Re: [Freesurfer] trac-all -prep error
Glad to hear it worked! Anastasia. From: freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Salar Dini, Elaheh Sent: Tuesday, December 21, 2021 6:54 PM To: Freesurfer support list 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-preproc<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-boun...@nmr.mgh.harvard.edu on behalf of Salar Dini, Elaheh Sent: Tuesday, December 21, 2021 1:46 PM To: Freesurfer support list 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 Sent: Tuesday, December 14, 2021 2:31 PM To: Freesurfer support list 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 on behalf of Yendiki, Anastasia Sent: Thursday, December 9, 2021 2:05 PM To: Freesurfer support list 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<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-caMGVrm6N2HVVkneMBsNIkNYG
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 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-boun...@nmr.mgh.harvard.edu on behalf of Salar Dini, Elaheh Sent: Tuesday, December 21, 2021 1:46 PM To: Freesurfer support list 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 Sent: Tuesday, December 14, 2021 2:31 PM To: Freesurfer support list 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 on behalf of Yendiki, Anastasia Sent: Thursday, December 9, 2021 2:05 PM To: Freesurfer support list 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_IbttKdqyuTMH986C9monmmZXi3wpndvbhE47lu6pp416hnKWOiQbhUWNiTpRIbk-Q-kkf8Q7umC-rgzzZCkzOJxRJYRdmfTNeKSdzhU479N5pYxb2UPA0LbjIVPydURLgdu4-TIN4b0mM8pjedmFBfVFhTYvgqSN6tdRkQsti77l6W_TG75Q5s6phbcwKXN3WUeEt26PULNuekqQmW1lg95oPzUEzgTHUbIwVja7l-_jdODCm98AUSRQFIuRrf1-MaGXEM-EMzxQMsOqfqaCUKx5xK2E-naQ/https%3A%2F%2Fgithub.com%2Ffreesurfer%2Ffreesurfer%2Fblob%2Fdev%2Fscripts%2Fdmri_bids_config<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%25
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 Sent: Tuesday, December 14, 2021 2:31 PM To: Freesurfer support list 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 on behalf of Yendiki, Anastasia Sent: Thursday, December 9, 2021 2:05 PM To: Freesurfer support list 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 on behalf of Salar Dini, Elaheh Sent: Thursday, December 9, 2021 10:31 AM To: 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 ti
Re: [Freesurfer] trac-all -prep error
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-boun...@nmr.mgh.harvard.edu on behalf of Yendiki, Anastasia Sent: Thursday, December 9, 2021 2:05 PM To: Freesurfer support list 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/1JsdOkZVCm1JcfRu9OvUzTC1tA9ukZ1oJ015-6VsyLvbwUpOAgdIbjC8m3025P6w4TBb6U45Cstp7Ss8KZCi2C1J3lSMuWuOMew_6IcuzoIndihwTOFqQvvkLF5FntGn0-PYW_4xhoTwcO_oUFWsrRPkRmqVZUGnt6bSbTGlnLTbR9_KW3Efh6-N2aufLDiPLoXxldesQTrSa28SFETUQ-VtsR63V33M_a-umjlDc2eVXAPA0KvE8CTZMaN-0hZ2DjB7bK6AlXya8NwvwRS6Nluy2QkdUsE1WBFX0MeBFfDpa1ZAvquCVErlmW3kP9JjsrL6NV8vlHHGBriY6_DxnHQ/https%3A%2F%2Fgithub.com%2Ffreesurfer%2Ffreesurfer%2Fblob%2Fdev%2Fscripts%2Fdmri_bids_config<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-boun...@nmr.mgh.harvard.edu on behalf of Salar Dini, Elaheh Sent: Thursday, December 9, 2021 10:31 AM To: 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 trac-all.log Description: trac-all.log dmriEla Description: dmriEla trac-all.error Description: trac-all.error ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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://github.com/freesurfer/freesurfer/blob/dev/scripts/dmri_bids_config Anastasia. From: freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Salar Dini, Elaheh Sent: Thursday, December 9, 2021 10:31 AM To: 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 The 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 http://www.massgeneralbrigham.org/complianceline . 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). If you do not wish to continue communication over unencrypted e-mail, please notify the sender of this message immediately. 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.
[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 dmriEla Description: dmriEla ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] trac-all -prep error
You're running the old version, you should install 7.2 From: freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Arman Avesta Sent: Wednesday, December 1, 2021 10:35 AM To: freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] trac-all -prep error External Email - Use Caution Hi gang, I'm trying to run trac-all -prep on a number of cases, and I'm getting an error. I've attached the config and log files for two cases. I would really appreciate your help. Best, Arman ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The 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 http://www.massgeneralbrigham.org/complianceline . 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). If you do not wish to continue communication over unencrypted e-mail, please notify the sender of this message immediately. 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.
Re: [Freesurfer] trac-all -prep error
External Email - Use Caution Hello Arman, The first error indicates there is a file missing from under fsl/bin, /usr/local/fsl/bin/eddy_correct: line 95: /usr/local/fsl/bin/imglob: No such file or directory - which makes me think something may not be correct with how fsl is setup/installed on your machine. - R. On Dec 1, 2021, at 10:35, Arman Avesta avesta.ar...@yahoo.com wrote:External Email - Use CautionHi gang,I'm trying to run trac-all -prep on a number of cases, and I'm getting an error. I've attached the config and log files for two cases.. I would really appreciate your help.Best,Armandmrirc1.txtdmrirc2.txttrac-all.logtrac-all.log___Freesurfer mailing listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] trac-all prep error
DICOMs may save each slice or each volume separately. This is not a problem per se, it's just a format, but it suggests that something may have changed in the protocol, which begs the question if other things changed in the protocol. I'd start by checking the converted nifti (dmri/dwi.nii.gz) to see if it's different than the others in an obvious way, then checking the gradient table (dmri/bvecs) and b-value table (dmri/bvals) to see if each of them has as many lines as volumes in the nifti. From: freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Zeng, Qi Sent: Wednesday, May 13, 2020 7:36 PM To: Freesurfer support list Subject: [Freesurfer] trac-all prep error External Email - Use Caution Hi, I have an error message when processing trac-all prep. attached the log file. error: "terminate called after throwing an instance of 'std::logic_error' what(): Mat::operator(): index out of bounds" Recon-all was finished without error. However, my raw DTI DCM file is 120 compared to others with over 2000 slices. Would that be a problem? Best, Qi -- Ph.D. candidate Icahn School of Medicine at Mount Sinai ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] trac-all -prep error field map error
Hi - I still have not been able to apply the field map correction within tracula. Tracula does not appear to recognize the format of my field maps in either dicom or nifti formats. However, as a work around I first did the field map correction outside tracula (using our wrapper script for epidewarp). Next I used this field map corrected image as the input diffusion image for tracula and set dob0 = 0 in my dmrirc file (so as to skip tracula's field map correction). This appears to be working. Eileen. -- Message: 5 Date: Wed, 27 Aug 2014 13:51:06 -0700 From: Eileen Moore eimo...@mail.sdsu.edu Subject: Re: [Freesurfer] trac-all -prep error field map error To: freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu Message-ID: CA++dajQo_2EF= lvufckbs+_061v7dctfc5t11pn0k4g9d-c...@mail.gmail.com Content-Type: text/plain; charset=utf-8 Anastasia, I'm not sure how I can give tracula the phase difference maps, can you provide an example? As a reminder, I've run a wrapper script around epidewarp which takes our dicom images and converts them into a phase difference map (it is based on the script that was authored by Doug Greve for the fBIRN consortium). In the tutorial dmrirc example I see only the 'set b0mlist' and 'set b0plist' options, and am unsure where I could give it the phase difference map. I've also tried converting the dicom magnitude and phase maps to nifti format and inputting these into the dmrirc file but I am still getting an error. (See attached log file). Thanks, Eileen. -- Message: 10 Date: Thu, 17 Jul 2014 04:14:16 -0400 (EDT) From: Anastasia Yendiki ayend...