External Email - Use Caution

Dear Anastasia,

Thank you so much for your help. So silly of me, the trac-all prep step went off alright after I fixed the config file but it now gives me the error:

ERROR: must set ANTSPATH environment variable to use ANTs

I noticed on a previous thread that another user had a similar issue, so I also decided to install ANTs. As with them, I am also running into a lot of issues installing ANTs and you mentioned in the thread that using ANTs for registration is optional in the new versions of TRACULA. Would you please recommend how to go about the option of not running ANTs? Is it an option I need to set/add to the config file for TRACULA?

Thanks again!

Best, Ashwati

-- Ashwati Vipin (PhD) Research Fellow – Dementia Research Centre (Singapore) Lee Kong Chian School of Medicine Nanyang Technological University, Singapore http://secure-web.cisco.com/1ALbfL6HUWQ102wtDdlcndwGvtRHHmAeUL5hyp7Au2LGf1D5...http://secure-web.cisco.com/1ALbfL6HUWQ102wtDdlcndwGvtRHHmAeUL5hyp7Au2LGf1D5ocwRxxevxGSl67YdnZtfgLO9yU82Ldn77UMeofTXSczAsXgl2wzcvfaJo3mMxawjSF8MpPn0bHQuT3I8Y02wqazYydoYY8jt8z0uEWUr4zbUj9CHzyI7dGZGvrdmgbuwtoDzSr11t4mLQbid5gaCZLDx-1L5rWx9UYA-6nGhndj5Cozc6YK0-xl_KIFSUN_yYholWOD9wMxhTYP7JNLTIzG7O67mV9Xsgv70Lj4KJF_V4LprJdiyub61bKrs4aaaWLqitYPmq4XXsYbIL/http%3A%2F%2Fwww.drcs.sg [signature_2362934844]

From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Yendiki, Anastasia AYENDIKI@MGH.HARVARD.EDU Date: Friday, 19 August 2022 at 2:39 AM To: freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Unable to run trac-all -prep : cannot file bvals bvecs file Dear Ashwati - Check out the instructions in the example config file: https://secure-web.cisco.com/1hfjFDlVnT9-TLUEkl2rZReuG3HJkCTuMOInrw3QQbM0TPj...

... # Diffusion gradient tables (file names can be relative to dcmroot) ... # Diffusion b-value tables (file names can be relative to dcmroot) ...

Because you defined dcmroot, these filenames should be relative paths (which you did correctly for the DWI nifti file). The error occurs because it prepends dcmroot to the filenames you provided, so there's a replication (check what the error says and you'll see that).

Best, Anastasia.

________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Ashwati Vipin (Dr) ashwati.vipin@ntu.edu.sg Sent: Tuesday, August 16, 2022 9:50 PM To: freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] Unable to run trac-all -prep : cannot file bvals bvecs file

External Email - Use Caution

Dear Freesurfer developers,

I am running the trac-all -prep for my DWI data on Freesurfer version 7.2.0. The configuration file seems to be alright but when I start running the -prep step it gives me the error:

writing to /Volumes/DRCS_MAIN_SERVER/DRCS/BIOCIS/Neuroimaging/Stats/Freesurfer/diffusion_tracula/BIOC_0001_v01_FS/dmri/dwi_orig.1.nii.gz...

/Volumes/DRCS_MAIN_SERVER/DRCS/BIOCIS/Neuroimaging/Stats/Freesurfer/diffusion_tracula//Volumes/DRCS_MAIN_SERVER/DRCS/BIOCIS/Neuroimaging/Stats/Freesurfer/diffusion_tracula/BIOC_0001_v01_FS/bvecs.txt: No such file or directory.

Darwin DRCSs-iMac.local 21.5.0 Darwin Kernel Version 21.5.0: Tue Apr 26 21:08:22 PDT 2022; root:xnu-8020.121.3~4/RELEASE_X86_64 x86_64

trac-preproc exited with ERRORS at Mon Aug 15 11:32:11 +08 2022

I have attached the log file, error file, bvals and bvecs and the configuration file and as the screenshot below shows: the directory does have the bvals.txt and bvecs.txt files, so I’m not sure why it’s giving me this error? I thought the error was because the bvals and bvecs were given in rows, so I transposed them so they are now in columns but it still doesn’t work.

[cid2203429043*image001.png@01D8B09D.94718010]

I have run tracula before with no issues so I’m really lost here. Could you please help?

Thank you so much!

Best,

Ashwati

--

Ashwati Vipin (PhD)

Research Fellow - Dementia Research Centre (Singapore)

Lee Kong Chian School of Medicine

Nanyang Technological University, Singapore

http://secure-web.cisco.com/1ALbfL6HUWQ102wtDdlcndwGvtRHHmAeUL5hyp7Au2LGf1D5...

[signature_3677307404]

From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Ashwati Vipin (Dr) ashwati.vipin@ntu.edu.sg Date: Monday, 15 August 2022 at 11:59 AM To: freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] Unable to run trac-all -prep : cannot file bvals bvecs file

External Email - Use Caution

Dear Freesurfer developers,

I am running the trac-all -prep for my DWI data on Freesurfer version 7.2.0. The configuration file seems to be alright but when I start running the -prep step it gives me the error:

writing to /Volumes/DRCS_MAIN_SERVER/DRCS/BIOCIS/Neuroimaging/Stats/Freesurfer/diffusion_tracula/BIOC_0001_v01_FS/dmri/dwi_orig.1.nii.gz...

