Re: [Freesurfer] error while running dt-recon all

2016-03-20 Thread Jasmin Alves
breaksw breaksw end end while ( $#argv != 0 ) while ( 5 != 0 ) set flag = $argv[1] ; shift ; set flag = --i shift switch ( $flag ) switch ( --i ) if ( $#argv < 1 ) goto arg1err ; if ( 4 < 1 ) goto arg1err set InputVol = "$argv[1]" ; shift ; set InputVol = DTI.nii.gz shift if ( ! -e

Re: [Freesurfer] error while running dt-recon all

2016-03-19 Thread Jasmin Alves
Do you mean, what ends up happening? I have attached a screen shot of what files are made. On Wed, Mar 16, 2016 at 7:31 AM, Douglas Greve wrote: > Can you send me what dt_recon prints to the screen when your run the > command below? > > > On 3/15/16 11:40 PM, Jasmin

Re: [Freesurfer] error while running dt-recon all

2016-03-19 Thread Douglas Greve
Can you send me what dt_recon prints to the screen when your run the command below? On 3/15/16 11:40 PM, Jasmin Alves wrote: Jasmins-MacBook-Pro:40 jasminalves$ dt_recon --i DTI.nii.gz --s 40 --o /Users/jasminalves/Desktop/data/FREESURFER/40 INFO: SUBJECTS_DIR is

Re: [Freesurfer] error while running dt-recon all

2016-03-19 Thread Douglas N Greve
No, I mean that when the command is run, it will print a lot of text to the screen. I want to know what that text is. You can run the following command and send me the dng.log file dt_recon --debug --i DTI.nii.gz --s 40 --o /Users/jasminalves/Desktop/data/FREESURFER/40 |& tee dng.log On

Re: [Freesurfer] error while running dt-recon all

2016-03-15 Thread Jasmin Alves
Jasmins-MacBook-Pro:40 jasminalves$ dt_recon --i DTI.nii.gz --s 40 --o /Users/jasminalves/Desktop/data/FREESURFER/40 INFO: SUBJECTS_DIR is /Users/jasminalves/Desktop/data/FREESURFER/ dt_recon logfile Tue Mar 15 20:37:35 PDT 2016 VERSION $Id: dt_recon,v 1.15 2011/01/25 21:53:04 greve Exp $

Re: [Freesurfer] error while running dt-recon all

2016-03-15 Thread Douglas N Greve
Can you send the full terminal output from when you run dt_recon with the nifti as input? On 03/15/2016 03:07 PM, Jasmin Alves wrote: > How was DTI.nii.gz created? DTI.nii.gz was converted from the raw > dicom data using dcm2nii. > > Response for: "What happens if you run mri_info DTI.nii.gz" >

Re: [Freesurfer] error while running dt-recon all

2016-03-15 Thread Jasmin Alves
How was DTI.nii.gz created? DTI.nii.gz was converted from the raw dicom data using dcm2nii. Response for: "What happens if you run mri_info DTI.nii.gz" Volume information for DTI.nii.gz type: nii dimensions: 128 x 128 x 70 x 65 voxel sizes: 2., 2., 2.

Re: [Freesurfer] error while running dt-recon all

2016-03-15 Thread Douglas N Greve
How was DTI.nii.gz created? What happens if you run mri_info DTI.nii.gz If the DICOM is a siemens dicom but has been stripped of special siemens info, then we cannot unpack it On 03/15/2016 02:02 PM, Jasmin Alves wrote: > > Still get the same error: > > WARNING: file

Re: [Freesurfer] error while running dt-recon all

2016-03-15 Thread Jasmin Alves
Still get the same error: WARNING: file /Users/jasminalves/Desktop/data/40/00010001 does not contain a Siemens ASCII header has this file been anonymized? ERROR: cannot unpack mosiacs without ASCII header The error I get when running in nifti format is actually found in the log file. ERROR:

Re: [Freesurfer] error while running dt-recon all

2016-03-15 Thread Douglas N Greve
if you run mri_convert 00010001 deleteme.nii what happens? what is the error when running with nifti? On 03/14/2016 05:59 PM, Jasmin Alves wrote: > > Dear Freesurfer experts, > > FREESURFER_HOME: /Applications/freesurfer > > Build stamp: freesurfer-Darwin-lion-stable-pub-v5.3.0 > > Kernel info:

[Freesurfer] error while running dt-recon all

2016-03-14 Thread Jasmin Alves
Dear Freesurfer experts, FREESURFER_HOME: /Applications/freesurfer Build stamp: freesurfer-Darwin-lion-stable-pub-v5.3.0 Kernel info: Darwin 14.5.0 x86_64 I received the following error while running the dt_recon --i 00010001 --s 40 --o /Users/jasminalves/Desktop/data/FREESURFER/40. The