External Email - Use Caution        

got you, thanks

Best,
Zeng



On Thu, Nov 11, 2021 at 4:06 PM Douglas N. Greve <dgr...@mgh.harvard.edu>
wrote:

> For DODS you would add 16 zeros (8 classes times 2 continuous variables)
>
> On 11/11/2021 4:00 PM, Zeng, Qi wrote:
>
>         External Email - Use Caution
> So for the DODS case, is "1 -1 1 -1 1 -1 1 -1 0 0 0 0" for the following
> FSGD:
>
> GroupDescriptorFile 1
> Title MyStudy
> Class CaseMaleWhite
> Class ControlMaleWhite
> Class CaseMaleNonWhite
> Class ControlMaleNonWhite
> Class CaseFemaleWhite
> Class ControlFemaleWhite
> Class CaseFemaleNonWhite
> Class ControlFemaleNonWhite
> Variables age_bl eTIV
> Input Sub001_base ControlFemaleWhite 85 1350519.71
> Input Sub002_base ControlFemaleWhite 81.3 1558515.86
>
> Best,
> Qi
>
> On Thu, Nov 11, 2021 at 3:28 PM Douglas N. Greve <dgr...@mgh.harvard.edu>
> wrote:
>
>> For the DOSS case, yes.
>>
>> On 11/11/2021 3:23 PM, Zeng, Qi wrote:
>>
>>         External Email - Use Caution
>> Hi  Douglas,
>>
>> If to set up the FSGD as below, is my design matrix for case and control
>> comparison as "1 -1 1 -1 1 -1 1 -1 0 0"  ?
>>
>> GroupDescriptorFile 1
>> Title MyStudy
>> Class CaseMaleWhite
>> Class ControlMaleWhite
>> Class CaseMaleNonWhite
>> Class ControlMaleNonWhite
>> Class CaseFemaleWhite
>> Class ControlFemaleWhite
>> Class CaseFemaleNonWhite
>> Class ControlFemaleNonWhite
>> Variables    Age eTIV
>> Input Sub001_base  Control   Female  White   85     1350519.71
>> Input Sub002_base  Control   Female  White   81.3   1558515.86
>>
>> Best,
>> Qi
>>
>> On Thu, Nov 11, 2021 at 3:06 PM Douglas N. Greve <dgr...@mgh.harvard.edu>
>> wrote:
>>
>>> I would advice setting up the FSGD files with 8 classes based on your 3
>>> discrete, 2-level variables, eg, MaleControlWhite then use two continuous
>>> variables Age and eTIV.
>>> You should definitely normalize the eTIV (and probably age too)
>>>
>>> On 11/10/2021 7:07 PM, Zeng, Qi wrote:
>>>
>>>         External Email - Use Caution
>>> Hi Douglas,
>>>
>>> Just to be clear, should I recode discrete variables as numeric as
>>> sample1) or change discrete variables into strings 2) or even change the
>>> comparison groups into strings too 3)?
>>> 1)
>>> Variables Age Gender Race eTIV
>>> Input Sub001_base Control 85 1 1 1350519.71
>>> Input Sub002_base Control 81.3   0 1 1558515.86
>>> Input Sub003_base Control 81.3   0 0 1558515.86
>>>
>>> or 2)
>>> Variables Age Gender Race eTIV
>>> Input Sub001_base Control 85 "Female" "White" 1350519.71
>>> Input Sub002_base Control 81.3  "Male" "White" 1558515.86
>>> Input Sub003_base Control 72.7  "Male" "White" 1187649.47
>>>
>>> or 3)
>>> Variables  Age Gender Race eTIV
>>> Input Sub001_base "Control" 85 "Female" "White" 1350519.71
>>> Input Sub002_base "Control" 81.3  "Male" "White" 1558515.86
>>> Input Sub003_base "Control" 72.7  "Male" "White" 1187649.47
>>>
>>>
>>> Best,
>>> Zeng
>>>
>>>
>>>
>>> On Wed, Nov 10, 2021 at 6:38 PM Douglas N. Greve <dgr...@mgh.harvard.edu>
>>> wrote:
>>>
>>>> Did you read the error message? It says:
>>>> Variable 2 has character string Female
>>>> Variables should be continuous numbers
>>>> You have listed Gender and Race as strings, they have to be numbers
>>>> (eg, 1, 2)
>>>> You probably want to have these be discrete variables instead of
>>>> continuous
>>>>
>>>> On 11/10/2021 6:20 PM, Zeng, Qi wrote:
>>>>
>>>>         External Email - Use Caution
>>>> Hi Douglas,
>>>>
>>>> Here is the command line:
>>>> mri_glmfit \
>>>>   --y rh.thickness-rate.MyStudy.10.mgh \
>>>>   --fsgd FSGD/MyStudy.fsgd dods\
>>>>   --C Contrasts/Case-Control_age_gender_race_etiv.mtx\
>>>>   --surf fsaverage rh \
>>>>   --cortex \
>>>>   --glmdir rh.thickness-rate.MyStudy.10.mgh_age_gender_race_etiv.glmdir
>>>> \
>>>>   --eres-save
>>>>
>>>> Also error message in terminal:
>>>> gdfRead(): reading FSGD/MyStudy.fsgd
>>>> WARNING: variable 1 is "Gender" which is often a discrete factor
>>>>   The proper way to handle discrete factors is to create classes.