/Volumes/DRCS_MAIN_SERVER/DRCS/BIOCIS/Neuroimaging/Stats/Freesurfer/diffusion_tracula//Volumes/DRCS_MAIN_SERVER/DRCS/BIOCIS/Neuroimaging/Stats/Freesurfer/diffusion_tracula/BIOC_0001_v01_FS/bvecs.txt: No such file or directory.

Darwin DRCSs-iMac.local 21.5.0 Darwin Kernel Version 21.5.0: Tue Apr 26 21:08:22 PDT 2022; root:xnu-8020.121.3~4/RELEASE_X86_64 x86_64

trac-preproc exited with ERRORS at Mon Aug 15 11:32:11 +08 2022

I have attached the log file, error file, bvals and bvecs and the configuration file and as the screenshot below shows: the directory does have the bvals.txt and bvecs.txt files, so I’m not sure why it’s giving me this error? I thought the error was because the bvals and bvecs were given in rows, so I transposed them so they are now in columns but it still doesn’t work.

[cid:image001.png@01D8B09D.94718010]

I have run tracula before with no issues so I’m really lost here. Could you please help?

Thank you so much!

Best,

Ashwati

________________________________

CONFIDENTIALITY: This email is intended solely for the person(s) named and may be confidential and/or privileged. If you are not the intended recipient, please delete it, notify us and do not copy, use, or disclose its contents. Towards a sustainable earth: Print only when necessary. Thank you.

External Email - Use Caution

Hi,

If you're having trouble building ANTs, you might be interested in the ANTs binaries now available from Github for Mac and Linux.

https://secure-web.cisco.com/1RXhqmCs7-WVg_KC9lhxGwKP70O312wiPAKH8FBHdof2b4d...

The zip files will unzip to a folder ants-2.4.1. So you would do (in bash)

export ANTSPATH=/path/to/ants-2.4.1/bin/

including the trailing slash, and replacing `/path/to` with wherever you unzipped the archive.

From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Ashwati Vipin (Dr) ashwati.vipin@ntu.edu.sg Date: Wednesday, August 24, 2022 at 1:14 AM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu, AYENDIKI@MGH.HARVARD.EDU AYENDIKI@mgh.harvard.edu Subject: [External] Re: [Freesurfer] Unable to run trac-all -prep : cannot file bvals bvecs file

External Email - Use Caution Dear Anastasia,

Thank you so much for your help. So silly of me, the trac-all prep step went off alright after I fixed the config file but it now gives me the error:

ERROR: must set ANTSPATH environment variable to use ANTs

I noticed on a previous thread that another user had a similar issue, so I also decided to install ANTs. As with them, I am also running into a lot of issues installing ANTs and you mentioned in the thread that using ANTs for registration is optional in the new versions of TRACULA. Would you please recommend how to go about the option of not running ANTs? Is it an option I need to set/add to the config file for TRACULA?

Thanks again!

Best, Ashwati

-- Ashwati Vipin (PhD) Research Fellow – Dementia Research Centre (Singapore) Lee Kong Chian School of Medicine Nanyang Technological University, Singapore MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be http://secure-web.cisco.com/1djs-LcxMXctrKK9R9AUoZZvddL6yg4XTbLx3g3Cwac8aIs-...http://secure-web.cisco.com/1s-YrY65w1FiOKsiW-0G9wV-PrOTvYBUtuqG6JSfx_h5LzzCIpe7EHL_5-qq7C2iDx7WVshhnF_iZBeXxpB_9ZEpXHj_IR4nYKMjs19yViLFzr5N_X0a1xt_51IwqkF4wptKuU6wCgYdEWgj_uLped9HZIKDpF3Y6iXJXxOk_bb3eqlk1n-9-1cVBLxbxLGvEtWnZSdEnS3hWxw6avRbXQz6tbrfP4JnyfBQXSNwV4kYHpaOXHCHr57SuKAPxBnw1MvUD7EpqnGm25IGiIxLY7XzsqHsRAyGw-NMeYZDugacU4nTn26on7aD5R-Ox3o7J/http%3A%2F%2Fwww.drcs.sg [signature_2362934844]

From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Yendiki, Anastasia AYENDIKI@MGH.HARVARD.EDU Date: Friday, 19 August 2022 at 2:39 AM To: freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Unable to run trac-all -prep : cannot file bvals bvecs file Dear Ashwati - Check out the instructions in the example config file: MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://secure-web.cisco.com/192xIRSZjbL42omDAsLZN7pBx2Ui3xwFNm44aHg-SqxXN7G...https://secure-web.cisco.com/1ET4-uSvOKpKyTr2DcbBV3NGuucGOuyiR0U8TloSTyLRfls8g1s0lzLXCh_VL4_en0-iwZv6waGGBXE04R5OlV7H-oUSRhxP1LIB8jLNx-1hH5GqFHSmstITlCa6lgPqR2NHg4ATD9VPX5mlAAe3qPOjiHwDFUKMT9xtOS92Hf6z39te_wcpf86f9V9Tg-YR07vCyyWmUeo6nfNa77lZ4wnSwnNTkI0OF7z4pGN9NlPEDjK870z5bXA4aJrTs07FWlBsJI4a3ujU1pFMgHpphEXqLAjsu6KZm0aqk771PXMfPvtK8bi7hW0RlwK4fi18GGZRnpsYqyoumbK9-rzEySQ/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2Fdmrirc

... # Diffusion gradient tables (file names can be relative to dcmroot) ... # Diffusion b-value tables (file names can be relative to dcmroot) ...