@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] trac-all -prep error field map error To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Message-ID: alpine.lrh.2.03.140717040.12...@nmr.mgh.harvard.edu Content-Type: TEXT/PLAIN; charset=US-ASCII; format=flowed Hi Eileen - All image formats that mri_convert (and thus any freesurfer program) can read will do, you don't need dicom. Try giving trac-all the phase difference maps you have and let's see what happens. Best, a.y On Wed, 16 Jul 2014, Eileen Moore wrote: Hi Anastasia, OK - our imaging physicists had developed a wrapper script around epidewarp which takes our dicom images and converts them into the phase difference map (it is based on the script that was authored by Doug Greve for the fBIRN consortium). It looks like the tracula script requires dicom images. Is there a way for me to do epidewarp manually and then follow through with the remaining steps using trac-all? Thanks, Eileen. Date: Mon, 14 Jul 2014 11:23:47 -0400 (EDT) From: Anastasia Yendiki ayend...@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] trac-all -prep error field map error To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Message-ID: alpine.lrh.2.03.1407141119560.23...@nmr.mgh.harvard.edu Content-Type: text/plain; charset=utf-8 Hi Eileen - That step is run with the program epidewarp.fsl, which you can run on the command line to see the available options. The input phase map volume is expected to have either 2 frames (2 separate phase maps) or 1 frame (the difference phase map). This error from trac-all means that it found that your input phase map has something other than 1 or 2 frames, so it doesn't know how to handle it. Hope this helps, a.y On Sat, 12 Jul 2014, Eileen Moore wrote: Hi - I'm using freesurfer 5.3 on an Ubuntu operating system. I'm tyring to run tracula on some? images acquired from a GE scanner. I am running into problems when I try to perform the registration-based B0-inhomogeneity compensation, getting an error in the terminal output: ERROR: Unrecognized format of phase map. However, trac-all -prep runs fine when I skip the B0-inhomogeneity compensation step. Is there something else I need to do to use field map correction? I've attached the trac-all.log and a copy of the terminal output. Thanks, Eileen. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The 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 Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent
Re: [Freesurfer] trac-all -prep error field map error
Hi Eileen - In b0plist you can give files that contain either 2 phase maps (a volume with 2 frames), or the difference of 2 phase maps (a volume with only 1 frame). Depending on whether the volume that you specified has 2 or 1 frame, trac-all will assume which of the above you're giving it. Your error seems to be that mri_convert doesn't recognize the format of your volume: mri_convert /home/image/FASD/call1285/call1285_dti_021210/proc/b0pha.nii /home/image/FASD/Shared/freesurfer/tracula/CIFASDII_T1-DTI/call1285_CIFASDII _T1_021210/dmri/b0pha.nii.gz niiRead(): unsupported datatype 32 (with scl_slope != 0) in /home/image/FASD/call1285/call1285_dti_021210/proc/b0pha.nii Can you view the volume in freeview, for example? If freesurfer tools can't recognize the format of your file, then it's not a tracula-specific problem. In that case, it's best to send a new email on the list about the mri_convert error, so that you get responses from the appropriate experts. a.y On Wed, 27 Aug 2014, Eileen Moore wrote: Anastasia, I'm not sure how I can give tracula the phase difference maps, can you provide an example? As a reminder, I've run a wrapper script around epidewarp which takes our dicom images and converts them into a phase difference map (it is based on the script that was authored by Doug Greve for the fBIRN consortium). In the tutorial dmrirc example I see only the 'set b0mlist' and 'set b0plist' options, and am unsure where I could give it the phase difference map. I've also tried converting the dicom magnitude and phase maps to nifti format and inputting these into the dmrirc file but I am still getting an error. (See attached log file). Thanks, Eileen. -- Message: 10 Date: Thu, 17 Jul 2014 04:14:16 -0400 (EDT) From: Anastasia Yendiki ayend...@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] trac-all -prep error field map error To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Message-ID: alpine.lrh.2.03.140717040.12...@nmr.mgh.harvard.edu Content-Type: TEXT/PLAIN; charset=US-ASCII; format=flowed Hi Eileen - All image formats that mri_convert (and thus any freesurfer program) can read will do, you don't need dicom. Try giving trac-all the phase difference maps you have and let's see what happens. Best, a.y On Wed, 16 Jul 2014, Eileen Moore wrote: Hi Anastasia, OK - our imaging physicists had developed a wrapper script around epidewarp which takes our dicom images and converts them into the phase difference map (it is based on the script that was authored by Doug Greve for the fBIRN consortium). It looks like the tracula script requires dicom images. Is there a way for me to do epidewarp manually and then follow through with the remaining steps using trac-all? Thanks, Eileen. Date: Mon, 14 Jul 2014 11:23:47 -0400 (EDT) From: Anastasia Yendiki ayend...@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] trac-all -prep error field map error To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Message-ID: alpine.lrh.2.03.1407141119560.23...@nmr.mgh.harvard.edu Content-Type: text/plain; charset=utf-8 Hi Eileen - That step is run with the program epidewarp.fsl, which you can run on the command line to see the available options. The input phase map volume is expected to have either 2 frames (2 separate phase maps) or 1 frame (the difference phase map). This error from trac-all means that it found that your input phase map has something other than 1 or 2 frames, so it doesn't know how to handle it. Hope this helps, a.y On Sat, 12 Jul 2014, Eileen Moore wrote: Hi - I'm using freesurfer 5.3 on an Ubuntu operating system. I'm tyring to run tracula on some? images acquired from a GE scanner. I am running into problems when I try to perform the registration-based B0-inhomogeneity compensation, getting an error in the terminal output: ERROR: Unrecognized format of phase map. However, trac-all -prep runs fine when I skip the B0-inhomogeneity compensation step. Is there something else I need to do to use field map correction? I've attached the trac-all.log and a copy of the terminal output. Thanks
Re: [Freesurfer] trac-all -prep error field map error
Anastasia, I'm not sure how I can give tracula the phase difference maps, can you provide an example? As a reminder, I've run a wrapper script around epidewarp which takes our dicom images and converts them into a phase difference map (it is based on the script that was authored by Doug Greve for the fBIRN consortium). In the tutorial dmrirc example I see only the 'set b0mlist' and 'set b0plist' options, and am unsure where I could give it the phase difference map. I've also tried converting the dicom magnitude and phase maps to nifti format and inputting these into the dmrirc file but I am still getting an error. (See attached log file). Thanks, Eileen. -- Message: 10 Date: Thu, 17 Jul 2014 04:14:16 -0400 (EDT) From: Anastasia Yendiki ayend...@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] trac-all -prep error field map error To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Message-ID: alpine.lrh.2.03.140717040.12...@nmr.mgh.harvard.edu Content-Type: TEXT/PLAIN; charset=US-ASCII; format=flowed Hi Eileen - All image formats that mri_convert (and thus any freesurfer program) can read will do, you don't need dicom. Try giving trac-all the phase difference maps you have and let's see what happens. Best, a.y On Wed, 16 Jul 2014, Eileen Moore wrote: Hi Anastasia, OK - our imaging physicists had developed a wrapper script around epidewarp which takes our dicom images and converts them into the phase difference map (it is based on the script that was authored by Doug Greve for the fBIRN consortium). It looks like the tracula script requires dicom images. Is there a way for me to do epidewarp manually and then follow through with the remaining steps using trac-all? Thanks, Eileen. Date: Mon, 14 Jul 2014 11:23:47 -0400 (EDT) From: Anastasia Yendiki ayend...