/pilot/dlabel/anatorig/aparc+aseg.nii.gz
>> Loading source LTA
>> /media/inrp/Data/Amir/SoldierSleep/AnalyzeDWI/pilot/dmri/xfms/anatorig2syn.bbr.lta
>> Loading GCAM
>> /media/inrp/Data/Amir/SoldierSleep/AnalyzeDWI/pilot/dmri/xfms/syn_warp.m3z
>> setting orig areas to linear transform determinant scaled 1.00
>> Loading destination LTA
>> /media/inrp/Data/Amir/SoldierSleep/AnalyzeDWI/pilot/dmri/xfms/syn2syn.lta
>> MRIvol2volGCAM(): VSM not used
>> MRIvol2volGCAM(): interpolation type is 0 nearest
>> MRIvol2volGCAM(): Inverting Source LTA
>> WARN: MRIvol2volGCAM(): neither src nor dst VG of Dest LTA is conformed
>> MRIvol2volGCAM(): Chaning Destination LTA type to vox2vox
>> MRIvol2volGCAM: t=0.4239
>> Writing to
>> /media/inrp/Data/Amir/SoldierSleep/AnalyzeDWI/pilot/dlabel/syn/aparc+aseg.nii.gz
>> mri_vol2vol gcam done
>> [and continues without error]
>>
>> The log file for one of the subjects is also attached plus the config
>> file. I'll be glad to know your opinion.
>>
>> Bests,
>> Amir
>>
>> On Wed, Jul 21, 2021 at 5:47 PM Yendiki, Anastasia <
>> ayend...@mgh.harvard.edu> wrote:
>>
>> Hi Amir - I should make it clearer in the documentation that, unless you
>> have a specific need to change one of the configuration variables, you
>> should just leave it out of your configuration file entirely. This is the
>> best way to make sure that the defaults are being used. Only have in your
>> config file the variables that you specifically need to change for your
>> study.
>>
>> The error is actually not in trac-all but in the example config file, in
>> the sense that $FREESURFER_HOME/trctrain/trainlist.txt is not actually the
>> default. The default is $FREESURFER_HOME/trctrain/hcp/trainlist.txt. If you
>> set your trainfile to that or, even better, leave that variable out of your
>> config file entirely, trac-all should run fine. Let me know how that goes.
>>
>> I'll fix the example file and make the documentation clearer on this
>> point.
>>
>> Thanks for bringing this to our attention,
>> Anastasia.
>>
>>
>>
>>
>> ------------------------------
>> *From:* freesurfer-boun...@nmr.mgh.harvard.edu <
>> freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of AmirHussein
>> Abdolalizadeh <amirhussei...@gmail.com>
>> *Sent:* Wednesday, July 21, 2021 2:54 AM
>> *To:* Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
>> *Subject:* Re: [Freesurfer] dwi_orig_las issue trac-all -prep
>>
>>
>>         External Email - Use Caution
>>
>> I used the default settings which is
>> $FREESURFER_HOME/trctrain/trainlist.txt. I couldn't find a place to type in
>> the pathlist.txt so I manually copied all the 42 paths into the config. I
>> have also attached the config file.
>>
>> Bests,
>> Amir
>>
>> On Tue, Jul 20, 2021 at 11:37 PM Yendiki, Anastasia <
>> ayend...@mgh.harvard.edu> wrote:
>>
>> Hi Amir - Glad the results were satisfying! I'm afraid that it's a bit
>> hard to address issues before they are reported 🙂
>>
>> About the second issue, was there something in your config file about
>> where to find the training data, or did you just use the default?
>>
>> Thanks,
>> Anastasia.
>>
>> ------------------------------
>> *From:* freesurfer-boun...@nmr.mgh.harvard.edu <
>> freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of AmirHussein
>> Abdolalizadeh <amirhussei...@gmail.com>
>> *Sent:* Tuesday, July 20, 2021 2:17 PM
>> *To:* Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
>> *Subject:* Re: [Freesurfer] dwi_orig_las issue trac-all -prep
>>
>>
>>         External Email - Use Caution
>>
>> Hi Anastasia,
>>
>> I installed the beta version and tried TRACULA on one of my subjects. The
>> results were satisfying but there were a few issues that I had to address
>> manually:
>>
>>    - I did thalamic segmentation using the T2 beside the T1 sequence,
>>    thus the thalamic segmentation had "*.T2.*" instead of T1 and I had to
>>    manually rename them.
>>    - During trac-all -prep there were errors of pathlist and trclist; it
>>    was looking for them in $FREESURFER_HOME/trclist instead of trclist/hcp. 