Because you defined dcmroot, these filenames should be relative paths (which you did correctly for the DWI nifti file). The error occurs because it prepends dcmroot to the filenames you provided, so there's a replication (check what the error says and you'll see that).

Best, Anastasia.

________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Ashwati Vipin (Dr) ashwati.vipin@ntu.edu.sg Sent: Tuesday, August 16, 2022 9:50 PM To: freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] Unable to run trac-all -prep : cannot file bvals bvecs file

External Email - Use Caution

Dear Freesurfer developers,

I am running the trac-all -prep for my DWI data on Freesurfer version 7.2.0. The configuration file seems to be alright but when I start running the -prep step it gives me the error:

writing to /Volumes/DRCS_MAIN_SERVER/DRCS/BIOCIS/Neuroimaging/Stats/Freesurfer/diffusion_tracula/BIOC_0001_v01_FS/dmri/dwi_orig.1.nii.gz...

/Volumes/DRCS_MAIN_SERVER/DRCS/BIOCIS/Neuroimaging/Stats/Freesurfer/diffusion_tracula//Volumes/DRCS_MAIN_SERVER/DRCS/BIOCIS/Neuroimaging/Stats/Freesurfer/diffusion_tracula/BIOC_0001_v01_FS/bvecs.txt: No such file or directory.

Darwin DRCSs-iMac.local 21.5.0 Darwin Kernel Version 21.5.0: Tue Apr 26 21:08:22 PDT 2022; root:xnu-8020.121.3~4/RELEASE_X86_64 x86_64

trac-preproc exited with ERRORS at Mon Aug 15 11:32:11 +08 2022

I have attached the log file, error file, bvals and bvecs and the configuration file and as the screenshot below shows: the directory does have the bvals.txt and bvecs.txt files, so I’m not sure why it’s giving me this error? I thought the error was because the bvals and bvecs were given in rows, so I transposed them so they are now in columns but it still doesn’t work.

[cid2203429043*image001.png@01D8B09D.94718010]

I have run tracula before with no issues so I’m really lost here. Could you please help?

Thank you so much!

Best,

Ashwati

--

Ashwati Vipin (PhD)

Research Fellow - Dementia Research Centre (Singapore)

Lee Kong Chian School of Medicine

Nanyang Technological University, Singapore

http://secure-web.cisco.com/1djs-LcxMXctrKK9R9AUoZZvddL6yg4XTbLx3g3Cwac8aIs-...

[signature_3677307404]

From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Ashwati Vipin (Dr) ashwati.vipin@ntu.edu.sg Date: Monday, 15 August 2022 at 11:59 AM To: freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] Unable to run trac-all -prep : cannot file bvals bvecs file

External Email - Use Caution

Dear Freesurfer developers,

I am running the trac-all -prep for my DWI data on Freesurfer version 7.2.0. The configuration file seems to be alright but when I start running the -prep step it gives me the error:

writing to /Volumes/DRCS_MAIN_SERVER/DRCS/BIOCIS/Neuroimaging/Stats/Freesurfer/diffusion_tracula/BIOC_0001_v01_FS/dmri/dwi_orig.1.nii.gz...

/Volumes/DRCS_MAIN_SERVER/DRCS/BIOCIS/Neuroimaging/Stats/Freesurfer/diffusion_tracula//Volumes/DRCS_MAIN_SERVER/DRCS/BIOCIS/Neuroimaging/Stats/Freesurfer/diffusion_tracula/BIOC_0001_v01_FS/bvecs.txt: No such file or directory.

Darwin DRCSs-iMac.local 21.5.0 Darwin Kernel Version 21.5.0: Tue Apr 26 21:08:22 PDT 2022; root:xnu-8020.121.3~4/RELEASE_X86_64 x86_64

trac-preproc exited with ERRORS at Mon Aug 15 11:32:11 +08 2022

I have attached the log file, error file, bvals and bvecs and the configuration file and as the screenshot below shows: the directory does have the bvals.txt and bvecs.txt files, so I’m not sure why it’s giving me this error? I thought the error was because the bvals and bvecs were given in rows, so I transposed them so they are now in columns but it still doesn’t work.

[cid:image001.png@01D8B09D.94718010]

I have run tracula before with no issues so I’m really lost here. Could you please help?

Thank you so much!

Best,

Ashwati

________________________________

CONFIDENTIALITY: This email is intended solely for the person(s) named and may be confidential and/or privileged. If you are not the intended recipient, please delete it, notify us and do not copy, use, or disclose its contents. Towards a sustainable earth: Print only when necessary. Thank you.

External Email - Use Caution

Thank you! I didn’t run into the ANTs error after following the steps you mentioned. However, my trac-all -prep keeps ending abruptly without any error warning as below:

[cid:image005.png@01D8B937.AC0099D0]

The subject’s scripts folder still has an IsRunning.trac file. I’ve attached the log files and my configuration file. Not sure what’s going wrong?

Best, Ashwati

-- Ashwati Vipin (PhD) Research Fellow - Dementia Research Centre (Singapore) Lee Kong Chian School of Medicine Nanyang Technological University, Singapore http://secure-web.cisco.com/1_zBE50d8KEwTelAmS63-BQF2XbKIhokBNy4i2O4AH_OrlHQ... [signature_2362934844]

From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Ashwati Vipin (Dr) ashwati.vipin@ntu.edu.sg Date: Friday, 26 August 2022 at 10:56 AM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu, cookpa@pennmedicine.upenn.edu cookpa@pennmedicine.upenn.edu Subject: Re: [Freesurfer] [External] Re: Unable to run trac-all -prep : cannot file bvals bvecs file

External Email - Use Caution Thank you! I didn’t run into the ANTs error after following the steps you mentioned. However, my trac-all -prep keeps ending abruptly without any error warning as below:

[cid:image005.png@01D8B937.AC0099D0]

The subject’s scripts folder still has an IsRunning.trac file. I’ve attached the log files and my configuration file. Not sure what’s going wrong?

Best, Ashwati

-- Ashwati Vipin (PhD) Research Fellow – Dementia Research Centre (Singapore) Lee Kong Chian School of Medicine Nanyang Technological University, Singapore MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be http://secure-web.cisco.com/1_zBE50d8KEwTelAmS63-BQF2XbKIhokBNy4i2O4AH_OrlHQ...http://secure-web.cisco.com/1Ecmi2uO8XbHDAozYYpNPzezLAdNwtcH3ZRYroa9azSgJmfIwbvkvHqL_WsyfeJ78QqhrB27hvXjF9-Q0ZTfO3yl2xfiu2Ldeg8QHwvxRAC0B1ez2vR7_B9zR8u3MndEYitq-MNdNjw_4eOvDLM1jGcXdi2_K1TikmH1OANKkCC20xksk4I4b0zyijj0DcgfDzmImmHBBlqq3P6d8yjDxrtYcxW3fkmUvH22GN74gidGdPWHkHasPtSdNIYG3TWs7y4gZ9hTMf37QAp6t3idUyinzoW0zu60XxqMm41yOz_Ae_svxCxLQKx7Iqhz8ENqR/http%3A%2F%2Fwww.drcs.sg [signature_2362934844]

From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Cook, Philip cookpa@pennmedicine.upenn.edu Date: Wednesday, 24 August 2022 at 9:23 PM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu, AYENDIKI@MGH.HARVARD.EDU AYENDIKI@MGH.HARVARD.EDU Subject: Re: [Freesurfer] [External] Re: Unable to run trac-all -prep : cannot file bvals bvecs file

External Email - Use Caution Hi,

If you're having trouble building ANTs, you might be interested in the ANTs binaries now available from Github for Mac and Linux.

MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://secure-web.cisco.com/1ljr0E8ExRz7THiBaOcihV8g_qsKN7bVoJjo4WnfagiLtJU...https://secure-web.cisco.com/1RXhqmCs7-WVg_KC9lhxGwKP70O312wiPAKH8FBHdof2b4d2NZH6ObWMEOg5iQwOZle7WB8yy-aLq3rNZDat3Afs3nxkhrjPuPcr9cObRWaVvpVc36Bq31xCUkMceOh_WphSZENnY7x4gT9ctwNV-cZqp_IxFWUv7yFTOP2hHm2djwPTpvlXsm2X9iUFOFebRKCQt5YXoYEEMxTDJPXj9W79lwbRYgiRS0eBGxoURg_tGfjoML1fr4xbCgnrMCT11RPzelJA_0tfqEu4cU6O9FQdjg-8udQLYiWdQXtwosizAYBLKKgX-pm-_tM9o_U9f__W-mqMq4DrQJ6GaC5exLA/https%3A%2F%2Fgithub.com%2FANTsX%2FANTs%2Freleases%2Ftag%2Fv2.4.1

The zip files will unzip to a folder ants-2.4.1. So you would do (in bash)

export ANTSPATH=/path/to/ants-2.4.1/bin/

including the trailing slash, and replacing `/path/to` with wherever you unzipped the archive.

From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Ashwati Vipin (Dr) ashwati.vipin@ntu.edu.sg Date: Wednesday, August 24, 2022 at 1:14 AM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu, AYENDIKI@MGH.HARVARD.EDU AYENDIKI@mgh.harvard.edu Subject: [External] Re: [Freesurfer] Unable to run trac-all -prep : cannot file bvals bvecs file

External Email - Use Caution Dear Anastasia,

Thank you so much for your help. So silly of me, the trac-all prep step went off alright after I fixed the config file but it now gives me the error:

ERROR: must set ANTSPATH environment variable to use ANTs

I noticed on a previous thread that another user had a similar issue, so I also decided to install ANTs. As with them, I am also running into a lot of issues installing ANTs and you mentioned in the thread that using ANTs for registration is optional in the new versions of TRACULA. Would you please recommend how to go about the option of not running ANTs? Is it an option I need to set/add to the config file for TRACULA?

Thanks again!

Best, Ashwati

-- Ashwati Vipin (PhD) Research Fellow – Dementia Research Centre (Singapore) Lee Kong Chian School of Medicine Nanyang Technological University, Singapore MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be http://secure-web.cisco.com/1_zBE50d8KEwTelAmS63-BQF2XbKIhokBNy4i2O4AH_OrlHQ...http://secure-web.cisco.com/1s-YrY65w1FiOKsiW-0G9wV-PrOTvYBUtuqG6JSfx_h5LzzCIpe7EHL_5-qq7C2iDx7WVshhnF_iZBeXxpB_9ZEpXHj_IR4nYKMjs19yViLFzr5N_X0a1xt_51IwqkF4wptKuU6wCgYdEWgj_uLped9HZIKDpF3Y6iXJXxOk_bb3eqlk1n-9-1cVBLxbxLGvEtWnZSdEnS3hWxw6avRbXQz6tbrfP4JnyfBQXSNwV4kYHpaOXHCHr57SuKAPxBnw1MvUD7EpqnGm25IGiIxLY7XzsqHsRAyGw-NMeYZDugacU4nTn26on7aD5R-Ox3o7J/http%3A%2F%2Fwww.drcs.sg [signature_2362934844]

