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
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://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
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
External Email - Use Caution
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: https://secure-web.cisco.com/1JsdOkZVCm1JcfRu9OvUzTC1tA9ukZ1oJ015-6VsyLvbwUp...https://secure-web.cisco.com/13oF5GAtEvjQHrdcYeKeP8PNC-iL5DQiYJy5dtKP1PjPoGqstZ8_u7cUzFflBt9yua6odxgRKwvwtIRhsXKgJqSbAYEpGYl4pmLTmpoqRe5tjBNbKcQwEmNb6szIN_oZUpJeOOu32eDDKEga1KTpQk7nTgEY1zWJbgMvP08eEd-uFTkU-7FjQYgSRT2_WD3ylHWmVYmAtHJ0opcqy9lUmh3r55cgGp-dnQrcwsE7kbALR4KlufKn9WLUObau49NpsIPmECMQsK-o2kkg8B69le7unHoxUVuu_pVkkXqOqr0f3wCAkN3gGA28KkBd8jw4-/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-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
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
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: https://secure-web.cisco.com/1QnguQ42otHDarKwoG5RdIlCXLNRkT1FwKRKnn8jwMfQ57G...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-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
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
External Email - Use Caution
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 https://secure-web.cisco.com/1P1sUoJL3537Cb9lrMyseEVWITurRXDbk5PflvQYRdmpLXK... 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://secure-web.cisco.com/1qttQJ3T8RYcpnVFDxb6TWQoEB5Lko_W_IbttKdqyuTMH98...https://secure-web.cisco.com/1-KfIK24Q80F1DSED9sXIlsb26yX1oLrHUaBB67ovEjdVHuuDPWJDdEcVIWTplSpIb7fBOApipPfkv_at9BaAgd87CJiIt1uVOy7ISgv4HEUsFdXIRdm4vQjovEuqNXqZllANuYOsHt9YmjKIZPGkdCGBB39bm5Q8_vildeqm-m9DiQwctH7hAIIw7f1FBp_DeSZ4NvAyziRRvbGECEFpo2meyq8O1EpxDMzy6K4XE0S2ZDxQv-XTLYQzJOBg6utULEwkos2ZbXSZmVakxlWKDZwm4TltIZXpsPj_hwKzv1VMYbFQHl9vjGtjPca8NNyQ/https%3A%2F%2Fnam12.safelinks.protection.outlook.com%2F%3Furl%3Dhttps%253A%252F%252Fsecure-web.cisco.com%252F1H-9mB5cXx6rp7wA8hpT_BzOZokigLP9EodDBvbhbwq2dNB7quKhofx60GML4lxCCydzj7VZBk5ZBY1mraR5jrwtxsZgwKjvq8t_72-CCqCgQ1RlizC_RDv4bxITXz-usybn5Win5Os2hbhv6TpvIBbE27HPgcHCMsgQuNOJLm50S-PvVxgjE2HDtc6647Y4jz8l6E8XpVJM-W1QStveGXXFCLOXgLTLysvSLq-fjGIqbwh7V8xSPyzuqeqsxQyx0YbSBtjHFJpYNCdhQBISV9GuMO088ysKCl0Vwd8YCDrifAxcGd54Q-caMGVrm6N2HVVkneMBsNIkNYGNwAuBmtw%252Fhttps%25253A%25252F%25252Fnam12.safelinks.protection.outlook.com%25252F%25253Furl%25253Dhttps%2525253A%2525252F%2525252Fgithub.com%2525252Ffreesurfer%2525252Ffreesurfer%2525252Fblob%2525252Fdev%2525252Fscripts%2525252Fdmri_bids_config%252526data%25253D04%2525257C01%2525257Celaheh.salardini%25252540yale.edu%2525257Cbdf6a67dbea54b46226808d9bb46f97a%2525257Cdd8cbebb21394df8b4114e3e87abeb5c%2525257C0%2525257C0%2525257C637746735775914576%2525257CUnknown%2525257CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%2525253D%2525257C3000%252526sdata%25253D0tciIgIkPmrifx8r1Fgwmjx3csGNkQXrsSD4p6ZSSeQ%2525253D%252526reserved%25253D0%26data%3D04%257C01%257Celaheh.salardini%2540yale.edu%257C0eb95ad632b048dbcb0a08d9c4b24cfa%257Cdd8cbebb21394df8b4114e3e87abeb5c%257C0%257C0%257C637757092356813034%257CUnknown%257CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%253D%257C3000%26sdata%3DVnEIZKZy5xjrc%252B%252F5LbQcHp9ZKv2AFq3cFFqMOWkek6c%253D%26reserved%3D0
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
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
Glad to hear it worked!
