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
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
I tried that and realized the images are very blurry so it probably will not run in any case.
Thank you! Idil ________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Bruce Fischl [fischl@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
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-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Bruce Fischl [fischl@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
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Yagmur Ozdemir 19