From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Yendiki, Anastasia AYENDIKI@MGH.HARVARD.EDU Date: Friday, 19 August 2022 at 2:39 AM To: freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Unable to run trac-all -prep : cannot file bvals bvecs file Dear Ashwati - Check out the instructions in the example config file: MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://secure-web.cisco.com/1X84TIzZ-YHDYCbf97Hoz65OrR1tHZn2ZMCDHYG1UOHmIXV...https://secure-web.cisco.com/1ET4-uSvOKpKyTr2DcbBV3NGuucGOuyiR0U8TloSTyLRfls8g1s0lzLXCh_VL4_en0-iwZv6waGGBXE04R5OlV7H-oUSRhxP1LIB8jLNx-1hH5GqFHSmstITlCa6lgPqR2NHg4ATD9VPX5mlAAe3qPOjiHwDFUKMT9xtOS92Hf6z39te_wcpf86f9V9Tg-YR07vCyyWmUeo6nfNa77lZ4wnSwnNTkI0OF7z4pGN9NlPEDjK870z5bXA4aJrTs07FWlBsJI4a3ujU1pFMgHpphEXqLAjsu6KZm0aqk771PXMfPvtK8bi7hW0RlwK4fi18GGZRnpsYqyoumbK9-rzEySQ/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2Fdmrirc

... # Diffusion gradient tables (file names can be relative to dcmroot) ... # Diffusion b-value tables (file names can be relative to dcmroot) ...

Because you defined dcmroot, these filenames should be relative paths (which you did correctly for the DWI nifti file). The error occurs because it prepends dcmroot to the filenames you provided, so there's a replication (check what the error says and you'll see that).

Best, Anastasia.

________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Ashwati Vipin (Dr) ashwati.vipin@ntu.edu.sg Sent: Tuesday, August 16, 2022 9:50 PM To: freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] Unable to run trac-all -prep : cannot file bvals bvecs file

External Email - Use Caution

Dear Freesurfer developers,

I am running the trac-all -prep for my DWI data on Freesurfer version 7.2.0. The configuration file seems to be alright but when I start running the -prep step it gives me the error:

writing to /Volumes/DRCS_MAIN_SERVER/DRCS/BIOCIS/Neuroimaging/Stats/Freesurfer/diffusion_tracula/BIOC_0001_v01_FS/dmri/dwi_orig.1.nii.gz...

/Volumes/DRCS_MAIN_SERVER/DRCS/BIOCIS/Neuroimaging/Stats/Freesurfer/diffusion_tracula//Volumes/DRCS_MAIN_SERVER/DRCS/BIOCIS/Neuroimaging/Stats/Freesurfer/diffusion_tracula/BIOC_0001_v01_FS/bvecs.txt: No such file or directory.

Darwin DRCSs-iMac.local 21.5.0 Darwin Kernel Version 21.5.0: Tue Apr 26 21:08:22 PDT 2022; root:xnu-8020.121.3~4/RELEASE_X86_64 x86_64

trac-preproc exited with ERRORS at Mon Aug 15 11:32:11 +08 2022

I have attached the log file, error file, bvals and bvecs and the configuration file and as the screenshot below shows: the directory does have the bvals.txt and bvecs.txt files, so I’m not sure why it’s giving me this error? I thought the error was because the bvals and bvecs were given in rows, so I transposed them so they are now in columns but it still doesn’t work.

[cid2203429043*image001.png@01D8B09D.94718010]

I have run tracula before with no issues so I’m really lost here. Could you please help?

Thank you so much!

Best,

Ashwati

--

Ashwati Vipin (PhD)

Research Fellow - Dementia Research Centre (Singapore)

Lee Kong Chian School of Medicine

Nanyang Technological University, Singapore

http://secure-web.cisco.com/1_zBE50d8KEwTelAmS63-BQF2XbKIhokBNy4i2O4AH_OrlHQ...

[signature_3677307404]

From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Ashwati Vipin (Dr) ashwati.vipin@ntu.edu.sg Date: Monday, 15 August 2022 at 11:59 AM To: freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] Unable to run trac-all -prep : cannot file bvals bvecs file

External Email - Use Caution

Dear Freesurfer developers,

I am running the trac-all -prep for my DWI data on Freesurfer version 7.2.0. The configuration file seems to be alright but when I start running the -prep step it gives me the error:

writing to /Volumes/DRCS_MAIN_SERVER/DRCS/BIOCIS/Neuroimaging/Stats/Freesurfer/diffusion_tracula/BIOC_0001_v01_FS/dmri/dwi_orig.1.nii.gz...

/Volumes/DRCS_MAIN_SERVER/DRCS/BIOCIS/Neuroimaging/Stats/Freesurfer/diffusion_tracula//Volumes/DRCS_MAIN_SERVER/DRCS/BIOCIS/Neuroimaging/Stats/Freesurfer/diffusion_tracula/BIOC_0001_v01_FS/bvecs.txt: No such file or directory.

Darwin DRCSs-iMac.local 21.5.0 Darwin Kernel Version 21.5.0: Tue Apr 26 21:08:22 PDT 2022; root:xnu-8020.121.3~4/RELEASE_X86_64 x86_64

trac-preproc exited with ERRORS at Mon Aug 15 11:32:11 +08 2022

I have attached the log file, error file, bvals and bvecs and the configuration file and as the screenshot below shows: the directory does have the bvals.txt and bvecs.txt files, so I’m not sure why it’s giving me this error? I thought the error was because the bvals and bvecs were given in rows, so I transposed them so they are now in columns but it still doesn’t work.

