Hi Idil
you have to figure out what the input volume has more than 1 frame (that is, why is it 4d). It could be because you saved phase and mag, or because there are multiple echoes, but until you understand what the additional frames are we can't process it. YOu can start by bringing the orig.mgz up in freeview and looking at it and seeing what the different frames look like. If one of them looks like the T1-weighted image and the other doesn't (maybe it's a phase map?) you would run:


cd  /home/lab/Desktop/freesurfer/subjects/sub-06-error/mri/orig/
mv 001.mgz 001.multiframe.mgz
mri_convert -nth 0 001.multiframe.mgz 001.mgz


assuming that the 0th (first) frame is the T1 weighted. If it was the next one you would do -nth 1 instead

cheers
Bruce


On Tue, 8 Aug 2017, Yagmur Ozdemir 19 wrote:

Hello FreeSurfer experts,

I am trying to run recon-all on a nifti file converted from PAR/SEC using
dcm2niix, and this error came up pretty soon after the script started to
run;

>> mri_convert.bin
/home/lab/Desktop/freesurfer/subjects/sub-06_run-01_T1w.nii.gz
/home/lab/Desktop/freesurfer/subjects/sub-06-error/mri/orig/001.mgz
$Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $
reading from
/home/lab/Desktop/freesurfer/subjects/sub-06_run-01_T1w.nii.gz...
TR=2000.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-1, 0, 0)
j_ras = (-0, 0.916013, -0.401149)
k_ras = (0, 0.401149, 0.916013)
writing to
/home/lab/Desktop/freesurfer/subjects/sub-06-error/mri/orig/001.mgz...
#--------------------------------------------
#@# MotionCor Tue AugĀ  8 17:42:13 EDT 2017
Found 1 runs
/home/lab/Desktop/freesurfer/subjects/sub-06-error/mri/orig/001.mgz
Checking for (invalid) multi-frame inputs...
ERROR: input(s) cannot have multiple frames!

I am pretty inexperienced with FreeSurfer, but does this error mean I need
to slice my file? I would really appreciate if someone could give me some
ideas for commands to use.

Thank you all!
Best,
Idil



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