Re: [Freesurfer] ERROR: cannot find RB_all_2008-03-26.gca & Now DYLD Variables

2016-11-30 Thread Douglas N Greve 
Doug, can you do me a favor and check to see if this modified version of 
recon-all works on your data?

https://gate.nmr.mgh.harvard.edu/safelinks/greve/recon-all



On 11/30/2016 11:41 AM, Douglas Merkitch wrote:
> Hmmm it is a dicom file. Could it be that the lack of file extension 
> gives it problems?
>
> Thanks,
>
> Doug
>
> Douglas Merkitch
> Neurological Sciences
> Rush University Medical Center
> Phone: (312) 563-3853 
> Fax: (312) 563-4660 
> Email: douglas_merki...@rush.edu 
>
>
>
>
>
> On Nov 29, 2016, at 5:01 PM, Douglas N Greve 
> mailto:gr...@nmr.mgh.harvard.edu>>
>  wrote:
>
>> It is not recognizing that the input is a dicom file. Is 4355-0005-1
>> a dicom file? Or is it a folder?
>>
>>
>> On 11/29/2016 05:51 PM, Douglas Merkitch wrote:
>>> Here is the command/output with the -debug flag:
>>>
>>> recon-all -debug -i
>>> /Volumes/JGG_WD_4TB_hard_drive_2/raw_data_UIC_3T/1039/raw_reordered/005-SAG_FSPGR_BRAVO_PURE/4355-0005-1
>>>  
>>>
>>> -i
>>> /Volumes/JGG_WD_4TB_hard_drive_2/raw_data_UIC_3T/1039/raw_reordered/006-SAG_FSPGR_BRAVO_PURE_REPEAT/4355-0006-1
>>>  
>>>
>>> -s 1039_test
>>> set echo = 1 ;
>>> breaksw
>>> breaksw
>>> end
>>> end
>>> while ( $#argv != 0 )
>>> while ( 6 != 0 )
>>>
>>> set flag = $argv[1] ; shift ;
>>> set flag = -i
>>> shift
>>>
>>> switch ( $flag )
>>> switch ( -i )
>>> if ( $#argv < 1 ) goto arg1err ;
>>> if ( 5 < 1 ) goto arg1err
>>> set InputVol = "$argv[1]" ; shift ;
>>> set InputVol =
>>> /Volumes/JGG_WD_4TB_hard_drive_2/raw_data_UIC_3T/1039/raw_reordered/005-SAG_FSPGR_BRAVO_PURE/4355-0005-1
>>> shift
>>> if ( ! -e "$InputVol" ) then
>>> if ( ! -e
>>> /Volumes/JGG_WD_4TB_hard_drive_2/raw_data_UIC_3T/1039/raw_reordered/005-SAG_FSPGR_BRAVO_PURE/4355-0005-1
>>>  
>>>
>>> ) then
>>> if ( -d "$InputVol" ) then
>>> if ( -d
>>> /Volumes/JGG_WD_4TB_hard_drive_2/raw_data_UIC_3T/1039/raw_reordered/005-SAG_FSPGR_BRAVO_PURE/4355-0005-1
>>>  
>>>
>>> ) then
>>> if ( ! -r "$InputVol" ) then
>>> if ( ! -r
>>> /Volumes/JGG_WD_4TB_hard_drive_2/raw_data_UIC_3T/1039/raw_reordered/005-SAG_FSPGR_BRAVO_PURE/4355-0005-1
>>>  
>>>
>>> ) then
>>> set InVolDir = `dirname  "$InputVol"` ;
>>> set InVolDir = `dirname  "$InputVol"`
>>> dirname
>>> /Volumes/JGG_WD_4TB_hard_drive_2/raw_data_UIC_3T/1039/raw_reordered/005-SAG_FSPGR_BRAVO_PURE/4355-0005-1
>>> set InVolBase = `basename "$InputVol"` ;
>>> set InVolBase = `basename "$InputVol"`
>>> basename
>>> /Volumes/JGG_WD_4TB_hard_drive_2/raw_data_UIC_3T/1039/raw_reordered/005-SAG_FSPGR_BRAVO_PURE/4355-0005-1
>>> pushd $InVolDir > /dev/null
>>> pushd
>>> /Volumes/JGG_WD_4TB_hard_drive_2/raw_data_UIC_3T/1039/raw_reordered/005-SAG_FSPGR_BRAVO_PURE
>>> set InVolDir = `pwd` ;
>>> set InVolDir = `pwd`
>>> pwd
>>> popd > /dev/null
>>> popd
>>> set InputVol = "$InVolDir/$InVolBase" ;
>>> set InputVol =
>>> /Volumes/JGG_WD_4TB_hard_drive_2/raw_data_UIC_3T/1039/raw_reordered/005-SAG_FSPGR_BRAVO_PURE/4355-0005-1
>>> set InputList = ( $InputList "$InputVol" ) ;
>>> set InputList = (
>>> /Volumes/JGG_WD_4TB_hard_drive_2/raw_data_UIC_3T/1039/raw_reordered/005-SAG_FSPGR_BRAVO_PURE/4355-0005-1
>>>  
>>>
>>> )
>>> set DoConvertInput = 1 ;
>>> set DoConvertInput = 1
>>> breaksw
>>> breaksw
>>> end
>>> end
>>> while ( $#argv != 0 )
>>> while ( 4 != 0 )
>>>
>>> set flag = $argv[1] ; shift ;
>>> set flag = -i
>>> shift
>>>
>>> switch ( $flag )
>>> switch ( -i )
>>> if ( $#argv < 1 ) goto arg1err ;
>>> if ( 3 < 1 ) goto arg1err
>>> set InputVol = "$argv[1]" ; shift ;
>>> set InputVol =
>>> /Volumes/JGG_WD_4TB_hard_drive_2/raw_data_UIC_3T/1039/raw_reordered/006-SAG_FSPGR_BRAVO_PURE_REPEAT/4355-0006-1
>>> shift
>>> if ( ! -e "$InputVol" ) then
>>> if ( ! -e
>>> /Volumes/JGG_WD_4TB_hard_drive_2/raw_data_UIC_3T/1039/raw_reordered/006-SAG_FSPGR_BRAVO_PURE_REPEAT/4355-0006-1
>>>  
>>>
>>> ) then
>>> if ( -d "$InputVol" ) then
>>> if ( -d
>>> /Volumes/JGG_WD_4TB_hard_drive_2/raw_data_UIC_3T/1039/raw_reordered/006-SAG_FSPGR_BRAVO_PURE_REPEAT/4355-0006-1
>>>  
>>>
>>> ) then
>>> if ( ! -r "$InputVol" ) then
>>> if ( ! -r
>>> /Volumes/JGG_WD_4TB_hard_drive_2/raw_data_UIC_3T/1039/raw_reordered/006-SAG_FSPGR_BRAVO_PURE_REPEAT/4355-0006-1
>>>  
>>>
>>> ) then
>>> set InVolDir = `dirname  "$InputVol"` ;
>>> set InVolDir = `dirname  "$InputVol"`
>>> dirname
>>> /Volumes/JGG_WD_4TB_hard_drive_2/raw_data_UIC_3T/1039/raw_reordered/006-SAG_FSPGR_BRAVO_PURE_REPEAT/4355-0006-1
>>> set InVolBase = `basename "$InputVol"` ;
>>> set InVolBase = `basename "$InputVol"`
>>> basename
>>> /Volumes/JGG_WD_4TB_hard_drive_2/raw_data_UIC_3T/1039/raw_reordered/006-SAG_FSPGR_BRAVO_PURE_REPEAT/4355-0006-1
>>> pushd $InVolDir > /dev/null
>>> pushd
>>> /Volumes/JGG_WD_4TB_hard_drive_2/raw_data_UIC_3T/1039/raw_reordered/006-SAG_FSPGR_BRAVO_PURE_REPEAT
>>> set InVolDir = `pwd` ;
>>> set InVolDir = `pwd`
>>> pwd
>>> popd > /dev/null
>>> popd
>>> set InputVol = "$InVolDir/$InVolBase" ;
>>> set InputVol =
>

