Hi Cecilia - Does the number of entries in the bvals and bvecs files match the number of volumes in data.nii.gz?

a.y ________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Mazzetti, C. (Cecilia) C.Mazzetti@donders.ru.nl Sent: Saturday, October 5, 2019 3:23:23 AM To: freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] Errors running TRACULA (data attached) - valid frame numbers

External Email - Use Caution

Dear members,

I've tried troubleshooting but can't wrap my head around this. Trying to run TRACULA after recon-all the subjects, but I keep getting:

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R: Subscript out of range. R: Subscript out of range. R: Subscript out of range. R: Subscript out of range. R: Subscript out of range. R: Subscript out of range. R: Subscript out of range. R: Subscript out of range. R: Subscript out of range. R: Subscript out of range. R: Subscript out of range. R: Subscript out of range. R: Subscript out of range. R: Subscript out of range. R: Subscript out of range. R: Subscript out of range. R: Subscript out of range. R: Subscript out of range. R: Subscript out of range. R: Subscript out of range. R: Subscript out of range. R: Subscript out of range. R: Subscript out of range. R: Subscript out of range. (a bunch of these)

TR=3670.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-0.989717, -0.110817, -0.0904434) j_ras = (-0.128995, 0.964706, 0.22957) k_ras = (-0.0618111, -0.238876, 0.969081)

keeping frames 0 1 12 23 34 45 56 67 78 89 100 ERROR: valid frame numbers are between 0 and 0

trac-preproc exited with ERRORS #####

I checked the # of bvals and bvecs in the dorm folder compared to orig ones, same.

I don't know what's wrong

below config file:

set subjlist = ( subject02_C ) set dcmlist = ( /myfolder/freesurfer/subject02_C/dmri/data.nii.gz )

set bveclist = ( /myfolder/freesurfer/subject02_C/dmri/bvecs ) set bvallist = ( /myfolder/freesurfer/subject02_C/dmri/bvals )

set doeddy = 1 set dorotbvecs = 1 set usemaskanat = 1 set thrbet = 0.3 set doregflt = 0 set doregbbr = 1 ​set doregmni = 1 set doregcvs = 0

set pathlist = ( lh.cst_AS rh.cst_AS \ lh.ilf_AS rh.ilf_AS \ lh.unc_AS rh.unc_AS \ fmajor_PP fminor_PP \ lh.atr_PP rh.atr_PP \ lh.cab_PP rh.cab_PP \ lh.ccg_PP rh.ccg_PP \ lh.slfp_PP rh.slfp_PP \ lh.slft_PP rh.slft_PP )

set ncpts = (6 6 5 5 5 5 7 5 5 5 5 5 4 4 5 5 5 5)

Please any sort of input/help is super appreciated.

Let me know if I can give more information

Cheers,

Cecilia

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