External Email - Use Caution
Hi all,
My input 001.mgz has data type short, but converted to unsigned byte. The plot shows the intensity of thee two images. How is the data conversion done? Thanks.
Best,
Ruifeng
External Email - Use Caution
Hi Ruifeng,
You can pass -nc (nochange) flag to mri_convert to keep the original data type.
Best,
Yujing
From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu On Behalf Of ruifeng14@gmail.com Sent: Thursday, May 25, 2023 2:45 PM To: freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] Question about mri_convert --conform
External Email - Use Caution Hi all,
My input 001.mgz has data type short, but converted to unsigned byte. The plot shows the intensity of thee two images. How is the data conversion done? Thanks.
Best, Ruifeng
External Email - Use Caution
Hi Yujing,
Thanks. I am wondering about the reason why Freesurfer converts data types to uchar. Doesn't this affect the non-uniformity bias correction that follows?
Best, Ruifeng
On Tue, Jun 13, 2023 at 9:37 AM Huang, Yujing YHUANG43@mgh.harvard.edu wrote:
External Email - Use CautionHi Ruifeng,
You can pass -nc (nochange) flag to mri_convert to keep the original data type.
Best,
Yujing
*From:* freesurfer-bounces@nmr.mgh.harvard.edu < freesurfer-bounces@nmr.mgh.harvard.edu> *On Behalf Of *ruifeng14@gmail.com *Sent:* Thursday, May 25, 2023 2:45 PM *To:* freesurfer@nmr.mgh.harvard.edu *Subject:* [Freesurfer] Question about mri_convert --conform
External Email - Use Caution *Hi all,
My input 001.mgz has data type short, but converted to unsigned byte. The plot shows the intensity of thee two images. How is the data conversion done? Thanks.
Best,
Ruifeng _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://secure-web.cisco.com/1Oj4X-li9veUPQ77Ng5C5fYnumIrh8h0zUT_pdbR2LreWt8... 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 https://secure-web.cisco.com/1T_w41mCOjAfMrbUQN-M5bhSyLBotzBigntZadS0EQkNg8r... < https://secure-web.cisco.com/1T_w41mCOjAfMrbUQN-M5bhSyLBotzBigntZadS0EQkNg8r... .
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This was done a long time ago to conserve space/memory. There is a rescaling that is done, so it should not affect the bias correction much
On 6/14/2023 3:35 PM, Ruifeng Dong wrote:
External Email - Use Caution
Hi Yujing,
Thanks. I am wondering about the reason why Freesurfer converts data types to uchar. Doesn't this affect the non-uniformity bias correction that follows?
Best, Ruifeng
On Tue, Jun 13, 2023 at 9:37 AM Huang, Yujing YHUANG43@mgh.harvard.edu wrote:
External Email - Use Caution Hi Ruifeng, You can pass -nc (nochange) flag to mri_convert to keep the original data type. Best, Yujing *From:*freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> *On Behalf Of *ruifeng14@gmail.com *Sent:* Thursday, May 25, 2023 2:45 PM *To:* freesurfer@nmr.mgh.harvard.edu *Subject:* [Freesurfer] Question about mri_convert --conform * External Email - Use Caution * Hi all, My input 001.mgz has data type short, but converted to unsigned byte. The plot shows the intensity of thee two images. How is the data conversion done? Thanks. Best, Ruifeng _______________________________________________ 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/1LfHD19PMDabgnN1B5iFxV19YNtAVwTk7I8ysCHSrQST9NT0C_evdMYHaoI4p9-_lfUaCpEV4jd1b0u_vz6TZn9YdkC80qiMORINUmXc0rpa1MK7R4RJQwjZbgsGW8rAQEh2Hl0ez9kNONeUESfKe3tIXHi8AYcQ3LGDbyrDWyG4X-TBpXzPNM8DkWN9MG7AidJ_GBnAiou17Vj5O5t3oHYxZ_VxRBbb4fk6AH7s-uDACbVuy-hFXZulLkH5GMVEGSUSNHqt9z0aKnOG3VFzdjw/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer <https://secure-web.cisco.com/1Oj4X-li9veUPQ77Ng5C5fYnumIrh8h0zUT_pdbR2LreWt8ZBEH0ek4eiz43BsKP4wWNB5q-d9I3FZAbeyWPufxRlhQcg4zfA52oxxyzTtB1FROHBvB8bj-TuVh1OifnbV7LOCFzZhA7Qruq5FAp7Vnn94Fd15w_12VLyJygNgaPcUjpuYr4vmIrlUyQ7pZtBJEEm6zXxYNNXftv_L5HrWmUm42gbgk_uKYJlGaPlXs05KsllJs0nh0tjIixl61i3bFujSTu6GZyufLAHnEfjjlrmnrvWxINMnclNyAtLGpNUiLNWdwm7GfxNoyI0n8V_/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* https://secure-web.cisco.com/1E9EtWcKJyUirBEP_SWNwA0X_q24kHi7jP0TXHHDVUdcr8q9Mpowi6FijNbYwagyLt6rDC4Y2fDf6YLbmF0rDBZUf2YHdulJ4ouaI7J7342eZKaeyZ2YSfueV1ANMfYHYhNGqzkro09R_A00mVSXyGm2vizJYucgMeaSVSJtHnCo21jcV4y51vPvg6EtIu2mST2UtJZ--oKt_mKr-bu3ps8EuLWrVtmUPYZO712CoxmrFoCUvnEtwI3ge-GofjaLAABEgfrajY6PMcXo2yrO7yQ/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline <https://secure-web.cisco.com/1T_w41mCOjAfMrbUQN-M5bhSyLBotzBigntZadS0EQkNg8rdZyxhoTMednnDrU0HQ9rxlR9niTu6p0Jkm-H3NnklEnFUrXuKK_1HBEn_QRdik-CWF45HqBQCqfDrLNSQ1gMuLPNbQjS3LFiygsTeOhClMX6hxotfs4Ig3HjITqxwd2SkD52bIGUzTU2woTSwfDmxjmqwK7Z5_rUv-wpWmBYIb574g0R9e-BD_JsCBFKUb4nnwM_dvjsO4Lrf0QpjWLWZ4AdtluNOveI3GA939qbN2j2_jFrTwCFLCpURhJsCyG2tbzeg9zpRLIk-thepf/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline> <*MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* https://secure-web.cisco.com/1E9EtWcKJyUirBEP_SWNwA0X_q24kHi7jP0TXHHDVUdcr8q9Mpowi6FijNbYwagyLt6rDC4Y2fDf6YLbmF0rDBZUf2YHdulJ4ouaI7J7342eZKaeyZ2YSfueV1ANMfYHYhNGqzkro09R_A00mVSXyGm2vizJYucgMeaSVSJtHnCo21jcV4y51vPvg6EtIu2mST2UtJZ--oKt_mKr-bu3ps8EuLWrVtmUPYZO712CoxmrFoCUvnEtwI3ge-GofjaLAABEgfrajY6PMcXo2yrO7yQ/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline <https://secure-web.cisco.com/1T_w41mCOjAfMrbUQN-M5bhSyLBotzBigntZadS0EQkNg8rdZyxhoTMednnDrU0HQ9rxlR9niTu6p0Jkm-H3NnklEnFUrXuKK_1HBEn_QRdik-CWF45HqBQCqfDrLNSQ1gMuLPNbQjS3LFiygsTeOhClMX6hxotfs4Ig3HjITqxwd2SkD52bIGUzTU2woTSwfDmxjmqwK7Z5_rUv-wpWmBYIb574g0R9e-BD_JsCBFKUb4nnwM_dvjsO4Lrf0QpjWLWZ4AdtluNOveI3GA939qbN2j2_jFrTwCFLCpURhJsCyG2tbzeg9zpRLIk-thepf/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline>> .
