Re: [Freesurfer] TRACULA error wrt to dwi_orig_las.1.bvals file - Freesurfer

9 Dec 2021


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Sorry, I should have said you need to directly invoke the script with bash,
$ bash bedpostx_mgh -n 2 -model 1 &lt;all other args&gt;
Alternately, if you can edit the script, then change the first line from:#!/bin/shto:#!/usr/bin/env bash
and you should not need to preface it with bash from the command line.
- R.
On Dec 9, 2021, at 03:01, juergen.haenggi@upd.unibe.ch wrote:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;External Email - Use Caution&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Dear expertthanks a lot for your suggestion.the error initially occurred using tcsh.if I use bash as you suggested, the same error is reported./usr/local/freesurfer/bin/bedpostx_mgh: 128: /usr/local/freesurfer/bin/bedpostx_mgh: Syntax error: "(„ unexpectedwrt the command&nbsp;fslver=(`cat $FSLDIR/etc/fslversion | sed 's/./ /g’`), the message "Badly placed ()’s.“ disappears when using bash instead of tcsh, but no output is produced.&nbsp;I do not understand for what purpose I have to run this command and what output, if any, should be expected.Any idea how to get bedpostx_mgh working is highly appreciated?Thanks in advanceRegardsJürgenAm 08.12.2021 um 18:25 schrieb fsbuild &lt;fsbuild@contbay.com&gt;:Hello&nbsp;Jürgen,Try running the bash shell from the terminal, e.g., before running anything type,$ bash- and then try your command again.If that works then I would set your login shell to bash (as the default is dash).- R.On Dec 7, 2021, at 01:46,&nbsp;juergen.haenggi@upd.unibe.ch&nbsp;wrote:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;External Email - Use Caution&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Dear Anastasiathank a lot for the answer.We use Ubuntu 18.04.6 LTS.When we run the command directly in the terminalbedpostx_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/dmriwe get the sane error/usr/local/freesurfer/bin/bedpostx_mgh: 128: /usr/local/freesurfer/bin/bedpostx_mgh: Syntax error: "(„ unexpectedwhen we run the command you sent in your last email, i.e. fslver=(`cat $FSLDIR/etc/fslversion | sed 's/./ /g’`)we get the following errorBadly placed ()’s.Thanks in advanceRegardsJürgenAm 03.12.2021 um 00:02 schrieb Yendiki, Anastasia &lt;AYENDIKI@mgh.harvard.edu&gt;:Hi&nbsp;Jürgen&nbsp;- I haven't been&nbsp;able to replicate your error locally. What operating system are you running it on? And what do you see if you try run the line that errors out directly on the command line? The line is:fslver=(`cat $FSLDIR/etc/fslversion | sed 's/./ /g'`)Thanks,Anastasia.From:&nbsp;freesurfer-bounces@nmr.mgh.harvard.edu&nbsp;&lt;freesurfer-bounces@nmr.mgh.harvard.edu&gt; on behalf of&nbsp;juergen.haenggi@upd.unibe.ch&nbsp;&lt;juergen.haenggi@upd.unibe.ch&gt;Sent:&nbsp;Thursday, November 25, 2021 1:40 AMTo:&nbsp;freesurfer@nmr.mgh.harvard.edu&nbsp;&lt;freesurfer@nmr.mgh..harvard.edu&gt;Subject:&nbsp;Re: [Freesurfer] TRACULA error wrt to dwi_orig_las.1.bvals file&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;External Email - Use Caution&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Dear Anastasiacat $FSLDIR/etc/fslversion reported6.0.5.1:57b01774I guess its the newest version availableThanksJürgenAm 24.11.2021 um 15:53 schrieb Yendiki, Anastasia &lt;AYENDIKI@MGH.HARVARD.EDU&gt;:Hi Jürgen - Can you check what's in this file: $FSLDIR/etc/fslversion ?Thanks,Anastasia.From:&nbsp;freesurfer-bounces@nmr.mgh.harvard.edu&nbsp;&lt;freesurfer-bounces@nmr.mgh.harvard.edu&gt; on behalf of&nbsp;juergen.haenggi@upd..unibe.ch&nbsp;&lt;juergen.haenggi@upd.unibe.ch&gt;Sent:&nbsp;Wednesday, November 24, 2021 12:53 AMTo:&nbsp;freesurfer@nmr.mgh.harvard.edu&nbsp;&lt;freesurfer@nmr.mgh.harvard.edu&gt;Subject:&nbsp;Re: [Freesurfer] TRACULA error wrt to dwi_orig_las.1.bvals file&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;External Email - Use Caution&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Dear Anastasiawhen 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 JürgenAm 24.11.2021 um 01:20 schrieb Yendiki, Anastasia &lt;AYENDIKI@mgh.harvard.edu&gt;:Hi Jürgen - What's your $FSLDIR set to?Anastasia.From:&nbsp;freesurfer-bounces@nmr.mgh.harvard.edu&nbsp;&lt;freesurfer-bounces@nmr.mgh.harvard.edu&gt; on behalf of&nbsp;juergen.haenggi@upd.unibe.ch&nbsp;&lt;juergen.haenggi@upd.unibe.ch&gt;Sent:&nbsp;Tuesday, November 23, 2021 9:36 AMTo:&nbsp;freesurfer@nmr.mgh.harvard.edu&nbsp;&lt;freesurfer@nmr.mgh.harvard.edu&gt;Subject:&nbsp;Re: [Freesurfer] TRACULA error wrt to dwi_orig_las.1.bvals file&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;External Email - Use Caution&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Dear Anastasiathank 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.txtINFO: SUBJECTS_DIR is /mnt/981dac6a-ec33-4a79-9c9e-588e004c6806/Juergen/01_IPS_Project/DTI_DATA/03_TRACULA_Test/00_FS_subjectsINFO: Diffusion root is /mnt/981dac6a-ec33-4a79-9c9e-588e004c6806/Juergen/01_IPS_Project/DTI_DATA/03_TRACULA_Test/00_TRACULA_Results_DICOMs_NIFTIs_FS720Actual FREESURFER_HOME /usr/local/freesurferln -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.gzWARN: Running bedbostx locally - this might take a whileWARN: It is recommended to run this step on a clusterbedpostx_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&nbsp;MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be&nbsp;https://secure-web.cisco.com/1PZw3Rw8y7Owkru69l62f3qrEeHiVBpRsvZg7RpGqSTgHTn... it meanwhile possible to run bedpostx_mgh also locally or do we have to run bedpostx directly as suggested in the link?BestJürgenAm 23.11.2021 um 01:14 schrieb Yendiki, Anastasia &lt;AYENDIKI@mgh.harvard.edu&gt;:Ah yes, I did say that this would be feasible in 7.2, before 7.2 came out&nbsp;��&nbsp;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&nbsp;https://secure-web.cisco.com/1BcqFiy7b_RheZDW7Y6dSsECFm81wUqvpTrx6GfnUNIyZFg... 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:&nbsp;freesurfer-bounces@nmr.mgh.harvard.edu&nbsp;&lt;freesurfer-bounces@nmr.mgh.harvard.edu&gt; on behalf of&nbsp;juergen.haenggi@upd..unibe.ch&nbsp;&lt;juergen.haenggi@upd.unibe.ch&gt;Sent:&nbsp;Monday, November 22, 2021 4:47 AMTo:&nbsp;freesurfer@nmr.mgh.harvard.edu&nbsp;&lt;freesurfer@nmr.mgh.harvard.edu&gt;Subject:&nbsp;Re: [Freesurfer] TRACULA error wrt to dwi_orig_las.1.bvals file&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;External Email - Use Caution&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Dear Anastasiathank 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 &gt; /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.datERROR: 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.dcmLinux 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/Linuxtrac-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 advanceBest,JürgenAm 20.11.2021 um 18:11 schrieb Yendiki, Anastasia &lt;AYENDIKI@mgh.harvard.edu&gt;: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&nbsp;https://secure-web.cisco.com/1vogQP6gWZ3A7n4EogQreDkBb-38S1C2taCJcrYZL6INyIn... 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:&nbsp;freesurfer-bounces@nmr.mgh.harvard.edu&nbsp;&lt;freesurfer-bounces@nmr.mgh.harvard.edu&gt; on behalf of&nbsp;juergen.haenggi@upd.unibe.ch&nbsp;&lt;juergen.haenggi@upd.unibe.ch&gt;Sent:&nbsp;Wednesday, October 27, 2021 8:19 AMTo:&nbsp;freesurfer@nmr.mgh.harvard.edu&nbsp;&lt;freesurfer@nmr.mgh.harvard.edu&gt;Subject:&nbsp;[Freesurfer] TRACULA error wrt to dwi_orig_las.1.bvals file&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;External Email - Use Caution&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Dear TRACULA expertsI 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&nbsp;https://secure-web.cisco.com/1kdXnIzyrqnSlUAKpjf6Ehu2NoR_fdE1tNkmf4n7Lq04PP3... the file "dwi_orig_las.1.bvals“ was renamed to „dwi_orig_las.bvals“ &nbsp;earlier in the runmv -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.bvalsit 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 advanceRegardsJürgen—————— 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/dwiEddyInputError: &nbsp;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.txtTerminating programLinux 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/Linuxtrac-preproc exited with ERRORS at Wed Oct 27 13:41:49 CEST 2021upd-159253:/mnt/981dac6a-ec33-4a79-9c9e-588e004c6806/Juergen/01_IPS_Project/DTI_DATA/03_TRACULA_Test&gt;——————_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduMailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be&nbsp;https://secure-web.cisco.com/1s2hfIaO8Fd-4kPJit80Ioh7TPfSykIu_rzSPDQUw2yIWUx... information in this e-mail is intended only for the person to whom it is addressed. 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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&nbsp;MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be&nbsp;http://secure-web.cisco.com/1AAfp-_alHB0TRruMwtGnwwgSfdBuy0Jaw1vM1xKcxx0ZSei... 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). &nbsp;If you do not wish to continue communication over unencrypted e-mail, please notify the sender of this message immediately. &nbsp;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..&nbsp;_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduMailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be&nbsp;https://secure-web.cisco.com/1s2hfIaO8Fd-4kPJit80Ioh7TPfSykIu_rzSPDQUw2yIWUx... 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&nbsp;MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be&nbsp;http://secure-web.cisco.com/1AAfp-_alHB0TRruMwtGnwwgSfdBuy0Jaw1vM1xKcxx0ZSei... 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). &nbsp;If you do not wish to continue communication over unencrypted e-mail, please notify the sender of this message immediately. &nbsp;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.&nbsp;_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer________________... mailing listFreesurfer@nmr.mgh..harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer