We are please to announce version 7.2. Mostly bug fixes and behind-the-scenes enhancements. But there are a few new goodies and one new "known issue" about defacing. Check out https://surfer.nmr.mgh.harvard.edu/fswiki/ReleaseNotes doug
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Dear Doug,
Thank you for the announcement of 7.2.0 update. I updated using freesurfer-linux-ubuntu18_amd64.tar.gz and noticed that the 'mni' directory is missing.
As a result, now the shell shows warning about MNI
===== -------- freesurfer-linux-ubuntu18_x86_64-7.2.0-20210714-aa8f76b -------- Setting up environment for FreeSurfer/FS-FAST (and FSL) FREESURFER_HOME /usr/local/freesurfer/7.2.0 FSFAST_HOME /usr/local/freesurfer/7.2.0/fsfast FSF_OUTPUT_FORMAT nii.gz SUBJECTS_DIR /home/username/freesurfer/7.2.0/subjects WARNING: MINC_BIN_DIR not defined. 'nu_correct' and other MINC tools are used by some Freesurfer utilities. Set NO_MINC to suppress this warning. WARNING: MINC_LIB_DIR not defined. Some Freesurfer utilities rely on the MINC toolkit libraries. Set NO_MINC to suppress this warning. FSL_DIR /usr/local/fsl =====
Is it intended?
Best regards,
Kiyotaka
On Tue, Jul 20, 2021 at 7:45 AM Douglas N. Greve dgreve@mgh.harvard.edu wrote:
We are please to announce version 7.2. Mostly bug fixes and behind-the-scenes enhancements. But there are a few new goodies and one new "known issue" about defacing. Check out https://secure-web.cisco.com/1Nq7OG4aqL5Xu5zmIj8jgt_aBH5sIzltmYEnh37LRCC02zU... doug
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Read the release notes. Can I with the new version run a recon-all over processed 7.1.1. I am interested in the ability to edit filled.mgz and applying this to 7.1.1 recons.
On Mon, Jul 19, 2021 at 5:46 PM Douglas N. Greve dgreve@mgh.harvard.edu wrote:
We are please to announce version 7.2. Mostly bug fixes and behind-the-scenes enhancements. But there are a few new goodies and one new "known issue" about defacing. Check out https://secure-web.cisco.com/1ncOzuZ5zSOChH82g2B5B18lsyS_oEgAlsOqNBwjRBfOX6d... doug
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Yes, just run recon-all with the -fill option to regenerated the filled.mgz (it will be the same filled.mgz but it will have a colortable embedded; it will also create filled.auto.mgz to help keep track of the edits). The just edit filled.mgz and proceed as normal. When you edit, make sure you use the right brush value depending on whether you are editing the left or right subcortical mass.
On 7/21/2021 1:43 PM, Aaron Tanenbaum wrote:
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Read the release notes. Can I with the new version run a recon-all over processed 7.1.1. I am interested in the ability to edit filled.mgz and applying this to 7.1.1 recons.
On Mon, Jul 19, 2021 at 5:46 PM Douglas N. Greve <dgreve@mgh.harvard.edu mailto:dgreve@mgh.harvard.edu> wrote:
We are please to announce version 7.2. Mostly bug fixes and behind-the-scenes enhancements. But there are a few new goodies and one new "known issue" about defacing. Check out *MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* https://surfer.nmr.mgh.harvard.edu/fswiki/ReleaseNotes <https://secure-web.cisco.com/1ncOzuZ5zSOChH82g2B5B18lsyS_oEgAlsOqNBwjRBfOX6dfCND4jEsGCslQiItXGhoadIOuNCP9Gdmotj05UDElZXc90oNGCyvZru1po1g8cNxA7SoCM43_jzv-wXfMs5Tj0EkP6TSPvm7uUDBsbHfFfclxf04AiFYRNhml_unsZDdggeQmLirCZ8UYNmHtG1ZHmG-PJVrMZpkjwzAtOS6RxZWBbuUaph-jzKfnDTTvy8xrvDR2st2Ue34xIf3G24-lzCJ1yyH-YVAjKWSfFqA/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FReleaseNotes> doug _______________________________________________ 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/1XSbp5peThU5W_dwhjz2xbhCbTKop8LCZLa0cWj_AnAFSlQ5yAy6-KkrPVDv1OTQacllvfwuxaIefGAxmct-a98awVcKwXrrUg6AehruujyopUHe_Idvet8BlY9sGSwGiooW_gBFNPMPmVgbEb7xVO7DU1qPQhsUif60aBrl2R_ns4gvcHDKfwdhvsQmmYW2tCwvxQJl5x7UAyzwFsCaUbeIsmUuV9o3xdEw825o9Y1OxkPvNGMajDZGk7nm5RbAjWarSeHhXIbbBysV1g9l2Jg/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer> 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 *MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* http://www.massgeneralbrigham.org/complianceline <http://secure-web.cisco.com/1qq4_8ro9DodC-PZ6JRYBPeNB95ntpAw2OWwwxEh8dqHq7tnX725uijGepyySfxl9wE1_gc49mPs8K01dPmAKPO-kZBbIsWRJWDHL9XXQhPX-Qx8gDTOLLvlOIQAKuhqMmO4PpYYMEfhpV6J4Gy-VfQb1-c3nu1D0mOb2floZHKt91MgV-N6_bN3iLoWbtxxnz76DzsLORDsE7RFUnIq88eKuzsVJyGMWdQguPuaBXwdMPFLs9Y--FuNz_ZP9Jd8xFu1w-z_y2Xo_NrDKc9g4Xg/http%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline> . 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.