Re: [Freesurfer] ERROR: cannot find RB_all_2008-03-26.gca & Now DYLD Variables

2016-11-30 Thread Douglas N Greve 
Actually, it is the lack of a dot (".") in the file name. This is a 
short-coming of recon-all. I'm really surprised that it took this long 
to manifest itself. The short-term fix is to convert the files to mgz, 
then pass the mgz files to recon-all.


On 11/30/2016 11:41 AM, Douglas Merkitch wrote:
> Hmmm it is a dicom file. Could it be that the lack of file extension 
> gives it problems?
>
> Thanks,
>
> Doug
>
> Douglas Merkitch
> Neurological Sciences
> Rush University Medical Center
> Phone: (312) 563-3853 
> Fax: (312) 563-4660 
> Email: douglas_merki...@rush.edu 
>
>
>
>
>
> On Nov 29, 2016, at 5:01 PM, Douglas N Greve 
> mailto:gr...@nmr.mgh.harvard.edu>>
>  wrote:
>
>> It is not recognizing that the input is a dicom file. Is 4355-0005-1
>> a dicom file? Or is it a folder?
>>
>>
>> On 11/29/2016 05:51 PM, Douglas Merkitch wrote:
>>> Here is the command/output with the -debug flag:
>>>
>>> recon-all -debug -i
>>> /Volumes/JGG_WD_4TB_hard_drive_2/raw_data_UIC_3T/1039/raw_reordered/005-SAG_FSPGR_BRAVO_PURE/4355-0005-1
>>>  
>>>
>>> -i
>>> /Volumes/JGG_WD_4TB_hard_drive_2/raw_data_UIC_3T/1039/raw_reordered/006-SAG_FSPGR_BRAVO_PURE_REPEAT/4355-0006-1
>>>  
>>>
>>> -s 1039_test
>>> set echo = 1 ;
>>> breaksw
>>> breaksw
>>> end
>>> end
>>> while ( $#argv != 0 )
>>> while ( 6 != 0 )
>>>
>>> set flag = $argv[1] ; shift ;
>>> set flag = -i
>>> shift
>>>
>>> switch ( $flag )
>>> switch ( -i )
>>> if ( $#argv < 1 ) goto arg1err ;
>>> if ( 5 < 1 ) goto arg1err
>>> set InputVol = "$argv[1]" ; shift ;
>>> set InputVol =
>>> /Volumes/JGG_WD_4TB_hard_drive_2/raw_data_UIC_3T/1039/raw_reordered/005-SAG_FSPGR_BRAVO_PURE/4355-0005-1
>>> shift
>>> if ( ! -e "$InputVol" ) then
>>> if ( ! -e
>>> /Volumes/JGG_WD_4TB_hard_drive_2/raw_data_UIC_3T/1039/raw_reordered/005-SAG_FSPGR_BRAVO_PURE/4355-0005-1
>>>  
>>>
>>> ) then
>>> if ( -d "$InputVol" ) then
>>> if ( -d
>>> /Volumes/JGG_WD_4TB_hard_drive_2/raw_data_UIC_3T/1039/raw_reordered/005-SAG_FSPGR_BRAVO_PURE/4355-0005-1
>>>  
>>>
>>> ) then
>>> if ( ! -r "$InputVol" ) then
>>> if ( ! -r
>>> /Volumes/JGG_WD_4TB_hard_drive_2/raw_data_UIC_3T/1039/raw_reordered/005-SAG_FSPGR_BRAVO_PURE/4355-0005-1
>>>  
>>>
>>> ) then
>>> set InVolDir = `dirname  "$InputVol"` ;
>>> set InVolDir = `dirname  "$InputVol"`
>>> dirname
>>> /Volumes/JGG_WD_4TB_hard_drive_2/raw_data_UIC_3T/1039/raw_reordered/005-SAG_FSPGR_BRAVO_PURE/4355-0005-1
>>> set InVolBase = `basename "$InputVol"` ;
>>> set InVolBase = `basename "$InputVol"`
>>> basename
