Hi Jürgen - Can you check what's in this file: $FSLDIR/etc/fslversion ?
Thanks,
Anastasia.
________________________________
From: freesurfer-boun...@nmr.mgh.harvard.edu
<freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of
juergen.haen...@upd.unibe.ch <juergen.haen...@upd.unibe.ch>
Sent: Wednesday, November 24, 2021 12:53 AM
To: freesurfer@nmr.mgh.harvard.edu <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] TRACULA error wrt to dwi_orig_las.1.bvals file
External Email - Use Caution
Dear Anastasia
when I type $FSLDIR in the terminal, I get /usr/local/fsl: permission denied.
this is the right path where fsl is installed.
however, I can start FSL GUI and also other FSL commands.
Best Jürgen
Am 24.11.2021 um 01:20 schrieb Yendiki, Anastasia
<ayend...@mgh.harvard.edu<mailto:ayend...@mgh.harvard.edu>>:
Hi Jürgen - What's your $FSLDIR set to?
Anastasia.
________________________________
From:
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
<freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
on behalf of juergen.haen...@upd.unibe.ch<mailto:juergen.haen...@upd.unibe.ch>
<juergen.haen...@upd.unibe.ch<mailto:juergen.haen...@upd.unibe.ch>>
Sent: Tuesday, November 23, 2021 9:36 AM
To: freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>
<freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] TRACULA error wrt to dwi_orig_las.1.bvals file
External Email - Use Caution
Dear Anastasia
thank you for the new option. It works. Now we were able to finish trac-all
-prep without any further problem.
However, when we try to run trac-all -bedp, the following error occurred:
----------
trac-all -bedp -c
/mnt/981dac6a-ec33-4a79-9c9e-588e004c6806/Juergen/01_IPS_Project/DTI_DATA/03_TRACULA_Test/tracula_config_IPS_all_example_DICOM_NIFTI_ANTs.txt
INFO: SUBJECTS_DIR is
/mnt/981dac6a-ec33-4a79-9c9e-588e004c6806/Juergen/01_IPS_Project/DTI_DATA/03_TRACULA_Test/00_FS_subjects
INFO: Diffusion root is
/mnt/981dac6a-ec33-4a79-9c9e-588e004c6806/Juergen/01_IPS_Project/DTI_DATA/03_TRACULA_Test/00_TRACULA_Results_DICOMs_NIFTIs_FS720
Actual FREESURFER_HOME /usr/local/freesurfer
ln -sf ../dlabel/diff/aparc+aseg_mask.bbr.nii.gz
/mnt/981dac6a-ec33-4a79-9c9e-588e004c6806/Juergen/01_IPS_Project/DTI_DATA/03_TRACULA_Test/00_TRACULA_Results_DICOMs_NIFTIs_FS720/IPS_CO_007_ANTs/dmri/nodif_brain_mask.nii.gz
WARN: Running bedbostx locally - this might take a while
WARN: It is recommended to run this step on a cluster
bedpostx_mgh -n 2 -model 1
/mnt/981dac6a-ec33-4a79-9c9e-588e004c6806/Juergen/01_IPS_Project/DTI_DATA/03_TRACULA_Test/00_TRACULA_Results_DICOMs_NIFTIs_FS720/IPS_CO_007_ANTs/dmri
/usr/local/freesurfer/bin/bedpostx_mgh: 128:
/usr/local/freesurfer/bin/bedpostx_mgh: Syntax error: "(" unexpected
——————
we have found this message from 2014
MailScanner has detected a possible fraud attempt from "secure-web.cisco.com"
claiming to be
https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg38004.html<https://secure-web.cisco.com/12TdwqJYjrGP9jwKUvFseyuooOre9yruBVjpdXSQMKwZ8dmhMcfy-UEGAPAeUcvmoaVtgAyUar30aRpEXEpVx6mYNB4zaWpN0hBfvTM40p--GecqImVQKLmB_C7XNt66dAwtMieMgF5whO7lbn1rEQYLC6ppJwIm-ZQKi4FB0K5ge-Ng-sevOl2PbKY05JLS4cCeMYkafxMCLQw5h_XKcXqzu5n_QReCxKTqIz6AwaCEY8TsYyhJdTvp_NorMMfapCUk5NuYdP9kSZDO9bpSbWSX2m4gX-F58YqdBZKR2Gn5ugsQLoezk825ZeYnceXNq/https%3A%2F%2Fwww.mail-archive.com%2Ffreesurfer%40nmr.mgh.harvard.edu%2Fmsg38004.html>
is it meanwhile possible to run bedpostx_mgh also locally or do we have to run
bedpostx directly as suggested in the link?
