External Email - Use Caution
Hi Experts,
Just a follow up to my issue below. I have extracted the time course from my pre-processed GIFTI data, despite the "DA[599] has coordsys with intent NIFTI_INTENT_TIME_SERIES (should be NIFTI_INTENT_POINTSET)" terminal messages and plotted it (see attached). It appears to have worked, but I am concerned with the messages. Can anyone let me know if it is suitable to use mri_segstats with --avgwf to extract time courses from GIFTI fMRI data?
Best wishes, Mason
Mason T Wells, MSc
PhD student
School of Optometry and Vision Sciences
& Cardiff University Brain Research
Imaging Centre (CUBRIC), School of Psychology
Cardiff University
Cardiff
CF24 4HQ
UK
Email: WellsMT1@cardiff.ac.ukmailto:WellsMT1@cardiff.ac.uk
Tel: 02920 879628
Web: Cardiff University webpagehttps://secure-web.cisco.com/1xA8x0osHI1FMTkn-2KisAaM1Z0K20yRUcdxxF5-OKrOssjA3KQs-umYT_7Xy0MCOY4eNQ1JTQz8hg7OKagVrU6CoBG8PYGxCPdTK2ATKvhRu_tI9xfhzeku9ebVkbHj4ZGPUOGwm8dZhffSD70a1zi7ox8cu3ULjfmIsYFi-mu1Op_twt250OR9s5YPcuMCPL8dvvO-yXmDzwub9jd4hoFgUfJQl8RWHJ4a7AnaJyrP7EoJ_DGRQd3ze8h7SrT0O/https%3A%2F%2Fwww.cardiff.ac.uk%2Fpeople%2Fresearch-students%2Fview%2F974214-http://secure-web.cisco.com/1ymLmooqzto7aTZFag66la7yrz4Gq_rt-Ott_BKPw40qDKFzQ_ZY1DgNrhKb0xNZsgsf7whRY0j-Ktz0ChI5615yALVAn7EqVtvtHj6mdYWIzzBUEaG_3mx-mH2KgiCoWfkl4M_g8iwPPRIrI0sori-YQd_8WQW9IFBCwlf050bZrAlcpPJgLmj_B6VkYqpsIB0O4gGFvMFVPGMv0cMDqx9bqO0VQCsNoDPfVuMzdaBeNc1Ed8wQFl7H925Jhu_w0/http%3A%2F%2Fwww.cardiff.ac.uk%2Fpeople%2Fresearch-students%2Fview%2F482937-
Mason T Wells, MSc
Myfyriwr PhD
Yr Ysgol Optometreg a Gwyddorau’r Golwg
& Canolfan Ymchwil Delweddu’r Ymennydd Prifysgol Caerdydd (CUBRIC), Yr Ysgol Seicoleg
Prifysgol Caerdydd
Heol Maindy
Caerdydd
CF24 4HQ
DU
E-bost: WellsMT1@caerdydd.ac.ukmailto:WellsMT1@caerdydd.ac.uk
Ffôn: 02920 879628
________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Mason Wells WellsMT1@cardiff.ac.uk Sent: Wednesday, December 9, 2020 11:05 AM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu; freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu Subject: [Freesurfer] Extracted mean timecourse from FS label
External Email - Use Caution
Hi Experts,
I have pre-processed some resting-state date using fMRI prep. I have the functional data on the fs_native surface in bold.func.gii format for each hemisphere. I have created some FS labels and I would like to extract the mean time course from vertices within these labels. Is it possible to use FreeSurfer tools to do this? I have a feeling mri_segstats might be the correct option, but I don't believe this can be used with GIFTI functional data. I tried the command below
* mri_segstats --slabel sub-0006 lh /home/masontwells/Documents/freesurfer/subjects/sub-0006/label/lh.wang2015atlas.V1v.label --avgwf out.dat --id 1 --i ../../post-fmriprep/sub-0006_ses-1_task-rest_acq-TR2000_space-fsnative_hemi-L_bold.func.gii
However, the terminal produces serval of these messages when the command runs:
* ** DA[599] has coordsys with intent NIFTI_INTENT_TIME_SERIES (should be NIFTI_INTENT_POINTSET)
I assume this is a sign that the command and data format are not compatible? If this is the case, can you advise on the best way to extract the mean time courses from my functional data? Will I have to resample the volume data to the surface with mri_vol2surf to get it into MGH format and then run mri_segstats?