>>> /Volumes/JGG_WD_4TB_hard_drive_2/raw_data_UIC_3T/1039/raw_reordered/005-SAG_FSPGR_BRAVO_PURE/4355-0005-1
>>> pushd $InVolDir > /dev/null
>>> pushd
>>> /Volumes/JGG_WD_4TB_hard_drive_2/raw_data_UIC_3T/1039/raw_reordered/005-SAG_FSPGR_BRAVO_PURE
>>> set InVolDir = `pwd` ;
>>> set InVolDir = `pwd`
>>> pwd
>>> popd > /dev/null
>>> popd
>>> set InputVol = "$InVolDir/$InVolBase" ;
>>> set InputVol =
>>> /Volumes/JGG_WD_4TB_hard_drive_2/raw_data_UIC_3T/1039/raw_reordered/005-SAG_FSPGR_BRAVO_PURE/4355-0005-1
>>> set InputList = ( $InputList "$InputVol" ) ;
>>> set InputList = (
>>> /Volumes/JGG_WD_4TB_hard_drive_2/raw_data_UIC_3T/1039/raw_reordered/005-SAG_FSPGR_BRAVO_PURE/4355-0005-1
>>>  
>>>
>>> )
>>> set DoConvertInput = 1 ;
>>> set DoConvertInput = 1
>>> breaksw
>>> breaksw
>>> end
>>> end
>>> while ( $#argv != 0 )
>>> while ( 4 != 0 )
>>>
>>> set flag = $argv[1] ; shift ;
>>> set flag = -i
>>> shift
>>>
>>> switch ( $flag )
>>> switch ( -i )
>>> if ( $#argv < 1 ) goto arg1err ;
>>> if ( 3 < 1 ) goto arg1err
>>> set InputVol = "$argv[1]" ; shift ;
>>> set InputVol =
>>> /Volumes/JGG_WD_4TB_hard_drive_2/raw_data_UIC_3T/1039/raw_reordered/006-SAG_FSPGR_BRAVO_PURE_REPEAT/4355-0006-1
>>> shift
>>> if ( ! -e "$InputVol" ) then
>>> if ( ! -e
>>> /Volumes/JGG_WD_4TB_hard_drive_2/raw_data_UIC_3T/1039/raw_reordered/006-SAG_FSPGR_BRAVO_PURE_REPEAT/4355-0006-1
>>>  
>>>
>>> ) then
>>> if ( -d "$InputVol" ) then
>>> if ( -d
>>> /Volumes/JGG_WD_4TB_hard_drive_2/raw_data_UIC_3T/1039/raw_reordered/006-SAG_FSPGR_BRAVO_PURE_REPEAT/4355-0006-1
>>>  
>>>
>>> ) then
>>> if ( ! -r "$InputVol" ) then
>>> if ( ! -r
>>> /Volumes/JGG_WD_4TB_hard_drive_2/raw_data_UIC_3T/1039/raw_reordered/006-SAG_FSPGR_BRAVO_PURE_REPEAT/4355-0006-1
>>>  
>>>
>>> ) then
>>> set InVolDir = `dirname  "$InputVol"` ;
>>> set InVolDir = `dirname  "$InputVol"`
>>> dirname
>>> /Volumes/JGG_WD_4TB_hard_drive_2/raw_data_UIC_3T/1039/raw_reordered/006-SAG_FSPGR_BRAVO_PURE_REPEAT/4355-0006-1
>>> set InVolBase = `basename "$InputVol"` ;
>>> set InVolBase = `basename "$InputVol"`
>>> basename
>>> /Volumes/JGG_WD_4TB_hard_drive_2/raw_data_UIC_3T/1039/raw_reordered/006-SAG_FSPGR_BRAVO_PURE_REPEAT/4355-0006-1
>>> pushd $InVolDir > /dev/null
>>> pushd
>>> /Volumes/JGG_WD_4TB_hard_drive_2/raw_data_UIC_3T/1039/raw_reordered/006-SAG_FSPGR_BRAVO_PURE_REPEAT
>>> set InVolDir = `pwd` ;
>>> set InVolDir = `pwd`
>>> pwd
>>> popd

Re: [Freesurfer] ERROR: cannot find RB_all_2008-03-26.gca & Now DYLD Variables

2016-11-29 Thread Douglas N Greve 
It is not recognizing that the input is a dicom file. Is 4355-0005-1 
a dicom file? Or is it a folder?