Best
Jürgen
Am 23.11.2021 um 01:14 schrieb Yendiki, Anastasia
<ayend...@mgh.harvard.edu<mailto:ayend...@mgh.harvard.edu>>:
Ah yes, I did say that this would be feasible in 7.2, before 7.2 came out ��
One more bug fix, in the same place (and then in the dev version):
MailScanner has detected a possible fraud attempt from "secure-web.cisco.com"
claiming to be
https://raw.githubusercontent.com/ayendiki/freesurfer/trcdev/scripts/trac-preproc<https://secure-web.cisco.com/1Y4QR7zMqS-P5ZMuFX5CW29WQG7q8VdLfH5Xj6op25PoQPb5cz8IOhb_ze2LaFMa_EDKXa9XOjy6ZjoLM4uTXjxAvfeInswYAPJClnZiR-R9F10WB2wT9Y0hO0Hci3vHQEBH2b981DSDPisct-IaANfoRoiItgBqQkYx-H__novSCl8nW_lcy8OXaBSqrXy6qjHSdn-sWYa43HZHwOqBheaTd2iqJt8wAS0ba5VrCWxq22Tg_PmwuhF1puRtKvGhFDL-NVvGJwHN4338vS94oi-w37RqEr_D5AJQw9nF5aybKZOaxAcDUr1O0W8YKkwEQ/https%3A%2F%2Fraw.githubusercontent.com%2Fayendiki%2Ffreesurfer%2Ftrcdev%2Fscripts%2Ftrac-preproc>
>From now on the dTE from the config file will supersede the one from the DICOM
>header. Thanks for finding this and let us know if there are any other issues.
Anastasia.
________________________________
From:
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
<freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
on behalf of juergen.haen...@upd.unibe.ch<mailto:juergen.haen...@upd.unibe.ch>
<juergen.haen...@upd.unibe.ch<mailto:juergen.haen...@upd.unibe.ch>>
Sent: Monday, November 22, 2021 4:47 AM
To: freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>
<freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] TRACULA error wrt to dwi_orig_las.1.bvals file
External Email - Use Caution
Dear Anastasia
thank you for providing the bug fix. It works and solved our problem.
However, another (old) problem occurred wrt the field map for which we did not
find any solution yet:
---------------------------------------------------------
writing to
/mnt/981dac6a-ec33-4a79-9c9e-588e004c6806/Juergen/01_IPS_Project/DTI_DATA/03_TRACULA_Test/00_TRACULA_Results_DICOMs_FS720/IPS_CO_007/dmri/b0pha.nii.gz...
mri_probedicom --i
/mnt/981dac6a-ec33-4a79-9c9e-588e004c6806/Juergen/01_IPS_Project/DTI_DATA/03_TRACULA_Test/00_TRACULA_Prepared_DICOMs_FS720/IPS_CO_007/Phase/33163229.dcm
>
/mnt/981dac6a-ec33-4a79-9c9e-588e004c6806/Juergen/01_IPS_Project/DTI_DATA/03_TRACULA_Test/00_TRACULA_Results_DICOMs_FS720/IPS_CO_007/dmri/b0info.dat
ERROR: Need dTE for field map
/mnt/981dac6a-ec33-4a79-9c9e-588e004c6806/Juergen/01_IPS_Project/DTI_DATA/03_TRACULA_Test/00_TRACULA_Prepared_DICOMs_FS720/IPS_CO_007/Phase/33163229.dcm
Linux upd-159253 4.15.0-162-lowlatency #170-Ubuntu SMP PREEMPT Mon Oct 18
13:19:21 UTC 2021 x86_64 x86_64 x86_64 GNU/Linux
trac-preproc exited with ERRORS at Mon Nov 22 09:18:01 CET 2021
-----------------------------------------------------------
For some reasons, dTE cannot be extracted from the b0info.dat file (see
attachment). Indeed, there is only one echo time entry (EchoTime 7.38) in the
b0info.dat file maybe due to the fact that there is also only one echo time
entry (EchoTime 7.38) in the DICOM header.
