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Hello Everyone, I hope you are doing well!
I am trying to recon-all a DICOM file, for the ultimate hope of being able to identify the location of M1 via parcellation. I have successfully been able to do so for 2 subjects already, though for some reason I am having a problem with the MRI convert stage from the .dcm file to the .nii.gz file. I copied/pasted the terminal shell I tried performing above. I am using a Mac (Yosemite 10.10.5) with FreeSurfer V6.0.0
Further, I think it might be helpful to note that I am a very extreme novice in computer science/coding--I have completed recon-all's of 2 subjects by following, essentially line-by-line, the "FreeSurfer Download and Install Page," and this process was the first time I ever used the terminal shell. (In this way, I would absolutely LOVE if anyone might be able to explain where I went wrong as simplistically as possible).
Thank you all so much for the help- I hope you have a great start to the week! - Justin
DBI 05 MRI Convert Error
Justins-Computer:~ justinarnett$ export FREESURFER_HOME=/Applications/freesurfer
Justins-Computer:~ justinarnett$ source $FREESURFER_HOME/SetUpFreeSurfer.sh
-------- freesurfer-Darwin-OSX-stable-pub-v6.0.0-2beb96c --------
Setting up environment for FreeSurfer/FS-FAST (and FSL)
FREESURFER_HOME /Applications/freesurfer
FSFAST_HOME /Applications/freesurfer/fsfast
FSF_OUTPUT_FORMAT nii.gz
SUBJECTS_DIR /Applications/freesurfer/subjects
-bash: [: /Users/justinarnett: binary operator expected
grep: /Users/justinarnett: Is a directory
grep: 1/matlab/startup.m: No such file or directory
grep: /Users/justinarnett: Is a directory
grep: 1/matlab/startup.m: No such file or directory
grep: /Users/justinarnett: Is a directory
grep: 1/matlab/startup.m: No such file or directory
MNI_DIR /Applications/freesurfer/mni
Justins-Computer:~ justinarnett$ export SUBJECTS_DIR=/Applications/freesurfer/subjects/DBI05MRI
Justins-Computer:~ justinarnett$ cd /Applications/freesurfer/subjects/DBI05MRI
Justins-Computer:DBI05MRI justinarnett$ cp $FREESURFER_HOME/subjects/DBI05MRI/Image1.dcm
usage: cp [-R [-H | -L | -P]] [-fi | -n] [-apvX] source_file target_file
cp [-R [-H | -L | -P]] [-fi | -n] [-apvX] source_file ... target_directory
Justins-Computer:DBI05MRI justinarnett$ mri_convert Image1.dcm Image1.nii.gz
/Applications/freesurfer/FreeSurferEnv.sh: line 226: [: /Users/justinarnett: binary operator expected
grep: /Users/justinarnett: Is a directory
grep: 1/matlab/startup.m: No such file or directory
grep: /Users/justinarnett: Is a directory
grep: 1/matlab/startup.m: No such file or directory
grep: /Users/justinarnett: Is a directory
grep: 1/matlab/startup.m: No such file or directory
mri_convert.bin Image1.dcm Image1.nii.gz
$Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $
reading from Image1.dcm...
Starting DICOMRead2()
dcmfile = /Applications/freesurfer/subjects/DBI05MRI/Image1.dcm
dcmdir = /Applications/freesurfer/subjects/DBI05MRI
Ref Series No = 401
Found 824 files, checking for dicoms
WARNING: tag ImageNumber not found in /Applications/freesurfer/subjects/DBI05MRI/DICOMDIR
WARNING: tag SeriesNumber not found in /Applications/freesurfer/subjects/DBI05MRI/DICOMDIR
WARNING: tag image orientation not found in /Applications/freesurfer/subjects/DBI05MRI/DICOMDIR
ERROR: GetDICOMInfo(): dcmGetDWIParams() 10
DICOM File: /Applications/freesurfer/subjects/DBI05MRI/DICOMDIR
break DICOMRead.c:5228
Found 164 dicom files in series.
WARNING: tag ImageNumber not found in /Applications/freesurfer/subjects/DBI05MRI/DICOMDIR
WARNING: tag SeriesNumber not found in /Applications/freesurfer/subjects/DBI05MRI/DICOMDIR
WARNING: tag image orientation not found in /Applications/freesurfer/subjects/DBI05MRI/DICOMDIR
ERROR: GetDICOMInfo(): dcmGetDWIParams() 10
DICOM File: /Applications/freesurfer/subjects/DBI05MRI/DICOMDIR
break DICOMRead.c:5228
First Sorting
Computing Slice Direction
Vs: -120.054 -103.192 34.4639
Vs: -0.741 -0.636922 0.212719
Second Sorting
IsDWI = 0, IsPhilipsDWI = 0
Counting frames
nframes = 1
nslices = 165
ndcmfiles = 165
MRIallocSequence(0, 0, 165, 1): bad parm
No such file or directory
ERROR: mri alloc failed