On 11/29/2016 05:51 PM, Douglas Merkitch wrote:
> Here is the command/output with the -debug flag:
>
> recon-all -debug -i 
> /Volumes/JGG_WD_4TB_hard_drive_2/raw_data_UIC_3T/1039/raw_reordered/005-SAG_FSPGR_BRAVO_PURE/4355-0005-1
>  
> -i 
> /Volumes/JGG_WD_4TB_hard_drive_2/raw_data_UIC_3T/1039/raw_reordered/006-SAG_FSPGR_BRAVO_PURE_REPEAT/4355-0006-1
>  
> -s 1039_test
> set echo = 1 ;
> breaksw
> breaksw
> end
> end
> while ( $#argv != 0 )
> while ( 6 != 0 )
>
> set flag = $argv[1] ; shift ;
> set flag = -i
> shift
>
> switch ( $flag )
> switch ( -i )
> if ( $#argv < 1 ) goto arg1err ;
> if ( 5 < 1 ) goto arg1err
> set InputVol = "$argv[1]" ; shift ;
> set InputVol = 
> /Volumes/JGG_WD_4TB_hard_drive_2/raw_data_UIC_3T/1039/raw_reordered/005-SAG_FSPGR_BRAVO_PURE/4355-0005-1
> shift
> if ( ! -e "$InputVol" ) then
> if ( ! -e 
> /Volumes/JGG_WD_4TB_hard_drive_2/raw_data_UIC_3T/1039/raw_reordered/005-SAG_FSPGR_BRAVO_PURE/4355-0005-1
>  
> ) then
> if ( -d "$InputVol" ) then
> if ( -d 
> /Volumes/JGG_WD_4TB_hard_drive_2/raw_data_UIC_3T/1039/raw_reordered/005-SAG_FSPGR_BRAVO_PURE/4355-0005-1
>  
> ) then
> if ( ! -r "$InputVol" ) then
> if ( ! -r 
> /Volumes/JGG_WD_4TB_hard_drive_2/raw_data_UIC_3T/1039/raw_reordered/005-SAG_FSPGR_BRAVO_PURE/4355-0005-1
>  
> ) then
> set InVolDir = `dirname  "$InputVol"` ;
> set InVolDir = `dirname  "$InputVol"`
> dirname 
> /Volumes/JGG_WD_4TB_hard_drive_2/raw_data_UIC_3T/1039/raw_reordered/005-SAG_FSPGR_BRAVO_PURE/4355-0005-1
> set InVolBase = `basename "$InputVol"` ;
> set InVolBase = `basename "$InputVol"`
> basename 
> /Volumes/JGG_WD_4TB_hard_drive_2/raw_data_UIC_3T/1039/raw_reordered/005-SAG_FSPGR_BRAVO_PURE/4355-0005-1
> pushd $InVolDir > /dev/null
> pushd 
> /Volumes/JGG_WD_4TB_hard_drive_2/raw_data_UIC_3T/1039/raw_reordered/005-SAG_FSPGR_BRAVO_PURE
> set InVolDir = `pwd` ;
> set InVolDir = `pwd`
> pwd
> popd > /dev/null
> popd
> set InputVol = "$InVolDir/$InVolBase" ;
> set InputVol = 
> /Volumes/JGG_WD_4TB_hard_drive_2/raw_data_UIC_3T/1039/raw_reordered/005-SAG_FSPGR_BRAVO_PURE/4355-0005-1
> set InputList = ( $InputList "$InputVol" ) ;
> set InputList = ( 
> /Volumes/JGG_WD_4TB_hard_drive_2/raw_data_UIC_3T/1039/raw_reordered/005-SAG_FSPGR_BRAVO_PURE/4355-0005-1
>  
> )
> set DoConvertInput = 1 ;
> set DoConvertInput = 1
> breaksw
> breaksw
> end
> end
> while ( $#argv != 0 )
> while ( 4 != 0 )
>
> set flag = $argv[1] ; shift ;
> set flag = -i
> shift
>
> switch ( $flag )
> switch ( -i )
> if ( $#argv < 1 ) goto arg1err ;
> if ( 3 < 1 ) goto arg1err
> set InputVol = "$argv[1]" ; shift ;
> set InputVol = 
> /Volumes/JGG_WD_4TB_hard_drive_2/raw_data_UIC_3T/1039/raw_reordered/006-SAG_FSPGR_BRAVO_PURE_REPEAT/4355-0006-1
> shift
> if ( ! -e "$InputVol" ) then
> if ( ! -e 
> /Volumes/JGG_WD_4TB_hard_drive_2/raw_data_UIC_3T/1039/raw_reordered/006-SAG_FSPGR_BRAVO_PURE_REPEAT/4355-0006-1
>  
> ) then
> if ( -d "$InputVol" ) then
> if ( -d 
> /Volumes/JGG_WD_4TB_hard_drive_2/raw_data_UIC_3T/1039/raw_reordered/006-SAG_FSPGR_BRAVO_PURE_REPEAT/4355-0006-1
>  
> ) then
> if ( ! -r "$InputVol" ) then
> if ( ! -r 
> /Volumes/JGG_WD_4TB_hard_drive_2/raw_data_UIC_3T/1039/raw_reordered/006-SAG_FSPGR_BRAVO_PURE_REPEAT/4355-0006-1
>  
> ) then
> set InVolDir = `dirname  "$InputVol"` ;
> set InVolDir = `dirname  "$InputVol"`
> dirname 
> /Volumes/JGG_WD_4TB_hard_drive_2/raw_data_UIC_3T/1039/raw_reordered/006-SAG_FSPGR_BRAVO_PURE_REPEAT/4355-0006-1
> set InVolBase = `basename "$InputVol"` ;
> set InVolBase = `basename "$InputVol"`
> basename 
> /Volumes/JGG_WD_4TB_hard_drive_2/raw_data_UIC_3T/1039/raw_reordered/006-SAG_FSPGR_BRAVO_PURE_REPEAT/4355-0006-1
> pushd $InVolDir > /dev/null
> pushd 
> /Volumes/JGG_WD_4TB_hard_drive_2/raw_data_UIC_3T/1039/raw_reordered/006-SAG_FSPGR_BRAVO_PURE_REPEAT
> set InVolDir = `pwd` ;
> set InVolDir = `pwd`
> pwd
> popd > /dev/null
> popd
> set InputVol = "$InVolDir/$InVolBase" ;
> set InputVol = 
> /Volumes/JGG_WD_4TB_hard_drive_2/raw_data_UIC_3T/1039/raw_reordered/006-SAG_FSPGR_BRAVO_PURE_REPEAT/4355-0006-1
> set InputList = ( $InputList "$InputVol" ) ;
> set InputList = ( 
> /Volumes/JGG_WD_4TB_hard_drive_2/raw_data_UIC_3T/1039/raw_reordered/005-SAG_FSPGR_BRAVO_PURE/4355-0005-1
>  
> /Volumes/JGG_WD_4TB_hard_drive_2/raw_data_UIC_3T/1039/raw_reordered/006-SAG_FSPGR_BRAVO_PURE_REPEAT/4355-0006-1
>  
> )
> set DoConvertInput = 1 ;
> set DoConvertInput = 1
> breaksw
> breaksw
> end
> end
> while ( $#argv != 0 )
> while ( 2 != 0 )
>
> set flag = $argv[1] ; shift ;
> set flag = -s
> shift
>
> switch ( $flag )
> switch ( -s )
> if ( $#argv < 1 ) goto arg1err ;
> if ( 1 < 1 ) goto arg1err
> set subjid = $argv[1] ; shift ;
> set subjid = 1039_test
> shift
> set subjid = `basename $subjid` ;
> set subjid = `basename $subjid`
> basename 1039_test
> breaksw
> breaksw
> end
> end
> wh