Specifying dTE = 2.46 in the config file does not solve the problem, neither
with NIFTI nor DICOM file format for the field map.
In a former email, you mentioned that this should be possible.
The log and config file are also attached.
Is there any work around for this problem?
Thanks in advance
Best,
Jürgen
Am 20.11.2021 um 18:11 schrieb Yendiki, Anastasia
<ayend...@mgh.harvard.edu<mailto:ayend...@mgh.harvard.edu>>:
Hi Jürgen - You have diagnosed the problem correctly. It's specific to the case
when you have 1 DWI run only. I committed a bug fix for this. For now you can
get it from here (and it should get merged into the dev version in a couple of
days):
MailScanner has detected a possible fraud attempt from "secure-web.cisco.com"
claiming to be
https://raw.githubusercontent.com/ayendiki/freesurfer/trcdev/scripts/trac-preproc<https://secure-web.cisco.com/1l0klX-YanhXQKwsaHZLsP2jyZS1-cdJ_xY-FMa2uG__1HM8l3SLLeLQZuMu-2cvUofKMq-vD-wUvzIVynW1T0Em5IOaD2qQSclP2b6o3k_3hZ7Fwv5ACz79H_LQ74LLXgbvm-3WtcytqQtgssL52R_2e4I7kWwGmLUHlQ7aO2b-_15ehHxVs_hhhECG0MjMvGsNK99qQCVwhJ8CM0R0FQR4X1WWEGF49sRvxkehr2TbddfuoOK2TTsuBK0My3m60bmnIIJOhFtHQ82K-GLbV0RAExDaZV2caJG4Wp8W1ODbVvzZGGvjx5Vl4H06KJ1XC/https%3A%2F%2Fraw.githubusercontent.com%2Fayendiki%2Ffreesurfer%2Ftrcdev%2Fscripts%2Ftrac-preproc>
Can you please save this version of trac-preproc to your $FREESURFER_HOME/bin/
and tell us if it fixes the problem? Thank you for bringing this to our
attention.
Best,
Anastasia.
________________________________
From:
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
<freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
on behalf of juergen.haen...@upd.unibe.ch<mailto:juergen.haen...@upd.unibe.ch>
<juergen.haen...@upd.unibe.ch<mailto:juergen.haen...@upd.unibe.ch>>
Sent: Wednesday, October 27, 2021 8:19 AM
To: freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>
<freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: [Freesurfer] TRACULA error wrt to dwi_orig_las.1.bvals file
External Email - Use Caution
Dear TRACULA experts
I try to run TRACULA FS7.2 on a Linux machine and get the following error (see
below). A similar problem has already been reported in the archives, but I
found no solution.
MailScanner has detected a possible fraud attempt from "secure-web.cisco.com"
claiming to be
https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg71032.html<https://secure-web.cisco.com/15ekCi1WQB-CkH0WPGgECXGvPn99_mRmsow_C5M9nEA423BRbW-FKtNsZUbezZE_QDLB9tTrAhEngv6e3pZzRpvDIkIm6KXSCKMpikqqr8I7UzDhYNp9r4WMD_cNPQ1H9iJM_mZEjcL74q2XaK_BJMKcDCUR2IEVhTB14V-0-KDoDCIvf8avZH8sAQdlpf1AtWVaBOzP_a_q2ytmsXQq_z-VTqwl4kZhDQUh3pe3qM0Xq2I8WgvFw4OeT6omPBozJ/https%3A%2F%2Fwww.mail-archive.com%2Ffreesurfer%40nmr.mgh.harvard.edu%2Fmsg71032.html>
Because the file "dwi_orig_las.1.bvals“ was renamed to „dwi_orig_las.bvals“
earlier in the run
mv -f
/mnt/981dac6a-ec33-4a79-9c9e-588e004c6806/Juergen/01_IPS_Project/DTI_DATA/03_TRACULA_Test/00_TRACULA_Results_DICOMs_FS720/IPS_CO_007/dmri/dwi_orig_las.1.bvals
/mnt/981dac6a-ec33-4a79-9c9e-588e004c6806/Juergen/01_IPS_Project/DTI_DATA/03_TRACULA_Test/00_TRACULA_Results_DICOMs_FS720/IPS_CO_007/dmri/dwi_orig_las.bvals
it cannot be found by awk and as a result, I guess, the index.txt file is empty
and therefore eddy_openmp terminated.