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: Tuesday, December 21, 2021 6:54 PM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] trac-all -prep error
External Email - Use Caution
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-pr...https://secure-web.cisco.com/1P1sUoJL3537Cb9lrMyseEVWITurRXDbk5PflvQYRdmpLXK2Hjt9Bdlc0XGkFamz66-pLShenoTy7fgR9bL-olCcNVpYj9RZHrDB8hGkF7hLevD8lQgYwRBII8A-ShsAy8qHf95o4G20QwUUZwSyWS8C2oPh1xQe3zNh1A6nSfKwmNSVYretONyagt4cg-DlrNCXBIFxN1oLT_EJXWMV-X5PiMberliPc_gf9MqcHbnEOnfRexemqwO8CC6jnSIw3SV_vcuFcMPJS-RBOqrL4ZovQ_f_nHLckqyly4EPwV6GlyerhQt_b_Hc6kMuyIH6K/https%3A%2F%2Fraw.githubusercontent.com%2Fayendiki%2Ffreesurfer%2Ftrcdev%2Fscripts%2Ftrac-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_confighttps://secure-web.cisco.com/1-KfIK24Q80F1DSED9sXIlsb26yX1oLrHUaBB67ovEjdVHuuDPWJDdEcVIWTplSpIb7fBOApipPfkv_at9BaAgd87CJiIt1uVOy7ISgv4HEUsFdXIRdm4vQjovEuqNXqZllANuYOsHt9YmjKIZPGkdCGBB39bm5Q8_vildeqm-m9DiQwctH7hAIIw7f1FBp_DeSZ4NvAyziRRvbGECEFpo2meyq8O1EpxDMzy6K4XE0S2ZDxQv-XTLYQzJOBg6utULEwkos2ZbXSZmVakxlWKDZwm4TltIZXpsPj_hwKzv1VMYbFQHl9vjGtjPca8NNyQ/https%3A%2F%2Fnam12.safelinks.protection.outlook.com%2F%3Furl%3Dhttps%253A%252F%252Fsecure-web.cisco.com%252F1H-9mB5cXx6rp7wA8hpT_BzOZokigLP9EodDBvbhbwq2dNB7quKhofx60GML4lxCCydzj7VZBk5ZBY1mraR5jrwtxsZgwKjvq8t_72-CCqCgQ1RlizC_RDv4bxITXz-usybn5Win5Os2hbhv6TpvIBbE27HPgcHCMsgQuNOJLm50S-PvVxgjE2HDtc6647Y4jz8l6E8XpVJM-W1QStveGXXFCLOXgLTLysvSLq-fjGIqbwh7V8xSPyzuqeqsxQyx0YbSBtjHFJpYNCdhQBISV9GuMO088ysKCl0Vwd8YCDrifAxcGd54Q-caMGVrm6N2HVVkneMBsNIkNYGNwAuBmtw%252Fhttps%25253A%25252F%25252Fnam12.safelinks.protection.outlook.com%25252F%25253Furl%25253Dhttps%2525253A%2525252F%2525252Fgithub.com%2525252Ffreesurfer%2525252Ffreesurfer%2525252Fblob%2525252Fdev%2525252Fscripts%2525252Fdmri_bids_config%252526data%25253D04%2525257C01%2525257Celaheh.salardini%25252540yale.edu%2525257Cbdf6a67dbea54b46226808d9bb46f97a%2525257Cdd8cbebb21394df8b4114e3e87abeb5c%2525257C0%2525257C0%2525257C637746735775914576%2525257CUnknown%2525257CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%2525253D%2525257C3000%252526sdata%25253D0tciIgIkPmrifx8r1Fgwmjx3csGNkQXrsSD4p6ZSSeQ%2525253D%252526reserved%25253D0%26data%3D04%257C01%257Celaheh.salardini%2540yale.edu%257C0eb95ad632b048dbcb0a08d9c4b24cfa%257Cdd8cbebb21394df8b4114e3e87abeb5c%257C0%257C0%257C637757092356813034%257CUnknown%257CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%253D%257C3000%26sdata%3DVnEIZKZy5xjrc%252B%252F5LbQcHp9ZKv2AFq3cFFqMOWkek6c%253D%26reserved%3D0
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
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@nmr.mgh.harvard.edu
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Salar Dini, Elaheh -
Yendiki, Anastasia