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Hi, I was wondering if anyone can point me to a good tutorial that would focus on how to upload and process DICOM data into FS / FreeView. I have a recent Triage Brain Atrophy report from NeuroQuant and would like to see how this compares to results generated in FS. I am a brand-new user and just installed FS on my computer.
Thank you,Allison O.
welcome to freesurfer! To convert from dicom to mgz, you can do a couple of things: use mri_convert, eg, mri_convert /path/to/dicomfile mprage.mgz Then run recon-all like recon-all -i mprage.mgz -s subjectname -all You can also use dcmunpack to unpack all volumes from a dicom directory See https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Practice for more info Also check out our tutorials
On 1/8/2025 4:18 PM, allio34218@aol.com wrote:
External Email - Use Caution
Hi, I was wondering if anyone can point me to a good tutorial that would focus on how to upload and process DICOM data into FS / FreeView.
I have a recent Triage Brain Atrophy report from NeuroQuant and would like to see how this compares to results generated in FS.
I am a brand-new user and just installed FS on my computer.
Thank you, Allison O.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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Hi, I'm following the tutorial for dcmunpack, but am getting stuck here: Any ideas on what I'm doing wrong?
Thanks,Allison O. On Thursday, January 9, 2025 at 08:32:09 AM EST, Douglas N. Greve dgreve@mgh.harvard.edu wrote:
welcome to freesurfer! To convert from dicom to mgz, you can do a couple of things: use mri_convert, eg, mri_convert /path/to/dicomfile mprage.mgz Then run recon-all like recon-all -i mprage.mgz -s subjectname -all You can also use dcmunpack to unpack all volumes from a dicom directory See https://secure-web.cisco.com/1vtfYtMQHqK4cgAEOfqmyXfcH0c-qin6tLFTm01aIjCqzO0... for more info Also check out our tutorials
On 1/8/2025 4:18 PM, allio34218@aol.com wrote:
External Email - Use Caution Hi, I was wondering if anyone can point me to a good tutorial that would focus on how to upload and process DICOM data into FS / FreeView. I have a recent Triage Brain Atrophy report from NeuroQuant and would like to see how this compares to results generated in FS. I am a brand-new user and just installed FS on my computer.
Thank you, Allison O.
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://secure-web.cisco.com/1v3AhU4sCFksxXi09El30OxRM3mbSAJIcJsX7jL1vgHWGbM...
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Hi Allison
The parameter you give the -i flag is the file name for a single slice in the correct dicom series (the t1-weighted scan).
Cheers Bruce
On Jan 11, 2025, at 3:51 PM, allio34218@aol.com wrote:
External Email - Use Caution
Hi, I'm following the tutorial for dcmunpack, but am getting stuck here:
Any ideas on what I'm doing wrong?
<1736628593324blob.jpg>
Thanks, Allison O.
On Thursday, January 9, 2025 at 08:32:09 AM EST, Douglas N. Greve dgreve@mgh.harvard.edu wrote:
welcome to freesurfer! To convert from dicom to mgz, you can do a couple of things: use mri_convert, eg, mri_convert /path/to/dicomfile mprage.mgz Then run recon-all like recon-all -i mprage.mgz -s subjectname -all You can also use dcmunpack to unpack all volumes from a dicom directory See MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Practicehttps://secure-web.cisco.com/1vtfYtMQHqK4cgAEOfqmyXfcH0c-qin6tLFTm01aIjCqzO08VQwL7Iv4xhxEvx_ADagViba3hAxYLfKAZFU4O_MBtTbqoQLXVNvI725QUCYQppof99a3V649Hymlo6xyBdeHwt5OCtbf93Y5pV2MZRkYsCYKglLALkQ-XQ2agenblfI8MKJW8PrlbN5BlqMiCP_q28QnDU4_iNXI2kBIEb5IZPt9-IGO2oBk98EH_9kGZC_PxDZ0VG_j2lsX17jZRa3MPocx87vrAJiXPRiLK-Ujg43u-XUkSs0wkuMgQfeMRBJGKXHeG6tqQYIHOQcl-QvbogGmlkYS6B1OKNJDq5w/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FFsTutorial%2FPractice for more info Also check out our tutorials
On 1/8/2025 4:18 PM, allio34218@aol.commailto:allio34218@aol.com wrote:
External Email - Use Caution
Hi, I was wondering if anyone can point me to a good tutorial that would focus on how to upload and process DICOM data into FS / FreeView.