@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] trac-all -prep error field map error To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Message-ID: alpine.lrh.2.03.1407141119560.23...@nmr.mgh.harvard.edu Content-Type: text/plain; charset=utf-8 Hi Eileen - That step is run with the program epidewarp.fsl, which you can run on the command line to see the available options. The input phase map volume is expected to have either 2 frames (2 separate phase maps) or 1 frame (the difference phase map). This error from trac-all means that it found that your input phase map has something other than 1 or 2 frames, so it doesn't know how to handle it. Hope this helps, a.y On Sat, 12 Jul 2014, Eileen Moore wrote: Hi - I'm using freesurfer 5.3 on an Ubuntu operating system. I'm tyring to run tracula on some? images acquired from a GE scanner. I am running into problems when I try to perform the registration-based B0-inhomogeneity compensation, getting an error in the terminal output: ERROR: Unrecognized format of phase map. However, trac-all -prep runs fine when I skip the B0-inhomogeneity compensation step. Is there something else I need to do to use field map correction? I've attached the trac-all.log and a copy of the terminal output. Thanks, Eileen. freesurfer-Linux-centos4_x86_64-stable-pub-v5.3.0 Setting up environment for FreeSurfer/FS-FAST (and FSL) FREESURFER_HOME /usr/local/freesurfer FSFAST_HOME /usr/local/freesurfer/fsfast FSF_OUTPUT_FORMAT nii.gz SUBJECTS_DIR /home/image/FASD/Shared/freesurfer/subjects MNI_DIR /usr/local/freesurfer/mni FSL_DIR /usr/local/fsl brain:~ cd freesurfer/ brain:~/freesurfer ls DICOM_FILES FreeSurfer_Scripts sessions subjects tracula brain:~/freesurfer cd tracula brain:~/freesurfer/tracula ls CIFASD2-DTI-pilot CIFASDII_T1-DTI dmrirc.example DTI-30 DTI-30_pilot error.log brain:~/freesurfer/tracula cd CIFASDII_T1-DTI/ brain:~/freesurfer/tracula/CIFASDII_T1-DTI ls bvals call1285_CIFASDII_T1_021210 dmrirc.CIFASDII_T1-DTI~ terminal-output-error.txt bvecs dmrirc.CIFASDII_T1-DTI dmrirc.file brain:~/freesurfer/tracula/CIFASDII_T1-DTI gedit dmri dmrirc.CIFASDII_T1-DTI~ dmrirc.CIFASDII_T1-DTI dmrirc.file brain:~/freesurfer/tracula/CIFASDII_T1-DTI gedit dmrirc.* brain:~/freesurfer/tracula/CIFASDII_T1-DTI trac-all -prep -c ERROR: flag -c requires one argument brain:~/freesurfer/tracula/CIFASDII_T1-DTI pwd /home/image/FASD/Shared/freesurfer/tracula/CIFASDII_T1-DTI brain:~/freesurfer/tracula/CIFASDII_T1-DTI trac-all -prep -c /home/image/FASD/Shared/freesurfer/tracula/CIFASDII_T1-DTI/dm dmrirc.CIFASDII_T1-DTI~ dmrirc.CIFASDII_T1-DTI dmrirc.file brain:~/freesurfer
Re: [Freesurfer] trac-all -prep error field map error
Hi Eileen - All image formats that mri_convert (and thus any freesurfer program) can read will do, you don't need dicom. Try giving trac-all the phase difference maps you have and let's see what happens. Best, a.y On Wed, 16 Jul 2014, Eileen Moore wrote: Hi Anastasia, OK - our imaging physicists had developed a wrapper script around epidewarp which takes our dicom images and converts them into the phase difference map (it is based on the script that was authored by Doug Greve for the fBIRN consortium). It looks like the tracula script requires dicom images. Is there a way for me to do epidewarp manually and then follow through with the remaining steps using trac-all? Thanks, Eileen. Date: Mon, 14 Jul 2014 11:23:47 -0400 (EDT) From: Anastasia Yendiki ayend...@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] trac-all -prep error field map error To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Message-ID: alpine.lrh.2.03.1407141119560.23...@nmr.mgh.harvard.edu Content-Type: text/plain; charset=utf-8 Hi Eileen - That step is run with the program epidewarp.fsl, which you can run on the command line to see the available options. The input phase map volume is expected to have either 2 frames (2 separate phase maps) or 1 frame (the difference phase map). This error from trac-all means that it found that your input phase map has something other than 1 or 2 frames, so it doesn't know how to handle it. Hope this helps, a.y On Sat, 12 Jul 2014, Eileen Moore wrote: Hi - I'm using freesurfer 5.3 on an Ubuntu operating system. I'm tyring to run tracula on some? images acquired from a GE scanner. I am running into problems when I try to perform the registration-based B0-inhomogeneity compensation, getting an error in the terminal output: ERROR: Unrecognized format of phase map. However, trac-all -prep runs fine when I skip the B0-inhomogeneity compensation step. Is there something else I need to do to use field map correction? I've attached the trac-all.log and a copy of the terminal output. Thanks, Eileen. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The 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 Partners Compliance HelpLine at http://www.partners.org/complianceline . 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.
Re: [Freesurfer] trac-all -prep error field map error
Hi Anastasia, OK - our imaging physicists had developed a wrapper script around epidewarp which takes our dicom images and converts them into the phase difference map (it is based on the script that was authored by Doug Greve for the fBIRN consortium). It looks like the tracula script requires dicom images. Is there a way for me to do epidewarp manually and then follow through with the remaining steps using trac-all? Thanks, Eileen. Date: Mon, 14 Jul 2014 11:23:47 -0400 (EDT) From: Anastasia Yendiki ayend...@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] trac-all -prep error field map error To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Message-ID: alpine.lrh.2.03.1407141119560.23...@nmr.mgh.harvard.edu Content-Type: text/plain; charset=utf-8 Hi Eileen - That step is run with the program epidewarp.fsl, which you can run on the command line to see the available options. The input phase map volume is expected to have either 2 frames (2 separate phase maps) or 1 frame (the difference phase map). This error from trac-all means that it found that your input phase map has something other than 1 or 2 frames, so it doesn't know how to handle it. Hope this helps, a.y On Sat, 12 Jul 2014, Eileen Moore wrote: Hi - I'm using freesurfer 5.3 on an Ubuntu operating system. I'm tyring to run tracula on some? images acquired from a GE scanner. I am running into problems when I try to perform the registration-based B0-inhomogeneity compensation, getting an error in the terminal output: ERROR: Unrecognized format of phase map. However, trac-all -prep runs fine when I skip the B0-inhomogeneity compensation step. Is there something else I need to do to use field map correction? I've attached the trac-all.log and a copy of the terminal output. Thanks, Eileen. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The 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 Partners Compliance HelpLine at http://www.partners.org/complianceline . 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.
Re: [Freesurfer] trac-all -prep error field map error
Hi Eileen - That step is run with the program epidewarp.fsl, which you can run on the command line to see the available options. The input phase map volume is expected to have either 2 frames (2 separate phase maps) or 1 frame (the difference phase map). This error from trac-all means that it found that your input phase map has something other than 1 or 2 frames, so it doesn't know how to handle it. Hope this helps, a.y On Sat, 12 Jul 2014, Eileen Moore wrote: Hi - I'm using freesurfer 5.3 on an Ubuntu operating system. I'm tyring to run tracula on some images acquired from a GE scanner. I am running into problems when I try to perform the registration-based B0-inhomogeneity compensation, getting an error in the terminal output: ERROR: Unrecognized format of phase map. However, trac-all -prep runs fine when I skip the B0-inhomogeneity compensation step. Is there something else I need to do to use field map correction? I've attached the trac-all.log and a copy of the terminal output. Thanks, Eileen. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The 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 Partners Compliance HelpLine at http://www.partners.org/complianceline . 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.