[cid:image001.png@01D8B09D.94718010]

I have run tracula before with no issues so I’m really lost here. Could you please help?

Thank you so much!

Best,

Ashwati

________________________________

CONFIDENTIALITY: This email is intended solely for the person(s) named and may be confidential and/or privileged. If you are not the intended recipient, please delete it, notify us and do not copy, use, or disclose its contents. Towards a sustainable earth: Print only when necessary. Thank you.

External Email - Use Caution

Sending this again – please help!

Thank you! I didn’t run into the ANTs error after following the steps you mentioned. However, my trac-all -prep keeps ending abruptly without any error warning as below:

[cid:image005.png@01D8B937.AC0099D0]

The subject’s scripts folder still has an IsRunning.trac file. I’ve attached the log files and my configuration file. Not sure what’s going wrong?

Best, Ashwati

-- Ashwati Vipin (PhD) Research Fellow - Dementia Research Centre (Singapore) Lee Kong Chian School of Medicine Nanyang Technological University, Singapore http://secure-web.cisco.com/1Mp1DylM5h6c4CIIcZWu72HiXi-zehmeWm1iKsSQx-2rMeCj... [signature_2362934844]

From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Ashwati Vipin (Dr) ashwati.vipin@ntu.edu.sg Date: Thursday, 1 September 2022 at 12:22 PM To: freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu Cc: Yendiki, Anastasia AYENDIKI@MGH.HARVARD.EDU, Cook, Philip cookpa@pennmedicine.upenn.edu Subject: Re: [Freesurfer] Unable to run trac-all -prep : cannot file bvals bvecs file

External Email - Use Caution Sending this again – please help!

Thank you! I didn’t run into the ANTs error after following the steps you mentioned. However, my trac-all -prep keeps ending abruptly without any error warning as below:

[cid:image005.png@01D8B937.AC0099D0]

The subject’s scripts folder still has an IsRunning.trac file. I’ve attached the log files and my configuration file. Not sure what’s going wrong?

Best, Ashwati

-- Ashwati Vipin (PhD) Research Fellow - Dementia Research Centre (Singapore) Lee Kong Chian School of Medicine Nanyang Technological University, Singapore http://secure-web.cisco.com/1Mp1DylM5h6c4CIIcZWu72HiXi-zehmeWm1iKsSQx-2rMeCj... [signature_2362934844]

From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Ashwati Vipin (Dr) ashwati.vipin@ntu.edu.sg Date: Monday, 29 August 2022 at 10:19 AM To: cookpa@pennmedicine.upenn.edu cookpa@pennmedicine.upenn.edu, freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] [External] Re: Unable to run trac-all -prep : cannot file bvals bvecs file

External Email - Use Caution Thank you! I didn’t run into the ANTs error after following the steps you mentioned. However, my trac-all -prep keeps ending abruptly without any error warning as below:

[cid:image005.png@01D8B937.AC0099D0]

The subject’s scripts folder still has an IsRunning.trac file. I’ve attached the log files and my configuration file. Not sure what’s going wrong?

Best, Ashwati

-- Ashwati Vipin (PhD) Research Fellow - Dementia Research Centre (Singapore) Lee Kong Chian School of Medicine Nanyang Technological University, Singapore http://secure-web.cisco.com/1Mp1DylM5h6c4CIIcZWu72HiXi-zehmeWm1iKsSQx-2rMeCj... [signature_2362934844]

From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Ashwati Vipin (Dr) ashwati.vipin@ntu.edu.sg Date: Friday, 26 August 2022 at 10:56 AM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu, cookpa@pennmedicine.upenn.edu cookpa@pennmedicine.upenn.edu Subject: Re: [Freesurfer] [External] Re: Unable to run trac-all -prep : cannot file bvals bvecs file

External Email - Use Caution Thank you! I didn’t run into the ANTs error after following the steps you mentioned. However, my trac-all -prep keeps ending abruptly without any error warning as below:

[cid:image005.png@01D8B937.AC0099D0]

The subject’s scripts folder still has an IsRunning.trac file. I’ve attached the log files and my configuration file. Not sure what’s going wrong?

Best, Ashwati

-- Ashwati Vipin (PhD) Research Fellow – Dementia Research Centre (Singapore) Lee Kong Chian School of Medicine Nanyang Technological University, Singapore MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be http://secure-web.cisco.com/1Mp1DylM5h6c4CIIcZWu72HiXi-zehmeWm1iKsSQx-2rMeCj...http://secure-web.cisco.com/1Ecmi2uO8XbHDAozYYpNPzezLAdNwtcH3ZRYroa9azSgJmfIwbvkvHqL_WsyfeJ78QqhrB27hvXjF9-Q0ZTfO3yl2xfiu2Ldeg8QHwvxRAC0B1ez2vR7_B9zR8u3MndEYitq-MNdNjw_4eOvDLM1jGcXdi2_K1TikmH1OANKkCC20xksk4I4b0zyijj0DcgfDzmImmHBBlqq3P6d8yjDxrtYcxW3fkmUvH22GN74gidGdPWHkHasPtSdNIYG3TWs7y4gZ9hTMf37QAp6t3idUyinzoW0zu60XxqMm41yOz_Ae_svxCxLQKx7Iqhz8ENqR/http%3A%2F%2Fwww.drcs.sg [signature_2362934844]

From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Cook, Philip cookpa@pennmedicine.upenn.edu Date: Wednesday, 24 August 2022 at 9:23 PM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu, AYENDIKI@MGH.HARVARD.EDU AYENDIKI@MGH.HARVARD.EDU Subject: Re: [Freesurfer] [External] Re: Unable to run trac-all -prep : cannot file bvals bvecs file

External Email - Use Caution Hi,

If you're having trouble building ANTs, you might be interested in the ANTs binaries now available from Github for Mac and Linux.

MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://secure-web.cisco.com/1fJXZwdWn4Ek6l2OALn-OMzweRBcmCYemYnKzoY4qOdUW0B...https://secure-web.cisco.com/1RXhqmCs7-WVg_KC9lhxGwKP70O312wiPAKH8FBHdof2b4d2NZH6ObWMEOg5iQwOZle7WB8yy-aLq3rNZDat3Afs3nxkhrjPuPcr9cObRWaVvpVc36Bq31xCUkMceOh_WphSZENnY7x4gT9ctwNV-cZqp_IxFWUv7yFTOP2hHm2djwPTpvlXsm2X9iUFOFebRKCQt5YXoYEEMxTDJPXj9W79lwbRYgiRS0eBGxoURg_tGfjoML1fr4xbCgnrMCT11RPzelJA_0tfqEu4cU6O9FQdjg-8udQLYiWdQXtwosizAYBLKKgX-pm-_tM9o_U9f__W-mqMq4DrQJ6GaC5exLA/https%3A%2F%2Fgithub.com%2FANTsX%2FANTs%2Freleases%2Ftag%2Fv2.4.1

The zip files will unzip to a folder ants-2.4.1. So you would do (in bash)

export ANTSPATH=/path/to/ants-2.4.1/bin/

including the trailing slash, and replacing `/path/to` with wherever you unzipped the archive.

From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Ashwati Vipin (Dr) ashwati.vipin@ntu.edu.sg Date: Wednesday, August 24, 2022 at 1:14 AM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu, AYENDIKI@MGH.HARVARD.EDU AYENDIKI@mgh.harvard.edu Subject: [External] Re: [Freesurfer] Unable to run trac-all -prep : cannot file bvals bvecs file

External Email - Use Caution Dear Anastasia,

Thank you so much for your help. So silly of me, the trac-all prep step went off alright after I fixed the config file but it now gives me the error:

ERROR: must set ANTSPATH environment variable to use ANTs

I noticed on a previous thread that another user had a similar issue, so I also decided to install ANTs. As with them, I am also running into a lot of issues installing ANTs and you mentioned in the thread that using ANTs for registration is optional in the new versions of TRACULA. Would you please recommend how to go about the option of not running ANTs? Is it an option I need to set/add to the config file for TRACULA?

Thanks again!

Best, Ashwati

-- Ashwati Vipin (PhD) Research Fellow – Dementia Research Centre (Singapore) Lee Kong Chian School of Medicine Nanyang Technological University, Singapore MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be http://secure-web.cisco.com/1Mp1DylM5h6c4CIIcZWu72HiXi-zehmeWm1iKsSQx-2rMeCj...http://secure-web.cisco.com/1s-YrY65w1FiOKsiW-0G9wV-PrOTvYBUtuqG6JSfx_h5LzzCIpe7EHL_5-qq7C2iDx7WVshhnF_iZBeXxpB_9ZEpXHj_IR4nYKMjs19yViLFzr5N_X0a1xt_51IwqkF4wptKuU6wCgYdEWgj_uLped9HZIKDpF3Y6iXJXxOk_bb3eqlk1n-9-1cVBLxbxLGvEtWnZSdEnS3hWxw6avRbXQz6tbrfP4JnyfBQXSNwV4kYHpaOXHCHr57SuKAPxBnw1MvUD7EpqnGm25IGiIxLY7XzsqHsRAyGw-NMeYZDugacU4nTn26on7aD5R-Ox3o7J/http%3A%2F%2Fwww.drcs.sg [signature_2362934844]

From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Yendiki, Anastasia AYENDIKI@MGH.HARVARD.EDU Date: Friday, 19 August 2022 at 2:39 AM To: freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Unable to run trac-all -prep : cannot file bvals bvecs file Dear Ashwati - Check out the instructions in the example config file: MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://secure-web.cisco.com/1eRGO3fptU5xGyrsp9r4mMZba1qFRYqw9m2qxlgAfMx1pEg...https://secure-web.cisco.com/1ET4-uSvOKpKyTr2DcbBV3NGuucGOuyiR0U8TloSTyLRfls8g1s0lzLXCh_VL4_en0-iwZv6waGGBXE04R5OlV7H-oUSRhxP1LIB8jLNx-1hH5GqFHSmstITlCa6lgPqR2NHg4ATD9VPX5mlAAe3qPOjiHwDFUKMT9xtOS92Hf6z39te_wcpf86f9V9Tg-YR07vCyyWmUeo6nfNa77lZ4wnSwnNTkI0OF7z4pGN9NlPEDjK870z5bXA4aJrTs07FWlBsJI4a3ujU1pFMgHpphEXqLAjsu6KZm0aqk771PXMfPvtK8bi7hW0RlwK4fi18GGZRnpsYqyoumbK9-rzEySQ/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2Fdmrirc

... # Diffusion gradient tables (file names can be relative to dcmroot) ... # Diffusion b-value tables (file names can be relative to dcmroot) ...