>>>>   See *MailScanner has detected a possible fraud attempt from
>>>> "secure-web.cisco.com" claiming to be*
>>>> https://secure-web.cisco.com/1yZjSb88ByC6LpqTpxoDlPxIRkwZ4AgKf-ntdFS_UoHQnXxr47np6gUrWYww844iJ0PNYnyHPxIOTdlFT0LNYQ4JY3PiUg6T3L4kV1etuizRdwe_N71AadQjNvW3b0_zSQ4PzW9zJkM8pGuPHdxO3kx6Agto8vYpWfmr41hvWBH4evReluISnXKavQPG-VQAOkIisi_CblVa1hNsjrO3QZ8GaPH8ITQkNZTAkhzzvrmiMBfzcrZm67LElwLA_XyIz0ToXi2fSM9sBljnY2_RG2Xu-K4K5zxnCTCU-0iWlVWmekV-F57Et2wbEuchTKBii/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FFsgdExamples
>>>> <https://secure-web.cisco.com/1NHVxBIRnha6EjEdEho81-VE9d-vjJ6ivzt10z28vhX9c94pCwosQpkLG4Hfu3nLYp7KMDne5wAk9mK45YIQJEZBe6UlteF2wwLohmZJzp070UjHvv6fqugRAkgBk0uNO3Fsgo5BzblW95J5iO5sXWwZLK-LGAZJJTBaU7mLTkO5L70JRSscCW3pdc-G5KchZMbVyeY65gGH4w5MMIYBSVHvX03spMjZ85XkHbkgYYmWXTFnzqUGhqGgHygP5sLeR7OWPKIzEb7X3pHi7POf0UyEHJAZpQLU9bgT2BnOcClt0kW4mll1ODQDC2Y0U7-0f/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FFsgdExamples>
>>>> ERROR: gdfReadV1: Format Error: Input line 1, subjid = sub001_base
>>>>  Variable 2 has character string Female
>>>>  Variables should be continuous numbers
>>>> FSGDF Format Error: file = FSGD/MyStudy.fsgd, tag=Input
>>>>
>>>> Also attached FSGD file below.
>>>> Thank you so much for the help!
>>>>
>>>> Best,
>>>> Zeng
>>>>
>>>>
>>>>
>>>>
>>>> On Wed, Nov 10, 2021 at 5:41 PM Douglas N. Greve <
>>>> dgr...@mgh.harvard.edu> wrote:
>>>>
>>>>> please send your command line and full terminal output as well as the
>>>>> fsgd file
>>>>>
>>>>> On 11/10/2021 5:12 PM, Zeng, Qi wrote:
>>>>>
>>>>>         External Email - Use Caution
>>>>> Hi Freesurfer experts,
>>>>>
>>>>> Here, I want to design a simple group comparison (two levels: Case vs.
>>>>> Control) and also count for 4 covariates (two continuous and two
>>>>> categoricals). However, the GLM model cannot recognize my discrete
>>>>> variables. What do you suggest to change?