Best wishes, Mason
Mason T Wells, MSc
PhD student
School of Optometry and Vision Sciences
& Cardiff University Brain Research
Imaging Centre (CUBRIC), School of Psychology
Cardiff University
Cardiff
CF24 4HQ
UK
Email: WellsMT1@cardiff.ac.ukmailto:WellsMT1@cardiff.ac.uk
Tel: 02920 879628
Web: Cardiff University webpagehttps://secure-web.cisco.com/16HDTfvtb7-0fbEJgBGRm8OCLZVIBQ0iVdl2kRJSd6NJgdYUh-dSldLoL9pWo5SzOzplcF8jLKZnARlVgriKAmfa1LtPEaXTgKhyTc70DF6o-32D4neb6KcKduoKgSTjUD5GKVvFM91wsdNrIhHhN1VbCx3mKtaXZcIL9gQDv-1JzwF0FN65YI4a1q8preURtxLzp0ZLIQ1fSjib9pR_UljQpqCVuChreORKZQoYZN_itwtbk-IP7tpy2XvM6dfb4/https%3A%2F%2Feur03.safelinks.protection.outlook.com%2F%3Furl%3Dhttps%253A%252F%252Fsecure-web.cisco.com%252F1qzj6G102Hp0-GTfeJ6322xQNXQcW4GkqaH5liYvjrdTN9mVH28bjGarCyUEt0zeoSD9XRNT3Js4tOz9xJGHHbBeWJmOjIuLaSBflgcs-ry00l7JVlWM4_8E8IS8UwxZHUMbRjGiskMLtCzmZ4SdKSyev3yrgz9p10unPLJKCRAsDxjOB4LvLe39zOOF1SVol3Q84N4dfg1KrWw0nkrnNDQiQHYKJ4fPUkE_E-24hdF3JUwNAUBhTcfLYiKM0nabl_NQZwKP4lhiOGf5J08oIAg%252Fhttps%25253A%25252F%25252Fwww.cardiff.ac.uk%25252Fpeople%25252Fresearch-students%25252Fview%25252F974214-%26data%3D04%257C01%257CWellsMT1%2540cardiff.ac.uk%257C4f5c1f20c6604568be6808d89c32dae9%257Cbdb74b3095684856bdbf06759778fcbc%257C1%257C0%257C637431089516312831%257CUnknown%257CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%253D%257C1000%26sdata%3DeLDzGu%252BhwRo2R3Oml8eYoRACIUvY5M6kSQfIYiKUHCY%253D%26reserved%3D0https://secure-web.cisco.com/1VauQFyyTrf4EdNwHRSmtsXZiE4Brm8PoKn5YTCjqc2DXeCPnCtQ0aAToudxh-DBN3D4jaQaCleIX_SAIk25vSgKq0G0tBA-MZvDUv9GaUqe8VMwDg6zbT8_YMEhoHbqHkg4mcX8Ipmo56Ovu0Jkx3PR115ACmxF-0Fvyexuf34I--YLvcoK4jLHJmxMA7fDtuP3PkKTJdO-JU3Qaq58EHm-E-wN-d-JQPOW4V9MpK1IYYI-95X0z9ipkf2sqvyqQ/https%3A%2F%2Feur03.safelinks.protection.outlook.com%2F%3Furl%3Dhttp%253A%252F%252Fsecure-web.cisco.com%252F1wKqfPd1L9yGr-NK1MFwwQm3aX2SenX1VtTlRgPt0wLl12m1S3gPKVuklTThQx5hYho6o7JRvNgFSJACPTxcEMbyloVNftwdvKXBDnY1wLcJefCiN6DPqde9TUnehUA7cYQUdSj9k2S7gezqMA0BiTKgsiB31IuF_aEAPAfITuUud8_bPUhIvfCr5Plom6p-YKBaFzDxbmKu1ApbYyWzH8R_5enHIskcMNg8jSksPE57VlCCjMHmzvhwIIRn0rOY0u-4Uak9j5yd13Yw_F2I1pA%252Fhttp%25253A%25252F%25252Fwww.cardiff.ac.uk%25252Fpeople%25252Fresearch-students%25252Fview%25252F482937-%26data%3D04%257C01%257CWellsMT1%2540cardiff.ac.uk%257C4f5c1f20c6604568be6808d89c32dae9%257Cbdb74b3095684856bdbf06759778fcbc%257C1%257C0%257C637431089516322825%257CUnknown%257CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%253D%257C1000%26sdata%3D0SgIJwGjOwk3vpINPyVps3g7%252F7POs%252BupklHtZ6wMylk%253D%26reserved%3D0
Mason T Wells, MSc
Myfyriwr PhD
Yr Ysgol Optometreg a Gwyddorau’r Golwg
& Canolfan Ymchwil Delweddu’r Ymennydd Prifysgol Caerdydd (CUBRIC), Yr Ysgol Seicoleg
Prifysgol Caerdydd
Heol Maindy
Caerdydd
CF24 4HQ
DU
E-bost: WellsMT1@caerdydd.ac.ukmailto:WellsMT1@caerdydd.ac.uk
Ffôn: 02920 879628
