Just give it one of the dicoms (ie, don't use the "*" wild card, just
give it the actual file name of one of the files in the series, it will
find the rest)
doug
On 2/11/15 4:28 PM, Sampada Sinha wrote:
Dear freesurfer experts,
Sorry for posting such a long message but I am trying to run dt_recon
command on DTI images acquired in dicom format using 3T_Toshiba
(Toshiba_MEC_MR3). Image parameters are: Scanning sequence =Spin Echo;
TR=9 ; TE=082.0 ; Flip angle = 90; Slice thickness= 3.0000;
acquisition matrix is 160. Howsoever, I used many tools to get the
bval and bvect gr
adient from the conversion of dcm files to nifti but couldn't get one
(dcm2nii, mricron). Even with freesurfer, I am getting following
error: (My dcm file is in directory:
/Users/Sampada/Desktop/DTIDCM/Raw/I*.dcm)
I used following command to get the dt_recon work:
Sampada$ export FREESURFER_HOME=/Applications/freesurfer
Sampada$ source $FREESURFER_HOME/SetUpFreeSurfer.sh
-------- freesurfer-Darwin-snowleopard-i686-stable-pub-v5.3.0 --------
Setting up environment for FreeSurfer/FS-FAST (and FSL)
FREESURFER_HOME /Applications/freesurfer
FSFAST_HOME /Applications/freesurfer/fsfast
FSF_OUTPUT_FORMAT nii.gz
SUBJECTS_DIR /Applications/freesurfer/subjects
MNI_DIR /Applications/freesurfer/mni
FSL_DIR /Applications/fsl
Sampada$ tcsh
Sampada% cd /Users/sampada/Desktop/DTIDCM/Raw/
~/Desktop/DTIDCM/Raw] Sampada% setenv SUBJECTS_DIR
/Users/Sampada/Desktop/DTIDCM/Raw
~/Desktop/DTIDCM/Raw] Sampada% set subj =Diff001
~/Desktop/DTIDCM/Raw] Sampada% dt_recon --i
/Users/Sampada/Desktop/DTIDCM/Raw/I*.dcm --s $subj --o
/Users/Sampada/Desktop/DTIDCM/Raw
Error Message: ERROR: Flag
/Users/Sampada/Desktop/DTIDCM/Raw/I0005130.dcm unrecognized.
--i /Users/Sampada/Desktop/DTIDCM/Raw/I0005129.dcm
/Users/Sampada/Desktop/DTIDCM/Raw/I0005130.dcm
/Users/Sampada/Desktop/DTIDCM/Raw/I0005131.dcm
/Users/Sampada/Desktop/DTIDCM/Raw/I0005132.dcm
/Users/Sampada/Desktop/DTIDCM/Raw/I0005133.dcm
/Users/Sampada/Desktop/DTIDCM/Raw/I0005134.dcm
and so on… (dt_recon exited with ERRORS at Wed Feb 11 01:47:01 CST 2015)
Then I used nii converted file instead of the dcm file and it shows
the following error
Sampada% dt_recon --i /Users/Sampada/Desktop/DTIDCM/Raw/s700a1001.nii
--s $subj --o /Users/Sampada/Desktop/DTIDCM/Raw
INFO: SUBJECTS_DIR is /Users/Sampada/Desktop/DTIDCM/Raw
dt_recon logfile
Wed Feb 11 15:02:47 CST 2015
VERSION $Id: dt_recon,v 1.15 2011/01/25 21:53:04 greve Exp $
setenv SUBJECTS_DIR /Users/Sampada/Desktop/DTIDCM/Raw
cd /Users/Sampada/Desktop/DTIDCM/Raw
/Applications/freesurfer/bin/dt_recon --i
/Users/Sampada/Desktop/DTIDCM/Raw/s700a1001.nii --s Diff001 --o
/Users/Sampada/Desktop/DTIDCM/Raw
rmbp.home
Sampada
/Applications/fsl/bin/eddy_correct
ECRefTP 0
#@#-------------------------------
Converting input
Wed Feb 11 15:02:47 CST 2015
cd /Users/Sampada/Desktop/DTIDCM/Raw
mri_convert /Users/Sampada/Desktop/DTIDCM/Raw/s700a1001.nii
/Users/Sampada/Desktop/DTIDCM/Raw/dwi.nii
mri_convert /Users/Sampada/Desktop/DTIDCM/Raw/s700a1001.nii
/Users/Sampada/Desktop/DTIDCM/Raw/dwi.nii
$Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $
reading from /Users/Sampada/Desktop/DTIDCM/Raw/s700a1001.nii...
TR=9000.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-0.994743, 0.0323186, 0.097165)
j_ras = (0.0525116, 0.97562, 0.21309)
k_ras = (0.0879093, -0.217072, 0.972189)
writing to /Users/Sampada/Desktop/DTIDCM/Raw/dwi.nii...
cd /Users/Sampada/Desktop/DTIDCM/Raw
mri_probedicom --i /Users/Sampada/Desktop/DTIDCM/Raw/s700a1001.nii
[rmbp:~/Desktop/DTIDCM/Raw] Sampada%
I would be very grateful if I any response and know where I am going
wrong. I am also attaching the dt_recon.log file with this query.
Much thanks for your time!
Kind regards,
Sampada
Post-Doctoral Associate
University of Minnesota (East Bank)
Molecular and neuroimaging laboratory
Department of Psychiatry
Minneapolis-55415
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