>>>>> >> FSDG file:
>>>>> GroupDescriptorFile 1
>>>>> Title MyStudy
>>>>> Class Control
>>>>> Class Case
>>>>> Variables age gender race  eTIV
>>>>> Input sub001_base Control 85 Female White 1350519
>>>>> Contrast:
>>>>> >> Design matrix for Case-Control and regress out the effect of age,
>>>>> gender, race, and eTIV.
>>>>> -1 1 0 0 0 0 0 0 0 0
>>>>>
>>>>> Best,
>>>>> Zeng
>>>>>
>>>>>
>>>>>
>>>>>
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>>>>>  
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>>>>
>>>>
>>>> --
>>>>
>>>> Ph.D. candidate
>>>> Icahn School of Medicine at Mount Sinai
>>>>
>>>>
>>>> _______________________________________________
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>>>>  
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>>>>
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>>>> <http://secure-web.cisco.com/1A0Ya5XLTopPJxtvY6W3BYdLWR_an51gQ8KKFgKuexXEwHqDE7UducPFqwa4W_f6drzqLO6TTfvJdl9TX8bb_Bun8KQdoN6jifg--1DaRPgK5vpDhmxdsEcl2bKSctpeFFx0GwtqNMhTRicmYN40mg6ODHXYoyJ1-uEoIcYfMbwV9kaf7Ggw7BjK35YGkFlfgKF0yB34izSkUcV650w8LfbSh3JDpiyby-RAkFWfC4xGWVUx456s63epPX2GtYCYeK0dWrdSxnJ5k_P7HsJkMjsgcVyRxWcP1EKJr322sUOkeAGLe3Oi_nxkSIy5LtzFFPkR_jNJ2FYtT4NHHqEgTvg/http%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline>
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>>>
>>>
>>> --
>>>
>>> Ph.D. candidate
>>> Icahn School of Medicine at Mount Sinai
>>>
>>>
>>> _______________________________________________
>>> Freesurfer mailing listfreesur...@nmr.mgh.harvard.edu*MailScanner has 
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>>>  
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>>>
>>>
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>>> "secure-web.cisco.com" claiming to be*
>>> https://secure-web.cisco.com/1UC5XBBHWs4PhHhTnXY1JAgn7lAGj-GdduWUKA7KWchESybtj9cbuzOUKeYSfBu-Hy8XcOrjz135OXDSqGsW_qE1A6nWQQWUHAGKRoqyxk83BvIngm8SWf_rlmjuMkifNxALBcWKzwA15T6sGR_6lt_2bzTRF1ZoVr1I1E2cY0cmDg5TVGXmRDqIXaKMr3_v9V4hfM4H9lZhzyE1HjTobG9n_19S77To3Fn6etCRSkZDRScVO81DqZnr-kcNL7Kf-43zD2q5Tq3p3wAe2OsY8g1u1Or6PWc2X3oNgx7drl8Ike8TWCRj1GQFopOhw1nK3/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer
>>> <https://secure-web.cisco.com/1DlZ2fTOF2AmzPXQrBuHInam5F1ZSU5iCJjKeJJqWAASMhfJ8i189eI_CZ7gpxiK9dX7CRMmSB4f-Zx7Im7ODFwlJoj2233ZFP1qJxD4VXSfJyrulgaWnSgifBjf0Psmnc33uWViiYCmCpRBUhWJG1LRYZ77cEqTBKU3aWhcMeYq8V7--0ZjTZ9IsonGh7ZLsjBqXj0ovIWso1L853fVjTdphN6Onhv4NagUX45XhqU4957lqTWsgHcMB1xQhazgsAxjOHe2VujiJJR5xYdOY2TAxbvci75FfG7B1hl6vIr7BxmiWamDP_FnLSlCA1GGAtJrOgACL8pGZTMpTHAWItg/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://secure-web.cisco.com/1CPf7JJ_yx4qG-w349MRVuTxdV1IL2mrTNtZ1Nvs3B-GOOrDcgYLdf5ad5cRLm58XyFhgwAGVqnl--TaYa5_1FfcMEExqU7FhO8MlxfWqvbdJRE3LSqQ4w_8CR8m1isCXasswhS-NA81WLmtcW7fjwTmfXhNtVQF96KrwIzRltRrvSMo4Y9rHF-SYBJPn-Ww71MR4ok_UXrh10t2Vll6_Gkr82KluEh-uX9ngO-nyP9YqIduZNdqi32n_FXXO2_kdRXlrwWK4Wc0jz3OezC711hr7bQLA4bu-3AlyICuJL2fljh2r2JkI_hd-T7XvD2zE/http%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline
>>> <http://secure-web.cisco.com/1-qjxHtsxsujfAJD78Q5f8o2Z_2grSqK7CGIEyXX1kcG0lM5l06jwYSp5S8eKA8HSSBV06Tlzy5tnybuvY6VDKAV3MTzcS2NCox67GmGepW59h5IXq1UvLq-HCBKg0-MAURQid2sgka7FhgPioBdIK32828K9UZNZEcDMT3aOXcC7jsTpE6Fhj___vPFdgCSrwXLUR14qQS15Q8Yx6k3pZg5xffs3FBipoVjwUnRuo-3zDgZ4bRU1kE7bC-nP3nbyEnJTU6nZaerOL8Dl0H9pFCuYutUjAmYqZiZUgGbdtuOmaK0AmfpKTKAtbndoWIk_p95FKHp1bXBqdeDH2Stc-Q/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.
