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Hi all,
The lab I work in recently upgrade to freesurfer-linux-centos7x_86_64-7.1.1 from freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0, and I am trying to use a series of shell scripts (that call freesurfer) which we successfully used to run to create flatmaps for non-human primate sessions. I am stuck when using recon-all to inflate the surface. Specifically, I am running the command: "recon-all -autorecon2-wm \ -subjid ${tmp_subj} ${corpcal_coord_string} ${pons_coord_string}\ -noaseg \ -mprage \ -xopts-use\ -debug" This step runs for quite some time, seemingly making progress and then "Exits with errors" . In the terminal the error message that I can see is: "ERROR: need seg for ripping". This is followed by: "recon-all - s SUBJECTNAME exited with ERRORS." (Screen shot of this error is attached). I will also attach the recon-all.log.
This issue does not seem to be a problem of quality of skull stripping or white matter segmentation, as the session can be completed with the older version of freesurfer, adn I get the same error with different sessions and subjects. Can you please shed some light on this? The machine I am using is running Linux 3.10.0-1127.18.2.e17.x86_64 .
As an aside - Do you have any references or outline for flat map creation (specifically for non-human primates) with the newer versions of Free surfer? It is possible adapting our old pipeline is not ideal / there are more efficient or "better" ways to do this now.
Thank you for your help.
Best,
Erin
There have been some changes that are breaking your stream. Try this
cd /mnt/data2/data/erink/cooked/2019/190124Jamie2/mri setenv SUBJECTS_DIR /mnt/data0/home/erink/subjects mris_place_surface --adgws-in ../surf/autodet.gw.stats.lh.dat --wm wm.mgz --threads 1 --invol brain.finalsurfs.mgz --lh --i ../surf/lh.orig --o ../surf/lh.white.preaparc --white --nsmooth 5 --no-rip-midline --no-rip-bg --no-rip-wmsa --no-rip-freeze --no-rip-lesion
If that works, then add this to your xopts file WhitePreAparc --no-rip-midline --no-rip-bg --no-rip-wmsa --no-rip-freeze --no-rip-lesion
On 12/14/2020 5:35 PM, Koch, Erin M. wrote:
External Email - Use Caution
Hi all,
The lab I work in recently upgrade to freesurfer-linux-centos7x_86_64-7.1.1 from freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0, and I am trying to use a series of shell scripts (that call freesurfer) which we successfully used to run to create flatmaps for non-human primate sessions. I am stuck when using recon-all to inflate the surface. Specifically, I am running the command: "recon-all -autorecon2-wm \ -subjid ${tmp_subj} ${corpcal_coord_string} ${pons_coord_string}\ -noaseg \ -mprage \ -xopts-use\ -debug" This step runs for quite some time, seemingly making progress and then "Exits with errors" . In the terminal the error message that I can see is: "ERROR: need seg for ripping". This is followed by: "recon-all - s SUBJECTNAME exited with ERRORS." (Screen shot of this error is attached). I will also attach the recon-all.log.
This issue does not seem to be a problem of quality of skull stripping or white matter segmentation, as the session can be completed with the older version of freesurfer, adn I get the same error with different sessions and subjects. Can you please shed some light on this? The machine I am using is running Linux 3.10.0-1127.18.2.e17.x86_64 .
As an aside - Do you have any references or outline for flat map creation (specifically for non-human primates) with the newer versions of Free surfer? It is possible adapting our old pipeline is not ideal / there are more efficient or "better" ways to do this now.
Thank you for your help.
Best,
Erin
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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Hi
Thanks for your help. Indeed the list of commands you sent worked, so I added the line you recommended to my xopts. This gets me beyond my previous exit point, but now recon-all is exiting with a new error. I will attach my recon-all log and terminal error. It seems recon-all is trying to load an aseg file; however, I include in my call -noaseg (and I tried adding -nosubcortseg). Please let me know if you need anything else.
Erin
________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Greve, Douglas N.,Ph.D. DGREVE@mgh.harvard.edu Sent: Wednesday, December 23, 2020 9:12 AM To: freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Recon-all exiting with Errors during surface inflation
There have been some changes that are breaking your stream. Try this
cd /mnt/data2/data/erink/cooked/2019/190124Jamie2/mri setenv SUBJECTS_DIR /mnt/data0/home/erink/subjects mris_place_surface --adgws-in ../surf/autodet.gw.stats.lh.dat --wm wm.mgz --threads 1 --invol brain.finalsurfs.mgz --lh --i ../surf/lh.orig --o ../surf/lh.white.preaparc --white --nsmooth 5 --no-rip-midline --no-rip-bg --no-rip-wmsa --no-rip-freeze --no-rip-lesion
If that works, then add this to your xopts file WhitePreAparc --no-rip-midline --no-rip-bg --no-rip-wmsa --no-rip-freeze --no-rip-lesion
On 12/14/2020 5:35 PM, Koch, Erin M. wrote:
External Email - Use Caution
Hi all,
The lab I work in recently upgrade to freesurfer-linux-centos7x_86_64-7.1.1 from freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0, and I am trying to use a series of shell scripts (that call freesurfer) which we successfully used to run to create flatmaps for non-human primate sessions. I am stuck when using recon-all to inflate the surface. Specifically, I am running the command: "recon-all -autorecon2-wm \ -subjid ${tmp_subj} ${corpcal_coord_string} ${pons_coord_string}\ -noaseg \ -mprage \ -xopts-use\ -debug" This step runs for quite some time, seemingly making progress and then "Exits with errors" . In the terminal the error message that I can see is: "ERROR: need seg for ripping". This is followed by: "recon-all - s SUBJECTNAME exited with ERRORS." (Screen shot of this error is attached). I will also attach the recon-all.log.
This issue does not seem to be a problem of quality of skull stripping or white matter segmentation, as the session can be completed with the older version of freesurfer, adn I get the same error with different sessions and subjects. Can you please shed some light on this? The machine I am using is running Linux 3.10.0-1127.18.2.e17.x86_64 .
As an aside - Do you have any references or outline for flat map creation (specifically for non-human primates) with the newer versions of Free surfer? It is possible adapting our old pipeline is not ideal / there are more efficient or "better" ways to do this now.
Thank you for your help.
Best,
Erin
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://secure-web.cisco.com/1_hNONTW7W5-OaDObXh6c_1aitbnlbI9-XJ6saE9Bghs0Ly...
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Just want to bump this message. Please let me know if you have any suggestions.
Best, Erin ________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Koch, Erin M. erink@caltech.edu Sent: Friday, January 15, 2021 2:40 PM To: freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Recon-all exiting with Errors during surface inflation
External Email - Use Caution
Hi
Thanks for your help. Indeed the list of commands you sent worked, so I added the line you recommended to my xopts. This gets me beyond my previous exit point, but now recon-all is exiting with a new error. I will attach my recon-all log and terminal error. It seems recon-all is trying to load an aseg file; however, I include in my call -noaseg (and I tried adding -nosubcortseg). Please let me know if you need anything else.
Erin
________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Greve, Douglas N.,Ph.D. DGREVE@mgh.harvard.edu Sent: Wednesday, December 23, 2020 9:12 AM To: freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Recon-all exiting with Errors during surface inflation
There have been some changes that are breaking your stream. Try this
cd /mnt/data2/data/erink/cooked/2019/190124Jamie2/mri setenv SUBJECTS_DIR /mnt/data0/home/erink/subjects mris_place_surface --adgws-in ../surf/autodet.gw.stats.lh.dat --wm wm.mgz --threads 1 --invol brain.finalsurfs.mgz --lh --i ../surf/lh.orig --o ../surf/lh.white.preaparc --white --nsmooth 5 --no-rip-midline --no-rip-bg --no-rip-wmsa --no-rip-freeze --no-rip-lesion
If that works, then add this to your xopts file WhitePreAparc --no-rip-midline --no-rip-bg --no-rip-wmsa --no-rip-freeze --no-rip-lesion
On 12/14/2020 5:35 PM, Koch, Erin M. wrote:
External Email - Use Caution
Hi all,
The lab I work in recently upgrade to freesurfer-linux-centos7x_86_64-7.1.1 from freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0, and I am trying to use a series of shell scripts (that call freesurfer) which we successfully used to run to create flatmaps for non-human primate sessions. I am stuck when using recon-all to inflate the surface. Specifically, I am running the command: "recon-all -autorecon2-wm \ -subjid ${tmp_subj} ${corpcal_coord_string} ${pons_coord_string}\ -noaseg \ -mprage \ -xopts-use\ -debug" This step runs for quite some time, seemingly making progress and then "Exits with errors" . In the terminal the error message that I can see is: "ERROR: need seg for ripping". This is followed by: "recon-all - s SUBJECTNAME exited with ERRORS." (Screen shot of this error is attached). I will also attach the recon-all.log.
This issue does not seem to be a problem of quality of skull stripping or white matter segmentation, as the session can be completed with the older version of freesurfer, adn I get the same error with different sessions and subjects. Can you please shed some light on this? The machine I am using is running Linux 3.10.0-1127.18.2.e17.x86_64 .
As an aside - Do you have any references or outline for flat map creation (specifically for non-human primates) with the newer versions of Free surfer? It is possible adapting our old pipeline is not ideal / there are more efficient or "better" ways to do this now.
Thank you for your help.
