External Email - Use Caution 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 sd...@pitt.edu<mailto:sd...@pitt.edu> Email 412.246.0460 Office 630.854.0547 Mobile Neuromuscular Research Laboratory<http://secure-web.cisco.com/1gDmNYco15T9f99NRgccbe-1Eqtrq8sIWRqDDP87gsAUUiDCx4Mnw-Yi-NV57bU_VKC9jrcZy72QAnR3Q-y9oqm-a7SwQK_o4PTKryjU2YFDqEPFa1TTUhE--mLZWEvuUuzxCN10iOdxzje4RDdEeFyyH4xZN4f--vBxiFGaXgPC0zD0hUpfrpNa_CW9I3NVyw2-lpEzoUAJ7mRYdOXESaaUY3mLq3CmDhY61kxtGkgtWjVgv1K7VQ9wokKwYdTmyUagN_zQvPuxaQ_YkxpKpCR4F60Z1PVPUcOlfV7-SBSIoZIyd0vHuIaPcnnBPvxeP/http%3A%2F%2Fwww.nmrl.pitt.edu%2F> ________________________________ From: freesurfer-boun...@nmr.mgh.harvard.edu <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Tim Schäfer <ts...@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 <sd...@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 > sd...@pitt.edu<mailto:sd...@pitt.edu> Email > 412.246.0460 Office > 630.854.0547 Mobile > > > Neuromuscular Research > Laboratory<https://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_tcocjfzkVrzIJt3kmhUrpi_KCXUIXY9hkyiyAdAe5NcLRDFVfVwUoTN-IS3yhf2ERrCaAJPFrV6BsbeDuLaMLXJfO4hlz2TlLBB0GdT7fndh4-mM2kwfJOi-MzHNKrxkUL6svv72RobgYAUJzj_zu6B5lLSMFVehbb71yXFbc3pdT3xWT4fswqpfg3o1gySHK2hS5nU3oWClJu4P_1JXn8BfxReiO4uo7ku6pgTsQgNDNvbXGwrnDR5Pi5-wvQJ0Grladjsd9RSkeYm0Ljz_lG2_HW/https%3A%2F%2Fnam12.safelinks.protection.outlook.com%2F%3Furl%3Dhttps%253A%252F%252Fsecure-web.cisco.com%252F1HJtky_oRPF1soh991aJ3DftXUf06gK_k14Ev7YDSp_TawY-kZYEx4YdMf7xM8uT7Om7o2Te7Wh-OLut-7Qp5pInZ-Mv0fkZcJhbnM4KvekfG1vMXIxkR02p0q_RlQ-rGP1Ul26nUGTXC0hIm0rRKnSxfxhqEK0J3LAQeMkH7qCWLKabYhg9mtSxOfW1Y8i87Q6GVj-jre0Yua7JLsKKA9b8FspEhVyzPyWJBB0bQX4-Ywy-Ym5kQljgAt-IoQ7ZndQKSTI1xj7fObJszNRO42UP_6JIvth793iA_w_lShgEgvuHvo5Uf9i_-Fqagkq-Y%252Fhttps%25253A%25252F%25252Fmail.nmr.mgh.harvard.edu%25252Fmailman%25252Flistinfo%25252Ffreesurfer%26data%3D04%257C01%257Csdf29%2540pitt.edu%257Caf14122026134e12943808d9ad92fd0a%257C9ef9f489e0a04eeb87cc3a526112fd0d%257C1%257C0%257C637731669393718831%257CUnknown%257CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%253D%257C1000%26sdata%3DnLIp0nMqVd8r02dUFjMb4sAi5WVNA482P4VxgwAFZAk%253D%26reserved%3D0
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