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://secure-web.cisco.com/1LfHD19PMDabgnN1B5iFxV19YNtAVwTk7I8ysCHSrQST9NT...
External Email - Use Caution
Hi Douglas,
Thanks. Out of curiosity, I kept the short data type in the mri_convert --conform by adding options -odt short -ns 1. Freesurfer 6.0 ran well until its default skull stripping, attached below. [image: Screenshot from 2023-06-20 10-20-03.png] Best, Ruifeng
On Tue, Jun 20, 2023 at 9:59 AM Douglas N. Greve dgreve@mgh.harvard.edu wrote:
External Email - Use CautionThis was done a long time ago to conserve space/memory. There is a rescaling that is done, so it should not affect the bias correction much
On 6/14/2023 3:35 PM, Ruifeng Dong wrote:
External Email - Use CautionHi Yujing,
Thanks. I am wondering about the reason why Freesurfer converts data types to uchar. Doesn't this affect the non-uniformity bias correction that follows?
Best, Ruifeng
On Tue, Jun 13, 2023 at 9:37 AM Huang, Yujing YHUANG43@mgh.harvard.edu wrote:
External Email - Use CautionHi Ruifeng,
You can pass -nc (nochange) flag to mri_convert to keep the original data type.
Best,
Yujing
*From:* freesurfer-bounces@nmr.mgh.harvard.edu < freesurfer-bounces@nmr.mgh.harvard.edu> *On Behalf Of * ruifeng14@gmail.com *Sent:* Thursday, May 25, 2023 2:45 PM *To:* freesurfer@nmr.mgh.harvard.edu *Subject:* [Freesurfer] Question about mri_convert --conform
External Email - Use Caution *Hi all,
My input 001.mgz has data type short, but converted to unsigned byte. The plot shows the intensity of thee two images. How is the data conversion done? Thanks.
Best,
Ruifeng _______________________________________________ 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/1eYGk7hMm8tpyxi-_vPicEOy6_kxpjkGkzYmxIsN_o4Sf-5... https://secure-web.cisco.com/1Oj4X-li9veUPQ77Ng5C5fYnumIrh8h0zUT_pdbR2LreWt8ZBEH0ek4eiz43BsKP4wWNB5q-d9I3FZAbeyWPufxRlhQcg4zfA52oxxyzTtB1FROHBvB8bj-TuVh1OifnbV7LOCFzZhA7Qruq5FAp7Vnn94Fd15w_12VLyJygNgaPcUjpuYr4vmIrlUyQ7pZtBJEEm6zXxYNNXftv_L5HrWmUm42gbgk_uKYJlGaPlXs05KsllJs0nh0tjIixl61i3bFujSTu6GZyufLAHnEfjjlrmnrvWxINMnclNyAtLGpNUiLNWdwm7GfxNoyI0n8V_/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* https://secure-web.cisco.com/1on1vZH8Q5LNFZ1ZHuewSmUVs_CicTtdr2mUh6PJgEDFHP4... https://secure-web.cisco.com/1T_w41mCOjAfMrbUQN-M5bhSyLBotzBigntZadS0EQkNg8rdZyxhoTMednnDrU0HQ9rxlR9niTu6p0Jkm-H3NnklEnFUrXuKK_1HBEn_QRdik-CWF45HqBQCqfDrLNSQ1gMuLPNbQjS3LFiygsTeOhClMX6hxotfs4Ig3HjITqxwd2SkD52bIGUzTU2woTSwfDmxjmqwK7Z5_rUv-wpWmBYIb574g0R9e-BD_JsCBFKUb4nnwM_dvjsO4Lrf0QpjWLWZ4AdtluNOveI3GA939qbN2j2_jFrTwCFLCpURhJsCyG2tbzeg9zpRLIk-thepf/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline <*MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* https://secure-web.cisco.com/1on1vZH8Q5LNFZ1ZHuewSmUVs_CicTtdr2mUh6PJgEDFHP4... https://secure-web.cisco.com/1T_w41mCOjAfMrbUQN-M5bhSyLBotzBigntZadS0EQkNg8rdZyxhoTMednnDrU0HQ9rxlR9niTu6p0Jkm-H3NnklEnFUrXuKK_1HBEn_QRdik-CWF45HqBQCqfDrLNSQ1gMuLPNbQjS3LFiygsTeOhClMX6hxotfs4Ig3HjITqxwd2SkD52bIGUzTU2woTSwfDmxjmqwK7Z5_rUv-wpWmBYIb574g0R9e-BD_JsCBFKUb4nnwM_dvjsO4Lrf0QpjWLWZ4AdtluNOveI3GA939qbN2j2_jFrTwCFLCpURhJsCyG2tbzeg9zpRLIk-thepf/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline> .