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Hi Doug,
I'm about to start edits on subjects that have been re-processed in 7.2 using the -fill flag. Before doing so, can you clarify/verify that we edit the new filled.mgz just the same as we would the wm.mgz (aside from the fill values being different for left vs right hemispheres)? I have also noticed a few spots where the filled.mgz extends beyond the wm surface from the wm.mgz file (see attached). Should these be edited to match the wm.mgz?
Thanks!
Corinna
On Wed, Jul 21, 2021 at 1:49 PM Douglas N. Greve dgreve@mgh.harvard.edu wrote:
Yes, just run recon-all with the -fill option to regenerated the filled.mgz (it will be the same filled.mgz but it will have a colortable embedded; it will also create filled.auto.mgz to help keep track of the edits). The just edit filled.mgz and proceed as normal. When you edit, make sure you use the right brush value depending on whether you are editing the left or right subcortical mass.
On 7/21/2021 1:43 PM, Aaron Tanenbaum wrote:
External Email - Use CautionRead the release notes. Can I with the new version run a recon-all over processed 7.1.1. I am interested in the ability to edit filled.mgz and applying this to 7.1.1 recons.
On Mon, Jul 19, 2021 at 5:46 PM Douglas N. Greve dgreve@mgh.harvard.edu wrote:
We are please to announce version 7.2. Mostly bug fixes and behind-the-scenes enhancements. But there are a few new goodies and one new "known issue" about defacing. Check out *MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* https://secure-web.cisco.com/1_auFsNRMCKZLLL7SpxBcBkBa0fTcS8MXW9ZT4oNn_ShJbk... https://secure-web.cisco.com/1ncOzuZ5zSOChH82g2B5B18lsyS_oEgAlsOqNBwjRBfOX6dfCND4jEsGCslQiItXGhoadIOuNCP9Gdmotj05UDElZXc90oNGCyvZru1po1g8cNxA7SoCM43_jzv-wXfMs5Tj0EkP6TSPvm7uUDBsbHfFfclxf04AiFYRNhml_unsZDdggeQmLirCZ8UYNmHtG1ZHmG-PJVrMZpkjwzAtOS6RxZWBbuUaph-jzKfnDTTvy8xrvDR2st2Ue34xIf3G24-lzCJ1yyH-YVAjKWSfFqA/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FReleaseNotes doug
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Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://secure-web.cisco.com/166nAjc5vMPt1Iz5Ci-hwATQOdIT5JZI2NPBttQu-s_h8ES... 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://secure-web.cisco.com/1v9jMvkZTMWTTI3Wpann3BuXm_bpaaZMxkzzOvqlUYjqMzl2... . 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.
On 9/23/2021 11:05 AM, Corinna Bauer wrote:
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Hi Doug,
I'm about to start edits on subjects that have been re-processed in 7.2 using the -fill flag. Before doing so, can you clarify/verify that we edit the new filled.mgz just the same as we would the wm.mgz (aside from the fill values being different for left vs right hemispheres)?
Correct.
I have also noticed a few spots where the filled.mgz extends beyond the wm surface from the wm.mgz file (see attached). Should these be edited to match the wm.mgz?
I'm not sure what you are pointing out. Both of those surfaces should be tessellated at 1mm, but I just see the white and pial.
Thanks!