>> So
>>    I copied them a directory above (into trclist).
>>    - trac-all -bedp had an ubuntu-related issue: bedpostx_mgh errored
>>    with a syntax error, and I had to change the first line of bedpostx_mgh
>>    into /bin/bash.
>>
>> I hope they've been addressed in the released 7.2 version.
>>
>> Bests,
>> Amir
>>
>> On Mon, Jul 19, 2021 at 6:06 AM Yendiki, Anastasia <
>> ayend...@mgh.harvard.edu> wrote:
>>
>> Hi Amir - You can check the build stamp in your log file:
>>
>> build-stamp.txt: freesurfer-linux-ubuntu18_x86_64-*dev-20210207*-440e8c2
>>
>> You're using a development version of freesurfer that was built on Feb
>> 7th, 2021 ("dev-20210207") . This is neither 7.1.1 (which was released on
>> July 27th, 2020: *MailScanner has detected a possible fraud attempt from
>> "secure-web.cisco.com" claiming to be*
>> https://secure-web.cisco.com/1qBLDmHvTEHeqS6J3zmWlC8rV8yM-EEnS9WQRuicbApuonldmcYZbfatl6tE5CvzCy6aY15Ke0pa0_s1GAFkpDq1zQpwxkkVExJ686SOcXoxbUvvq4HKpISLztTOg2GYAS6pVzqK0APJ3XtKrS0-FKIDvnExYGRiI1KXyLBK6g3Fv462V5XAKnFGMbwsDiYRB8N0no-wXH8JSd2xKO8jBxIBpsaCRKd6fB0SiY45zfBG8lfvWdDv-CdxmslT7Ntess17A_6l7qcceC3jEKxHDkQ/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FReleaseNotes
>> <https://secure-web.cisco.com/1WvPRjsqUvLcDnvLYoFDVPqDm8_TjDHwRNJm4IIMIdyA6Ty_EUKNSEo66F7YNmVoxfH3sqArHg8B3QopYClSCDPJY_SC3ETIn5vrDXB4g7hKfjMCzhwv4cvm88aLcn-F91rylg6yIYiAawFXpcVkdnepCh7uXkCPA8MaJq6RqxaKteOg4eOUu_v_yqp56LW_O7SSCuTr6z1DFF004lyJUyty_IVdQ4Vf08nwb_dJEQZIdtspfefXe7B2sexiEl5F46G0E217c5in2LAPRoURWIw/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FReleaseNotes>),
>> nor 7.2 (which is about to be released). It's an unstable version somewhere
>> in between.
>>
>> I checked your trac-all output against the trac-all in 7.2, and I don't
>> expect that you'll get this error in 7.2. You can try out the 7.2 beta
>> here: *MailScanner has detected a possible fraud attempt from
>> "secure-web.cisco.com" claiming to be*
>> https://secure-web.cisco.com/190as38pI3YOKXutSDLsB0SvK6KIyCDP5VnebfQqnA0RUrO5YVFIfFfEq9zwEIpH7WJPXiPPug3yEhn5uq6h_ZHi4sLG75ww3GUHp8mAqg0Es3ZjFa5hFk9glyWkH9C3chAfaYnFfpl9KNqnI-_DE_NpSdJl6R9x5D4njg-u572NSHJqjfJIWFXt7zBYgkOw4gw2Z5jO7RtoZlzFhoJIUM4EgVmmYB3lW4aIaPcxcG4m_GRCt5D-YG_EnasPxfMDlmGXP0hkJTjKcaD_t133dMQ/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Fpub%2Fdist%2Ffreesurfer%2F7.2.0-beta%2F
>> <https://secure-web.cisco.com/1cj1SgkkGGbnVwrDeUlw1jR7O0jCdIDXqhTwWUb6tGXTsvGfOA-6Nc5QTGa0iS7G8_W9HhNNlgd0vhd2sQwQDGuH23ThOReTds7XOiYNJTSxHaPow0HJzA2b2cc-I5-F2U2-C24PwPHgPMdpc8TaBEyC9kEwLrSEbg7nW1Xpx3XyqZwB_YJUKtHWPMqdxqYcKUqMpUB60tiEbELoQCU_YqYQ6Kq6m3Flzk-n-UjCwL4IBkk-MyU4HBGDPaqPGlmGehx6OB0z9cdF0vi8JgFuY4w/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Fpub%2Fdist%2Ffreesurfer%2F7.2.0-beta%2F>
>>
>> Let us know how it goes! 🙂
>>
>> Anastasia.
>>
>>
>>
>> ------------------------------
>> *From:* freesurfer-boun...@nmr.mgh.harvard.edu <
>> freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of AmirHussein
>> Abdolalizadeh <amirhussei...@gmail.com>
>> *Sent:* Sunday, July 18, 2021 2:18 AM
>> *To:* freesurfer@nmr.mgh.harvard.edu <freesurfer@nmr.mgh.harvard.edu>
>> *Subject:* Re: [Freesurfer] dwi_orig_las issue trac-all -prep
>>
>>
>>         External Email - Use Caution
>>
>> Hi Anastasia and thanks for your reply. Here I have attached
>> trac-all.log. I think I installed the official FS 7.1.1 version and not the
>> beta (not sure btw). Is there a way to get which one that I am using?
>> _______________________________________________
>> Freesurfer mailing list
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>> e-mail contains patient information, please contact the Mass General
>> Brigham Compliance HelpLine at *MailScanner has detected a possible
>> fraud attempt from "secure-web.cisco.com" claiming to be*
>> http://secure-web.cisco.com/16sV2GpeCBR-Yo8KAaWBbygc9Aquky9Pvbmru2pkk5_NzAhjL2DIB-qP2mG8rA5lR7jdoFDrU5MBZWjLvZFXbe7lwrj4W4zAdJ_62hidvnw_-50XOAc1_gz_a4ZSE34m_flOqrpc2ylQZGa9fgcTt6jszI_XbRQ0zPL-2a0V-zhYjUnh32prcdoqOMrFmlcI1D89hm1k3ouvr1p1MWSVYZTh3w19UbajaBQytB9cxlpbzPMKFCR7UXSfTf9Z-m_6vERjN14t0yiFjQSdZhptrDA/http%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline
>> <http://secure-web.cisco.com/1euc3IZmziNkQEGPrbT3j3xXlUcAxPPaKWiZ0CYjU1kQqaDUPudeZyWWdPmpxLCWV3etlACxTgRvGdl9WmqVa8St7IYhE7HLp92jXQDm-q8fPwPq233YI65axoTEFCIjzN1qLOWKO0QJfk6s03MAbDjBd9n7RgxlzRYztIFE7sxbtCiqxsGAy8ZtY2AMyM579UQQetSsSxxMDo3YbPlSEc8DNnBnc8_iZ5ubwi3N0qOmtH_GeiZkgP256KqzZo5sElkwSDWlys_y4dU4ao1l5LA/http%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline>
>> . 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.
>> Please note that this e-mail is not secure (encrypted).  If you do not
>> wish to continue communication over unencrypted e-mail, please notify the
>> sender of this message immediately.  Continuing to send or respond to
>> e-mail after receiving this message means you understand and accept this
>> risk and wish to continue to communicate over unencrypted e-mail.
>>
>> _______________________________________________
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu
>> https://secure-web.cisco.com/1_v1DsFrOupq_QuuHJvsFmYh4D4P78giQPV_uNo7cXwJF_UJ4i0Sg0LnGI4ZT5sozgGwkrgOGj3p8q1kvFJg8kvQHKfipMLQyIgvVW7m2-6JaatjkkaN7pmN5oqKHzWc5YLa5prCH2EmRN7MGMxZ9HtqONDy-Ujm7mW_wEnX2Dsz-1DS14fCRy4L45wO-fbyx6M-tvH-3RJ3BzHwDzkpFbDZ_lq4dC1csjAcM9B5ghpF-ueg2xjQ3GxKQRXQC-dnwokmFGH8Z59HzGKJKhQFkxg/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer
>> 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 Mass General
>> Brigham Compliance HelpLine at
>> http://secure-web.cisco.com/16sV2GpeCBR-Yo8KAaWBbygc9Aquky9Pvbmru2pkk5_NzAhjL2DIB-qP2mG8rA5lR7jdoFDrU5MBZWjLvZFXbe7lwrj4W4zAdJ_62hidvnw_-50XOAc1_gz_a4ZSE34m_flOqrpc2ylQZGa9fgcTt6jszI_XbRQ0zPL-2a0V-zhYjUnh32prcdoqOMrFmlcI1D89hm1k3ouvr1p1MWSVYZTh3w19UbajaBQytB9cxlpbzPMKFCR7UXSfTf9Z-m_6vERjN14t0yiFjQSdZhptrDA/http%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline
>>  . 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.
>> Please note that this e-mail is not secure (encrypted).  If you do not
>> wish to continue communication over unencrypted e-mail, please notify the
>> sender of this message immediately.  Continuing to send or respond to
>> e-mail after receiving this message means you understand and accept this
>> risk and wish to continue to communicate over unencrypted e-mail.
>>
>
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