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Dear Sir/Madam,
I hope you are doing well. I'm having a ADNI T1 weighted MRI database. I have run the recon-all command successfully and got a couple of default stats files in the stats folder. Then fornix.mgz is estimated using command "mri_cc -aseg aseg.auto_noCCseg.mgz -o aseg.auto_CCseg.mgz -f folder_name" successfully. Now what can be done to generate the stats for only fornix.mgz? I've been struggling with this for a long time, please help me with this.
I'm using linux-ubuntu. [image: IMG-20230526-WA0000.jpg]
With Regards Ahsan --------------------------------------------- Ahsan Ali Ph.D Scholar Department of Applied Mechanics and Biomedical Engineering (AMBE) Indian Institute of Technology Madras Chennai-600036, Tamil Nadu, INDIA Mob.:- +91-8899605552
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I have not used mri_cc for that. I would use mri_sclimbic_seg; that will also segment the fornix and create a stats files that you can use as normal
On 5/26/2023 3:37 AM, Ahsan Ali wrote:
External Email - Use Caution
Dear Sir/Madam,
I hope you are doing well. I'm having a ADNI T1 weighted MRI database. I have run the recon-all command successfully and got a couple of default stats files in the stats folder. Then fornix.mgz is estimated using command "mri_cc -aseg aseg.auto_noCCseg.mgz -o aseg.auto_CCseg.mgz -f folder_name" successfully. Now what can be done to generate the stats for only fornix.mgz? I've been struggling with this for a long time, please help me with this.
I'm using linux-ubuntu. IMG-20230526-WA0000.jpg
With Regards Ahsan
Ahsan Ali Ph.D Scholar Department of Applied Mechanics and Biomedical Engineering (AMBE) Indian Institute of Technology Madras Chennai-600036, Tamil Nadu, INDIA Mob.:- +91-8899605552
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://secure-web.cisco.com/1v5zfthjwtgCog9YOSM9g5pQFVlhSG0OmfNKod48iCshm8Q...
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Dear Greve,
How did you do with this line of code? I'm getting a error, would you please explain me with one image?
With Regards Ahsan --------------------------------------------- Ahsan Ali Ph.D Scholar Department of Applied Mechanics (Biomedical Engineering Group) Indian Institute of Technology Madras Chennai-600036, Tamil Nadu, INDIA Mob.:- +91-8899605552
On Tue, 20 Jun, 2023, 6:58 pm Douglas N. Greve, dgreve@mgh.harvard.edu wrote:
External Email - Use CautionI have not used mri_cc for that. I would use mri_sclimbic_seg; that will also segment the fornix and create a stats files that you can use as normal
On 5/26/2023 3:37 AM, Ahsan Ali wrote:
External Email - Use CautionDear Sir/Madam,
I hope you are doing well. I'm having a ADNI T1 weighted MRI database. I have run the recon-all command successfully and got a couple of default stats files in the stats folder. Then fornix.mgz is estimated using command "mri_cc -aseg aseg.auto_noCCseg.mgz -o aseg.auto_CCseg.mgz -f folder_name" successfully. Now what can be done to generate the stats for only fornix.mgz? I've been struggling with this for a long time, please help me with this.
I'm using linux-ubuntu. [image: IMG-20230526-WA0000.jpg]
With Regards Ahsan
Ahsan Ali Ph.D Scholar Department of Applied Mechanics and Biomedical Engineering (AMBE) Indian Institute of Technology Madras Chennai-600036, Tamil Nadu, INDIA Mob.:- +91-8899605552
Freesurfer mailing listFreesurfer@nmr.mgh.harvard.edu*MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* https://secure-web.cisco.com/1A8qDWiwrJk2qFG0KlDL8HUi6Ortx-0hbS5ZY3-FhX3pyHH... https://secure-web.cisco.com/1v5zfthjwtgCog9YOSM9g5pQFVlhSG0OmfNKod48iCshm8QnnHKDCJNkRIMc_KgVcAM-boqzU-c8LejHR3UkGI2Wp_sDHstdkIgl9AHCpoPFv2uWeqoHhim9FtkDdeM4RJoiGwZiFFCb32m80wGd66HYpQinQYT95Peqp8rl0506bNTIAWTe9-wHeCpUyto8K2yb5C2p_FhS8h9gxkHBIXJFcFXvfkFsG5DDtdrnHX8pYcdhIDv59DEML_FuaROXFFqrEtjJAQoZ8xkLcHupwkQ/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer
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Do what? If you want to run mri_sclimbic_seg, then just run something like mri_sclimbic_seg --i input-t1.mgz --o sclimbic.mgz
On 6/21/2023 2:13 PM, Ahsan Ali wrote:
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Dear Greve,
How did you do with this line of code? I'm getting a error, would you please explain me with one image?
