Re: [Freesurfer] Extracted mean timecourse from FS label

I don't know, that msg probably comes from the gifti code we link to. It looks like it is just a warning. Do the output waveforms look ok?

On 12/9/2020 6:05 AM, Mason Wells wrote:

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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/1qzj6G102Hp0-GTfeJ6322xQNXQcW4GkqaH5liYvjrdTN9mVH28bjGarCyUEt0zeoSD9XRNT3Js4tOz9xJGHHbBeWJmOjIuLaSBflgcs-ry00l7JVlWM4_8E8IS8UwxZHUMbRjGiskMLtCzmZ4SdKSyev3yrgz9p10unPLJKCRAsDxjOB4LvLe39zOOF1SVol3Q84N4dfg1KrWw0nkrnNDQiQHYKJ4fPUkE_E-24hdF3JUwNAUBhTcfLYiKM0nabl_NQZwKP4lhiOGf5J08oIAg/https%3A%2F%2Fwww.cardiff.ac.uk%2Fpeople%2Fresearch-students%2Fview%2F974214-

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

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