I have a recent Triage Brain Atrophy report from NeuroQuant and would like to see how this compares to results generated in FS.
I am a brand-new user and just installed FS on my computer.
Thank you, Allison O.
_______________________________________________ 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/1v3AhU4sCFksxXi09El30OxRM3mbSAJIcJsX7jL1vgHWGbM6vM3mHfhyRYqpqfrxppGwW-yTpargN5MvJ_l4Ob61bNm_K0vVurB5DAu7zb6yrRdO5Vrh8oZaVzx3bkzInrw-rLwNxxxznjQLNn7bFlB8OlGwxBDkfUp8znlYW6W3BAkwvGRVcptJtezVHFEgwGdu2TAk7_o1eV0VNOTzniBpR_AONeBQcpIB5Eg3ywm3eKRNCYTasnKJGCttOBC-1RRPGnGmV5KSvA8floXokYTozCaecUyd0iwoveXCJwwN1bKp42bmxzjdPajegngysji7yjxbwWOT9jxN-GG5F5w/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer
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Thanks, I realized it was in another folder called DICOM in the practice area:
On Saturday, January 11, 2025 at 03:58:01 PM EST, Fischl, Bruce R.,PHD bfischl@mgh.harvard.edu wrote:
Hi Allison The parameter you give the -i flag is the file name for a single slice in the correct dicom series (the t1-weighted scan). CheersBruce
On Jan 11, 2025, at 3:51 PM, allio34218@aol.com wrote:
External Email - Use Caution
Hi, I'm following the tutorial for dcmunpack, but am getting stuck here: Any ideas on what I'm doing wrong? <1736628593324blob.jpg>
Thanks,Allison O. On Thursday, January 9, 2025 at 08:32:09 AM EST, Douglas N. Greve dgreve@mgh.harvard.edu wrote:
welcome to freesurfer! To convert from dicom to mgz, you can do a couple of things: use mri_convert, eg, mri_convert /path/to/dicomfile mprage.mgz Then run recon-all like recon-all -i mprage.mgz -s subjectname -all You can also use dcmunpack to unpack all volumes from a dicom directory See MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://secure-web.cisco.com/1HYGk_mCltdhJSL42sxRJAFURtPc3rntpDHh7xjyv8crh7B... for more info Also check out our tutorials
On 1/8/2025 4:18 PM, allio34218@aol.com wrote:
External Email - Use Caution Hi, I was wondering if anyone can point me to a good tutorial that would focus on how to upload and process DICOM data into FS / FreeView. I have a recent Triage Brain Atrophy report from NeuroQuant and would like to see how this compares to results generated in FS. I am a brand-new user and just installed FS on my computer.
Thank you,Allison O.
_______________________________________________ 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/1JPhbFQ2OD_Is1CKEV8iwsqMGIT12zWMdMGBEhNZRXU82K_...
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If an MRI scan produced many folders with many images in each folder, how do you know which to run the dcmunpack command on? For example:
On Saturday, January 11, 2025 at 03:58:01 PM EST, Fischl, Bruce R.,PHD bfischl@mgh.harvard.edu wrote:
Hi Allison The parameter you give the -i flag is the file name for a single slice in the correct dicom series (the t1-weighted scan). CheersBruce
On Jan 11, 2025, at 3:51 PM, allio34218@aol.com wrote:
External Email - Use Caution
Hi, I'm following the tutorial for dcmunpack, but am getting stuck here: Any ideas on what I'm doing wrong? <1736628593324blob.jpg>
Thanks,Allison O. On Thursday, January 9, 2025 at 08:32:09 AM EST, Douglas N. Greve dgreve@mgh.harvard.edu wrote:
welcome to freesurfer! To convert from dicom to mgz, you can do a couple of things: use mri_convert, eg, mri_convert /path/to/dicomfile mprage.mgz Then run recon-all like recon-all -i mprage.mgz -s subjectname -all You can also use dcmunpack to unpack all volumes from a dicom directory See MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://secure-web.cisco.com/1RoYKZZjxPO0WWjb1cn44ROEIOXlEH-VSRs16jyfwti8a_A... for more info Also check out our tutorials
On 1/8/2025 4:18 PM, allio34218@aol.com wrote:
External Email - Use Caution Hi, I was wondering if anyone can point me to a good tutorial that would focus on how to upload and process DICOM data into FS / FreeView. I have a recent Triage Brain Atrophy report from NeuroQuant and would like to see how this compares to results generated in FS. I am a brand-new user and just installed FS on my computer.
