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Hello,

I've just realized that one of our fellow freesurfer user, Jürgen, has faced the same problem which was originating from the file "dwi_orig_las.1.bvals“ was renamed to „dwi_orig_las.bvals“ . Based on Dr. Yendiki's direction is specific to the case when you have 1 DWI run only. Good news is that the bug fix available at 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 did fix the problem. I just saved this version of trac-preproc to my $FREESURFER_HOME/bin/ and it worked. Thanks Anastasia and Jürgen for your previous messages and bug fix. There is no further need to follow-up on this message/email chain as the problem is solved.

Thank you,

Ela

From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Salar Dini, Elaheh <elaheh.salardini@yale.edu>
Sent: Tuesday, December 21, 2021 1:46 PM
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] trac-all -prep error

External Email - Use Caution

Dear Anastasia,

I just wanted to follow-up on my previous message with having this in mind:

the index.txt file should be a line of twenty-six 1, i.e. 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1, in our case. For some reason, Freesurfer or FSL can't extract this from the header of our dwi dicom files. Is there a way I can manually make an index.txt file that won't be overwritten by running trac-all -prep -c and put it in dmri folder , so eddy can be run successfully all the way to the end?

Thank you and all the best

Ela

P.S: Happy holidays

From: Salar Dini, Elaheh <elaheh.salardini@yale.edu>
Sent: Tuesday, December 14, 2021 2:31 PM
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: trac-all -prep error

Good day Anastasia,

Thank you for replying back. It worked like a charm, I also had to add set epifactor, but after that, it started to run, and a dmri folder was created in subject directory as well. However, I'm getting this error right now:

EddyInputError: Error when attempting to read --index file /home2/am2359/fs6_data/TRACULA/subjects_dir/57/dmri/index.txt
Terminating program

In the dmri folder, I can see the index.txt file but when I open the file, it is empty: there is no text in it.

I am attaching trac-all log, trac-all.error and my config file which is named dmriEla. Can you please help me with this error.

Again, if this helps: I'm running freesurfer on Linux Centos7, the version of freesurfer is 7.2.0 and the installed package is freesurfer-linux-centos7_x86_64-7.2.0.tar.gz. The installed fsl version is 6.0.5.1 .

Thank you as always.

Kindly,

Ela

From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Yendiki, Anastasia <AYENDIKI@mgh.harvard.edu>
Sent: Thursday, December 9, 2021 2:05 PM
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] trac-all -prep error

Hi Ela - Do you know what phase-encode direction your DWIs were collected with (e.g. AP, PA, LR, etc.)? Then add it to the config file like this: "set pedir = (AP)"

Otherwise, if your data are stored in BIDS format, there's a new script that will figure all this out and generate the configuration file automatically:

MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://github.com/freesurfer/freesurfer/blob/dev/scripts/dmri_bids_config

Anastasia.

From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Salar Dini, Elaheh <elaheh.salardini@yale.edu>
Sent: Thursday, December 9, 2021 10:31 AM
To: freesurfer@nmr.mgh.harvard.edu <freesurfer@nmr.mgh.harvard.edu>
Subject: [Freesurfer] trac-all -prep error

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Dear freesurfer developers and Dr. Yendiki,

I am trying to run trac-all -prep -c dmriEla, dmriEla being my config file. I am attaching the config file here. If I perform registration-based correction with eddy_correct, doeddy=1, things start to run. However, if I use doeddy=2, model-based correction with eddy, I get the following error:

ERROR: for B0 distortion correction with reverse-polarity DWIs

ERROR: or for model-based eddy-current distortion correction,

ERROR: must specify PE direction

No Trac-all.log file is created. If needed, I can also send you a few anonymized slices from the acquired DTI series, so you can check the header. Moreover, I can send you the acquisition sequence properties as a PDF file if needed.

Is there a way to fix this problem? In other words, can we do something to be able to use model-based correction instead of registration-based questions since it seems to be a more sophisticated method?

I'm running freesurfer on Linux Centos7, the version of freesurfer is 7.2.0 and the installed package is freesurfer-linux-centos7_x86_64-7.2.0.tar.gz.

I really do appreciate your time and help.

Ela