External Email - Use Caution
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/1jYJlRtsG56HVKexWP536EPiFzT0mvnrG_krTS2DBuokAmIFihDxzOWiQzRxQtbY6rcxI0VZQdAuYRVtOn3S1tQASqbRO0_QvAB8HI_-1ln73TTo7WKjmZa34lyAXn1tFzM3p-7u_6kb5UMzfUgeWND4_xETfbiYf9MLGt4YAi3h2SxgaaYHTgnUdRTJ0eoXzdbrWfO17VbycfgFtxrfzjW0KOfcrLckmJHqUWjqEU47N1uTPvUCDFbQ93H57hARTP0CdILDYOXD5SEK0TFmjvQ/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*
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>
> 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?
> _______________________________________________
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> Brigham Compliance HelpLine at *MailScanner has detected a possible fraud
> attempt from "secure-web.cisco.com" claiming to be*
> http://secure-web.cisco.com/1VCPhXJJj3kFaSfTmXjzu21XvmKrPR2G-Q3SLwCL2mYfHJsY-SJOS3sLAlsjzt0IbRwCf8viFt8YGVmE3irxl3eTUqe6p3fYJS8LugFEs0p3ignyMxEVwNwlQoYRm6SSevdz6IYyGzuO3OGMAyCBgT47Au_HvAKaknF0e8Cn5chRgbbvXVXNyPhvmAxxyoVg97nxh-S7U9ojHiEz6uORui_dJXjdy6L-6RBryb8FbRt5eEOF1RigA3L7B6vs8ltF6aWpPrv7TzzeApY-P-4u4Ww/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.
>
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> Freesurfer@nmr.mgh.harvard.edu
> https://secure-web.cisco.com/1sobX6uQs1B6SFJhnUYURbnrHgMFWVA2OPXbCy3pOYnv_4pK-kxv4AdXHxvUiz72zDprcihnSL80qZibnsQH4Vb1HQKQtTV2_TlqXV9AMTz60t5SDchey80F_VngWlzhWfW6ORT4SVGK3FUX-_r92orpk0LL1KFYmbc374na_7HvDyUuCUwqBNN7m59pqvWbOqc5qAgvW4CUMzmy3WrPCo2ATAgHKTf5gprC9wlluxVjYorHhUYH_92pONPWwv3z5ztZEJAmD26rNG87OMLS_tw/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/1VCPhXJJj3kFaSfTmXjzu21XvmKrPR2G-Q3SLwCL2mYfHJsY-SJOS3sLAlsjzt0IbRwCf8viFt8YGVmE3irxl3eTUqe6p3fYJS8LugFEs0p3ignyMxEVwNwlQoYRm6SSevdz6IYyGzuO3OGMAyCBgT47Au_HvAKaknF0e8Cn5chRgbbvXVXNyPhvmAxxyoVg97nxh-S7U9ojHiEz6uORui_dJXjdy6L-6RBryb8FbRt5eEOF1RigA3L7B6vs8ltF6aWpPrv7TzzeApY-P-4u4Ww/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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