>>>
>>
>>
>> --
>>
>> Ph.D. candidate
>> Icahn School of Medicine at Mount Sinai
>>
>>
>> _______________________________________________
>> Freesurfer mailing listfreesur...@nmr.mgh.harvard.edu*MailScanner has 
>> detected a possible fraud attempt from "secure-web.cisco.com" claiming to 
>> be* 
>> https://secure-web.cisco.com/1UC5XBBHWs4PhHhTnXY1JAgn7lAGj-GdduWUKA7KWchESybtj9cbuzOUKeYSfBu-Hy8XcOrjz135OXDSqGsW_qE1A6nWQQWUHAGKRoqyxk83BvIngm8SWf_rlmjuMkifNxALBcWKzwA15T6sGR_6lt_2bzTRF1ZoVr1I1E2cY0cmDg5TVGXmRDqIXaKMr3_v9V4hfM4H9lZhzyE1HjTobG9n_19S77To3Fn6etCRSkZDRScVO81DqZnr-kcNL7Kf-43zD2q5Tq3p3wAe2OsY8g1u1Or6PWc2X3oNgx7drl8Ike8TWCRj1GQFopOhw1nK3/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer
>>  
>> <https://secure-web.cisco.com/1riQwbV7SivOWmdRI3o8g5unLSLoMUwk1_Fe2aJGWmlht2oA0tkB_pfg7aJpN2VZ4rdRk9wchQhy7dHG840cTDmQyLjxhOeNa8jDlUwt4bjgokARlChK0GQhA8Y58s0frdc4RK3WP8MTsDM2NIQ6KZQixcFPOmCBh2FkGCVF4QxgS7b4SEPFHSHMIqTCPorlGC6izGZs4cwDb5HHQq1FgLwsN0_Mgj9u_oPnftJrsLBP8Tb-iLVQiAsO08g7FpP4n4jRj_j4hyu73-rC21XlibZmnyhNuZXD4RX0RSD5rOWZflVfrl3_fNpXgcdTPfTyQ/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer>
>>
>>
>> _______________________________________________
>> Freesurfer mailing list
>> 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/1UC5XBBHWs4PhHhTnXY1JAgn7lAGj-GdduWUKA7KWchESybtj9cbuzOUKeYSfBu-Hy8XcOrjz135OXDSqGsW_qE1A6nWQQWUHAGKRoqyxk83BvIngm8SWf_rlmjuMkifNxALBcWKzwA15T6sGR_6lt_2bzTRF1ZoVr1I1E2cY0cmDg5TVGXmRDqIXaKMr3_v9V4hfM4H9lZhzyE1HjTobG9n_19S77To3Fn6etCRSkZDRScVO81DqZnr-kcNL7Kf-43zD2q5Tq3p3wAe2OsY8g1u1Or6PWc2X3oNgx7drl8Ike8TWCRj1GQFopOhw1nK3/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer
>> <https://secure-web.cisco.com/1riQwbV7SivOWmdRI3o8g5unLSLoMUwk1_Fe2aJGWmlht2oA0tkB_pfg7aJpN2VZ4rdRk9wchQhy7dHG840cTDmQyLjxhOeNa8jDlUwt4bjgokARlChK0GQhA8Y58s0frdc4RK3WP8MTsDM2NIQ6KZQixcFPOmCBh2FkGCVF4QxgS7b4SEPFHSHMIqTCPorlGC6izGZs4cwDb5HHQq1FgLwsN0_Mgj9u_oPnftJrsLBP8Tb-iLVQiAsO08g7FpP4n4jRj_j4hyu73-rC21XlibZmnyhNuZXD4RX0RSD5rOWZflVfrl3_fNpXgcdTPfTyQ/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://secure-web.cisco.com/1CPf7