Re: [Freesurfer] ERROR: cannot find RB_all_2008-03-26.gca & Now DYLD Variables

2016-11-29 Thread Douglas N Greve 
Can you run it with -debug and send the terminal output?


On 11/29/2016 05:39 PM, Douglas Merkitch wrote:
> Hello Bruce & Doug,
>
> There are no spaces in the filenames (just a lot of underscores and 
> dashes!).
>
> I don't think it's a permissions issue because it is able to write the 
> first of the two files that I input (regardless of which one I feed it 
> first), but fails to write the second file (what would be 002.mgz). My 
> current work around is to set it up as two different subjects for the 
> dicom conversion and then copy and rename one of the T1 outputs to 
> 002.mgz. I am currently processing this subject through the recon-all 
> -all pipeline after employing this work around, which suggests to me 
> that it's not a permissions issue?
>
> Thanks,
>
> Doug
>
> Douglas Merkitch
> Neurological Sciences
> Rush University Medical Center
> Phone: (312) 563-3853 
> Fax: (312) 563-4660 
> Email: douglas_merki...@rush.edu 
>
>
>
>
>
> On Nov 29, 2016, at 4:15 PM, Douglas N Greve 
> mailto:gr...@nmr.mgh.harvard.edu>>
>  wrote:
>
>> Do you have write permission into that folder, ie,
>> /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T/1039/mri/orig ? Can
>> you run it with -debug as the first argument and send the terminal 
>> output?
>>
>>
>> On 11/29/2016 05:00 PM, Douglas Merkitch wrote:
>>> Hello again,
>>>
>>> I did, in fact, encounter another error that resulted in only the
>>> first mri/orig/001.mgz and not the mr/orig/002.mgz file to be written.
>>> Below is the command line and terminal output:
>>>
>>>
>>> ===
>>> recon-all -i
>>> /Volumes/JGG_WD_4TB_hard_drive_2/raw_data_UIC_3T/1039/raw_reordered/005-SAG_FSPGR_BRAVO_PURE/4355-0005-1
>>>  
>>>
>>> -i
>>> /Volumes/JGG_WD_4TB_hard_drive_2/raw_data_UIC_3T/1039/raw_reordered/006-SAG_FSPGR_BRAVO_PURE_REPEAT/4355-0006-1
>>>  
>>>
>>> -s 1039
>>> Subject Stamp: freesurfer-Darwin-OSX-stable-v6-beta-20161116-5037eae
>>> Current Stamp: freesurfer-Darwin-OSX-stable-v6-beta-20161116-5037eae
>>> INFO: SUBJECTS_DIR is 
>>> /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T
>>> Actual FREESURFER_HOME /Applications/freesurfer_v6beta_16Nov2016
>>> Darwin glenn-stebbins-computer.local 12.6.0 Darwin Kernel Version
>>> 12.6.0: Wed Mar 18 16:23:48 PDT 2015;
>>> root:xnu-2050.48.19~1/RELEASE_X86_64 x86_64
>>> dyld: DYLD_ environment variables being ignored because main
>>> executable (/usr/bin/top) is setuid or setgid
>>> /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T/1039
>>> \n mri_convert
>>> /Volumes/JGG_WD_4TB_hard_drive_2/raw_data_UIC_3T/1039/raw_reordered/005-SAG_FSPGR_BRAVO_PURE/4355-0005-1
>>>  
>>>
>>> /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T/1039/mri/orig/001.mgz 
>>>
>>> \n
>>> mri_convert.bin
>>> /Volumes/JGG_WD_4TB_hard_drive_2/raw_data_UIC_3T/1039/raw_reordered/005-SAG_FSPGR_BRAVO_PURE/4355-0005-1
>>>  
>>>
>>> /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T/1039/mri/orig/001.mgz 
>>>
>>>
>>> $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $
>>> reading from
>>> /Volumes/JGG_WD_4TB_hard_drive_2/raw_data_UIC_3T/1039/raw_reordered/005-SAG_FSPGR_BRAVO_PURE/4355-0005-1...
>>> Starting DICOMRead2()
>>> dcmfile =
>>> /Volumes/JGG_WD_4TB_hard_drive_2/raw_data_UIC_3T/1039/raw_reordered/005-SAG_FSPGR_BRAVO_PURE/4355-0005-1
>>> dcmdir =
>>> /Volumes/JGG_WD_4TB_hard_drive_2/raw_data_UIC_3T/1039/raw_reordered/005-SAG_FSPGR_BRAVO_PURE
>>> Ref Series No = 5
>>> Found 138 files, checking for dicoms
>>> Found 136 dicom files in series.
>>> First Sorting
>>> Computing Slice Direction
>>> Vs: -1.2 0 0
>>> Vs: -1 0 0
>>> Second Sorting
>>> IsDWI = 0, IsPhilipsDWI = 0
>>> Counting frames
>>> nframes = 1
>>> nslices = 136
>>> ndcmfiles = 136
>>> PE Dir = ROW (dicom read)
>>> Loading pixel data
>>> TR=9.23, TE=3.72, TI=450.00, flip angle=13.00
>>> i_ras = (0, -1, 0)
>>> j_ras = (0, 0, -1)
>>> k_ras = (1, -0, 0)
>>> writing to
>>> /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T/1039/mri/orig/001.mgz...
>>> if: Expression Syntax.
>>> ===
>>>
>>> I did a quick search of the mail archives involving Mac and dyld
>>> variables, and it seems like this may be something that you may
>>> provide a fix for?
>>>
>>>
>>> Thanks,
>>>
>>> Doug
>>>
>>> Douglas Merkitch
>>> Neurological Sciences
>>> Rush University Medical Center
>>> Phone: (312) 563-3853 
>>> Fax: (312) 563-4660 
>>> Email: douglas_merki...@rush.edu  
>>> 
>>>
>>>
>>>
>>>
>>>
>>> On Nov 29, 2016, at 3:36 PM, Z K >> 
>>> >
>>> wrote:
>>>
 Hello Douglas,