Best,
Erin
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://secure-web.cisco.com/1ZDP9LB9JYY4rHR2OKt2xxeX9_TxwAvwjSLYF2AJvPo3U-j...https://secure-web.cisco.com/1_hNONTW7W5-OaDObXh6c_1aitbnlbI9-XJ6saE9Bghs0LyK-mDnSULttW89oQb38CkKoqGXcGoExhXC_PXo-5aqo3nGhKVNY2ABAENCVvjhyCeyt3NVeMHHT-WH7lHlcX3hyr9gVBrs1EJSfVlvTggckNssK7A_7fZY_-qzoKx2w1UQIk0ppXzYZBUBKBZIwobSHHRPcMXiG27nhQ9We5VoUF9iRk3Mvee8JEv2tKpIwGbmnc_nIBMZQO497bulhtNcmlejLCnzu79oXblsg6w/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer
The problem is that it expects there to be an aseg.presurf.mgz, but you have turned the creation of it off. Because this is NHP?
On 1/15/2021 5:40 PM, Koch, Erin M. wrote:
External Email - Use Caution
Hi
Thanks for your help. Indeed the list of commands you sent worked, so I added the line you recommended to my xopts. This gets me beyond my previous exit point, but now recon-all is exiting with a new error. I will attach my recon-all log and terminal error. It seems recon-all is trying to load an aseg file; however, I include in my call -noaseg (and I tried adding -nosubcortseg). Please let me know if you need anything else.
Erin
*From:* freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Greve, Douglas N.,Ph.D. DGREVE@mgh.harvard.edu *Sent:* Wednesday, December 23, 2020 9:12 AM *To:* freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu *Subject:* Re: [Freesurfer] Recon-all exiting with Errors during surface inflation There have been some changes that are breaking your stream. Try this
cd /mnt/data2/data/erink/cooked/2019/190124Jamie2/mri setenv SUBJECTS_DIR /mnt/data0/home/erink/subjects mris_place_surface --adgws-in ../surf/autodet.gw.stats.lh.dat --wm wm.mgz --threads 1 --invol brain.finalsurfs.mgz --lh --i ../surf/lh.orig --o ../surf/lh.white.preaparc --white --nsmooth 5 --no-rip-midline --no-rip-bg --no-rip-wmsa --no-rip-freeze --no-rip-lesion
If that works, then add this to your xopts file WhitePreAparc --no-rip-midline --no-rip-bg --no-rip-wmsa --no-rip-freeze --no-rip-lesion
On 12/14/2020 5:35 PM, Koch, Erin M. wrote:
External Email - Use Caution
Hi all,
The lab I work in recently upgrade to freesurfer-linux-centos7x_86_64-7.1.1 from freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0, and I am trying to use a series of shell scripts (that call freesurfer) which we successfully used to run to create flatmaps for non-human primate sessions. I am stuck when using recon-all to inflate the surface. Specifically, I am running the command: "recon-all -autorecon2-wm \ -subjid ${tmp_subj} ${corpcal_coord_string} ${pons_coord_string}\ -noaseg \ -mprage \ -xopts-use\ -debug" This step runs for quite some time, seemingly making progress and then "Exits with errors" . In the terminal the error message that I can see is: "ERROR: need seg for ripping". This is followed by: "recon-all - s SUBJECTNAME exited with ERRORS." (Screen shot of this error is attached). I will also attach the recon-all.log.
This issue does not seem to be a problem of quality of skull stripping or white matter segmentation, as the session can be completed with the older version of freesurfer, adn I get the same error with different sessions and subjects. Can you please shed some light on this? The machine I am using is running Linux 3.10.0-1127.18.2.e17.x86_64 .
As an aside - Do you have any references or outline for flat map creation (specifically for non-human primates) with the newer versions of Free surfer? It is possible adapting our old pipeline is not ideal / there are more efficient or "better" ways to do this now.
Thank you for your help.
Best,
Erin
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu *MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer https://secure-web.cisco.com/1_hNONTW7W5-OaDObXh6c_1aitbnlbI9-XJ6saE9Bghs0LyK-mDnSULttW89oQb38CkKoqGXcGoExhXC_PXo-5aqo3nGhKVNY2ABAENCVvjhyCeyt3NVeMHHT-WH7lHlcX3hyr9gVBrs1EJSfVlvTggckNssK7A_7fZY_-qzoKx2w1UQIk0ppXzYZBUBKBZIwobSHHRPcMXiG27nhQ9We5VoUF9iRk3Mvee8JEv2tKpIwGbmnc_nIBMZQO497bulhtNcmlejLCnzu79oXblsg6w/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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Yes. I turned off aseg because this is NHP. In previous versions of freesurfer this was fine. Do I need to add something more my xopts file? How do I get around this problem?
Thanks,
Erin
Get Outlook for iOShttps://secure-web.cisco.com/1DmYXz9AvDs-8SzQ0hBvO0ciJ2KHeyjiheztEzwGHZ-eGDy03rJ8WleExBnEpox-gBx3Ssa0i_H6MCTY3EgMW-U4BzTyCSUkc5dTaNnLsHRux6UyYQdVMYOSmznSH1OAq1gsHihjOXeao-bJyLvt-uZyKU3wAMr18UT-UhnMTafbK9PU_qJQ1WwH7Pf0Ay1Nz3ylb-1O9evs7EpGe4echU9Rdknkx20O2pm_pdSN4_rwh4tLyok4bDwBp5kx1UXLhWrBtYA0YPWv8sV74P7cVVQ/https%3A%2F%2Faka.ms%2Fo0ukef ________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Douglas N. Greve dgreve@mgh.harvard.edu Sent: Monday, January 25, 2021 8:01:12 PM To: freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Recon-all exiting with Errors during surface inflation
The problem is that it expects there to be an aseg.presurf.mgz, but you have turned the creation of it off. Because this is NHP?
On 1/15/2021 5:40 PM, Koch, Erin M. wrote:
External Email - Use Caution
Hi
Thanks for your help. Indeed the list of commands you sent worked, so I added the line you recommended to my xopts. This gets me beyond my previous exit point, but now recon-all is exiting with a new error. I will attach my recon-all log and terminal error. It seems recon-all is trying to load an aseg file; however, I include in my call -noaseg (and I tried adding -nosubcortseg). Please let me know if you need anything else.
Erin
________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Greve, Douglas N.,Ph.D. DGREVE@mgh.harvard.edumailto:DGREVE@mgh.harvard.edu Sent: Wednesday, December 23, 2020 9:12 AM To: freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Recon-all exiting with Errors during surface inflation
There have been some changes that are breaking your stream. Try this
cd /mnt/data2/data/erink/cooked/2019/190124Jamie2/mri setenv SUBJECTS_DIR /mnt/data0/home/erink/subjects mris_place_surface --adgws-in ../surf/autodet.gw.stats.lh.dat --wm wm.mgz --threads 1 --invol brain.finalsurfs.mgz --lh --i ../surf/lh.orig --o ../surf/lh.white.preaparc --white --nsmooth 5 --no-rip-midline --no-rip-bg --no-rip-wmsa --no-rip-freeze --no-rip-lesion
If that works, then add this to your xopts file WhitePreAparc --no-rip-midline --no-rip-bg --no-rip-wmsa --no-rip-freeze --no-rip-lesion
On 12/14/2020 5:35 PM, Koch, Erin M. wrote:
External Email - Use Caution
Hi all,
The lab I work in recently upgrade to freesurfer-linux-centos7x_86_64-7.1.1 from freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0, and I am trying to use a series of shell scripts (that call freesurfer) which we successfully used to run to create flatmaps for non-human primate sessions. I am stuck when using recon-all to inflate the surface. Specifically, I am running the command: "recon-all -autorecon2-wm \ -subjid ${tmp_subj} ${corpcal_coord_string} ${pons_coord_string}\ -noaseg \ -mprage \ -xopts-use\ -debug" This step runs for quite some time, seemingly making progress and then "Exits with errors" . In the terminal the error message that I can see is: "ERROR: need seg for ripping". This is followed by: "recon-all - s SUBJECTNAME exited with ERRORS." (Screen shot of this error is attached). I will also attach the recon-all.log.
This issue does not seem to be a problem of quality of skull stripping or white matter segmentation, as the session can be completed with the older version of freesurfer, adn I get the same error with different sessions and subjects. Can you please shed some light on this? The machine I am using is running Linux 3.10.0-1127.18.2.e17.x86_64 .
As an aside - Do you have any references or outline for flat map creation (specifically for non-human primates) with the newer versions of Free surfer? It is possible adapting our old pipeline is not ideal / there are more efficient or "better" ways to do this now.
Thank you for your help.
Best,
Erin
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://secure-web.cisco.com/1ti0YqeboWO4wmYzCGnRbvZ3P1wiehVYQ8e4iqb1fcWS-Di...https://secure-web.cisco.com/1_hNONTW7W5-OaDObXh6c_1aitbnlbI9-XJ6saE9Bghs0LyK-mDnSULttW89oQb38CkKoqGXcGoExhXC_PXo-5aqo3nGhKVNY2ABAENCVvjhyCeyt3NVeMHHT-WH7lHlcX3hyr9gVBrs1EJSfVlvTggckNssK7A_7fZY_-qzoKx2w1UQIk0ppXzYZBUBKBZIwobSHHRPcMXiG27nhQ9We5VoUF9iRk3Mvee8JEv2tKpIwGbmnc_nIBMZQO497bulhtNcmlejLCnzu79oXblsg6w/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer
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Or, are you saying that I do not need to turn it off for NHP?
