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