Because you defined dcmroot, these filenames should be relative paths (which you did correctly for the DWI nifti file). The error occurs because it prepends dcmroot to the filenames you provided, so there's a replication (check what the error says and you'll see that).

Best, Anastasia.

________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Ashwati Vipin (Dr) ashwati.vipin@ntu.edu.sg Sent: Tuesday, August 16, 2022 9:50 PM To: freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] Unable to run trac-all -prep : cannot file bvals bvecs file

External Email - Use Caution

Dear Freesurfer developers,

I am running the trac-all -prep for my DWI data on Freesurfer version 7.2.0. The configuration file seems to be alright but when I start running the -prep step it gives me the error:

writing to /Volumes/DRCS_MAIN_SERVER/DRCS/BIOCIS/Neuroimaging/Stats/Freesurfer/diffusion_tracula/BIOC_0001_v01_FS/dmri/dwi_orig.1.nii.gz...

/Volumes/DRCS_MAIN_SERVER/DRCS/BIOCIS/Neuroimaging/Stats/Freesurfer/diffusion_tracula//Volumes/DRCS_MAIN_SERVER/DRCS/BIOCIS/Neuroimaging/Stats/Freesurfer/diffusion_tracula/BIOC_0001_v01_FS/bvecs.txt: No such file or directory.

Darwin DRCSs-iMac.local 21.5.0 Darwin Kernel Version 21.5.0: Tue Apr 26 21:08:22 PDT 2022; root:xnu-8020.121.3~4/RELEASE_X86_64 x86_64

trac-preproc exited with ERRORS at Mon Aug 15 11:32:11 +08 2022

I have attached the log file, error file, bvals and bvecs and the configuration file and as the screenshot below shows: the directory does have the bvals.txt and bvecs.txt files, so I’m not sure why it’s giving me this error? I thought the error was because the bvals and bvecs were given in rows, so I transposed them so they are now in columns but it still doesn’t work.

[cid2203429043*image001.png@01D8B09D.94718010]

I have run tracula before with no issues so I’m really lost here. Could you please help?

Thank you so much!

Best,

Ashwati

--

Ashwati Vipin (PhD)

Research Fellow - Dementia Research Centre (Singapore)

Lee Kong Chian School of Medicine

Nanyang Technological University, Singapore

http://secure-web.cisco.com/1Mp1DylM5h6c4CIIcZWu72HiXi-zehmeWm1iKsSQx-2rMeCj...

[signature_3677307404]

From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Ashwati Vipin (Dr) ashwati.vipin@ntu.edu.sg Date: Monday, 15 August 2022 at 11:59 AM To: freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] Unable to run trac-all -prep : cannot file bvals bvecs file

External Email - Use Caution

Dear Freesurfer developers,

I am running the trac-all -prep for my DWI data on Freesurfer version 7.2.0. The configuration file seems to be alright but when I start running the -prep step it gives me the error:

writing to /Volumes/DRCS_MAIN_SERVER/DRCS/BIOCIS/Neuroimaging/Stats/Freesurfer/diffusion_tracula/BIOC_0001_v01_FS/dmri/dwi_orig.1.nii.gz...

/Volumes/DRCS_MAIN_SERVER/DRCS/BIOCIS/Neuroimaging/Stats/Freesurfer/diffusion_tracula//Volumes/DRCS_MAIN_SERVER/DRCS/BIOCIS/Neuroimaging/Stats/Freesurfer/diffusion_tracula/BIOC_0001_v01_FS/bvecs.txt: No such file or directory.

Darwin DRCSs-iMac.local 21.5.0 Darwin Kernel Version 21.5.0: Tue Apr 26 21:08:22 PDT 2022; root:xnu-8020.121.3~4/RELEASE_X86_64 x86_64

trac-preproc exited with ERRORS at Mon Aug 15 11:32:11 +08 2022

I have attached the log file, error file, bvals and bvecs and the configuration file and as the screenshot below shows: the directory does have the bvals.txt and bvecs.txt files, so I’m not sure why it’s giving me this error? I thought the error was because the bvals and bvecs were given in rows, so I transposed them so they are now in columns but it still doesn’t work.

[cid:image001.png@01D8B09D.94718010]

I have run tracula before with no issues so I’m really lost here. Could you please help?

Thank you so much!

Best,

Ashwati

________________________________

CONFIDENTIALITY: This email is intended solely for the person(s) named and may be confidential and/or privileged. If you are not the intended recipient, please delete it, notify us and do not copy, use, or disclose its contents. Towards a sustainable earth: Print only when necessary. Thank you.

External Email - Use Caution

Dear Freesurfer Developers

my trac-all -prep keeps ending abruptly without any error warning as below:

[cid1124726394*image002.png@01D8C207.8F0775A0]

The subject’s scripts folder still has an IsRunning.trac file. I’ve attached the log files and my configuration file. Not sure what’s going wrong?

Best, Ashwati

-- Ashwati Vipin (PhD) Research Fellow - Dementia Research Centre (Singapore) Lee Kong Chian School of Medicine Nanyang Technological University, Singapore http://secure-web.cisco.com/1U5OXT4QHxissUFZWlvPE9WX4wqaSozTmZOUbpigsORsr3CD... [signature_2362934844]

________________________________

CONFIDENTIALITY: This email is intended solely for the person(s) named and may be confidential and/or privileged. If you are not the intended recipient, please delete it, notify us and do not copy, use, or disclose its contents. Towards a sustainable earth: Print only when necessary. Thank you.