they probably aren't from the right dicom series then. On Wed, 9 Aug 2017, Yagmur Ozdemir 19 wrote:
> I tried that and realized the images are very blurry so it probably will not > run in any case. > > Thank you! > Idil > ________________________________________ > From: freesurfer-boun...@nmr.mgh.harvard.edu > [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Bruce Fischl > [fis...@nmr.mgh.harvard.edu] > 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 > > 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 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 >> >> >> >> > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
