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Hello,
I would like to use the Brainnectome atlas for cortical thickness analysis parcellations. The T1 template volume (nifti file type) is attached if helpful. I have seen a couple of posts on this, but am not clear about the process. For example, the response to a similar comment was to “run recon-all on the AAL anatomical T1w volume template”. At this point, I do not know what files, transformations, and/or code modifications are needed. For example, does the brainnectome template volume need to be preprocessed in any way, does it need to be saved in the MGH format? If so, how is this done? Does the process require any other files or subroutines?
In summary, I am wondering if you can “walk me through” the process or provide a detailed example. Any help would be greatly appreciated! Thank you for your time.
Best,
Shawn
--- Shawn Flanagan, Ph.D. Assistant Professor University of Pittsburgh School of Health and Rehabilitation Sciences Department of Sports Medicine and Nutrition Neuromuscular Research Laboratory Warrior Human Performance Research Center
3860 South Water Street Pittsburgh, PA 15203 sdf29@pitt.edumailto:sdf29@pitt.edu Email 412.246.0460 Office 630.854.0547 Mobile
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Dear Shawn,
I can't fully answer your question, but maybe as a start:
I think the idea behind the suggestion to run recon-all on the template is that this would allow you to map the results of the FreeSurfer thickness analysis (which are in by default mapped to the fsaverage template if you run qcache) back to your template. I think you could even leave fsaverage out and map directly to it.
I have had a look at the NIFTI file you provided though (a preview image is attached to this email for others), and it looks like it is not a complete T1 image but a scull-stripped brain only. I think simply running recon-all on the file (you need nothing but a T1-weighted NIFTI file to run recon-all) will not work. You could start the recon-all pipeline at a later stage (after skull stripping), but maybe you should wait for another answer before proceeding any further.
Tim
-- Dr. Tim Schäfer Postdoc Computational Neuroimaging Department of Child and Adolescent Psychiatry, Psychosomatics and Psychotherapy University Hospital Frankfurt, Goethe University Frankfurt am Main, Germany
On 11/21/2021 9:29 PM Flanagan, Shawn D sdf29@pitt.edu wrote:
External Email - Use Caution
Hello,
I would like to use the Brainnectome atlas for cortical thickness analysis parcellations. The T1 template volume (nifti file type) is attached if helpful. I have seen a couple of posts on this, but am not clear about the process. For example, the response to a similar comment was to “run recon-all on the AAL anatomical T1w volume template”. At this point, I do not know what files, transformations, and/or code modifications are needed. For example, does the brainnectome template volume need to be preprocessed in any way, does it need to be saved in the MGH format? If so, how is this done? Does the process require any other files or subroutines?
In summary, I am wondering if you can “walk me through” the process or provide a detailed example. Any help would be greatly appreciated! Thank you for your time.
Best,
Shawn
Shawn Flanagan, Ph.D. Assistant Professor University of Pittsburgh School of Health and Rehabilitation Sciences Department of Sports Medicine and Nutrition Neuromuscular Research Laboratory Warrior Human Performance Research Center
3860 South Water Street Pittsburgh, PA 15203 sdf29@pitt.edumailto:sdf29@pitt.edu Email 412.246.0460 Office 630.854.0547 Mobile
Neuromuscular Research Laboratoryhttp://secure-web.cisco.com/1w-f2b1Sv8FoWJqjWBtRI_gzdJ3kwmFPg5ehq75ANa6Is4a60cD4QsEg-p7ca-iH_zi2WeZISZxCc5jTRjVeUtMzIWpoPfSlAlQ642Vjv2fnVIOGVGDukxBLJIoy_xIb8UzkQ1zzHHw_0tvkXbIoza4dvXCPKYcVHGW3ZWBdI5zzzLCchWdMHOnoASLlk71snqyiM_V6jZBqfaYEJeWCFzhGTgqIwHnvNoE0S3Pj9-hZL5NN8MkqAXAY2YQKVAVEJebgwaw8tuU9Mb2f2wbb41NRc2_3cAtI5lOA_2VXU8ZFDHkmRumdUQn28osudmw0r/http%3A%2F%2Fwww.nmrl.pitt.edu%2F _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://secure-web.cisco.com/1HJtky_oRPF1soh991aJ3DftXUf06gK_k14Ev7YDSp_TawY...
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Thank you Tim!
Does someone from Freesurfer have any insight on this?
Best,
Shawn
--- Shawn Flanagan, Ph.D. Assistant Professor University of Pittsburgh School of Health and Rehabilitation Sciences Department of Sports Medicine and Nutrition Neuromuscular Research Laboratory Warrior Human Performance Research Center
3860 South Water Street Pittsburgh, PA 15203 sdf29@pitt.edumailto:sdf29@pitt.edu Email 412.246.0460 Office 630.854.0547 Mobile
________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Tim Schäfer ts+ml@rcmd.org Sent: Monday, November 22, 2021 3:34 AM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] [WARNING: ATTACHMENT UNSCANNED]Using a Different Atlas for Anatomical ROI Analysis
External Email - Use Caution
Dear Shawn,
I can't fully answer your question, but maybe as a start:
I think the idea behind the suggestion to run recon-all on the template is that this would allow you to map the results of the FreeSurfer thickness analysis (which are in by default mapped to the fsaverage template if you run qcache) back to your template. I think you could even leave fsaverage out and map directly to it.
I have had a look at the NIFTI file you provided though (a preview image is attached to this email for others), and it looks like it is not a complete T1 image but a scull-stripped brain only. I think simply running recon-all on the file (you need nothing but a T1-weighted NIFTI file to run recon-all) will not work. You could start the recon-all pipeline at a later stage (after skull stripping), but maybe you should wait for another answer before proceeding any further.
Tim
-- Dr. Tim Schäfer Postdoc Computational Neuroimaging Department of Child and Adolescent Psychiatry, Psychosomatics and Psychotherapy University Hospital Frankfurt, Goethe University Frankfurt am Main, Germany
On 11/21/2021 9:29 PM Flanagan, Shawn D sdf29@pitt.edu wrote:
External Email - Use Caution
Hello,
I would like to use the Brainnectome atlas for cortical thickness analysis parcellations. The T1 template volume (nifti file type) is attached if helpful. I have seen a couple of posts on this, but am not clear about the process. For example, the response to a similar comment was to “run recon-all on the AAL anatomical T1w volume template”. At this point, I do not know what files, transformations, and/or code modifications are needed. For example, does the brainnectome template volume need to be preprocessed in any way, does it need to be saved in the MGH format? If so, how is this done? Does the process require any other files or subroutines?
In summary, I am wondering if you can “walk me through” the process or provide a detailed example. Any help would be greatly appreciated! Thank you for your time.
Best,
Shawn
Shawn Flanagan, Ph.D. Assistant Professor University of Pittsburgh School of Health and Rehabilitation Sciences Department of Sports Medicine and Nutrition Neuromuscular Research Laboratory Warrior Human Performance Research Center
3860 South Water Street Pittsburgh, PA 15203 sdf29@pitt.edumailto:sdf29@pitt.edu Email 412.246.0460 Office 630.854.0547 Mobile
Neuromuscular Research Laboratoryhttps://secure-web.cisco.com/1_5aqZUkO6YoUcAIQvPRF1n7NYTO1H9P7qpq75KFnL3XFNjOVi6GNvBKYhiXAzXKH8J2pU4600LHnA2SXxBwzp6xIUIH7_uCuCzJ3MjbqiG7zi39gGBzKTs0Gt6hoENNdkACfh5un3s7FxoXNZ3tZsxAp9H9JNpDtPxN7SeqJYDHymDKgoltXy-LRGEOrfp6Nki74LR0pTW32oYOSxOwk-U03wudDOVdKJblrq9Un0F7Db5B1dKbvQW-LpNdQCPus7EizMF55_7t6vtCCD4MJhn2QHmWbtVN_iLsRoVROfyqcZCj2kLkU0QtGt9rrCmlH/https%3A%2F%2Fnam12.safelinks.protection.outlook.com%2F%3Furl%3Dhttp%253A%252F%252Fsecure-web.cisco.com%252F1w-f2b1Sv8FoWJqjWBtRI_gzdJ3kwmFPg5ehq75ANa6Is4a60cD4QsEg-p7ca-iH_zi2WeZISZxCc5jTRjVeUtMzIWpoPfSlAlQ642Vjv2fnVIOGVGDukxBLJIoy_xIb8UzkQ1zzHHw_0tvkXbIoza4dvXCPKYcVHGW3ZWBdI5zzzLCchWdMHOnoASLlk71snqyiM_V6jZBqfaYEJeWCFzhGTgqIwHnvNoE0S3Pj9-hZL5NN8MkqAXAY2YQKVAVEJebgwaw8tuU9Mb2f2wbb41NRc2_3cAtI5lOA_2VXU8ZFDHkmRumdUQn28osudmw0r%252Fhttp%25253A%25252F%25252Fwww.nmrl.pitt.edu%25252F%26data%3D04%257C01%257Csdf29%2540pitt.edu%257Caf14122026134e12943808d9ad92fd0a%257C9ef9f489e0a04eeb87cc3a526112fd0d%257C1%257C0%257C637731669393708879%257CUnknown%257CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%253D%257C1000%26sdata%3D9hoo4%252FJ7p9AznCYrNm5SoUSFBlYxI1t7q5881aYK7eo%253D%26reserved%3D0 _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://secure-web.cisco.com/1GSwDOXX9PZtWEoDMuTjYRZkZ7M3R6W0bErVm3_tcocjfzk...
freesurfer@nmr.mgh.harvard.edu
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Flanagan, Shawn D -
Tim Schäfer