How can I fix this problem?
The terminal output, log and config files are attached.
Thank you for any advise in advance
Regards
Jürgen
—————— error ————
awk: fatal: cannot open file
`/mnt/981dac6a-ec33-4a79-9c9e-588e004c6806/Juergen/01_IPS_Project/DTI_DATA/03_TRACULA_Test/00_TRACULA_Results_DICOMs_FS720/IPS_CO_007/dmri/dwi_orig_las.1.bvals'
for reading (No such file or directory)
eddy_openmp
--imain=/mnt/981dac6a-ec33-4a79-9c9e-588e004c6806/Juergen/01_IPS_Project/DTI_DATA/03_TRACULA_Test/00_TRACULA_Results_DICOMs_FS720/IPS_CO_007/dmri/dwi_orig_las.nii.gz
--mask=/mnt/981dac6a-ec33-4a79-9c9e-588e004c6806/Juergen/01_IPS_Project/DTI_DATA/03_TRACULA_Test/00_TRACULA_Results_DICOMs_FS720/IPS_CO_007/dmri/lowb_orig_las_brain_mask.nii.gz
--bvecs=/mnt/981dac6a-ec33-4a79-9c9e-588e004c6806/Juergen/01_IPS_Project/DTI_DATA/03_TRACULA_Test/00_TRACULA_Results_DICOMs_FS720/IPS_CO_007/dmri/dwi_orig_las.bvecs
--bvals=/mnt/981dac6a-ec33-4a79-9c9e-588e004c6806/Juergen/01_IPS_Project/DTI_DATA/03_TRACULA_Test/00_TRACULA_Results_DICOMs_FS720/IPS_CO_007/dmri/dwi_orig_las.bvals
--acqp=/mnt/981dac6a-ec33-4a79-9c9e-588e004c6806/Juergen/01_IPS_Project/DTI_DATA/03_TRACULA_Test/00_TRACULA_Results_DICOMs_FS720/IPS_CO_007/dmri/acqp.txt
--index=/mnt/981dac6a-ec33-4a79-9c9e-588e004c6806/Juergen/01_IPS_Project/DTI_DATA/03_TRACULA_Test/00_TRACULA_Results_DICOMs_FS720/IPS_CO_007/dmri/index.txt
--data_is_shelled
--out=/mnt/981dac6a-ec33-4a79-9c9e-588e004c6806/Juergen/01_IPS_Project/DTI_DATA/03_TRACULA_Test/00_TRACULA_Results_DICOMs_FS720/IPS_CO_007/dmri/dwi
EddyInputError: Error when attempting to read --index file
/mnt/981dac6a-ec33-4a79-9c9e-588e004c6806/Juergen/01_IPS_Project/DTI_DATA/03_TRACULA_Test/00_TRACULA_Results_DICOMs_FS720/IPS_CO_007/dmri/index.txt
Terminating program
Linux upd-159253 4.15.0-147-lowlatency #151-Ubuntu SMP PREEMPT Fri Jun 18
20:06:19 UTC 2021 x86_64 x86_64 x86_64 GNU/Linux
trac-preproc exited with ERRORS at Wed Oct 27 13:41:49 CEST 2021
upd-159253:/mnt/981dac6a-ec33-4a79-9c9e-588e004c6806/Juergen/01_IPS_Project/DTI_DATA/03_TRACULA_Test>
——————
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Compliance HelpLine at MailScanner has detected a possible fraud attempt from
"secure-web.cisco.com" claiming to be
http://www.massgeneralbrigham.org/complianceline<http://secure-web.cisco.com/1ss1949x0kMWgnOjZq6KT7mMCrTrDPubYHg8EF6WC2HuWplsEvRZbTijyhlEJU_cbrPyTSDJW5OoSq51naskKpW4XbGxAzyhX0ZILkl-EViGvOmNSr56o0RBmccYgS5nWnL01rFAgfLCISHh-MN4x_C-8fVg2VhulieAQnfE46PAOyb35soXXKUHN1ikPn8Lw_xx8v73fROouXBiTTTxKPGigaV0FdPpGKZmc0LHyPzQk_cigGECHwYPj2RYc5c1P8iH0c2Ol2m-e7EpKadaPqyLVuNWYhgyDVX6i1eW6W5lkpSJsjgVefwZG2rpcRAbP/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 mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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://www.massgeneralbrigham.org/complianceline . 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.
