I tried that and realized the images are very blurry so it probably will not 
run in any case. 

Thank you!
From: freesurfer-boun...@nmr.mgh.harvard.edu 
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Bruce Fischl 
Sent: Wednesday, August 09, 2017 1:20 AM
To: Freesurfer support list
Subject: Re: [Freesurfer] multi-frame input error with PAR/SEC origin file

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


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 Aug  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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