External Email - Use Caution Hello Freesurfer Developers,
I want to extract the beta values for an fMRI dataset that I analyzed with FSFAST, so that I get one beta map (in the ras space) per condition/regressor. The dataset has 5 conditions/regressors specified in the paradigm file and each participant has 4 runs. I used the following commands when running FSFAST (example for left hemisphere): mkanalysis-sess -analysis localiser.sm5.lh -surface fsaverage lh -fwhm 5 -paradigm parbench.par -event-related -spmhrf 0 -refeventdur 4 -polyfit 2 -nskip 4 -TR 2 -nconditions 5 -per-run -fsd bold mkcontrast-sess -analysis localiser.sm5.lh -contrast right-vs-left -c 3 -c 5 -a 2 -a 4 selxavg3-sess -sf sessid -analysis localiser.sm5.lh >From the output when I navigate to PARTICIPANT_FOLDER/bold/localiser.sm5.lh >and examine the beta file with mri_info, I get: mri_info beta.nii.gz --dim 163842 1 1 33 My understanding is that the first number is the actual beta values for a given regressor in ras space and the last number (33) is the different betas. From an archived post I found that the first N betas represent the first N conditions. Is that per run, or collapsed over runs? Or is it that the first five betas are the five conditions for run 1, the second five for run 2, etc until 20? What are the other nuisance regressors used to make the rest of the betas then? Kind Regards, Deyan Mae croeso i chi gysylltu gyda'r Brifysgol yn Gymraeg neu Saesneg. Ni fydd gohebu yn Gymraeg yn arwain at oedi. You are welcome to contact the University in Welsh or English. Corresponding in Welsh will not lead to delay. Rhif Elusen Gofrestredig 1141565 - Registered Charity No. 1141565 Gall y neges e-bost hon, ac unrhyw atodiadau a anfonwyd gyda hi, gynnwys deunydd cyfrinachol ac wedi eu bwriadu i'w defnyddio'n unig gan y sawl y cawsant eu cyfeirio ato (atynt). Os ydych wedi derbyn y neges e-bost hon trwy gamgymeriad, rhowch wybod i'r anfonwr ar unwaith a dilewch y neges. Os na fwriadwyd anfon y neges atoch chi, rhaid i chi beidio a defnyddio, cadw neu ddatgelu unrhyw wybodaeth a gynhwysir ynddi. Mae unrhyw farn neu safbwynt yn eiddo i'r sawl a'i hanfonodd yn unig ac nid yw o anghenraid yn cynrychioli barn Prifysgol Bangor. Nid yw Prifysgol Bangor yn gwarantu bod y neges e-bost hon neu unrhyw atodiadau yn rhydd rhag firysau neu 100% yn ddiogel. Oni bai fod hyn wedi ei ddatgan yn uniongyrchol yn nhestun yr e-bost, nid bwriad y neges e-bost hon yw ffurfio contract rhwymol - mae rhestr o lofnodwyr awdurdodedig ar gael o Swyddfa Cyllid Prifysgol Bangor. This email and any attachments may contain confidential material and is solely for the use of the intended recipient(s). If you have received this email in error, please notify the sender immediately and delete this email. If you are not the intended recipient(s), you must not use, retain or disclose any information contained in this email. Any views or opinions are solely those of the sender and do not necessarily represent those of Bangor University. Bangor University does not guarantee that this email or any attachments are free from viruses or 100% secure. Unless expressly stated in the body of the text of the email, this email is not intended to form a binding contract - a list of authorised signatories is available from the Bangor University Finance Office.
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