Thank you,Allison O.
_______________________________________________ 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/13toh_0FB-PM_wuvTWprb_18hf3Adw4fNB6Z9szpCgGhtFA...
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dcmunpack scans the top folder and extracts all dicom series numbers. By default, all dicom series in the directory will be converted.
Yujing
From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu On Behalf Of allio34218@aol.com Sent: Sunday, January 12, 2025 3:01 PM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] New user
External Email - Use Caution If an MRI scan produced many folders with many images in each folder, how do you know which to run the dcmunpack command on?
For example: [Inline image]
[Inline image]
On Saturday, January 11, 2025 at 03:58:01 PM EST, Fischl, Bruce R.,PHD <bfischl@mgh.harvard.edumailto:bfischl@mgh.harvard.edu> wrote:
Hi Allison
The parameter you give the -i flag is the file name for a single slice in the correct dicom series (the t1-weighted scan).
Cheers Bruce
On Jan 11, 2025, at 3:51 PM, allio34218@aol.commailto:allio34218@aol.com wrote:
External Email - Use Caution Hi, I'm following the tutorial for dcmunpack, but am getting stuck here:
Any ideas on what I'm doing wrong?
<1736628593324blob.jpg>
Thanks, Allison O.
On Thursday, January 9, 2025 at 08:32:09 AM EST, Douglas N. Greve <dgreve@mgh.harvard.edumailto:dgreve@mgh.harvard.edu> wrote:
welcome to freesurfer! To convert from dicom to mgz, you can do a couple of things: use mri_convert, eg, mri_convert /path/to/dicomfile mprage.mgz Then run recon-all like recon-all -i mprage.mgz -s subjectname -all You can also use dcmunpack to unpack all volumes from a dicom directory See MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Practicehttps://secure-web.cisco.com/1vtfYtMQHqK4cgAEOfqmyXfcH0c-qin6tLFTm01aIjCqzO08VQwL7Iv4xhxEvx_ADagViba3hAxYLfKAZFU4O_MBtTbqoQLXVNvI725QUCYQppof99a3V649Hymlo6xyBdeHwt5OCtbf93Y5pV2MZRkYsCYKglLALkQ-XQ2agenblfI8MKJW8PrlbN5BlqMiCP_q28QnDU4_iNXI2kBIEb5IZPt9-IGO2oBk98EH_9kGZC_PxDZ0VG_j2lsX17jZRa3MPocx87vrAJiXPRiLK-Ujg43u-XUkSs0wkuMgQfeMRBJGKXHeG6tqQYIHOQcl-QvbogGmlkYS6B1OKNJDq5w/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FFsTutorial%2FPractice for more info Also check out our tutorials
On 1/8/2025 4:18 PM, allio34218@aol.commailto:allio34218@aol.com wrote:
External Email - Use Caution Hi, I was wondering if anyone can point me to a good tutorial that would focus on how to upload and process DICOM data into FS / FreeView.
I have a recent Triage Brain Atrophy report from NeuroQuant and would like to see how this compares to results generated in FS.
I am a brand-new user and just installed FS on my computer.
Thank you, Allison O.