With Regards Ahsan
Ahsan Ali Ph.D Scholar Department of Applied Mechanics (Biomedical Engineering Group) Indian Institute of Technology Madras Chennai-600036, Tamil Nadu, INDIA Mob.:- +91-8899605552
On Tue, 20 Jun, 2023, 6:58 pm Douglas N. Greve, dgreve@mgh.harvard.edu wrote:
External Email - Use Caution I have not used mri_cc for that. I would use mri_sclimbic_seg; that will also segment the fornix and create a stats files that you can use as normal On 5/26/2023 3:37 AM, Ahsan Ali wrote:External Email - Use Caution Dear Sir/Madam, I hope you are doing well. I'm having a ADNI T1 weighted MRI database. I have run the recon-all command successfully and got a couple of default stats files in the stats folder. Then fornix.mgz is estimated using command "mri_cc -aseg aseg.auto_noCCseg.mgz -o aseg.auto_CCseg.mgz -f folder_name" successfully. Now what can be done to generate the stats for only fornix.mgz? I've been struggling with this for a long time, please help me with this. I'm using linux-ubuntu. IMG-20230526-WA0000.jpg With Regards Ahsan --------------------------------------------- Ahsan Ali Ph.D Scholar Department of Applied Mechanics and Biomedical Engineering (AMBE) Indian Institute of Technology Madras Chennai-600036, Tamil Nadu, INDIA Mob.:- +91-8899605552 _______________________________________________ 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/1bhmqFrrImYzczQ2qTzkYtDaLrOCWbGhUAPOJtSxVoVwFNIv2CMRMkwcax2V1zwRYI_wx1eSO3IRKPGlRcXHDbRzhxcV3eYWWwuvZ62x9v3yWq6msFMSfKWGfWPhY4vaKf6KZXw41wDHl-m2VyS-KTonf6udQH_5Ig33d6RWQ4_hqMOTR6ljElK2tGAfiSoNTvPjC2D-dnR7kJpWmuCKG4Xghp7SOMvLcktloqBGsIKJi8cjpmlIMuPOURpVXr3jIFD8yjpbbuCt5Vjw3tJ6k8A/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer <https://secure-web.cisco.com/1v5zfthjwtgCog9YOSM9g5pQFVlhSG0OmfNKod48iCshm8QnnHKDCJNkRIMc_KgVcAM-boqzU-c8LejHR3UkGI2Wp_sDHstdkIgl9AHCpoPFv2uWeqoHhim9FtkDdeM4RJoiGwZiFFCb32m80wGd66HYpQinQYT95Peqp8rl0506bNTIAWTe9-wHeCpUyto8K2yb5C2p_FhS8h9gxkHBIXJFcFXvfkFsG5DDtdrnHX8pYcdhIDv59DEML_FuaROXFFqrEtjJAQoZ8xkLcHupwkQ/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/1bhmqFrrImYzczQ2qTzkYtDaLrOCWbGhUAPOJtSxVoVwFNIv2CMRMkwcax2V1zwRYI_wx1eSO3IRKPGlRcXHDbRzhxcV3eYWWwuvZ62x9v3yWq6msFMSfKWGfWPhY4vaKf6KZXw41wDHl-m2VyS-KTonf6udQH_5Ig33d6RWQ4_hqMOTR6ljElK2tGAfiSoNTvPjC2D-dnR7kJpWmuCKG4Xghp7SOMvLcktloqBGsIKJi8cjpmlIMuPOURpVXr3jIFD8yjpbbuCt5Vjw3tJ6k8A/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer <https://secure-web.cisco.com/1A8qDWiwrJk2qFG0KlDL8HUi6Ortx-0hbS5ZY3-FhX3pyHHii3RHPL2WOwXksJnB8r9crE0hvySgIYylub6nYhBJPxLxVuFdTS5acrQvQnq-XcpgygagTraAx0b_Te8m_dKoND01OdIWkvHazRWtnWB4GlDnXsomi9tOU0nyrcpriI0DYgiC5nrTPjF_G9ENJH5lA2Xpixf27K5kRnh_NZFSpo34NmvNfCNEKfY_1hZZLKQ3mjQ4MNvba4m-FIuMxurYhN-MeuCxnjArCWZhxm-wYdfaBKD7z6kj9-pvnDoc_lEMAFw8nFMYDJN9xLY7CzgsYbxiT1FFVW4QYOWOeDg/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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