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Was that caused by using short? Ie, if you don't use short, is there still a problem?
On 6/20/2023 10:21 AM, Ruifeng Dong wrote:
External Email - Use Caution
Hi Douglas,
Thanks. Out of curiosity, I kept the short data type in the mri_convert --conform by adding options -odt short -ns 1. Freesurfer 6.0 ran well until its default skull stripping, attached below. Screenshot from 2023-06-20 10-20-03.png Best, Ruifeng
On Tue, Jun 20, 2023 at 9:59 AM Douglas N. Greve dgreve@mgh.harvard.edu wrote:
External Email - Use Caution This was done a long time ago to conserve space/memory. There is a rescaling that is done, so it should not affect the bias correction much On 6/14/2023 3:35 PM, Ruifeng Dong wrote:External Email - Use Caution Hi Yujing, Thanks. I am wondering about the reason why Freesurfer converts data types to uchar. Doesn't this affect the non-uniformity bias correction that follows? Best, Ruifeng On Tue, Jun 13, 2023 at 9:37 AM Huang, Yujing <YHUANG43@mgh.harvard.edu> wrote: External Email - Use Caution Hi Ruifeng, You can pass -nc (nochange) flag to mri_convert to keep the original data type. Best, Yujing *From:*freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> *On Behalf Of *ruifeng14@gmail.com *Sent:* Thursday, May 25, 2023 2:45 PM *To:* freesurfer@nmr.mgh.harvard.edu *Subject:* [Freesurfer] Question about mri_convert --conform * External Email - Use Caution * Hi all, My input 001.mgz has data type short, but converted to unsigned byte. The plot shows the intensity of thee two images. How is the data conversion done? Thanks. Best, Ruifeng _______________________________________________ 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/19Z4xW19nqqveFGOGnspiDGKBy5TPNvFQL9-MFj2ScKCxKMos-v_oKBl9ytyMcUxi9luMR5zgr_AK8FHPOZfUZa1bRWuRRP4W3sNS7l1qrOx67cd6iUCGZ71AW4GkyYxOd4ehgLTfzIQQWQsVoWj85ZvOtV2AB-7EQPFTC4GVUIm2rMjVEbuiajT_YD2Hq6DATc_v8Fn6jlonLzCBNJ9njYuamsFGJ-C48rlwUT8RPHbPWKJKMhX82-KcAawN5Jv2heAuET__P-GWwKBQCt-XmQ/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer <https://secure-web.cisco.com/1Oj4X-li9veUPQ77Ng5C5fYnumIrh8h0zUT_pdbR2LreWt8ZBEH0ek4eiz43BsKP4wWNB5q-d9I3FZAbeyWPufxRlhQcg4zfA52oxxyzTtB1FROHBvB8bj-TuVh1OifnbV7LOCFzZhA7Qruq5FAp7Vnn94Fd15w_12VLyJygNgaPcUjpuYr4vmIrlUyQ7pZtBJEEm6zXxYNNXftv_L5HrWmUm42gbgk_uKYJlGaPlXs05KsllJs0nh0tjIixl61i3bFujSTu6GZyufLAHnEfjjlrmnrvWxINMnclNyAtLGpNUiLNWdwm7GfxNoyI0n8V_/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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