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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/1v3AhU4sCFksxXi09El30OxRM3mbSAJIcJsX7jL1vgHWGbM6vM3mHfhyRYqpqfrxppGwW-yTpargN5MvJ_l4Ob61bNm_K0vVurB5DAu7zb6yrRdO5Vrh8oZaVzx3bkzInrw-rLwNxxxznjQLNn7bFlB8OlGwxBDkfUp8znlYW6W3BAkwvGRVcptJtezVHFEgwGdu2TAk7_o1eV0VNOTzniBpR_AONeBQcpIB5Eg3ywm3eKRNCYTasnKJGCttOBC-1RRPGnGmV5KSvA8floXokYTozCaecUyd0iwoveXCJwwN1bKp42bmxzjdPajegngysji7yjxbwWOT9jxN-GG5F5w/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://www.massgeneralbrigham.org/compliancelinehttps://secure-web.cisco.com/1zm1-_scPPeE8Ql8XSw5-UxI7XyuScXAdlT1_gpU8dVLlYOPO-7aOVnNraZw3efFl4F7SbpUm5lPikzfwBhaBHKAjjYEvnl-_EL98kuc2q_CjLtjXs-rGMrHI_07OI3hmDX6h-xAxvO171x11vbpqo4ca2_xT5nCF3LmZf5zzUf_Xa5udGrL9N45k3NTOtzeBI8pj8Vt-xzjwgWYR9YsokD9p7I-ixsqww-PAzof9ha1nx4NXOK46d02eJJzIHNnAKevbkXZADE_5y-_1ZE5kVBOidSg7ULG3oCyY6iHAeXzdGiDtjCPb608REelMMUQPxceAH20xO7hsEDaZDPREyg/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline <MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://www.massgeneralbrigham.org/compliancelinehttps://secure-web.cisco.com/1zm1-_scPPeE8Ql8XSw5-UxI7XyuScXAdlT1_gpU8dVLlYOPO-7aOVnNraZw3efFl4F7SbpUm5lPikzfwBhaBHKAjjYEvnl-_EL98kuc2q_CjLtjXs-rGMrHI_07OI3hmDX6h-xAxvO171x11vbpqo4ca2_xT5nCF3LmZf5zzUf_Xa5udGrL9N45k3NTOtzeBI8pj8Vt-xzjwgWYR9YsokD9p7I-ixsqww-PAzof9ha1nx4NXOK46d02eJJzIHNnAKevbkXZADE_5y-_1ZE5kVBOidSg7ULG3oCyY6iHAeXzdGiDtjCPb608REelMMUQPxceAH20xO7hsEDaZDPREyg/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline> . 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. <1736628593324blob.jpg> _______________________________________________
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer _______________________________________________ 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/13toh_0FB-PM_wuvTWprb_18hf3Adw4fNB6Z9szpCgGhtFAwCYGSQKKyhFeIuKXMd21WGTzOaWaqTvCGqOJiYRtOojQji3t-wgA8FbiKYolyDqfVGepWmiCzpLevaWvQ_-TDv4NfgencCKrx_J9mjAdZ64-jV8rH9z6bACdZtlnDe9GiZprECRDC2Abz_I7oOXJxhlTbiQWFqewWrlKqIWCxLkr2FaK_44zD_yC5mT5OePbttkbkqi8XUbLCMlyHY9hgFS7XIcAcILOExJD2nSzNquDIQMNKqQ3utLBk2U9DIFmi5on5-gNDbF5BkjBvq/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://www.massgeneralbrigham.org/compliancelinehttps://secure-web.cisco.com/18fUd7XHlhffGfNkEoiz3MKNMcH_ixVwj04CjQ4gSI7UxWMq7QrcD0pZbNRB3RR8nZPD-ZTQ_NObIqdN7YBK8_9rpfmRHwQYv7_cqI-nMthP3RSHqtQB5zJMA4S0zQDU8ABtF190rWRHF8ZCJSo--Y0GUl0yzeg1_32PNMsqkhmQ17HQ8zjdJUF9_hDESPhDV7yX6Ez7_PcbHI_eqER46GMhu9se9z8xFyHS6DjAdTKNgko1ekDBtIYVlMOyk_AFh4PUe8Z2C8pTU9M0E7ZhowE0e90nDuMNJtyssUJhZde8khSlOgeSZ1vqLHbu45ps4/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline <MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://www.massgeneralbrigham.org/compliancelinehttps://secure-web.cisco.com/18fUd7XHlhffGfNkEoiz3MKNMcH_ixVwj04CjQ4gSI7UxWMq7QrcD0pZbNRB3RR8nZPD-ZTQ_NObIqdN7YBK8_9rpfmRHwQYv7_cqI-nMthP3RSHqtQB5zJMA4S0zQDU8ABtF190rWRHF8ZCJSo--Y0GUl0yzeg1_32PNMsqkhmQ17HQ8zjdJUF9_hDESPhDV7yX6Ez7_PcbHI_eqER46GMhu9se9z8xFyHS6DjAdTKNgko1ekDBtIYVlMOyk_AFh4PUe8Z2C8pTU9M0E7ZhowE0e90nDuMNJtyssUJhZde8khSlOgeSZ1vqLHbu45ps4/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline> . 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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