 Any chance you can upload the two data files
 005-SAG_FSPGR_BRAVO_PURE/4355-0005-1 and 4355-0006-1:

 https://urldefense.proofpoint.com/v2/url?u=https-3A__surfer.nmr.mgh.harvard.edu_fswiki_FtpFileExchange&d=DgIBAg&c=XxU8ngzB_WPJXKyiin_6iQ&r=GRn28rC6ssBi3WYtpTHXUZZiKgdhzFrFkzz7_Ref9iw&m=tZ1

Re: [Freesurfer] ERROR: cannot find RB_all_2008-03-26.gca & Now DYLD Variables

2016-11-29 Thread Douglas Merkitch 
Hello Bruce & Doug,

There are no spaces in the filenames (just a lot of underscores and dashes!).

I don't think it's a permissions issue because it is able to write the first of 
the two files that I input (regardless of which one I feed it first), but fails 
to write the second file (what would be 002.mgz). My current work around is to 
set it up as two different subjects for the dicom conversion and then copy and 
rename one of the T1 outputs to 002.mgz. I am currently processing this subject 
through the recon-all -all pipeline after employing this work around, which 
suggests to me that it's not a permissions issue?

Thanks,

Doug

Douglas Merkitch
Neurological Sciences
Rush University Medical Center
Phone: (312) 563-3853
Fax: (312) 563-4660
Email: douglas_merki...@rush.edu





On Nov 29, 2016, at 4:15 PM, Douglas N Greve 
mailto:gr...@nmr.mgh.harvard.edu>>
 wrote:

Do you have write permission into that folder, ie,
/Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T/1039/mri/orig ? Can
you run it with -debug as the first argument and send the terminal output?


On 11/29/2016 05:00 PM, Douglas Merkitch wrote:
Hello again,

I did, in fact, encounter another error that resulted in only the
first mri/orig/001.mgz and not the mr/orig/002.mgz file to be written.
Below is the command line and terminal output:


===
recon-all -i
/Volumes/JGG_WD_4TB_hard_drive_2/raw_data_UIC_3T/1039/raw_reordered/005-SAG_FSPGR_BRAVO_PURE/4355-0005-1
-i
/Volumes/JGG_WD_4TB_hard_drive_2/raw_data_UIC_3T/1039/raw_reordered/006-SAG_FSPGR_BRAVO_PURE_REPEAT/4355-0006-1
-s 1039
Subject Stamp: freesurfer-Darwin-OSX-stable-v6-beta-20161116-5037eae
Current Stamp: freesurfer-Darwin-OSX-stable-v6-beta-20161116-5037eae
INFO: SUBJECTS_DIR is /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T
Actual FREESURFER_HOME /Applications/freesurfer_v6beta_16Nov2016
Darwin glenn-stebbins-computer.local 12.6.0 Darwin Kernel Version
12.6.0: Wed Mar 18 16:23:48 PDT 2015;
root:xnu-2050.48.19~1/RELEASE_X86_64 x86_64
dyld: DYLD_ environment variables being ignored because main
executable (/usr/bin/top) is setuid or setgid
/Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T/1039
\n mri_convert
/Volumes/JGG_WD_4TB_hard_drive_2/raw_data_UIC_3T/1039/raw_reordered/005-SAG_FSPGR_BRAVO_PURE/4355-0005-1
/Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T/1039/mri/orig/001.mgz
\n
mri_convert.bin
/Volumes/JGG_WD_4TB_hard_drive_2/raw_data_UIC_3T/1039/raw_reordered/005-SAG_FSPGR_BRAVO_PURE/4355-0005-1
/Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T/1039/mri/orig/001.mgz

$Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $
reading from
/Volumes/JGG_WD_4TB_hard_drive_2/raw_data_UIC_3T/1039/raw_reordered/005-SAG_FSPGR_BRAVO_PURE/4355-0005-1...
Starting DICOMRead2()
dcmfile =
/Volumes/JGG_WD_4TB_hard_drive_2/raw_data_UIC_3T/1039/raw_reordered/005-SAG_FSPGR_BRAVO_PURE/4355-0005-1
dcmdir =
/Volumes/JGG_WD_4TB_hard_drive_2/raw_data_UIC_3T/1039/raw_reordered/005-SAG_FSPGR_BRAVO_PURE
Ref Series No = 5
Found 138 files, checking for dicoms
Found 136 dicom files in series.
First Sorting
Computing Slice Direction
Vs: -1.2 0 0
Vs: -1 0 0
Second Sorting
IsDWI = 0, IsPhilipsDWI = 0
Counting frames
nframes = 1
nslices = 136
ndcmfiles = 136
PE Dir = ROW (dicom read)
Loading pixel data
TR=9.23, TE=3.72, TI=450.00, flip angle=13.00
i_ras = (0, -1, 0)
j_ras = (0, 0, -1)
k_ras = (1, -0, 0)
writing to
/Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T/1039/mri/orig/001.mgz...
if: Expression Syntax.
===

I did a quick search of the mail archives involving Mac and dyld
variables, and it seems like this may be something that you may
provide a fix for?


Thanks,

Doug

Douglas Merkitch
Neurological Sciences
Rush University Medical Center
Phone: (312) 563-3853 
Fax: (312) 563-4660 
Email: douglas_merki...@rush.edu 






On Nov 29, 2016, at 3:36 PM, Z K 
mailto:zkauf...@nmr.mgh.harvard.edu>
>
wrote:

Hello Douglas,

Any chance you can upload the two data files
005-SAG_FSPGR_BRAVO_PURE/4355-0005-1 and 4355-0006-1:

https://urldefense.proofpoint.com/v2/url?u=https-3A__surfer.nmr.mgh.harvard.edu_fswiki_FtpFileExchange&d=DgIBAg&c=XxU8ngzB_WPJXKyiin_6iQ&r=GRn28rC6ssBi3WYtpTHXUZZiKgdhzFrFkzz7_Ref9iw&m=tZ1yGlSjLRqbYLtgmRPVoSSCpQd1kptkk2pxdtqLxSM&s=t6LIHJ4FymbrNntHP5rjaeG3EwBFHeEkINY_hAxr--w&e=


Ide like to try and reproduce this. Thanks.

-Zeke




On 11/29/2016 04:20 PM, Douglas Merkitch wrote:
Hello Doug,

Command line & terminal output:

recon-all -i
/Volumes/JGG_WD_4TB_hard_drive_2/raw_data_UIC_3T/1039/raw_reordered/005-SAG_FSPGR_BRAVO_PURE/4355-0005-1
-i
/Volumes/JGG_WD_4TB_hard_drive_2/raw_data_UIC_3T/1039/raw_reordered/006-SAG_FSPGR_BRAVO_PURE_REPEAT/4355-0006-1
-s 1039
ERROR: cannot find
/Applications/freesurfer_v6beta_16Nov2016/average/RB_all_2008-03-26.gca

I do have the following simil

Re: [Freesurfer] ERROR: cannot find RB_all_2008-03-26.gca & Now DYLD Variables

2016-11-29 Thread Douglas N Greve 
Do you have write permission into that folder, ie, 
/Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T/1039/mri/orig ? Can 
you run it with -debug as the first argument and send the terminal output?