Re: [Freesurfer] trac-all -prep error during inter-subject registration with mri_cvs_register
Hi Verena - Which version of freesurfer are you using? In the public release of 5.1 the CVS registration option in trac-all is disabled. a.y On Tue, 23 Oct 2012, Verena Gramse wrote: From: Verena Gramse Sent: Monday, October 22, 2012 8:19 PM To: freesur...@nmr.mgh.harvard Subject: trac-all -prep error during inter-subject registration with mri_cvs_register Dear Tracula Team, I have been running into problems during Inter-subject registration at the mri_cvs_register step: it aborts with Image Exception : #22 :: ERROR: Could not open image /gablab/p/BGFU/data/freesurfer/cvs_avg35/mri//norm.mgz. But norm.mgz exists at the specified location and it can be opened with freeview without problems. Did I oversee anything? Thanks in advance! Verena Find attached my dmrirc and the error.log ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The 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 Partners Compliance HelpLine at http://www.partners.org/complianceline . 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.
Re: [Freesurfer] trac-all -prep error during inter-subject registration with mri_cvs_register
Hi Anastasia, Ahh.. I used the regular 5.1 and pointed to our dev folder where the cvs_avg35 (and cvs_avg_inMNI152) live. So, do you recommend skipping cvs registration for now? Thanks in advance! Verena From: Anastasia Yendiki [ayend...@nmr.mgh.harvard.edu] Sent: Tuesday, October 23, 2012 12:00 PM To: Verena Gramse Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] trac-all -prep error during inter-subject registration with mri_cvs_register Hi Verena - Which version of freesurfer are you using? In the public release of 5.1 the CVS registration option in trac-all is disabled. a.y On Tue, 23 Oct 2012, Verena Gramse wrote: From: Verena Gramse Sent: Monday, October 22, 2012 8:19 PM To: freesur...@nmr.mgh.harvard Subject: trac-all -prep error during inter-subject registration with mri_cvs_register Dear Tracula Team, I have been running into problems during Inter-subject registration at the mri_cvs_register step: it aborts with Image Exception : #22 :: ERROR: Could not open image /gablab/p/BGFU/data/freesurfer/cvs_avg35/mri//norm.mgz. But norm.mgz exists at the specified location and it can be opened with freeview without problems. Did I oversee anything? Thanks in advance! Verena Find attached my dmrirc and the error.log The 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 Partners Compliance HelpLine at http://www.partners.org/complianceline . 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. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] trac-all -prep error during inter-subject registration with mri_cvs_register
From: Verena Gramse Sent: Monday, October 22, 2012 8:19 PM To: freesur...@nmr.mgh.harvard Subject: trac-all -prep error during inter-subject registration with mri_cvs_register Dear Tracula Team, I have been running into problems during Inter-subject registration at the mri_cvs_register step: it aborts with Image Exception : #22 :: ERROR: Could not open image /gablab/p/BGFU/data/freesurfer/cvs_avg35/mri//norm.mgz. But norm.mgz exists at the specified location and it can be opened with freeview without problems. Did I oversee anything? Thanks in advance! Verena Find attached my dmrirc and the error.log dmrirc5 Description: dmrirc5 10301_to_cvs_avg35.mri_cvs_register.1210221939.log Description: 10301_to_cvs_avg35.mri_cvs_register.1210221939.log ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The 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 Partners Compliance HelpLine at http://www.partners.org/complianceline . 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.
Re: [Freesurfer] trac-all -prep error
Hi Sarina - You'll have to specify the list of gradient directions (bvecfile) and b-values (bvalfile), see here for more info: http://surfer.nmr.mgh.harvard.edu/fswiki/dmrirc Please send email to the freesurfer list and not to me directly. Emails sent to the freesurfer list are saved in a searchable archive so that other users can benefit from these pearls of wisdom. http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/ a.y On Wed, 11 Apr 2012, Sarina Sacco wrote: Ciao Anastasia ho risolto il problema di FSL,ora l'installazione è corretta,però mi si presenta sempre un errore inerente al bvecs non li trova,potrebbe forse dipendere dai files DICOM che utilizzo? Questo è l'errore: sarina@thunder:/opt/freesurfer/subjects$ trac-all -prep -c $SUBJECTS_DIR/subjects_trac_all/scripts/dmrircFiles/dmrirc_Diff001_F.B. INFO: SUBJECTS_DIR is /opt/freesurfer/subjects/subjects_recon_all INFO: Diffusion root is /opt/freesurfer/subjects/subjects_trac_all Actual FREESURFER_HOME /opt/freesurfer trac-preproc -c /opt/freesurfer/subjects/subjects_trac_all/Diff001_F.B./scripts/dmrirc.local -log /opt/freesurfer/subjects/subjects_trac_all/Diff001_F.B./scripts/trac-all.log -cmd /opt/freesurfer/subjects/subjects_trac_all/Diff001_F.B./scripts/trac-all.cmd #- /opt/freesurfer/bin/trac-preproc #- #@# Image corrections Wed Apr 11 18:01:15 CEST 2012 mri_convert /opt/freesurfer/subjects/subjects_trac_all//Diff001_F.B./orig/1.2.840.113619.2.260.6945.224896.29441.1274773115.263.dcm /opt/freesurfer/subjects/subjects_trac_all/Diff001_F.B./dmri/dwi_orig.nii.gz mri_convert /opt/freesurfer/subjects/subjects_trac_all//Diff001_F.B./orig/1.2.840.113619.2.260.6945.224896.29441.1274773115.263.dcm /opt/freesurfer/subjects/subjects_trac_all/Diff001_F.B./dmri/dwi_orig.nii.gz $Id: mri_convert.c,v 1.179.2.2 2011/05/16 20:53:47 greve Exp $ reading from /opt/freesurfer/subjects/subjects_trac_all//Diff001_F.B./orig/1.2.840.113619.2.260.6945.224896.29441.1274773115.263.dcm... Starting DICOMRead2() dcmfile = /opt/freesurfer/subjects/subjects_trac_all//Diff001_F.B./orig/1.2.840.113619.2.260.6945.224896.29441.1274773115.263.dcm