Dear All,
I want to segment white matter into 131xx and 141xx label series. I used aparc.a2009s but it just gave me cortex labels (111xx and 121xx). Can anyone guide me how could I do this?
Regards, Fari
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see http://www.mail-archive.com/freesurfer%40nmr.mgh.harvard.edu/msg47157.html
On 05/24/2016 05:44 PM, Mahmoudi, Fariborz wrote:
Dear All,
I want to segment white matter into 131xx and 141xx label series. I used aparc.a2009s but it just gave me cortex labels (111xx and 121xx). Can anyone guide me how could I do this?
Regards,
Fari
CONFIDENTIALITY NOTICE: This email contains information from the sender that may be CONFIDENTIAL, LEGALLY PRIVILEGED, PROPRIETARY or otherwise protected from disclosure. This email is intended for use only by the person or entity to whom it is addressed. If you are not the intended recipient, any use, disclosure, copying, distribution, printing, or any action taken in reliance on the contents of this email, is strictly prohibited. If you received this email in error, please contact the sending party by reply email, delete the email from your computer system and shred any paper copies.
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I added --2009s to my command (mri_vol2vol) but it didn't give me the white matter labels yet. I used following code can you tell me how should I modify it?
/usr/local/freesurfer/bin/recon-all -subjid $ID -autorecon1 /usr/local/freesurfer/bin/recon-all -subjid $ID -autorecon2 /usr/local/freesurfer/bin/recon-all -subjid $ID -autorecon3
mri_vol2vol --mov ./FreeSurfer_Subjects/MGZ/${ID}/mri/aparc.a2009s+aseg.mgz --targ ./FreeSurfer_Subjects/MGZ/${ID}/mri/rawavg.mgz --regheader --o ./FreeSurfer_Subjects/MGZ/${ID}/mri/aparc.a2009s+aseg_org.mgz --a2009s --no-save-reg --keep-precision --interp nearest
Thanks, Fari
-----Original Message----- From: freesurfer-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] On Behalf Of Douglas N Greve Sent: Tuesday, May 24, 2016 6:45 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] White matter segmentation
see https://urldefense.proofpoint.com/v2/url?u=http-3A__www.mail-2Darchive.com_f...
On 05/24/2016 05:44 PM, Mahmoudi, Fariborz wrote:
Dear All,
I want to segment white matter into 131xx and 141xx label series. I used aparc.a2009s but it just gave me cortex labels (111xx and 121xx). Can anyone guide me how could I do this?
Regards,
Fari
--
CONFIDENTIALITY NOTICE: This email contains information from the sender that may be CONFIDENTIAL, LEGALLY PRIVILEGED, PROPRIETARY or otherwise protected from disclosure. This email is intended for use only by the person or entity to whom it is addressed. If you are not the intended recipient, any use, disclosure, copying, distribution, printing, or any action taken in reliance on the contents of this email, is strictly prohibited. If you received this email in error, please contact the sending party by reply email, delete the email from your computer system and shred any paper copies.
Note to Patients: There are a number of risks you should consider before using e-mail to communicate with us. See our Privacy & Security page on www.henryford.com for more detailed information as well as information concerning MyChart, our new patient portal. If you do not believe that our policy gives you the privacy and security protection you need, do not send e-mail or Internet communications to us.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://urldefense.proofpoint.com/v2/url?u=https-3A__mail.nmr.mgh.harv ard.edu_mailman_listinfo_freesurfer&d=CwIBAg&c=aLnS6P8Ng0zSNhCF04OWImQ _He2L69sNWG3PbxeyieE&r=OSYmVYk3jPR6JSZwGSUjf1P4YyJXtRWvghayjS8UAMU&m=7 7QFGWjiRTdsKBaqbcq6AW2Nqzqwn4EZbuERJUedD-4&s=rUw6-oY4aqF1qMO7L6i--S2ZL tmvZ2Gaqxke-5oeOOk&e=
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
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That link says to use mri_aparc2aseg, not mri_vol2vol
On 05/25/2016 11:21 AM, Mahmoudi, Fariborz wrote:
I added --2009s to my command (mri_vol2vol) but it didn't give me the white matter labels yet. I used following code can you tell me how should I modify it?
/usr/local/freesurfer/bin/recon-all -subjid $ID -autorecon1 /usr/local/freesurfer/bin/recon-all -subjid $ID -autorecon2 /usr/local/freesurfer/bin/recon-all -subjid $ID -autorecon3
mri_vol2vol --mov ./FreeSurfer_Subjects/MGZ/${ID}/mri/aparc.a2009s+aseg.mgz --targ ./FreeSurfer_Subjects/MGZ/${ID}/mri/rawavg.mgz --regheader --o ./FreeSurfer_Subjects/MGZ/${ID}/mri/aparc.a2009s+aseg_org.mgz --a2009s --no-save-reg --keep-precision --interp nearest
Thanks, Fari
-----Original Message----- From: freesurfer-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] On Behalf Of Douglas N Greve Sent: Tuesday, May 24, 2016 6:45 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] White matter segmentation
see https://urldefense.proofpoint.com/v2/url?u=http-3A__www.mail-2Darchive.com_f...
On 05/24/2016 05:44 PM, Mahmoudi, Fariborz wrote:
Dear All,
I want to segment white matter into 131xx and 141xx label series. I used aparc.a2009s but it just gave me cortex labels (111xx and 121xx). Can anyone guide me how could I do this?
Regards,
Fari
--
CONFIDENTIALITY NOTICE: This email contains information from the sender that may be CONFIDENTIAL, LEGALLY PRIVILEGED, PROPRIETARY or otherwise protected from disclosure. This email is intended for use only by the person or entity to whom it is addressed. If you are not the intended recipient, any use, disclosure, copying, distribution, printing, or any action taken in reliance on the contents of this email, is strictly prohibited. If you received this email in error, please contact the sending party by reply email, delete the email from your computer system and shred any paper copies.
Note to Patients: There are a number of risks you should consider before using e-mail to communicate with us. See our Privacy & Security page on www.henryford.com for more detailed information as well as information concerning MyChart, our new patient portal. If you do not believe that our policy gives you the privacy and security protection you need, do not send e-mail or Internet communications to us.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://urldefense.proofpoint.com/v2/url?u=https-3A__mail.nmr.mgh.harv ard.edu_mailman_listinfo_freesurfer&d=CwIBAg&c=aLnS6P8Ng0zSNhCF04OWImQ _He2L69sNWG3PbxeyieE&r=OSYmVYk3jPR6JSZwGSUjf1P4YyJXtRWvghayjS8UAMU&m=7 7QFGWjiRTdsKBaqbcq6AW2Nqzqwn4EZbuERJUedD-4&s=rUw6-oY4aqF1qMO7L6i--S2ZL tmvZ2Gaqxke-5oeOOk&e=
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: https://urldefense.proofpoint.com/v2/url?u=http-3A__surfer.nmr.mgh.harvard.e... FileDrop: https://urldefense.proofpoint.com/v2/url?u=https-3A__gate.nmr.mgh.harvard.ed... https://urldefense.proofpoint.com/v2/url?u=http-3A__www.nmr.mgh.harvard.edu_... Outgoing: https://urldefense.proofpoint.com/v2/url?u=ftp-3A__surfer.nmr.mgh.harvard.ed...
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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 Partners Compliance HelpLine at https://urldefense.proofpoint.com/v2/url?u=http-3A__www.partners.org_complia... . 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.
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freesurfer@nmr.mgh.harvard.edu
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Mahmoudi, Fariborz