JJ_yx4qG-w349MRVuTxdV1IL2mrTNtZ1Nvs3B-GOOrDcgYLdf5ad5cRLm58XyFhgwAGVqnl--TaYa5_1FfcMEExqU7FhO8MlxfWqvbdJRE3LSqQ4w_8CR8m1isCXasswhS-NA81WLmtcW7fjwTmfXhNtVQF96KrwIzRltRrvSMo4Y9rHF-SYBJPn-Ww71MR4ok_UXrh10t2Vll6_Gkr82KluEh-uX9ngO-nyP9YqIduZNdqi32n_FXXO2_kdRXlrwWK4Wc0jz3OezC711hr7bQLA4bu-3AlyICuJL2fljh2r2JkI_hd-T7XvD2zE/http%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline
>> <http://secure-web.cisco.com/1JRy54pbXKb77KSi4tMhaphr0O2nBInhKvQlsk55n57cg20qYgjB52YXhXN14SwoCDvkT2vAC32wT2pAc4W05kn2eb3aTI0Q4IpHCADXrAGOke-7iILcuRXVGaQ8Et7Ck6Eg9We8GlCs4DcmntSm6z0X8J3jaZHoAdAodil48D5kIg-lkxUx6yZMMxMZpLwgHoVMLBAmD45HLos9CdjdOf755jjmNSdV6UOLlF0HyXpP_2Pe32ih-az3IoNQOyBwmCQIqhkZaJN7JzlnuK3MuN_IW8pM0WUslv6kDp5K723cFPuuFSHHwNsQjUCdTpDk1/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.
>>
>
>
> --
>
> Ph.D. candidate
> Icahn School of Medicine at Mount Sinai
>
>
> _______________________________________________
> Freesurfer mailing 
> listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
> _______________________________________________
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://secure-web.cisco.com/1UC5XBBHWs4PhHhTnXY1JAgn7lAGj-GdduWUKA7KWchESybtj9cbuzOUKeYSfBu-Hy8XcOrjz135OXDSqGsW_qE1A6nWQQWUHAGKRoqyxk83BvIngm8SWf_rlmjuMkifNxALBcWKzwA15T6sGR_6lt_2bzTRF1ZoVr1I1E2cY0cmDg5TVGXmRDqIXaKMr3_v9V4hfM4H9lZhzyE1HjTobG9n_19S77To3Fn6etCRSkZDRScVO81DqZnr-kcNL7Kf-43zD2q5Tq3p3wAe2OsY8g1u1Or6PWc2X3oNgx7drl8Ike8TWCRj1GQFopOhw1nK3/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
> http://secure-web.cisco.com/1CPf7JJ_yx4qG-w349MRVuTxdV1IL2mrTNtZ1Nvs3B-GOOrDcgYLdf5ad5cRLm58XyFhgwAGVqnl--TaYa5_1FfcMEExqU7FhO8MlxfWqvbdJRE3LSqQ4w_8CR8m1isCXasswhS-NA81WLmtcW7fjwTmfXhNtVQF96KrwIzRltRrvSMo4Y9rHF-SYBJPn-Ww71MR4ok_UXrh10t2Vll6_Gkr82KluEh-uX9ngO-nyP9YqIduZNdqi32n_FXXO2_kdRXlrwWK4Wc0jz3OezC711hr7bQLA4bu-3AlyICuJL2fljh2r2JkI_hd-T7XvD2zE/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.
>


-- 

Ph.D. candidate
Icahn School of Medicine at Mount Sinai
_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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