dcmdir = /opt/freesurfer/subjects/subjects_trac_all//Diff001_F.B./orig Ref Series No = 7 Found 2242 files, checking for dicoms Found 2240 dicom files in series. First Sorting Computing Slice Direction Vs: 0.029 0.321 1.9739 Vs: 0.0144997 0.160497 0.98693 Second Sorting Counting frames nframes = 28 nslices = 80 ndcmfiles = 2240 PE Dir = COL (dicom read) TransferSyntaxUID: --1.2.840.10008.1.2-- jpegUID: --1.2.840.10008.1.2.4-- Loading pixel data TR=10050.00, TE=87.10, TI=0.00, flip angle=90.00 i_ras = (-0.999859, -0.0058291, -0.0157782) j_ras = (0.00830111, -0.987041, -0.160255) k_ras = (-0.0144997, -0.160497, 0.98693) writing to /opt/freesurfer/subjects/subjects_trac_all/Diff001_F.B./dmri/dwi_orig.nii.gz... mri_probedicom --i /opt/freesurfer/subjects/subjects_trac_all//Diff001_F.B./orig/1.2.840.113619.2.260.6945.224896.29441.1274773115.263.dcm /opt/freesurfer/subjects/subjects_trac_all/Diff001_F.B./dmri/dcminfo.dat flip4fsl /opt/freesurfer/subjects/subjects_trac_all/Diff001_F.B./dmri/dwi_orig.nii.gz /opt/freesurfer/subjects/subjects_trac_all/Diff001_F.B./dmri/dwi_orig_flip.nii.gz INFO: input image orientation is LPS INFO: input image determinant is 2 fslswapdim /opt/freesurfer/subjects/subjects_trac_all/Diff001_F.B./dmri/dwi_orig.nii.gz x -y z /opt/freesurfer/subjects/subjects_trac_all/Diff001_F.B./dmri/dwi_orig_flip.nii.gz INFO: left-right orientation was flipped by fslswapdim fslorient -forceradiological /opt/freesurfer/subjects/subjects_trac_all/Diff001_F.B./dmri/dwi_orig_flip.nii.gz mv -f /opt/freesurfer/subjects/subjects_trac_all/Diff001_F.B./dmri/dwi_orig_flip.mghdti.bvecs /opt/freesurfer/subjects/subjects_trac_all/Diff001_F.B./dmri/bvecs mv: cannot stat `/opt/freesurfer/subjects/subjects_trac_all/Diff001_F.B./dmri/dwi_orig_flip.mghdti.bvecs': No such file or directory Linux thunder 2.6.38-8-generic #42-Ubuntu SMP Mon Apr 11 03:31:24 UTC 2011 x86_64 x86_64 x86_64 GNU/Linux trac-preproc exited with ERRORS at Wed Apr 11 18:03:33 CEST 2012 2012/3/27 Anastasia Yendiki ayend...@nmr.mgh.harvard.edu: Ciao Sarina - The problem is here fslorient: Command not found. You have to make sure that FSL is properly installed and the FSL executables are in your path, as trac-all calls a few of them. Hope this helps, a.y On Tue, 27 Mar 2012, Sarina Sacco wrote: quando avvio il trac-all (relase FS5.1) mi crea questo errore: /opt/freesurfer/bin/trac-preproc #- #@# Image corrections Tue Mar 27 11:17:27 CEST 2012 mri_convert /opt/freesurfer/subjects/subjects_trac_all/Diff001_F.B./orig/1.2.840.113619.2.260.6945.224896.29441.1274773115.263.dcm /opt/freesurfer/subjects/subjects_trac_all/Diff001_F.B./dmri/dwi_orig.nii.gz mri_convert
[Freesurfer] trac-all -prep error
quando avvio il trac-all (relase FS5.1) mi crea questo errore: /opt/freesurfer/bin/trac-preproc #- #@# Image corrections Tue Mar 27 11:17:27 CEST 2012 mri_convert /opt/freesurfer/subjects/subjects_trac_all/Diff001_F.B./orig/1.2.840.113619.2.260.6945.224896.29441.1274773115.263.dcm /opt/freesurfer/subjects/subjects_trac_all/Diff001_F.B./dmri/dwi_orig.nii.gz mri_convert /opt/freesurfer/subjects/subjects_trac_all/Diff001_F.B./orig/1.2.840.113619.2.260.6945.224896.29441.1274773115.263.dcm /opt/freesurfer/subjects/subjects_trac_all/Diff001_F.B./dmri/dwi_orig.nii.gz $Id: mri_convert.c,v 1.179.2.2 2011/05/16 20:53:47 greve Exp $ reading from /opt/freesurfer/subjects/subjects_trac_all/Diff001_F.B./orig/1.2.840.113619.2.260.6945.224896.29441.1274773115.263.dcm... Starting DICOMRead2() dcmfile = /opt/freesurfer/subjects/subjects_trac_all/Diff001_F.B./orig/1.2.840.113619.2.260.6945.224896.29441.1274773115.263.dcm dcmdir = /opt/freesurfer/subjects/subjects_trac_all/Diff001_F.B./orig Ref Series No = 7 Found 2242 files, checking for dicoms Found 2240 dicom files in series. First Sorting Computing Slice Direction Vs: 0.029 0.321 1.9739 Vs: 0.0144997 0.160497 0.98693 Second Sorting Counting frames nframes = 28 nslices = 80 ndcmfiles = 2240 PE Dir = COL (dicom read) TransferSyntaxUID: --1.2.840.10008.1.2-- jpegUID: --1.2.840.10008.1.2.4-- Loading pixel data TR=10050.00, TE=87.10, TI=0.00, flip angle=90.00 i_ras = (-0.999859, -0.0058291, -0.0157782) j_ras = (0.00830111, -0.987041, -0.160255) k_ras = (-0.0144997, -0.160497, 0.98693) writing to /opt/freesurfer/subjects/subjects_trac_all/Diff001_F.B./dmri/dwi_orig.nii.gz... mri_probedicom --i /opt/freesurfer/subjects/subjects_trac_all/Diff001_F.B./orig/1.2.840.113619.2.260.6945.224896.29441.1274773115.263.dcm /opt/freesurfer/subjects/subjects_trac_all/Diff001_F.B./dmri/dcminfo.dat flip4fsl /opt/freesurfer/subjects/subjects_trac_all/Diff001_F.B./dmri/dwi_orig.nii.gz /opt/freesurfer/subjects/subjects_trac_all/Diff001_F.B./dmri/dwi_orig_flip.nii.gz INFO: input image orientation is LPS INFO: input image determinant is 2 fslswapdim /opt/freesurfer/subjects/subjects_trac_all/Diff001_F.B./dmri/dwi_orig.nii.gz x -y z /opt/freesurfer/subjects/subjects_trac_all/Diff001_F.B./dmri/dwi_orig_flip.nii.gz fslorient -forceradiological /opt/freesurfer/subjects/subjects_trac_all/Diff001_F.B./dmri/dwi_orig_flip.nii.gz fslorient: Command not found. mv -f /opt/freesurfer/subjects/subjects_trac_all/Diff001_F.B./dmri/dwi_orig_flip.mghdti.bvecs /opt/freesurfer/subjects/subjects_trac_all/Diff001_F.B./dmri/bvecs mv: cannot stat `/opt/freesurfer/subjects/subjects_trac_all/Diff001_F.B./dmri/dwi_orig_flip.mghdti.bvecs': No such file or directory Linux thunder 2.6.38-8-generic #42-Ubuntu SMP Mon Apr 11 03:31:24 UTC 2011 x86_64 x86_64 x86_64 GNU/Linux trac-preproc exited with ERRORS at Tue Mar 27 11:18:21 CEST 2012 Non riesco a capire perchè,da cosa può dipendere? ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The 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 Partners Compliance HelpLine at http://www.partners.org/complianceline . 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.
Re: [Freesurfer] trac-all -prep error
Ciao Sarina - The problem is here fslorient: Command not found. You have to make sure that FSL is properly installed and the FSL executables are in your path, as trac-all calls a few of them. Hope this helps, a.y On Tue, 27 Mar 2012, Sarina Sacco wrote: quando avvio il trac-all (relase FS5.1) mi crea questo errore: /opt/freesurfer/bin/trac-preproc #- #@# Image corrections Tue Mar 27 11:17:27 CEST 2012 mri_convert /opt/freesurfer/subjects/subjects_trac_all/Diff001_F.B./orig/1.2.840.113619.2.260.6945.224896.29441.1274773115.263.dcm /opt/freesurfer/subjects/subjects_trac_all/Diff001_F.B./dmri/dwi_orig.nii.gz mri_convert /opt/freesurfer/subjects/subjects_trac_all/Diff001_F.B./orig/1.2.840.113619.2.260.6945.224896.29441.1274773115.263.dcm /opt/freesurfer/subjects/subjects_trac_all/Diff001_F.B./dmri/dwi_orig.nii.gz $Id: mri_convert.c,v 1.179.2.2 2011/05/16 20:53:47 greve Exp $ reading from /opt/freesurfer/subjects/subjects_trac_all/Diff001_F.B./orig/1.2.840.113619.2.260.6945.224896.29441.1274773115.263.dcm... Starting DICOMRead2() dcmfile = /opt/freesurfer/subjects/subjects_trac_all/Diff001_F.B./orig/1.2.840.113619.2.260.6945.224896.29441.1274773115.263.dcm dcmdir = /opt/freesurfer/subjects/subjects_trac_all/Diff001_F.B./orig Ref Series No = 7 Found 2242 files, checking for dicoms Found 2240 dicom files in series. First Sorting Computing Slice Direction Vs: 0.029 0.321 1.9739 Vs: 0.0144997 0.160497 0.98693 Second Sorting Counting frames nframes = 28 nslices = 80 ndcmfiles = 2240 PE Dir = COL (dicom read) TransferSyntaxUID: --1.2.840.10008.1.2-- jpegUID: --1.2.840.10008.1.2.4-- Loading pixel data TR=10050.00, TE=87.10, TI=0.00, flip angle=90.00 i_ras = (-0.999859, -0.0058291, -0.0157782) j_ras = (0.00830111, -0.987041, -0.160255) k_ras = (-0.0144997, -0.160497, 0.98693) writing to /opt/freesurfer/subjects/subjects_trac_all/Diff001_F.B./dmri/dwi_orig.nii.gz... mri_probedicom --i /opt/freesurfer/subjects/subjects_trac_all/Diff001_F.B./orig/1.2.840.113619.2.260.6945.224896.29441.1274773115.263.dcm /opt/freesurfer/subjects/subjects_trac_all/Diff001_F.B./dmri/dcminfo.dat flip4fsl /opt/freesurfer/subjects/subjects_trac_all/Diff001_F.B./dmri/dwi_orig.nii.gz /opt/freesurfer/subjects/subjects_trac_all/Diff001_F.B./dmri/dwi_orig_flip.nii.gz INFO: input image orientation is LPS INFO: input image determinant is 2 fslswapdim /opt/freesurfer/subjects/subjects_trac_all/Diff001_F.B./dmri/dwi_orig.nii.gz x -y z /opt/freesurfer/subjects/subjects_trac_all/Diff001_F.B./dmri/dwi_orig_flip.nii.gz fslorient -forceradiological /opt/freesurfer/subjects/subjects_trac_all/Diff001_F.B./dmri/dwi_orig_flip.nii.gz fslorient: Command not found. mv -f /opt/freesurfer/subjects/subjects_trac_all/Diff001_F.B./dmri/dwi_orig_flip.mghdti.bvecs /opt/freesurfer/subjects/subjects_trac_all/Diff001_F.B./dmri/bvecs mv: cannot stat `/opt/freesurfer/subjects/subjects_trac_all/Diff001_F.B./dmri/dwi_orig_flip.mghdti.bvecs': No such file or directory Linux thunder 2.6.38-8-generic #42-Ubuntu SMP Mon Apr 11 03:31:24 UTC 2011 x86_64 x86_64 x86_64 GNU/Linux trac-preproc exited with ERRORS at Tue Mar 27 11:18:21 CEST 2012 Non riesco a capire perchè,da cosa può dipendere? ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The 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 Partners Compliance HelpLine at http://www.partners.org/complianceline . 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.
[Freesurfer] trac-all -prep error
Hello, in running trac-all -prep, I get an error saying that it can't open lowb.nii.gz.hdr: fslroi /raid2/fmri8/fontan/volumetric/freesurfer/1.5T/cardiac/foo_b/dmri/dwi.nii.gz /raid2/fmri8/fontan/volumetric/freesurfer/1.5T/cardiac/foo_b/dmri/lowb.nii.gz 0 1 fslmaths /raid2/fmri8/fontan/volumetric/freesurfer/1.5T/cardiac/foo_b/dmri/lowb.nii.gz -Tmean /raid2/fmri8/fontan/volumetric/freesurfer/1.5T/cardiac/foo_b/dmri/lowb.nii.gz bet /raid2/fmri8/fontan/volumetric/freesurfer/1.5T/cardiac/foo_b/dmri/lowb.nii.gz /raid2/fmri8/fontan/volumetric/freesurfer/1.5T/cardiac/foo_b/dmri/lowb_brain.nii.gz -m -f 0.3 Can't open /raid2/fmri8/fontan/volumetric/freesurfer/1.5T/cardiac/foo_b/dmri/lowb.nii.gz.hdr Linux occipital.tch.harvard.edu 2.6.18-274.17.1.el5 #1 SMP Tue Jan 10 17:25:58 EST 2012 x86_64 x86_64 x86_64 GNU/Linux trac-preproc exited with ERRORS at Wed Feb 15 15:15:52 EST 2012 The variable FSLOUTPUTTYPE is set to NIFTI_GZ. I don't encounter this problem with other subjects that I am processing. Any thoughts? Thanks, Chris ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The 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 Partners Compliance HelpLine at http://www.partners.org/complianceline . 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.
Re: [Freesurfer] trac-all -prep error
Hey Chris - That is strange. The FSLOUTPUTTYPE would've been my first guess, too. Does this lowb.nii.gz actually exist? Anything looks strange when you run mri_info/freeview/fslview on it? a.y On Wed, 15 Feb 2012, Chris Watson wrote: Hello, in running trac-all -prep, I get an error saying that it can't open lowb.nii.gz.hdr: fslroi /raid2/fmri8/fontan/volumetric/freesurfer/1.5T/cardiac/foo_b/dmri/dwi.nii.gz /raid2/fmri8/fontan/volumetric/freesurfer/1.5T/cardiac/foo_b/dmri/lowb.nii.gz 0 1 fslmaths /raid2/fmri8/fontan/volumetric/freesurfer/1.5T/cardiac/foo_b/dmri/lowb.nii.gz -Tmean /raid2/fmri8/fontan/volumetric/freesurfer/1.5T/cardiac/foo_b/dmri/lowb.nii.gz bet /raid2/fmri8/fontan/volumetric/freesurfer/1.5T/cardiac/foo_b/dmri/lowb.nii.gz /raid2/fmri8/fontan/volumetric/freesurfer/1.5T/cardiac/foo_b/dmri/lowb_brain.nii.gz -m -f 0.3 Can't open /raid2/fmri8/fontan/volumetric/freesurfer/1.5T/cardiac/foo_b/dmri/lowb.nii.gz.hdr Linux occipital.tch.harvard.edu 2.6.18-274.17.1.el5 #1 SMP Tue Jan 10 17:25:58 EST 2012 x86_64 x86_64 x86_64 GNU/Linux trac-preproc exited with ERRORS at Wed Feb 15 15:15:52 EST 2012 The variable FSLOUTPUTTYPE is set to NIFTI_GZ. I don't encounter this problem with other subjects that I am processing. Any thoughts? Thanks, Chris ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The 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 Partners Compliance HelpLine at http://www.partners.org/complianceline . 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.
