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.salard...@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-boun...@nmr.mgh.harvard.edu <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Yendiki, Anastasia <ayend...@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: https://secure-web.cisco.com/1QnguQ42otHDarKwoG5RdIlCXLNRkT1FwKRKnn8jwMfQ57GLPXdDoNARFIF6Fs3QGeru2CW2fxEwpULdDljkQFA8DSLPxE9XNRO-9YXhG1EBED9ih5BC-XYo367P_0rLRP_kXSBnOQYlMLBhJ_faly_bdFB5Ts-gLCd4a1WS-GL3M_8rgS0VSWDEHeAe2tk3Ocu0572_1hWu2uouekRhQyP_kR2ojtg7Sn-Mn7iD3ltlAA-eWeT2KncSlj73Z_65IaDAu4wK_cBor2jmGiFaqZoI5miK9vOtYhBrNh2qldX0B-LoIcP7xuA2MvEQvkFfKpyZdaalaOtfbuMNFyOW10g/https%3A%2F%2Fgithub.com%2Ffreesurfer%2Ffreesurfer%2Fblob%2Fdev%2Fscripts%2Fdmri_bids_config<https://secure-web.cisco.com/1H-9mB5cXx6rp7wA8hpT_BzOZokigLP9EodDBvbhbwq2dNB7quKhofx60GML4lxCCydzj7VZBk5ZBY1mraR5jrwtxsZgwKjvq8t_72-CCqCgQ1RlizC_RDv4bxITXz-usybn5Win5Os2hbhv6TpvIBbE27HPgcHCMsgQuNOJLm50S-PvVxgjE2HDtc6647Y4jz8l6E8XpVJM-W1QStveGXXFCLOXgLTLysvSLq-fjGIqbwh7V8xSPyzuqeqsxQyx0YbSBtjHFJpYNCdhQBISV9GuMO088ysKCl0Vwd8YCDrifAxcGd54Q-caMGVrm6N2HVVkneMBsNIkNYGNwAuBmtw/https%3A%2F%2Fnam12.safelinks.protection.outlook.com%2F%3Furl%3Dhttps%253A%252F%252Fgithub.com%252Ffreesurfer%252Ffreesurfer%252Fblob%252Fdev%252Fscripts%252Fdmri_bids_config%26data%3D04%257C01%257Celaheh.salardini%2540yale.edu%257Cbdf6a67dbea54b46226808d9bb46f97a%257Cdd8cbebb21394df8b4114e3e87abeb5c%257C0%257C0%257C637746735775914576%257CUnknown%257CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%253D%257C3000%26sdata%3D0tciIgIkPmrifx8r1Fgwmjx3csGNkQXrsSD4p6ZSSeQ%253D%26reserved%3D0> Anastasia. ________________________________ From: freesurfer-boun...@nmr.mgh.harvard.edu <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Salar Dini, Elaheh <elaheh.salard...@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 External Email - Use Caution 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
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