Corinna
On Wed, Jul 21, 2021 at 1:49 PM Douglas N. Greve <dgreve@mgh.harvard.edu mailto:dgreve@mgh.harvard.edu> wrote:
Yes, just run recon-all with the -fill option to regenerated the filled.mgz (it will be the same filled.mgz but it will have a colortable embedded; it will also create filled.auto.mgz to help keep track of the edits). The just edit filled.mgz and proceed as normal. When you edit, make sure you use the right brush value depending on whether you are editing the left or right subcortical mass. On 7/21/2021 1:43 PM, Aaron Tanenbaum wrote:External Email - Use Caution Read the release notes. Can I with the new version run a recon-all over processed 7.1.1. I am interested in the ability to edit filled.mgz and applying this to 7.1.1 recons. On Mon, Jul 19, 2021 at 5:46 PM Douglas N. Greve <dgreve@mgh.harvard.edu <mailto:dgreve@mgh.harvard.edu>> wrote: We are please to announce version 7.2. Mostly bug fixes and behind-the-scenes enhancements. But there are a few new goodies and one new "known issue" about defacing. Check out *MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* https://surfer.nmr.mgh.harvard.edu/fswiki/ReleaseNotes <https://secure-web.cisco.com/1ncOzuZ5zSOChH82g2B5B18lsyS_oEgAlsOqNBwjRBfOX6dfCND4jEsGCslQiItXGhoadIOuNCP9Gdmotj05UDElZXc90oNGCyvZru1po1g8cNxA7SoCM43_jzv-wXfMs5Tj0EkP6TSPvm7uUDBsbHfFfclxf04AiFYRNhml_unsZDdggeQmLirCZ8UYNmHtG1ZHmG-PJVrMZpkjwzAtOS6RxZWBbuUaph-jzKfnDTTvy8xrvDR2st2Ue34xIf3G24-lzCJ1yyH-YVAjKWSfFqA/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FReleaseNotes> doug _______________________________________________ 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/1XSbp5peThU5W_dwhjz2xbhCbTKop8LCZLa0cWj_AnAFSlQ5yAy6-KkrPVDv1OTQacllvfwuxaIefGAxmct-a98awVcKwXrrUg6AehruujyopUHe_Idvet8BlY9sGSwGiooW_gBFNPMPmVgbEb7xVO7DU1qPQhsUif60aBrl2R_ns4gvcHDKfwdhvsQmmYW2tCwvxQJl5x7UAyzwFsCaUbeIsmUuV9o3xdEw825o9Y1OxkPvNGMajDZGk7nm5RbAjWarSeHhXIbbBysV1g9l2Jg/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer> 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 *MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* http://www.massgeneralbrigham.org/complianceline <http://secure-web.cisco.com/1qq4_8ro9DodC-PZ6JRYBPeNB95ntpAw2OWwwxEh8dqHq7tnX725uijGepyySfxl9wE1_gc49mPs8K01dPmAKPO-kZBbIsWRJWDHL9XXQhPX-Qx8gDTOLLvlOIQAKuhqMmO4PpYYMEfhpV6J4Gy-VfQb1-c3nu1D0mOb2floZHKt91MgV-N6_bN3iLoWbtxxnz76DzsLORDsE7RFUnIq88eKuzsVJyGMWdQguPuaBXwdMPFLs9Y--FuNz_ZP9Jd8xFu1w-z_y2Xo_NrDKc9g4Xg/http%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline> . 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 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/166nAjc5vMPt1Iz5Ci-hwATQOdIT5JZI2NPBttQu-s_h8ESKqhOhKoBTjJxqalU1UievBNYVjn-lCHjeFbFefHeOQ80Rs3-HZZyQWvzdx9TFGxnyvmHgN4vQS_dB7vLEx0UJkCk-rF8iVVxw06UWz3IsIhHaUNe59edtBLfY0emGf9DdGAYk5GZ9eptqcNUs2IxNd_1MCCvBS4-lIPGxrTGEKVFK8tz1s5Etdc49wBK3ZN4aOc5yNPyhPsnjrkDDZAzWM0618kXoSTITFdGvEfw/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer>_______________________________________________ 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/166nAjc5vMPt1Iz5Ci-hwATQOdIT5JZI2NPBttQu-s_h8ESKqhOhKoBTjJxqalU1UievBNYVjn-lCHjeFbFefHeOQ80Rs3-HZZyQWvzdx9TFGxnyvmHgN4vQS_dB7vLEx0UJkCk-rF8iVVxw06UWz3IsIhHaUNe59edtBLfY0emGf9DdGAYk5GZ9eptqcNUs2IxNd_1MCCvBS4-lIPGxrTGEKVFK8tz1s5Etdc49wBK3ZN4aOc5yNPyhPsnjrkDDZAzWM0618kXoSTITFdGvEfw/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer> The information in this e-mail is intended only for the person to whom it is addressed. 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Kiyotaka Nemoto