Re: [Freesurfer] trac-all -prep error
Here's output from mri_info: [freesurfer@occipital dmri]$ mri_info lowb.nii.gz Volume information for lowb.nii.gz type: nii dimensions: 96 x 96 x 56 voxel sizes: 2.5000, 2.5000, 2.5000 type: FLOAT (3) fov: 240.000 dof: 0 xstart: -120.0, xend: 120.0 ystart: -120.0, yend: 120.0 zstart: -70.0, zend: 70.0 TR: 1000.00 msec, TE: 0.00 msec, TI: 0.00 msec, flip angle: 0.00 degrees nframes: 1 PhEncDir: UNKNOWN ras xform present xform info: x_r = -1., y_r = 0., z_r = 0., c_r = 0.9450 : x_a = 0., y_a = 1., z_a = 0., c_a = 31.8560 : x_s = 0., y_s = 0., z_s = 1., c_s = 25.3936 Orientation : LAS Primary Slice Direction: axial voxel to ras transform: -2.5000 0. 0. 120.9450 0. 2.5000 0. -88.1440 0. 0. 2.5000 -44.6064 0. 0. 0. 1. voxel-to-ras determinant -15.625 ras to voxel transform: -0.4000 0. 0.48.3780 -0. 0.4000 -0.35.2576 -0. -0. 0.400017.8426 0. 0. 0. 1. It looks normal in fslview/freeview. Chris Anastasia Yendiki wrote: Hey Chris - That is strange. The FSLOUTPUTTYPE would've been my first guess, too. Does this lowb.nii.gz actually exist? Anything looks strange when you run mri_info/freeview/fslview on it? a.y On Wed, 15 Feb 2012, Chris Watson wrote: Hello, in running trac-all -prep, I get an error saying that it can't open lowb.nii.gz.hdr: fslroi /raid2/fmri8/fontan/volumetric/freesurfer/1.5T/cardiac/foo_b/dmri/dwi.nii.gz /raid2/fmri8/fontan/volumetric/freesurfer/1.5T/cardiac/foo_b/dmri/lowb.nii.gz 0 1 fslmaths /raid2/fmri8/fontan/volumetric/freesurfer/1.5T/cardiac/foo_b/dmri/lowb.nii.gz -Tmean /raid2/fmri8/fontan/volumetric/freesurfer/1.5T/cardiac/foo_b/dmri/lowb.nii.gz bet /raid2/fmri8/fontan/volumetric/freesurfer/1.5T/cardiac/foo_b/dmri/lowb.nii.gz /raid2/fmri8/fontan/volumetric/freesurfer/1.5T/cardiac/foo_b/dmri/lowb_brain.nii.gz -m -f 0.3 Can't open /raid2/fmri8/fontan/volumetric/freesurfer/1.5T/cardiac/foo_b/dmri/lowb.nii.gz.hdr Linux occipital.tch.harvard.edu 2.6.18-274.17.1.el5 #1 SMP Tue Jan 10 17:25:58 EST 2012 x86_64 x86_64 x86_64 GNU/Linux trac-preproc exited with ERRORS at Wed Feb 15 15:15:52 EST 2012 The variable FSLOUTPUTTYPE is set to NIFTI_GZ. I don't encounter this problem with other subjects that I am processing. Any thoughts? Thanks, Chris ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The 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 Partners Compliance HelpLine at http://www.partners.org/complianceline . 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. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] trac-all -prep error
When you run that bet command line outside of trac-all, does it give you the same error? On Wed, 15 Feb 2012, Chris Watson wrote: Here's output from mri_info: [freesurfer@occipital dmri]$ mri_info lowb.nii.gz Volume information for lowb.nii.gz type: nii dimensions: 96 x 96 x 56 voxel sizes: 2.5000, 2.5000, 2.5000 type: FLOAT (3) fov: 240.000 dof: 0 xstart: -120.0, xend: 120.0 ystart: -120.0, yend: 120.0 zstart: -70.0, zend: 70.0 TR: 1000.00 msec, TE: 0.00 msec, TI: 0.00 msec, flip angle: 0.00 degrees nframes: 1 PhEncDir: UNKNOWN ras xform present xform info: x_r = -1., y_r = 0., z_r = 0., c_r = 0.9450 : x_a = 0., y_a = 1., z_a = 0., c_a = 31.8560 : x_s = 0., y_s = 0., z_s = 1., c_s = 25.3936 Orientation : LAS Primary Slice Direction: axial voxel to ras transform: -2.5000 0. 0. 120.9450 0. 2.5000 0. -88.1440 0. 0. 2.5000 -44.6064 0. 0. 0. 1. voxel-to-ras determinant -15.625 ras to voxel transform: -0.4000 0. 0.48.3780 -0. 0.4000 -0.35.2576 -0. -0. 0.400017.8426 0. 0. 0. 1. It looks normal in fslview/freeview. Chris Anastasia Yendiki wrote: Hey Chris - That is strange. The FSLOUTPUTTYPE would've been my first guess, too. Does this lowb.nii.gz actually exist? Anything looks strange when you run mri_info/freeview/fslview on it? a.y On Wed, 15 Feb 2012, Chris Watson wrote: Hello, in running trac-all -prep, I get an error saying that it can't open lowb.nii.gz.hdr: fslroi /raid2/fmri8/fontan/volumetric/freesurfer/1.5T/cardiac/foo_b/dmri/dwi.nii.gz /raid2/fmri8/fontan/volumetric/freesurfer/1.5T/cardiac/foo_b/dmri/lowb.nii.gz 0 1 fslmaths /raid2/fmri8/fontan/volumetric/freesurfer/1.5T/cardiac/foo_b/dmri/lowb.nii.gz -Tmean /raid2/fmri8/fontan/volumetric/freesurfer/1.5T/cardiac/foo_b/dmri/lowb.nii.gz bet /raid2/fmri8/fontan/volumetric/freesurfer/1.5T/cardiac/foo_b/dmri/lowb.nii.gz /raid2/fmri8/fontan/volumetric/freesurfer/1.5T/cardiac/foo_b/dmri/lowb_brain.nii.gz -m -f 0.3 Can't open /raid2/fmri8/fontan/volumetric/freesurfer/1.5T/cardiac/foo_b/dmri/lowb.nii.gz.hdr Linux occipital.tch.harvard.edu 2.6.18-274.17.1.el5 #1 SMP Tue Jan 10 17:25:58 EST 2012 x86_64 x86_64 x86_64 GNU/Linux trac-preproc exited with ERRORS at Wed Feb 15 15:15:52 EST 2012 The variable FSLOUTPUTTYPE is set to NIFTI_GZ. I don't encounter this problem with other subjects that I am processing. Any thoughts? Thanks, Chris ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The 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 Partners Compliance HelpLine at http://www.partners.org/complianceline . 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. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] trac-all -prep error
Yes, the same error. Chris Anastasia Yendiki wrote: When you run that bet command line outside of trac-all, does it give you the same error? On Wed, 15 Feb 2012, Chris Watson wrote: Here's output from mri_info: [freesurfer@occipital dmri]$ mri_info lowb.nii.gz Volume information for lowb.nii.gz type: nii dimensions: 96 x 96 x 56 voxel sizes: 2.5000, 2.5000, 2.5000 type: FLOAT (3) fov: 240.000 dof: 0 xstart: -120.0, xend: 120.0 ystart: -120.0, yend: 120.0 zstart: -70.0, zend: 70.0 TR: 1000.00 msec, TE: 0.00 msec, TI: 0.00 msec, flip angle: 0.00 degrees nframes: 1 PhEncDir: UNKNOWN ras xform present xform info: x_r = -1., y_r = 0., z_r = 0., c_r = 0.9450 : x_a = 0., y_a = 1., z_a = 0., c_a = 31.8560 : x_s = 0., y_s = 0., z_s = 1., c_s = 25.3936 Orientation : LAS Primary Slice Direction: axial voxel to ras transform: -2.5000 0. 0. 120.9450 0. 2.5000 0. -88.1440 0. 0. 2.5000 -44.6064 0. 0. 0. 1. voxel-to-ras determinant -15.625 ras to voxel transform: -0.4000 0. 0.48.3780 -0. 0.4000 -0.35.2576 -0. -0. 0.400017.8426 0. 0. 0. 