Sorry, there are a lot of things going on down there, it is hard to figure out
what is happening. It looks like the sourcing of SetUpFreeSurfer.sh is failing
is that right? Then it looks like the copy (cp) is failing. Then when you run
mri_convert, it looks like another bash error. It looks like mri_convert is
trying to unpack it as a diffusion file and that may be what is causing the
final error. Try
export FS_LOAD_DWI=0
On 10/8/18 9:54 PM, Justin Arnett wrote:
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
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