Get Outlook for iOShttps://secure-web.cisco.com/1dONy4vR-n6Y0a9Bp50DjAYEcab4XFWNYEp12Bg12m_cvRNSc_qJGeaJVW6sP25kGw-PeSPgjoIaMpSg5Eilgf0CTGogwucNX_MvODoK-ntWBQIlY8z3gZZEo_aEQagsOr7STbtigUfaQvhNOgC5cFcSYKv9RVE8z1fTN_0bLnWOZaSQ59jS9F8sAsTFxVukQKh7rpeYhybgrqbVtoNBde_-F48f8d1L3d-58wF2DvbKfLy-J_M5FJHKFZQv_FF1p-xHplxEHNxPf7kK1H9zLaQ/https%3A%2F%2Faka.ms%2Fo0ukef ________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Koch, Erin M. erink@caltech.edu Sent: Monday, January 25, 2021 10:47:34 PM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Recon-all exiting with Errors during surface inflation
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Yes. I turned off aseg because this is NHP. In previous versions of freesurfer this was fine. Do I need to add something more my xopts file? How do I get around this problem?
Thanks,
Erin
Get Outlook for iOShttps://secure-web.cisco.com/1DmYXz9AvDs-8SzQ0hBvO0ciJ2KHeyjiheztEzwGHZ-eGDy03rJ8WleExBnEpox-gBx3Ssa0i_H6MCTY3EgMW-U4BzTyCSUkc5dTaNnLsHRux6UyYQdVMYOSmznSH1OAq1gsHihjOXeao-bJyLvt-uZyKU3wAMr18UT-UhnMTafbK9PU_qJQ1WwH7Pf0Ay1Nz3ylb-1O9evs7EpGe4echU9Rdknkx20O2pm_pdSN4_rwh4tLyok4bDwBp5kx1UXLhWrBtYA0YPWv8sV74P7cVVQ/https%3A%2F%2Faka.ms%2Fo0ukef ________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Douglas N. Greve dgreve@mgh.harvard.edu Sent: Monday, January 25, 2021 8:01:12 PM To: freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Recon-all exiting with Errors during surface inflation
The problem is that it expects there to be an aseg.presurf.mgz, but you have turned the creation of it off. Because this is NHP?
On 1/15/2021 5:40 PM, Koch, Erin M. wrote:
External Email - Use Caution
Hi
Thanks for your help. Indeed the list of commands you sent worked, so I added the line you recommended to my xopts. This gets me beyond my previous exit point, but now recon-all is exiting with a new error. I will attach my recon-all log and terminal error. It seems recon-all is trying to load an aseg file; however, I include in my call -noaseg (and I tried adding -nosubcortseg). Please let me know if you need anything else.
Erin
________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Greve, Douglas N.,Ph.D. DGREVE@mgh.harvard.edumailto:DGREVE@mgh.harvard.edu Sent: Wednesday, December 23, 2020 9:12 AM To: freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Recon-all exiting with Errors during surface inflation
There have been some changes that are breaking your stream. Try this
cd /mnt/data2/data/erink/cooked/2019/190124Jamie2/mri setenv SUBJECTS_DIR /mnt/data0/home/erink/subjects mris_place_surface --adgws-in ../surf/autodet.gw.stats.lh.dat --wm wm.mgz --threads 1 --invol brain.finalsurfs.mgz --lh --i ../surf/lh.orig --o ../surf/lh.white.preaparc --white --nsmooth 5 --no-rip-midline --no-rip-bg --no-rip-wmsa --no-rip-freeze --no-rip-lesion
If that works, then add this to your xopts file WhitePreAparc --no-rip-midline --no-rip-bg --no-rip-wmsa --no-rip-freeze --no-rip-lesion
On 12/14/2020 5:35 PM, Koch, Erin M. wrote:
External Email - Use Caution
Hi all,
The lab I work in recently upgrade to freesurfer-linux-centos7x_86_64-7.1.1 from freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0, and I am trying to use a series of shell scripts (that call freesurfer) which we successfully used to run to create flatmaps for non-human primate sessions. I am stuck when using recon-all to inflate the surface. Specifically, I am running the command: "recon-all -autorecon2-wm \ -subjid ${tmp_subj} ${corpcal_coord_string} ${pons_coord_string}\ -noaseg \ -mprage \ -xopts-use\ -debug" This step runs for quite some time, seemingly making progress and then "Exits with errors" . In the terminal the error message that I can see is: "ERROR: need seg for ripping". This is followed by: "recon-all - s SUBJECTNAME exited with ERRORS." (Screen shot of this error is attached). I will also attach the recon-all.log.
This issue does not seem to be a problem of quality of skull stripping or white matter segmentation, as the session can be completed with the older version of freesurfer, adn I get the same error with different sessions and subjects. Can you please shed some light on this? The machine I am using is running Linux 3.10.0-1127.18.2.e17.x86_64 .
As an aside - Do you have any references or outline for flat map creation (specifically for non-human primates) with the newer versions of Free surfer? It is possible adapting our old pipeline is not ideal / there are more efficient or "better" ways to do this now.
Thank you for your help.
Best,
Erin
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It needs to be there. Sorry, I rewrote parts of the stream for v7 and did not consider the impact on NHP streams (since they are not part of our package). You might have to use older versions of FS to make this work.
On 1/26/2021 11:10 PM, Koch, Erin M. wrote:
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Or, are you saying that I do not need to turn it off for NHP?
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*From:* freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Koch, Erin M. erink@caltech.edu *Sent:* Monday, January 25, 2021 10:47:34 PM *To:* Freesurfer support list freesurfer@nmr.mgh.harvard.edu *Subject:* Re: [Freesurfer] Recon-all exiting with Errors during surface inflation
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Yes. I turned off aseg because this is NHP. In previous versions of freesurfer this was fine. Do I need to add something more my xopts file? How do I get around this problem?
Thanks,
Erin
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*From:* freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Douglas N. Greve dgreve@mgh.harvard.edu *Sent:* Monday, January 25, 2021 8:01:12 PM *To:* freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu *Subject:* Re: [Freesurfer] Recon-all exiting with Errors during surface inflation
The problem is that it expects there to be an aseg.presurf.mgz, but you have turned the creation of it off. Because this is NHP?
On 1/15/2021 5:40 PM, Koch, Erin M. wrote:
External Email - Use Caution
Hi
Thanks for your help. Indeed the list of commands you sent worked, so I added the line you recommended to my xopts. This gets me beyond my previous exit point, but now recon-all is exiting with a new error. I will attach my recon-all log and terminal error. It seems recon-all is trying to load an aseg file; however, I include in my call -noaseg (and I tried adding -nosubcortseg). Please let me know if you need anything else.
Erin
*From:* freesurfer-bounces@nmr.mgh.harvard.edu mailto:freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu mailto:freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Greve, Douglas N.,Ph.D. DGREVE@mgh.harvard.edu mailto:DGREVE@mgh.harvard.edu *Sent:* Wednesday, December 23, 2020 9:12 AM *To:* freesurfer@nmr.mgh.harvard.edu mailto:freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu mailto:freesurfer@nmr.mgh.harvard.edu *Subject:* Re: [Freesurfer] Recon-all exiting with Errors during surface inflation There have been some changes that are breaking your stream. Try this
cd /mnt/data2/data/erink/cooked/2019/190124Jamie2/mri setenv SUBJECTS_DIR /mnt/data0/home/erink/subjects mris_place_surface --adgws-in ../surf/autodet.gw.stats.lh.dat --wm wm.mgz --threads 1 --invol brain.finalsurfs.mgz --lh --i ../surf/lh.orig --o ../surf/lh.white.preaparc --white --nsmooth 5 --no-rip-midline --no-rip-bg --no-rip-wmsa --no-rip-freeze --no-rip-lesion
If that works, then add this to your xopts file WhitePreAparc --no-rip-midline --no-rip-bg --no-rip-wmsa --no-rip-freeze --no-rip-lesion
On 12/14/2020 5:35 PM, Koch, Erin M. wrote:
External Email - Use Caution
Hi all,
The lab I work in recently upgrade to freesurfer-linux-centos7x_86_64-7.1.1 from freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0, and I am trying to use a series of shell scripts (that call freesurfer) which we successfully used to run to create flatmaps for non-human primate sessions. I am stuck when using recon-all to inflate the surface. Specifically, I am running the command: "recon-all -autorecon2-wm \ -subjid ${tmp_subj} ${corpcal_coord_string} ${pons_coord_string}\ -noaseg \ -mprage \ -xopts-use\ -debug" This step runs for quite some time, seemingly making progress and then "Exits with errors" . In the terminal the error message that I can see is: "ERROR: need seg for ripping". This is followed by: "recon-all - s SUBJECTNAME exited with ERRORS." (Screen shot of this error is attached). I will also attach the recon-all.log.
This issue does not seem to be a problem of quality of skull stripping or white matter segmentation, as the session can be completed with the older version of freesurfer, adn I get the same error with different sessions and subjects. Can you please shed some light on this? The machine I am using is running Linux 3.10.0-1127.18.2.e17.x86_64 .
As an aside - Do you have any references or outline for flat map creation (specifically for non-human primates) with the newer versions of Free surfer? It is possible adapting our old pipeline is not ideal / there are more efficient or "better" ways to do this now.
Thank you for your help.
Best,
Erin
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Thanks for the info. Is it possible to put in a "fake" aseg.presurf.mgz file? Do you think this is a possible work around, or is the inflation for flat map generation somehow reliant on this file now?
Erin ________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Douglas N. Greve dgreve@mgh.harvard.edu Sent: Wednesday, January 27, 2021 7:40 AM To: freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Recon-all exiting with Errors during surface inflation
It needs to be there. Sorry, I rewrote parts of the stream for v7 and did not consider the impact on NHP streams (since they are not part of our package). You might have to use older versions of FS to make this work.
On 1/26/2021 11:10 PM, Koch, Erin M. wrote:
External Email - Use Caution
Or, are you saying that I do not need to turn it off for NHP?
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Yes. I turned off aseg because this is NHP. In previous versions of freesurfer this was fine. Do I need to add something more my xopts file? How do I get around this problem?
Thanks,
Erin
Get Outlook for iOShttps://secure-web.cisco.com/1DmYXz9AvDs-8SzQ0hBvO0ciJ2KHeyjiheztEzwGHZ-eGDy03rJ8WleExBnEpox-gBx3Ssa0i_H6MCTY3EgMW-U4BzTyCSUkc5dTaNnLsHRux6UyYQdVMYOSmznSH1OAq1gsHihjOXeao-bJyLvt-uZyKU3wAMr18UT-UhnMTafbK9PU_qJQ1WwH7Pf0Ay1Nz3ylb-1O9evs7EpGe4echU9Rdknkx20O2pm_pdSN4_rwh4tLyok4bDwBp5kx1UXLhWrBtYA0YPWv8sV74P7cVVQ/https%3A%2F%2Faka.ms%2Fo0ukef ________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Douglas N. Greve dgreve@mgh.harvard.edumailto:dgreve@mgh.harvard.edu Sent: Monday, January 25, 2021 8:01:12 PM To: freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Recon-all exiting with Errors during surface inflation
The problem is that it expects there to be an aseg.presurf.mgz, but you have turned the creation of it off. Because this is NHP?
On 1/15/2021 5:40 PM, Koch, Erin M. wrote:
External Email - Use Caution
Hi
Thanks for your help. Indeed the list of commands you sent worked, so I added the line you recommended to my xopts. This gets me beyond my previous exit point, but now recon-all is exiting with a new error. I will attach my recon-all log and terminal error. It seems recon-all is trying to load an aseg file; however, I include in my call -noaseg (and I tried adding -nosubcortseg). Please let me know if you need anything else.
Erin
________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Greve, Douglas N.,Ph.D. DGREVE@mgh.harvard.edumailto:DGREVE@mgh.harvard.edu Sent: Wednesday, December 23, 2020 9:12 AM To: freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Recon-all exiting with Errors during surface inflation
There have been some changes that are breaking your stream. Try this
cd /mnt/data2/data/erink/cooked/2019/190124Jamie2/mri setenv SUBJECTS_DIR /mnt/data0/home/erink/subjects mris_place_surface --adgws-in ../surf/autodet.gw.stats.lh.dat --wm wm.mgz --threads 1 --invol brain.finalsurfs.mgz --lh --i ../surf/lh.orig --o ../surf/lh.white.preaparc --white --nsmooth 5 --no-rip-midline --no-rip-bg --no-rip-wmsa --no-rip-freeze --no-rip-lesion
If that works, then add this to your xopts file WhitePreAparc --no-rip-midline --no-rip-bg --no-rip-wmsa --no-rip-freeze --no-rip-lesion
On 12/14/2020 5:35 PM, Koch, Erin M. wrote:
External Email - Use Caution
Hi all,
The lab I work in recently upgrade to freesurfer-linux-centos7x_86_64-7.1.1 from freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0, and I am trying to use a series of shell scripts (that call freesurfer) which we successfully used to run to create flatmaps for non-human primate sessions. I am stuck when using recon-all to inflate the surface. Specifically, I am running the command: "recon-all -autorecon2-wm \ -subjid ${tmp_subj} ${corpcal_coord_string} ${pons_coord_string}\ -noaseg \ -mprage \ -xopts-use\ -debug" This step runs for quite some time, seemingly making progress and then "Exits with errors" . In the terminal the error message that I can see is: "ERROR: need seg for ripping". This is followed by: "recon-all - s SUBJECTNAME exited with ERRORS." (Screen shot of this error is attached). I will also attach the recon-all.log.
This issue does not seem to be a problem of quality of skull stripping or white matter segmentation, as the session can be completed with the older version of freesurfer, adn I get the same error with different sessions and subjects. Can you please shed some light on this? The machine I am using is running Linux 3.10.0-1127.18.2.e17.x86_64 .
As an aside - Do you have any references or outline for flat map creation (specifically for non-human primates) with the newer versions of Free surfer? It is possible adapting our old pipeline is not ideal / there are more efficient or "better" ways to do this now.
Thank you for your help.
Best,
Erin
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It should not need it for the inflation. You can try adding -no-cortex-label and see how far you get
On 1/27/2021 12:39 PM, Koch, Erin M. wrote:
External Email - Use Caution
Thanks for the info. Is it possible to put in a "fake" aseg.presurf.mgz file? Do you think this is a possible work around, or is the inflation for flat map generation somehow reliant on this file now?
Erin
*From:* freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Douglas N. Greve dgreve@mgh.harvard.edu *Sent:* Wednesday, January 27, 2021 7:40 AM *To:* freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu *Subject:* Re: [Freesurfer] Recon-all exiting with Errors during surface inflation It needs to be there. Sorry, I rewrote parts of the stream for v7 and did not consider the impact on NHP streams (since they are not part of our package). You might have to use older versions of FS to make this work.
On 1/26/2021 11:10 PM, Koch, Erin M. wrote:
External Email - Use Caution
Or, are you saying that I do not need to turn it off for NHP?
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*From:* freesurfer-bounces@nmr.mgh.harvard.edu mailto:freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu mailto:freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Koch, Erin M. erink@caltech.edu mailto:erink@caltech.edu *Sent:* Monday, January 25, 2021 10:47:34 PM *To:* Freesurfer support list freesurfer@nmr.mgh.harvard.edu mailto:freesurfer@nmr.mgh.harvard.edu *Subject:* Re: [Freesurfer] Recon-all exiting with Errors during surface inflation
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Yes. I turned off aseg because this is NHP. In previous versions of freesurfer this was fine. Do I need to add something more my xopts file? How do I get around this problem?
Thanks,
Erin
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*From:* freesurfer-bounces@nmr.mgh.harvard.edu mailto:freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu mailto:freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Douglas N. Greve dgreve@mgh.harvard.edu mailto:dgreve@mgh.harvard.edu *Sent:* Monday, January 25, 2021 8:01:12 PM *To:* freesurfer@nmr.mgh.harvard.edu mailto:freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu mailto:freesurfer@nmr.mgh.harvard.edu *Subject:* Re: [Freesurfer] Recon-all exiting with Errors during surface inflation
The problem is that it expects there to be an aseg.presurf.mgz, but you have turned the creation of it off. Because this is NHP?
On 1/15/2021 5:40 PM, Koch, Erin M. wrote:
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Hi
Thanks for your help. Indeed the list of commands you sent worked, so I added the line you recommended to my xopts. This gets me beyond my previous exit point, but now recon-all is exiting with a new error. I will attach my recon-all log and terminal error. It seems recon-all is trying to load an aseg file; however, I include in my call -noaseg (and I tried adding -nosubcortseg). Please let me know if you need anything else.
Erin
*From:* freesurfer-bounces@nmr.mgh.harvard.edu mailto:freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu mailto:freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Greve, Douglas N.,Ph.D. DGREVE@mgh.harvard.edu mailto:DGREVE@mgh.harvard.edu *Sent:* Wednesday, December 23, 2020 9:12 AM *To:* freesurfer@nmr.mgh.harvard.edu mailto:freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu mailto:freesurfer@nmr.mgh.harvard.edu *Subject:* Re: [Freesurfer] Recon-all exiting with Errors during surface inflation There have been some changes that are breaking your stream. Try this
cd /mnt/data2/data/erink/cooked/2019/190124Jamie2/mri setenv SUBJECTS_DIR /mnt/data0/home/erink/subjects mris_place_surface --adgws-in ../surf/autodet.gw.stats.lh.dat --wm wm.mgz --threads 1 --invol brain.finalsurfs.mgz --lh --i ../surf/lh.orig --o ../surf/lh.white.preaparc --white --nsmooth 5 --no-rip-midline --no-rip-bg --no-rip-wmsa --no-rip-freeze --no-rip-lesion
If that works, then add this to your xopts file WhitePreAparc --no-rip-midline --no-rip-bg --no-rip-wmsa --no-rip-freeze --no-rip-lesion
On 12/14/2020 5:35 PM, Koch, Erin M. wrote:
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Hi all,
The lab I work in recently upgrade to freesurfer-linux-centos7x_86_64-7.1.1 from freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0, and I am trying to use a series of shell scripts (that call freesurfer) which we successfully used to run to create flatmaps for non-human primate sessions. I am stuck when using recon-all to inflate the surface. Specifically, I am running the command: "recon-all -autorecon2-wm \ -subjid ${tmp_subj} ${corpcal_coord_string} ${pons_coord_string}\ -noaseg \ -mprage \ -xopts-use\ -debug" This step runs for quite some time, seemingly making progress and then "Exits with errors" . In the terminal the error message that I can see is: "ERROR: need seg for ripping". This is followed by: "recon-all - s SUBJECTNAME exited with ERRORS." (Screen shot of this error is attached). I will also attach the recon-all.log.
This issue does not seem to be a problem of quality of skull stripping or white matter segmentation, as the session can be completed with the older version of freesurfer, adn I get the same error with different sessions and subjects. Can you please shed some light on this? The machine I am using is running Linux 3.10.0-1127.18.2.e17.x86_64 .
As an aside - Do you have any references or outline for flat map creation (specifically for non-human primates) with the newer versions of Free surfer? It is possible adapting our old pipeline is not ideal / there are more efficient or "better" ways to do this now.
Thank you for your help.
Best,
Erin
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It completed! Thank you the help.
Get Outlook for iOShttps://secure-web.cisco.com/1_WItVCzVRuS3M0QN_QNypKBF6kPwV4f4xHS_QoUmiLcxgU2_7tDO78bo30PgyMj7yGDCGa9mSYk_I5XZPGaCnwzx29Brxoq-rO_Q8lQ6jekeEgm_pBhSayqqcHE4VDcfbF1LG5ZgB6fIqs3OJ87ihOCcCQ6iTVNXF96z9WOxgI0tn7Pu8y32vB6qWET_WZJOS_IC5Wqonm9UuAptYt7vthr4GiGqEHDMvz54azabLLHk5MS_ZQJBmxGGlsJ1ibOjkCb5MpRDepX_BJHPYIkGeA/https%3A%2F%2Faka.ms%2Fo0ukef ________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Douglas N. Greve dgreve@mgh.harvard.edu Sent: Wednesday, January 27, 2021 10:00:54 AM To: freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Recon-all exiting with Errors during surface inflation
It should not need it for the inflation. You can try adding -no-cortex-label and see how far you get
On 1/27/2021 12:39 PM, Koch, Erin M. wrote:
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Thanks for the info. Is it possible to put in a "fake" aseg.presurf.mgz file? Do you think this is a possible work around, or is the inflation for flat map generation somehow reliant on this file now?
Erin ________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Douglas N. Greve dgreve@mgh.harvard.edumailto:dgreve@mgh.harvard.edu Sent: Wednesday, January 27, 2021 7:40 AM To: freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Recon-all exiting with Errors during surface inflation
It needs to be there. Sorry, I rewrote parts of the stream for v7 and did not consider the impact on NHP streams (since they are not part of our package). You might have to use older versions of FS to make this work.
On 1/26/2021 11:10 PM, Koch, Erin M. wrote:
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Or, are you saying that I do not need to turn it off for NHP?
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Yes. I turned off aseg because this is NHP. In previous versions of freesurfer this was fine. Do I need to add something more my xopts file? How do I get around this problem?
Thanks,
Erin
Get Outlook for iOShttps://secure-web.cisco.com/1DmYXz9AvDs-8SzQ0hBvO0ciJ2KHeyjiheztEzwGHZ-eGDy03rJ8WleExBnEpox-gBx3Ssa0i_H6MCTY3EgMW-U4BzTyCSUkc5dTaNnLsHRux6UyYQdVMYOSmznSH1OAq1gsHihjOXeao-bJyLvt-uZyKU3wAMr18UT-UhnMTafbK9PU_qJQ1WwH7Pf0Ay1Nz3ylb-1O9evs7EpGe4echU9Rdknkx20O2pm_pdSN4_rwh4tLyok4bDwBp5kx1UXLhWrBtYA0YPWv8sV74P7cVVQ/https%3A%2F%2Faka.ms%2Fo0ukef ________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Douglas N. Greve dgreve@mgh.harvard.edumailto:dgreve@mgh.harvard.edu Sent: Monday, January 25, 2021 8:01:12 PM To: freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Recon-all exiting with Errors during surface inflation
The problem is that it expects there to be an aseg.presurf.mgz, but you have turned the creation of it off. Because this is NHP?
On 1/15/2021 5:40 PM, Koch, Erin M. wrote:
External Email - Use Caution
Hi
Thanks for your help. Indeed the list of commands you sent worked, so I added the line you recommended to my xopts. This gets me beyond my previous exit point, but now recon-all is exiting with a new error. I will attach my recon-all log and terminal error. It seems recon-all is trying to load an aseg file; however, I include in my call -noaseg (and I tried adding -nosubcortseg). Please let me know if you need anything else.
Erin
________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Greve, Douglas N.,Ph.D. DGREVE@mgh.harvard.edumailto:DGREVE@mgh.harvard.edu Sent: Wednesday, December 23, 2020 9:12 AM To: freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Recon-all exiting with Errors during surface inflation
There have been some changes that are breaking your stream. Try this
cd /mnt/data2/data/erink/cooked/2019/190124Jamie2/mri setenv SUBJECTS_DIR /mnt/data0/home/erink/subjects mris_place_surface --adgws-in ../surf/autodet.gw.stats.lh.dat --wm wm.mgz --threads 1 --invol brain.finalsurfs.mgz --lh --i ../surf/lh.orig --o ../surf/lh.white.preaparc --white --nsmooth 5 --no-rip-midline --no-rip-bg --no-rip-wmsa --no-rip-freeze --no-rip-lesion
If that works, then add this to your xopts file WhitePreAparc --no-rip-midline --no-rip-bg --no-rip-wmsa --no-rip-freeze --no-rip-lesion
On 12/14/2020 5:35 PM, Koch, Erin M. wrote:
External Email - Use Caution
Hi all,
The lab I work in recently upgrade to freesurfer-linux-centos7x_86_64-7.1.1 from freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0, and I am trying to use a series of shell scripts (that call freesurfer) which we successfully used to run to create flatmaps for non-human primate sessions. I am stuck when using recon-all to inflate the surface. Specifically, I am running the command: "recon-all -autorecon2-wm \ -subjid ${tmp_subj} ${corpcal_coord_string} ${pons_coord_string}\ -noaseg \ -mprage \ -xopts-use\ -debug" This step runs for quite some time, seemingly making progress and then "Exits with errors" . In the terminal the error message that I can see is: "ERROR: need seg for ripping". This is followed by: "recon-all - s SUBJECTNAME exited with ERRORS." (Screen shot of this error is attached). I will also attach the recon-all.log.
This issue does not seem to be a problem of quality of skull stripping or white matter segmentation, as the session can be completed with the older version of freesurfer, adn I get the same error with different sessions and subjects. Can you please shed some light on this? The machine I am using is running Linux 3.10.0-1127.18.2.e17.x86_64 .
As an aside - Do you have any references or outline for flat map creation (specifically for non-human primates) with the newer versions of Free surfer? It is possible adapting our old pipeline is not ideal / there are more efficient or "better" ways to do this now.
Thank you for your help.
Best,
Erin
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Hi Douglas,
I am sorry I have to bug you once more. While the inflation step completed with the suggested flag, as did the flattening step (for creating a flat map), when I went to register a functional scan to the inflated and flat map the command:
mri_vol2surf -src 'PVal_resliced' -srcreg reg.dat -projfrac 0.5 -interp nearest -hemi lh -out 'PVal_lh') mri_vol2surf -src 'PVal_resliced' -srcreg reg.dat -projfrac 0.5 -interp nearest -hemi rh -out 'PVal_rh')
failed because the recon-all did not create a few files including: lh.white, and rh.white
Is this due to the flags and expert options that were needed to complete the inflation? Can I run a separate command to create these files?
thanks,
Erin ________________________________ From: Koch, Erin M. erink@caltech.edu Sent: Wednesday, January 27, 2021 10:04 PM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Recon-all exiting with Errors during surface inflation
It completed! Thank you the help.
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It should not need it for the inflation. You can try adding -no-cortex-label and see how far you get
On 1/27/2021 12:39 PM, Koch, Erin M. wrote:
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Thanks for the info. Is it possible to put in a "fake" aseg.presurf.mgz file? Do you think this is a possible work around, or is the inflation for flat map generation somehow reliant on this file now?
Erin ________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Douglas N. Greve dgreve@mgh.harvard.edumailto:dgreve@mgh.harvard.edu Sent: Wednesday, January 27, 2021 7:40 AM To: freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Recon-all exiting with Errors during surface inflation
It needs to be there. Sorry, I rewrote parts of the stream for v7 and did not consider the impact on NHP streams (since they are not part of our package). You might have to use older versions of FS to make this work.
On 1/26/2021 11:10 PM, Koch, Erin M. wrote:
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Or, are you saying that I do not need to turn it off for NHP?
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Yes. I turned off aseg because this is NHP. In previous versions of freesurfer this was fine. Do I need to add something more my xopts file? How do I get around this problem?
Thanks,
Erin
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The problem is that it expects there to be an aseg.presurf.mgz, but you have turned the creation of it off. Because this is NHP?
On 1/15/2021 5:40 PM, Koch, Erin M. wrote:
External Email - Use Caution
Hi
Thanks for your help. Indeed the list of commands you sent worked, so I added the line you recommended to my xopts. This gets me beyond my previous exit point, but now recon-all is exiting with a new error. I will attach my recon-all log and terminal error. It seems recon-all is trying to load an aseg file; however, I include in my call -noaseg (and I tried adding -nosubcortseg). Please let me know if you need anything else.
Erin
________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Greve, Douglas N.,Ph.D. DGREVE@mgh.harvard.edumailto:DGREVE@mgh.harvard.edu Sent: Wednesday, December 23, 2020 9:12 AM To: freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Recon-all exiting with Errors during surface inflation
There have been some changes that are breaking your stream. Try this
cd /mnt/data2/data/erink/cooked/2019/190124Jamie2/mri setenv SUBJECTS_DIR /mnt/data0/home/erink/subjects mris_place_surface --adgws-in ../surf/autodet.gw.stats.lh.dat --wm wm.mgz --threads 1 --invol brain.finalsurfs.mgz --lh --i ../surf/lh.orig --o ../surf/lh.white.preaparc --white --nsmooth 5 --no-rip-midline --no-rip-bg --no-rip-wmsa --no-rip-freeze --no-rip-lesion
If that works, then add this to your xopts file WhitePreAparc --no-rip-midline --no-rip-bg --no-rip-wmsa --no-rip-freeze --no-rip-lesion
On 12/14/2020 5:35 PM, Koch, Erin M. wrote:
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Hi all,
The lab I work in recently upgrade to freesurfer-linux-centos7x_86_64-7.1.1 from freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0, and I am trying to use a series of shell scripts (that call freesurfer) which we successfully used to run to create flatmaps for non-human primate sessions. I am stuck when using recon-all to inflate the surface. Specifically, I am running the command: "recon-all -autorecon2-wm \ -subjid ${tmp_subj} ${corpcal_coord_string} ${pons_coord_string}\ -noaseg \ -mprage \ -xopts-use\ -debug" This step runs for quite some time, seemingly making progress and then "Exits with errors" . In the terminal the error message that I can see is: "ERROR: need seg for ripping". This is followed by: "recon-all - s SUBJECTNAME exited with ERRORS." (Screen shot of this error is attached). I will also attach the recon-all.log.
This issue does not seem to be a problem of quality of skull stripping or white matter segmentation, as the session can be completed with the older version of freesurfer, adn I get the same error with different sessions and subjects. Can you please shed some light on this? The machine I am using is running Linux 3.10.0-1127.18.2.e17.x86_64 .
As an aside - Do you have any references or outline for flat map creation (specifically for non-human primates) with the newer versions of Free surfer? It is possible adapting our old pipeline is not ideal / there are more efficient or "better" ways to do this now.
Thank you for your help.
Best,
Erin
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What surfaces are there?
On 2/11/2021 4:35 PM, Koch, Erin M. wrote:
External Email - Use Caution
Hi Douglas,
I am sorry I have to bug you once more. While the inflation step completed with the suggested flag, as did the flattening step (for creating a flat map), when I went to register a functional scan to the inflated and flat map the command:
mri_vol2surf —src 'PVal_resliced' —srcreg reg.dat —projfrac 0.5 —interp nearest —hemi lh —out 'PVal_lh') mri_vol2surf —src 'PVal_resliced' —srcreg reg.dat —projfrac 0.5 —interp nearest —hemi rh —out 'PVal_rh')
failed because the recon-all did not create a few files including: lh.white, and rh.white
Is this due to the flags and expert options that were needed to complete the inflation? Can I run a separate command to create these files?
thanks,
Erin
*From:* Koch, Erin M. erink@caltech.edu *Sent:* Wednesday, January 27, 2021 10:04 PM *To:* Freesurfer support list freesurfer@nmr.mgh.harvard.edu *Subject:* Re: [Freesurfer] Recon-all exiting with Errors during surface inflation It completed! Thank you the help.
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*From:* freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Douglas N. Greve dgreve@mgh.harvard.edu *Sent:* Wednesday, January 27, 2021 10:00:54 AM *To:* freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu *Subject:* Re: [Freesurfer] Recon-all exiting with Errors during surface inflation It should not need it for the inflation. You can try adding -no-cortex-label and see how far you get
On 1/27/2021 12:39 PM, Koch, Erin M. wrote:
External Email - Use Caution
Thanks for the info. Is it possible to put in a "fake" aseg.presurf.mgz file? Do you think this is a possible work around, or is the inflation for flat map generation somehow reliant on this file now?
Erin
*From:* freesurfer-bounces@nmr.mgh.harvard.edu mailto:freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu mailto:freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Douglas N. Greve dgreve@mgh.harvard.edu mailto:dgreve@mgh.harvard.edu *Sent:* Wednesday, January 27, 2021 7:40 AM *To:* freesurfer@nmr.mgh.harvard.edu mailto:freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu mailto:freesurfer@nmr.mgh.harvard.edu *Subject:* Re: [Freesurfer] Recon-all exiting with Errors during surface inflation It needs to be there. Sorry, I rewrote parts of the stream for v7 and did not consider the impact on NHP streams (since they are not part of our package). You might have to use older versions of FS to make this work.
On 1/26/2021 11:10 PM, Koch, Erin M. wrote:
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Or, are you saying that I do not need to turn it off for NHP?
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*From:* freesurfer-bounces@nmr.mgh.harvard.edu mailto:freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu mailto:freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Koch, Erin M. erink@caltech.edu mailto:erink@caltech.edu *Sent:* Monday, January 25, 2021 10:47:34 PM *To:* Freesurfer support list freesurfer@nmr.mgh.harvard.edu mailto:freesurfer@nmr.mgh.harvard.edu *Subject:* Re: [Freesurfer] Recon-all exiting with Errors during surface inflation
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Yes. I turned off aseg because this is NHP. In previous versions of freesurfer this was fine. Do I need to add something more my xopts file? How do I get around this problem?
Thanks,
Erin
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*From:* freesurfer-bounces@nmr.mgh.harvard.edu mailto:freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu mailto:freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Douglas N. Greve dgreve@mgh.harvard.edu mailto:dgreve@mgh.harvard.edu *Sent:* Monday, January 25, 2021 8:01:12 PM *To:* freesurfer@nmr.mgh.harvard.edu mailto:freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu mailto:freesurfer@nmr.mgh.harvard.edu *Subject:* Re: [Freesurfer] Recon-all exiting with Errors during surface inflation
The problem is that it expects there to be an aseg.presurf.mgz, but you have turned the creation of it off. Because this is NHP?
On 1/15/2021 5:40 PM, Koch, Erin M. wrote:
External Email - Use Caution
Hi
Thanks for your help. Indeed the list of commands you sent worked, so I added the line you recommended to my xopts. This gets me beyond my previous exit point, but now recon-all is exiting with a new error. I will attach my recon-all log and terminal error. It seems recon-all is trying to load an aseg file; however, I include in my call -noaseg (and I tried adding -nosubcortseg). Please let me know if you need anything else.
Erin
*From:* freesurfer-bounces@nmr.mgh.harvard.edu mailto:freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu mailto:freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Greve, Douglas N.,Ph.D. DGREVE@mgh.harvard.edu mailto:DGREVE@mgh.harvard.edu *Sent:* Wednesday, December 23, 2020 9:12 AM *To:* freesurfer@nmr.mgh.harvard.edu mailto:freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu mailto:freesurfer@nmr.mgh.harvard.edu *Subject:* Re: [Freesurfer] Recon-all exiting with Errors during surface inflation There have been some changes that are breaking your stream. Try this
cd /mnt/data2/data/erink/cooked/2019/190124Jamie2/mri setenv SUBJECTS_DIR /mnt/data0/home/erink/subjects mris_place_surface --adgws-in ../surf/autodet.gw.stats.lh.dat --wm wm.mgz --threads 1 --invol brain.finalsurfs.mgz --lh --i ../surf/lh.orig --o ../surf/lh.white.preaparc --white --nsmooth 5 --no-rip-midline --no-rip-bg --no-rip-wmsa --no-rip-freeze --no-rip-lesion
If that works, then add this to your xopts file WhitePreAparc --no-rip-midline --no-rip-bg --no-rip-wmsa --no-rip-freeze --no-rip-lesion
On 12/14/2020 5:35 PM, Koch, Erin M. wrote:
External Email - Use Caution
Hi all,
The lab I work in recently upgrade to freesurfer-linux-centos7x_86_64-7.1.1 from freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0, and I am trying to use a series of shell scripts (that call freesurfer) which we successfully used to run to create flatmaps for non-human primate sessions. I am stuck when using recon-all to inflate the surface. Specifically, I am running the command: "recon-all -autorecon2-wm \ -subjid ${tmp_subj} ${corpcal_coord_string} ${pons_coord_string}\ -noaseg \ -mprage \ -xopts-use\ -debug" This step runs for quite some time, seemingly making progress and then "Exits with errors" . In the terminal the error message that I can see is: "ERROR: need seg for ripping". This is followed by: "recon-all - s SUBJECTNAME exited with ERRORS." (Screen shot of this error is attached). I will also attach the recon-all.log.
This issue does not seem to be a problem of quality of skull stripping or white matter segmentation, as the session can be completed with the older version of freesurfer, adn I get the same error with different sessions and subjects. Can you please shed some light on this? The machine I am using is running Linux 3.10.0-1127.18.2.e17.x86_64 .
As an aside - Do you have any references or outline for flat map creation (specifically for non-human primates) with the newer versions of Free surfer? It is possible adapting our old pipeline is not ideal / there are more efficient or "better" ways to do this now.
Thank you for your help.
Best,
Erin
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I am attaching a screen shot of the files in my subjects surf subfolder. Note in the image you only see the lh.*** surfaces. All correspoinding rh.*** files are there as well.
Thanks! ________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Douglas N. Greve dgreve@mgh.harvard.edu Sent: Friday, February 12, 2021 6:54 AM To: freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Recon-all exiting with Errors during surface inflation
What surfaces are there?
On 2/11/2021 4:35 PM, Koch, Erin M. wrote:
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Hi Douglas,
I am sorry I have to bug you once more. While the inflation step completed with the suggested flag, as did the flattening step (for creating a flat map), when I went to register a functional scan to the inflated and flat map the command:
mri_vol2surf —src 'PVal_resliced' —srcreg reg.dat —projfrac 0.5 —interp nearest —hemi lh —out 'PVal_lh') mri_vol2surf —src 'PVal_resliced' —srcreg reg.dat —projfrac 0.5 —interp nearest —hemi rh —out 'PVal_rh')
failed because the recon-all did not create a few files including: lh.white, and rh.white
Is this due to the flags and expert options that were needed to complete the inflation? Can I run a separate command to create these files?
thanks,
Erin ________________________________ From: Koch, Erin M. erink@caltech.edumailto:erink@caltech.edu Sent: Wednesday, January 27, 2021 10:04 PM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Recon-all exiting with Errors during surface inflation
It completed! Thank you the help.
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It should not need it for the inflation. You can try adding -no-cortex-label and see how far you get
On 1/27/2021 12:39 PM, Koch, Erin M. wrote:
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Thanks for the info. Is it possible to put in a "fake" aseg.presurf.mgz file? Do you think this is a possible work around, or is the inflation for flat map generation somehow reliant on this file now?
Erin ________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Douglas N. Greve dgreve@mgh.harvard.edumailto:dgreve@mgh.harvard.edu Sent: Wednesday, January 27, 2021 7:40 AM To: freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Recon-all exiting with Errors during surface inflation
It needs to be there. Sorry, I rewrote parts of the stream for v7 and did not consider the impact on NHP streams (since they are not part of our package). You might have to use older versions of FS to make this work.
On 1/26/2021 11:10 PM, Koch, Erin M. wrote:
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Or, are you saying that I do not need to turn it off for NHP?
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Yes. I turned off aseg because this is NHP. In previous versions of freesurfer this was fine. Do I need to add something more my xopts file? How do I get around this problem?
Thanks,
Erin
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The problem is that it expects there to be an aseg.presurf.mgz, but you have turned the creation of it off. Because this is NHP?
On 1/15/2021 5:40 PM, Koch, Erin M. wrote:
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Hi
Thanks for your help. Indeed the list of commands you sent worked, so I added the line you recommended to my xopts. This gets me beyond my previous exit point, but now recon-all is exiting with a new error. I will attach my recon-all log and terminal error. It seems recon-all is trying to load an aseg file; however, I include in my call -noaseg (and I tried adding -nosubcortseg). Please let me know if you need anything else.
Erin
________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Greve, Douglas N.,Ph.D. DGREVE@mgh.harvard.edumailto:DGREVE@mgh.harvard.edu Sent: Wednesday, December 23, 2020 9:12 AM To: freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Recon-all exiting with Errors during surface inflation
There have been some changes that are breaking your stream. Try this
cd /mnt/data2/data/erink/cooked/2019/190124Jamie2/mri setenv SUBJECTS_DIR /mnt/data0/home/erink/subjects mris_place_surface --adgws-in ../surf/autodet.gw.stats.lh.dat --wm wm.mgz --threads 1 --invol brain.finalsurfs.mgz --lh --i ../surf/lh.orig --o ../surf/lh.white.preaparc --white --nsmooth 5 --no-rip-midline --no-rip-bg --no-rip-wmsa --no-rip-freeze --no-rip-lesion
If that works, then add this to your xopts file WhitePreAparc --no-rip-midline --no-rip-bg --no-rip-wmsa --no-rip-freeze --no-rip-lesion
On 12/14/2020 5:35 PM, Koch, Erin M. wrote:
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Hi all,
The lab I work in recently upgrade to freesurfer-linux-centos7x_86_64-7.1.1 from freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0, and I am trying to use a series of shell scripts (that call freesurfer) which we successfully used to run to create flatmaps for non-human primate sessions. I am stuck when using recon-all to inflate the surface. Specifically, I am running the command: "recon-all -autorecon2-wm \ -subjid ${tmp_subj} ${corpcal_coord_string} ${pons_coord_string}\ -noaseg \ -mprage \ -xopts-use\ -debug" This step runs for quite some time, seemingly making progress and then "Exits with errors" . In the terminal the error message that I can see is: "ERROR: need seg for ripping". This is followed by: "recon-all - s SUBJECTNAME exited with ERRORS." (Screen shot of this error is attached). I will also attach the recon-all.log.
This issue does not seem to be a problem of quality of skull stripping or white matter segmentation, as the session can be completed with the older version of freesurfer, adn I get the same error with different sessions and subjects. Can you please shed some light on this? The machine I am using is running Linux 3.10.0-1127.18.2.e17.x86_64 .
As an aside - Do you have any references or outline for flat map creation (specifically for non-human primates) with the newer versions of Free surfer? It is possible adapting our old pipeline is not ideal / there are more efficient or "better" ways to do this now.
Thank you for your help.
Best,
Erin
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Is there anyway to get the lh.white and rh.white with noaseg? Or is there a file in the attachment of the previous email that is a stand in for those missing files?
Thanks for your help. Erin ________________________________ From: Koch, Erin M. erink@caltech.edu Sent: Wednesday, February 17, 2021 11:14 AM To: freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Recon-all exiting with Errors during surface inflation
I am attaching a screen shot of the files in my subjects surf subfolder. Note in the image you only see the lh.*** surfaces. All correspoinding rh.*** files are there as well.
Thanks! ________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Douglas N. Greve dgreve@mgh.harvard.edu Sent: Friday, February 12, 2021 6:54 AM To: freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Recon-all exiting with Errors during surface inflation
What surfaces are there?
On 2/11/2021 4:35 PM, Koch, Erin M. wrote:
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Hi Douglas,
I am sorry I have to bug you once more. While the inflation step completed with the suggested flag, as did the flattening step (for creating a flat map), when I went to register a functional scan to the inflated and flat map the command:
mri_vol2surf —src 'PVal_resliced' —srcreg reg.dat —projfrac 0.5 —interp nearest —hemi lh —out 'PVal_lh') mri_vol2surf —src 'PVal_resliced' —srcreg reg.dat —projfrac 0.5 —interp nearest —hemi rh —out 'PVal_rh')
failed because the recon-all did not create a few files including: lh.white, and rh.white
Is this due to the flags and expert options that were needed to complete the inflation? Can I run a separate command to create these files?
thanks,
Erin ________________________________ From: Koch, Erin M. erink@caltech.edumailto:erink@caltech.edu Sent: Wednesday, January 27, 2021 10:04 PM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Recon-all exiting with Errors during surface inflation
It completed! Thank you the help.
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It should not need it for the inflation. You can try adding -no-cortex-label and see how far you get
On 1/27/2021 12:39 PM, Koch, Erin M. wrote:
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Thanks for the info. Is it possible to put in a "fake" aseg.presurf.mgz file? Do you think this is a possible work around, or is the inflation for flat map generation somehow reliant on this file now?
Erin ________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Douglas N. Greve dgreve@mgh.harvard.edumailto:dgreve@mgh.harvard.edu Sent: Wednesday, January 27, 2021 7:40 AM To: freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Recon-all exiting with Errors during surface inflation
It needs to be there. Sorry, I rewrote parts of the stream for v7 and did not consider the impact on NHP streams (since they are not part of our package). You might have to use older versions of FS to make this work.
On 1/26/2021 11:10 PM, Koch, Erin M. wrote:
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Or, are you saying that I do not need to turn it off for NHP?
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Yes. I turned off aseg because this is NHP. In previous versions of freesurfer this was fine. Do I need to add something more my xopts file? How do I get around this problem?
Thanks,
Erin
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The problem is that it expects there to be an aseg.presurf.mgz, but you have turned the creation of it off. Because this is NHP?
On 1/15/2021 5:40 PM, Koch, Erin M. wrote:
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Hi
Thanks for your help. Indeed the list of commands you sent worked, so I added the line you recommended to my xopts. This gets me beyond my previous exit point, but now recon-all is exiting with a new error. I will attach my recon-all log and terminal error. It seems recon-all is trying to load an aseg file; however, I include in my call -noaseg (and I tried adding -nosubcortseg). Please let me know if you need anything else.
Erin
________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Greve, Douglas N.,Ph.D. DGREVE@mgh.harvard.edumailto:DGREVE@mgh.harvard.edu Sent: Wednesday, December 23, 2020 9:12 AM To: freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Recon-all exiting with Errors during surface inflation
There have been some changes that are breaking your stream. Try this
cd /mnt/data2/data/erink/cooked/2019/190124Jamie2/mri setenv SUBJECTS_DIR /mnt/data0/home/erink/subjects mris_place_surface --adgws-in ../surf/autodet.gw.stats.lh.dat --wm wm.mgz --threads 1 --invol brain.finalsurfs.mgz --lh --i ../surf/lh.orig --o ../surf/lh.white.preaparc --white --nsmooth 5 --no-rip-midline --no-rip-bg --no-rip-wmsa --no-rip-freeze --no-rip-lesion
If that works, then add this to your xopts file WhitePreAparc --no-rip-midline --no-rip-bg --no-rip-wmsa --no-rip-freeze --no-rip-lesion
On 12/14/2020 5:35 PM, Koch, Erin M. wrote:
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Hi all,
The lab I work in recently upgrade to freesurfer-linux-centos7x_86_64-7.1.1 from freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0, and I am trying to use a series of shell scripts (that call freesurfer) which we successfully used to run to create flatmaps for non-human primate sessions. I am stuck when using recon-all to inflate the surface. Specifically, I am running the command: "recon-all -autorecon2-wm \ -subjid ${tmp_subj} ${corpcal_coord_string} ${pons_coord_string}\ -noaseg \ -mprage \ -xopts-use\ -debug" This step runs for quite some time, seemingly making progress and then "Exits with errors" . In the terminal the error message that I can see is: "ERROR: need seg for ripping". This is followed by: "recon-all - s SUBJECTNAME exited with ERRORS." (Screen shot of this error is attached). I will also attach the recon-all.log.
This issue does not seem to be a problem of quality of skull stripping or white matter segmentation, as the session can be completed with the older version of freesurfer, adn I get the same error with different sessions and subjects. Can you please shed some light on this? The machine I am using is running Linux 3.10.0-1127.18.2.e17.x86_64 .
As an aside - Do you have any references or outline for flat map creation (specifically for non-human primates) with the newer versions of Free surfer? It is possible adapting our old pipeline is not ideal / there are more efficient or "better" ways to do this now.
Thank you for your help.
Best,
Erin
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Just bumping this inquiry. Thanks for the help.
Erin ________________________________ From: Koch, Erin M. erink@caltech.edu Sent: Tuesday, February 23, 2021 9:51 AM To: freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Recon-all exiting with Errors during surface inflation
Is there anyway to get the lh.white and rh.white with noaseg? Or is there a file in the attachment of the previous email that is a stand in for those missing files?
Thanks for your help. Erin ________________________________ From: Koch, Erin M. erink@caltech.edu Sent: Wednesday, February 17, 2021 11:14 AM To: freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Recon-all exiting with Errors during surface inflation
I am attaching a screen shot of the files in my subjects surf subfolder. Note in the image you only see the lh.*** surfaces. All correspoinding rh.*** files are there as well.
Thanks! ________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Douglas N. Greve dgreve@mgh.harvard.edu Sent: Friday, February 12, 2021 6:54 AM To: freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Recon-all exiting with Errors during surface inflation
What surfaces are there?
On 2/11/2021 4:35 PM, Koch, Erin M. wrote:
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Hi Douglas,
I am sorry I have to bug you once more. While the inflation step completed with the suggested flag, as did the flattening step (for creating a flat map), when I went to register a functional scan to the inflated and flat map the command:
mri_vol2surf —src 'PVal_resliced' —srcreg reg.dat —projfrac 0.5 —interp nearest —hemi lh —out 'PVal_lh') mri_vol2surf —src 'PVal_resliced' —srcreg reg.dat —projfrac 0.5 —interp nearest —hemi rh —out 'PVal_rh')
failed because the recon-all did not create a few files including: lh.white, and rh.white
Is this due to the flags and expert options that were needed to complete the inflation? Can I run a separate command to create these files?
thanks,
Erin ________________________________ From: Koch, Erin M. erink@caltech.edumailto:erink@caltech.edu Sent: Wednesday, January 27, 2021 10:04 PM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Recon-all exiting with Errors during surface inflation
It completed! Thank you the help.
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It should not need it for the inflation. You can try adding -no-cortex-label and see how far you get
On 1/27/2021 12:39 PM, Koch, Erin M. wrote:
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Thanks for the info. Is it possible to put in a "fake" aseg.presurf.mgz file? Do you think this is a possible work around, or is the inflation for flat map generation somehow reliant on this file now?
Erin ________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Douglas N. Greve dgreve@mgh.harvard.edumailto:dgreve@mgh.harvard.edu Sent: Wednesday, January 27, 2021 7:40 AM To: freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Recon-all exiting with Errors during surface inflation
It needs to be there. Sorry, I rewrote parts of the stream for v7 and did not consider the impact on NHP streams (since they are not part of our package). You might have to use older versions of FS to make this work.
On 1/26/2021 11:10 PM, Koch, Erin M. wrote:
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Or, are you saying that I do not need to turn it off for NHP?
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Yes. I turned off aseg because this is NHP. In previous versions of freesurfer this was fine. Do I need to add something more my xopts file? How do I get around this problem?
Thanks,
Erin
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The problem is that it expects there to be an aseg.presurf.mgz, but you have turned the creation of it off. Because this is NHP?
On 1/15/2021 5:40 PM, Koch, Erin M. wrote:
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Hi
Thanks for your help. Indeed the list of commands you sent worked, so I added the line you recommended to my xopts. This gets me beyond my previous exit point, but now recon-all is exiting with a new error. I will attach my recon-all log and terminal error. It seems recon-all is trying to load an aseg file; however, I include in my call -noaseg (and I tried adding -nosubcortseg). Please let me know if you need anything else.
Erin
________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Greve, Douglas N.,Ph.D. DGREVE@mgh.harvard.edumailto:DGREVE@mgh.harvard.edu Sent: Wednesday, December 23, 2020 9:12 AM To: freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Recon-all exiting with Errors during surface inflation
There have been some changes that are breaking your stream. Try this
cd /mnt/data2/data/erink/cooked/2019/190124Jamie2/mri setenv SUBJECTS_DIR /mnt/data0/home/erink/subjects mris_place_surface --adgws-in ../surf/autodet.gw.stats.lh.dat --wm wm.mgz --threads 1 --invol brain.finalsurfs.mgz --lh --i ../surf/lh.orig --o ../surf/lh.white.preaparc --white --nsmooth 5 --no-rip-midline --no-rip-bg --no-rip-wmsa --no-rip-freeze --no-rip-lesion
If that works, then add this to your xopts file WhitePreAparc --no-rip-midline --no-rip-bg --no-rip-wmsa --no-rip-freeze --no-rip-lesion
On 12/14/2020 5:35 PM, Koch, Erin M. wrote:
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Hi all,
The lab I work in recently upgrade to freesurfer-linux-centos7x_86_64-7.1.1 from freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0, and I am trying to use a series of shell scripts (that call freesurfer) which we successfully used to run to create flatmaps for non-human primate sessions. I am stuck when using recon-all to inflate the surface. Specifically, I am running the command: "recon-all -autorecon2-wm \ -subjid ${tmp_subj} ${corpcal_coord_string} ${pons_coord_string}\ -noaseg \ -mprage \ -xopts-use\ -debug" This step runs for quite some time, seemingly making progress and then "Exits with errors" . In the terminal the error message that I can see is: "ERROR: need seg for ripping". This is followed by: "recon-all - s SUBJECTNAME exited with ERRORS." (Screen shot of this error is attached). I will also attach the recon-all.log.
This issue does not seem to be a problem of quality of skull stripping or white matter segmentation, as the session can be completed with the older version of freesurfer, adn I get the same error with different sessions and subjects. Can you please shed some light on this? The machine I am using is running Linux 3.10.0-1127.18.2.e17.x86_64 .
As an aside - Do you have any references or outline for flat map creation (specifically for non-human primates) with the newer versions of Free surfer? It is possible adapting our old pipeline is not ideal / there are more efficient or "better" ways to do this now.
Thank you for your help.
Best,
Erin
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_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurferhttps://secure-web.cisco.com/1uXr4l76qw91ZuxiF1h3SDEEu0eCh2pnx-b5n4X0g2ACVl2HmijilZ8ZFvIDOUwkb9B-7BOUhsXNjXYqLOG1I1QCJDJ-ljWK6dApFC6oQdPZn_hD9bd6xvcUV_vBtBXZzfyxPnt14_toOVN6qkUSnDE3dCNpAF1cSZc-WUkNlTr19xIjMzJFEUleyIp0Tqbvo9kjo_-dAerADFP1jfeGRR_d6j0preJEIGCWoy_c6Cuht5_o-WU0OYVEmDI3TEGKKxVyMthR-0TZYPhZq1INFUA/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurferhttps://secure-web.cisco.com/1RHRIst2cqa_F4R4pzoERTGFBEewHr2F-OnO_Xay4VBjYF2LQGMbqORta0GmNfQo1y9mOn7MF5bP7Ssi5WR0U0HE05s1Ospn4s8XzhGPAqz1ZWQ2D85OCinOW3giX8ZH14dbrmiZ5Lcy7WTiZwqPKfa91L67AHtbFLGRBHOLE-ebw5E1VhVH1NM20oXDhrQewZ9A5feodHveNaMpvLK__YYqIsr2AkOwPNc4ycDkobVyD06doz3F7ACbp70s4Cs4rv00BwMrK41QI4jqsQVb6Rg/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
freesurfer@nmr.mgh.harvard.edu
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Douglas N. Greve -
Greve, Douglas N.,Ph.D.
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Koch, Erin M.