1. It looks normal in fslview/freeview. Chris Anastasia Yendiki wrote: Hey Chris - That is strange. The FSLOUTPUTTYPE would've been my first guess, too. Does this lowb.nii.gz actually exist? Anything looks strange when you run mri_info/freeview/fslview on it? a.y On Wed, 15 Feb 2012, Chris Watson wrote: Hello, in running trac-all -prep, I get an error saying that it can't open lowb.nii.gz.hdr: fslroi /raid2/fmri8/fontan/volumetric/freesurfer/1.5T/cardiac/foo_b/dmri/dwi.nii.gz /raid2/fmri8/fontan/volumetric/freesurfer/1.5T/cardiac/foo_b/dmri/lowb.nii.gz 0 1 fslmaths /raid2/fmri8/fontan/volumetric/freesurfer/1.5T/cardiac/foo_b/dmri/lowb.nii.gz -Tmean /raid2/fmri8/fontan/volumetric/freesurfer/1.5T/cardiac/foo_b/dmri/lowb.nii.gz bet /raid2/fmri8/fontan/volumetric/freesurfer/1.5T/cardiac/foo_b/dmri/lowb.nii.gz /raid2/fmri8/fontan/volumetric/freesurfer/1.5T/cardiac/foo_b/dmri/lowb_brain.nii.gz -m -f 0.3 Can't open /raid2/fmri8/fontan/volumetric/freesurfer/1.5T/cardiac/foo_b/dmri/lowb.nii.gz.hdr Linux occipital.tch.harvard.edu 2.6.18-274.17.1.el5 #1 SMP Tue Jan 10 17:25:58 EST 2012 x86_64 x86_64 x86_64 GNU/Linux trac-preproc exited with ERRORS at Wed Feb 15 15:15:52 EST 2012 The variable FSLOUTPUTTYPE is set to NIFTI_GZ. I don't encounter this problem with other subjects that I am processing. Any thoughts? Thanks, Chris ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The 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 Partners Compliance HelpLine at http://www.partners.org/complianceline . 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. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] trac-all -prep error
Actually, it now works when I re-source my .bash_profile and .bashrc files. Not sure why that would be. Chris Chris Watson wrote: Yes, the same error. Chris Anastasia Yendiki wrote: When you run that bet command line outside of trac-all, does it give you the same error? On Wed, 15 Feb 2012, Chris Watson wrote: Here's output from mri_info: [freesurfer@occipital dmri]$ mri_info lowb.nii.gz Volume information for lowb.nii.gz type: nii dimensions: 96 x 96 x 56 voxel sizes: 2.5000, 2.5000, 2.5000 type: FLOAT (3) fov: 240.000 dof: 0 xstart: -120.0, xend: 120.0 ystart: -120.0, yend: 120.0 zstart: -70.0, zend: 70.0 TR: 1000.00 msec, TE: 0.00 msec, TI: 0.00 msec, flip angle: 0.00 degrees nframes: 1 PhEncDir: UNKNOWN ras xform present xform info: x_r = -1., y_r = 0., z_r = 0., c_r = 0.9450 : x_a = 0., y_a = 1., z_a = 0., c_a = 31.8560 : x_s = 0., y_s = 0., z_s = 1., c_s = 25.3936 Orientation : LAS Primary Slice Direction: axial voxel to ras transform: -2.5000 0. 0. 120.9450 0. 2.5000 0. -88.1440 0. 0. 2.5000 -44.6064 0. 0. 0. 1. voxel-to-ras determinant -15.625 ras to voxel transform: -0.4000 0. 0.48.3780 -0. 0.4000 -0.35.2576 -0. -0. 0.400017.8426 0. 0. 0. 1. It looks normal in fslview/freeview. Chris Anastasia Yendiki wrote: Hey Chris - That is strange. The FSLOUTPUTTYPE would've been my first guess, too. Does this lowb.nii.gz actually exist? Anything looks strange when you run mri_info/freeview/fslview on it? a.y On Wed, 15 Feb 2012, Chris Watson wrote: Hello, in running trac-all -prep, I get an error saying that it can't open lowb.nii.gz.hdr: fslroi /raid2/fmri8/fontan/volumetric/freesurfer/1.5T/cardiac/foo_b/dmri/dwi.nii.gz /raid2/fmri8/fontan/volumetric/freesurfer/1.5T/cardiac/foo_b/dmri/lowb.nii.gz 0 1 fslmaths /raid2/fmri8/fontan/volumetric/freesurfer/1.5T/cardiac/foo_b/dmri/lowb.nii.gz -Tmean /raid2/fmri8/fontan/volumetric/freesurfer/1.5T/cardiac/foo_b/dmri/lowb.nii.gz bet /raid2/fmri8/fontan/volumetric/freesurfer/1.5T/cardiac/foo_b/dmri/lowb.nii.gz /raid2/fmri8/fontan/volumetric/freesurfer/1.5T/cardiac/foo_b/dmri/lowb_brain.nii.gz -m -f 0.3 Can't open /raid2/fmri8/fontan/volumetric/freesurfer/1.5T/cardiac/foo_b/dmri/lowb.nii.gz.hdr Linux occipital.tch.harvard.edu 2.6.18-274.17.1.el5 #1 SMP Tue Jan 10 17:25:58 EST 2012 x86_64 x86_64 x86_64 GNU/Linux trac-preproc exited with ERRORS at Wed Feb 15 15:15:52 EST 2012 The variable FSLOUTPUTTYPE is set to NIFTI_GZ. I don't encounter this problem with other subjects that I am processing. Any thoughts? Thanks, Chris ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The 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 Partners Compliance HelpLine at http://www.partners.org/complianceline . 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. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] trac-all -prep error
Weird. Glad it got fixed, let us know if you have any more trouble. On Wed, 15 Feb 2012, Chris Watson wrote: Actually, it now works when I re-source my .bash_profile and .bashrc files. Not sure why that would be. Chris Chris Watson wrote: Yes, the same error. Chris Anastasia Yendiki wrote: When you run that bet command line outside of trac-all, does it give you the same error? On Wed, 15 Feb 2012, Chris Watson wrote: Here's output from mri_info: [freesurfer@occipital dmri]$ mri_info lowb.nii.gz Volume information for lowb.nii.gz type: nii dimensions: 96 x 96 x 56 voxel sizes: 2.5000, 2.5000, 2.5000 type: FLOAT (3) fov: 240.000 dof: 0 xstart: -120.0, xend: 120.0 ystart: -120.0, yend: 120.0 zstart: -70.0, zend: 70.0 TR: 1000.00 msec, TE: 0.00 msec, TI: 0.00 msec, flip angle: 0.00 degrees nframes: 1 PhEncDir: UNKNOWN ras xform present xform info: x_r = -1., y_r = 0., z_r = 0., c_r = 0.9450 : x_a = 0., y_a = 1., z_a = 0., c_a = 31.8560 : x_s = 0., y_s = 0., z_s = 1., c_s = 25.3936 Orientation : LAS Primary Slice Direction: axial voxel to ras transform: -2.5000 0. 0. 120.9450 0. 2.5000 0. -88.1440 0. 0. 2.5000 -44.6064 0. 0. 0. 1. voxel-to-ras determinant -15.625 ras to voxel transform: -0.4000 0. 0.48.3780 -0. 0.4000 -0.35.2576 -0. -0. 0.400017.8426 0. 0. 0. 1. It looks normal in fslview/freeview. Chris Anastasia Yendiki wrote: Hey Chris - That is strange. The FSLOUTPUTTYPE would've been my first guess, too. Does this lowb.nii.gz actually exist? Anything looks strange when you run mri_info/freeview/fslview on it? a.y On Wed, 15 Feb 2012, Chris Watson wrote: Hello, in running trac-all -prep, I get an error saying that it can't open lowb.nii.gz.hdr: fslroi /raid2/fmri8/fontan/volumetric/freesurfer/1.5T/cardiac/foo_b/dmri/dwi.nii.gz /raid2/fmri8/fontan/volumetric/freesurfer/1.5T/cardiac/foo_b/dmri/lowb.nii.gz 0 1 fslmaths /raid2/fmri8/fontan/volumetric/freesurfer/1.5T/cardiac/foo_b/dmri/lowb.nii.gz -Tmean /raid2/fmri8/fontan/volumetric/freesurfer/1.5T/cardiac/foo_b/dmri/lowb.nii.gz bet /raid2/fmri8/fontan/volumetric/freesurfer/1.5T/cardiac/foo_b/dmri/lowb.nii.gz /raid2/fmri8/fontan/volumetric/freesurfer/1.5T/cardiac/foo_b/dmri/lowb_brain.nii.gz -m -f 0.3 Can't open /raid2/fmri8/fontan/volumetric/freesurfer/1.5T/cardiac/foo_b/dmri/lowb.nii.gz.hdr Linux occipital.tch.harvard.edu 2.6.18-274.17.1.el5 #1 SMP Tue Jan 10 17:25:58 EST 2012 x86_64 x86_64 x86_64 GNU/Linux trac-preproc exited with ERRORS at Wed Feb 15 15:15:52 EST 2012 The variable FSLOUTPUTTYPE is set to NIFTI_GZ. I don't encounter this problem with other subjects that I am processing. Any thoughts? Thanks, Chris ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The 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 Partners Compliance HelpLine at http://www.partners.org/complianceline . 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. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu
