Run
mri_concat input.mgz --rms --o 001.mgz
then pass 001.mgz to recon-all
On 1/28/2021 3:13 AM, 南修司郎 wrote:
External Email - Use Caution
Hello FreeSurfer Developers,
I'm attempting to recon-all a subject, but i got the following error.
Checking for (invalid) multi-frame inputs...
ERROR: input(s) cannot have multiple frames!
/home/shujirominami/freesurfer/subjects/todai_test/mri/orig/001.mgz
has 4 frames
I checked mri_info, and the dimensions are 256 x 256 x 176 x 4.
I asked the radiation technologist to change the dimensions to 256 x
256 x 176, but he told me it's impossible because of the multi echo
sequence.
I'd appreciate if someone help me out with this and resolve this error.
Shujiro Minami M.D., Ph.D.
Dpt. of Otolaryngology National Tokyo Medical Center
2-5-1 Higashigaoka, Meguro, Tokyo 152-8902, Japan
E-mail shujiromin...@me.com <mailto:shujiromin...@me.com>
1) FreeSurfer version:freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c
2) Platform:Ubuntu 18.04.5 LTS (GNU/Linux 5.4.0-1034-gcp x86_64)
3) uname -a: Linux instance-1 5.4.0-1034-gcp #37~18.04.1-Ubuntu SMP Wed Jan 6
19:44:48 UTC 2021 x86_64 x86_64 x86_64 GNU/Linux
4) recon-all.log: see attached
User: shujirominami Machine: instance-1 Platform: Linux PlatformVersion:
5.4.0-1034-gcp CompilerName: GCC CompilerVersion: 40400
ProgramName: mri_relabel_hypointensities ProgramArguments: -all-info
ProgramVersion: $Name: stable6 $ TimeStamp: 2021/01/27-10:28:02-GMT
BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_relabel_hypointensities.c,v
1.13 2015/05/15 18:44:10 nicks Exp $ User: shujirominami Machine: instance-1
Platform: Linux PlatformVersion: 5.4.0-1034-gcp CompilerName: GCC
CompilerVersion: 40400
#######################################
GCADIR /usr/local/freesurfer/average
GCA RB_all_2016-05-10.vc700.gca
GCASkull RB_all_withskull_2016-05-10.vc700.gca
AvgCurvTif folding.atlas.acfb40.noaparc.i12.2016-08-02.tif
GCSDIR /usr/local/freesurfer/average
GCS DKaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs
#######################################
/home/shujirominami/freesurfer/subjects/todai_test
mri_convert /home/shujirominami/NIFTI/todai_test.nii.gz
/home/shujirominami/freesurfer/subjects/todai_test/mri/orig/001.mgz
mri_convert.bin /home/shujirominami/NIFTI/todai_test.nii.gz
/home/shujirominami/freesurfer/subjects/todai_test/mri/orig/001.mgz
$Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $
reading from /home/shujirominami/NIFTI/todai_test.nii.gz...
TR=2530.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (0, -1, 0)
j_ras = (0, 0, 1)
k_ras = (1, 0, 0)
writing to
/home/shujirominami/freesurfer/subjects/todai_test/mri/orig/001.mgz...
#--------------------------------------------
#@# MotionCor Wed Jan 27 10:29:57 UTC 2021
Found 1 runs
/home/shujirominami/freesurfer/subjects/todai_test/mri/orig/001.mgz
Checking for (invalid) multi-frame inputs...
ERROR: input(s) cannot have multiple frames!
/home/shujirominami/freesurfer/subjects/todai_test/mri/orig/001.mgz has 4 frames
If this is a multi-frame MEMPRAGE image,
use mri_concat --rms to combine echo frames.
Linux instance-1 5.4.0-1034-gcp #37~18.04.1-Ubuntu SMP Wed Jan 6 19:44:48 UTC
2021 x86_64 x86_64 x86_64 GNU/Linux
recon-all -s todai_test exited with ERRORS at Wed Jan 27 10:30:01 UTC 2021
To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
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