But do you know why it has multiple frames? We collect multi-echo T1
MPRAGEs that will have multiple frames. We then reduce it to one frame
by computing the RMS across frames (actually the scanner can output a
separate RMS series). Check to see whether you got an RMS series in
their. If not, check with whoever collected the data to find out why it
has multiple frames.
On 8/2/2021 4:08 PM, Frank Chau wrote:
External Email - Use Caution
Dear Bruce,
I have briefly read a article about multiple framesDICOM. As my
understanding, it can reduce the amount of data repetition and
decreases the time required to read and parse DICOM studies.
Yes, I want to use T1-weighted seriesas input. I have converted a
DICOM series, which the name of the series is "SAG T1 MPRAGE (INC
UPPERCX AS MUCH)", to Nifti format. When I input the Nifti T1 file.
The multiple frameserror occurred.
Below are log record:
---------------------------------------------------------------------------------------
PFCs-MacBook-Pro:T1 PFC$ recon-all -all -i101.nii -s101
Subject Stamp: freesurfer-Darwin-OSX-stable-pub-v6.0.0-2beb96c
Current Stamp: freesurfer-Darwin-OSX-stable-pub-v6.0.0-2beb96c
INFO: SUBJECTS_DIR is /Users/PFC/SPM12/T1
Actual FREESURFER_HOME /Applications/freesurfer
Darwin PFCs-MacBook-Pro.local 18.7.0 Darwin Kernel Version 18.7.0: Mon
May3 20:41:19 PDT 2021; root:xnu-4903.278.68~1/RELEASE_X86_64 x86_64
/Users/PFC/SPM12/T1/101
\n mri_convert /Users/PFC/SPM12/T1/101.nii
/Users/PFC/SPM12/T1/101/mri/orig/001.mgz \n
mri_convert.bin /Users/PFC/SPM12/T1/101.nii
/Users/PFC/SPM12/T1/101/mri/orig/001.mgz
$Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $
reading from /Users/PFC/SPM12/T1/101.nii...
TR=7.24, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (0.135649, -0.98975, -0.0446586)
j_ras = (0.0870012, -0.0330015, 0.995661)
k_ras = (0.98693, 0.138946, -0.0816328)
writing to /Users/PFC/SPM12/T1/101/mri/orig/001.mgz...
#--------------------------------------------
#@# MotionCor Sat Jul 31 18:01:46 HKT 2021
Found 1 runs
/Users/PFC/SPM12/T1/101/mri/orig/001.mgz
Checking for (invalid) multi-frame inputs...
ERROR: input(s) cannot have multiple frames!
/Users/PFC/SPM12/T1/101/mri/orig/001.mgz has 2 frames
Darwin PFCs-MacBook-Pro.local 18.7.0 Darwin Kernel Version 18.7.0: Mon
May3 20:41:19 PDT 2021; root:xnu-4903.278.68~1/RELEASE_X86_64 x86_64
recon-all -s 101 exited with ERRORS at Sat Jul 31 18:01:48 HKT 2021
For more details, see the log file
/Users/PFC/SPM12/T1/101/scripts/recon-all.log
To report a problem, see
http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
---------------------------------------------------------------------------------------
Regards
Frank
------------------------------------------------------------------------
*From:* freesurfer-boun...@nmr.mgh.harvard.edu
<freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Fischl, Bruce
<bfis...@mgh.harvard.edu>
*Sent:* 03 August 2021 03:56:31
*To:* freesurfer@nmr.mgh.harvard.edu
*Cc:* Jacky Lee; Jacky LEE
*Subject:* Re: [Freesurfer] ERROR- input(s) cannot have multiple
frames on Recon-all
Hi Frank
Do you know why there are multiple frames? What kind of MRI
acquisition are you trying to use as input? Most standard T1-weighted
series only have a single frame
Bruce
*From:* freesurfer-boun...@nmr.mgh.harvard.edu
<freesurfer-boun...@nmr.mgh.harvard.edu> *On Behalf Of *Frank Chau
*Sent:* Monday, August 2, 2021 3:49 PM
*To:* freesurfer@nmr.mgh.harvard.edu
*Cc:* Jacky Lee <cyle...@gmail.com>; Jacky LEE <lcy...@ha.org.hk>
*Subject:* [Freesurfer] ERROR- input(s) cannot have multiple frames on
Recon-all
* External Email - Use Caution *
Dear Freesurfer experts,
I tried to run Recon-all on a T1 series .nii file. A error occurred:
"ERROR: input(s) cannot have multiple frames!". I tried to google the
method of converting multi frame dicom to single frame dicom. I found
software of "dicom2" stated that it could perform the conversion but
their manual guide are too hard for me to understand. May I know there
are any easier method to perform the conversion? Thank you.
Regards
Frank
---------------------------
*FRANK C Y CHAU*
Research assistant
Division of Neurology
Department of Medicine
Tel: +852 6340 2553
Fax: 2872 5828
E-mail : cyfr...@hku.hk <mailto:cyfr...@hku.hk>
Rm 304, 3/F, New Clinical building, Queen Mary Hospital, 102 Pokfulam
Road, Hong Kong
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