On 11/29/2016 05:00 PM, Douglas Merkitch wrote:
> Hello again,
>
> I did, in fact, encounter another error that resulted in only the 
> first mri/orig/001.mgz and not the mr/orig/002.mgz file to be written. 
> Below is the command line and terminal output:
>
>
> ===
> recon-all -i 
> /Volumes/JGG_WD_4TB_hard_drive_2/raw_data_UIC_3T/1039/raw_reordered/005-SAG_FSPGR_BRAVO_PURE/4355-0005-1
>  
> -i 
> /Volumes/JGG_WD_4TB_hard_drive_2/raw_data_UIC_3T/1039/raw_reordered/006-SAG_FSPGR_BRAVO_PURE_REPEAT/4355-0006-1
>  
> -s 1039
> Subject Stamp: freesurfer-Darwin-OSX-stable-v6-beta-20161116-5037eae
> Current Stamp: freesurfer-Darwin-OSX-stable-v6-beta-20161116-5037eae
> INFO: SUBJECTS_DIR is /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T
> Actual FREESURFER_HOME /Applications/freesurfer_v6beta_16Nov2016
> Darwin glenn-stebbins-computer.local 12.6.0 Darwin Kernel Version 
> 12.6.0: Wed Mar 18 16:23:48 PDT 2015; 
> root:xnu-2050.48.19~1/RELEASE_X86_64 x86_64
> dyld: DYLD_ environment variables being ignored because main 
> executable (/usr/bin/top) is setuid or setgid
> /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T/1039
> \n mri_convert 
> /Volumes/JGG_WD_4TB_hard_drive_2/raw_data_UIC_3T/1039/raw_reordered/005-SAG_FSPGR_BRAVO_PURE/4355-0005-1
>  
> /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T/1039/mri/orig/001.mgz 
> \n
> mri_convert.bin 
> /Volumes/JGG_WD_4TB_hard_drive_2/raw_data_UIC_3T/1039/raw_reordered/005-SAG_FSPGR_BRAVO_PURE/4355-0005-1
>  
> /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T/1039/mri/orig/001.mgz 
>
> $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $
> reading from 
> /Volumes/JGG_WD_4TB_hard_drive_2/raw_data_UIC_3T/1039/raw_reordered/005-SAG_FSPGR_BRAVO_PURE/4355-0005-1...
> Starting DICOMRead2()
> dcmfile = 
> /Volumes/JGG_WD_4TB_hard_drive_2/raw_data_UIC_3T/1039/raw_reordered/005-SAG_FSPGR_BRAVO_PURE/4355-0005-1
> dcmdir = 
> /Volumes/JGG_WD_4TB_hard_drive_2/raw_data_UIC_3T/1039/raw_reordered/005-SAG_FSPGR_BRAVO_PURE
> Ref Series No = 5
> Found 138 files, checking for dicoms
> Found 136 dicom files in series.
> First Sorting
> Computing Slice Direction
> Vs: -1.2 0 0
> Vs: -1 0 0
> Second Sorting
> IsDWI = 0, IsPhilipsDWI = 0
> Counting frames
> nframes = 1
> nslices = 136
> ndcmfiles = 136
> PE Dir = ROW (dicom read)
> Loading pixel data
> TR=9.23, TE=3.72, TI=450.00, flip angle=13.00
> i_ras = (0, -1, 0)
> j_ras = (0, 0, -1)
> k_ras = (1, -0, 0)
> writing to 
> /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T/1039/mri/orig/001.mgz...
> if: Expression Syntax.
> ===
>
> I did a quick search of the mail archives involving Mac and dyld 
> variables, and it seems like this may be something that you may 
> provide a fix for?
>
>
> Thanks,
>
> Doug
>
> Douglas Merkitch
> Neurological Sciences
> Rush University Medical Center
> Phone: (312) 563-3853 
> Fax: (312) 563-4660 
> Email: douglas_merki...@rush.edu 
>
>
>
>
>
> On Nov 29, 2016, at 3:36 PM, Z K  >
>  wrote:
>
>> Hello Douglas,
>>
>> Any chance you can upload the two data files
>> 005-SAG_FSPGR_BRAVO_PURE/4355-0005-1 and 4355-0006-1:
>>
>> https://urldefense.proofpoint.com/v2/url?u=https-3A__surfer.nmr.mgh.harvard.edu_fswiki_FtpFileExchange&d=DgIBAg&c=XxU8ngzB_WPJXKyiin_6iQ&r=GRn28rC6ssBi3WYtpTHXUZZiKgdhzFrFkzz7_Ref9iw&m=tZ1yGlSjLRqbYLtgmRPVoSSCpQd1kptkk2pxdtqLxSM&s=t6LIHJ4FymbrNntHP5rjaeG3EwBFHeEkINY_hAxr--w&e=
>>  
>>
>>
>> Ide like to try and reproduce this. Thanks.
>>
>> -Zeke
>>
>>
>>
>>
>> On 11/29/2016 04:20 PM, Douglas Merkitch wrote:
>>> Hello Doug,
>>>
>>> Command line & terminal output:
>>>
>>> recon-all -i
>>> /Volumes/JGG_WD_4TB_hard_drive_2/raw_data_UIC_3T/1039/raw_reordered/005-SAG_FSPGR_BRAVO_PURE/4355-0005-1
>>> -i
>>> /Volumes/JGG_WD_4TB_hard_drive_2/raw_data_UIC_3T/1039/raw_reordered/006-SAG_FSPGR_BRAVO_PURE_REPEAT/4355-0006-1
>>> -s 1039
>>> ERROR: cannot find
>>> /Applications/freesurfer_v6beta_16Nov2016/average/RB_all_2008-03-26.gca
>>>
>>> I do have the following similarly-named files in the v6 beta average
>>> directory:
>>> RB_all_2008-03-26.mni152.2mm.lta
>>> RB_all_2016-05-10.vc700.gca
>>> RB_all_withskull_2016-05-10.vc700.gca
>>>
>>> Thanks for the prompt response!
>>>
>>> Thanks,
>>>
>>> Doug
>>>
>>> Douglas Merkitch
>>> Neurological Sciences
>>> Rush University Medical Center
>>> Email: douglas_merki...@rush.edu  
>>> 
>>>
>>>
>>>
>>>
>>>
>>> On Nov 29, 2016, at 3:12 PM, Douglas N Greve 
>>> mailto:gr...@nmr.mgh.harvard.edu>
>>> > wrote:
>>>
 can you send your command line and full terminal output?


 On 11/29/2016 04:10 PM, Douglas Merki

Re: [Freesurfer] ERROR: cannot find RB_all_2008-03-26.gca & Now DYLD Variables

2016-11-29 Thread Bruce Fischl 

Hi Doug

do you have any spaces in your filenames? That can cause this kind of 
thing. It's hard to tell from your email



cheers
Bruce
On Tue, 29 Nov 2016, Douglas Merkitch wrote:


Hello again,
I did, in fact, encounter another error that resulted in only the first 
mri/orig/001.mgz
and not the mr/orig/002.mgz file to be written. Below is the command line and 
terminal
output:


===
recon-all 
-i/Volumes/JGG_WD_4TB_hard_drive_2/raw_data_UIC_3T/1039/raw_reordered/005-SAG_FSPGR_BRAVO_
PURE/4355-0005-1 
-i/Volumes/JGG_WD_4TB_hard_drive_2/raw_data_UIC_3T/1039/raw_reordered/006-SAG_FSPGR_BRAVO_
PURE_REPEAT/4355-0006-1 -s 1039
Subject Stamp: freesurfer-Darwin-OSX-stable-v6-beta-20161116-5037eae
Current Stamp: freesurfer-Darwin-OSX-stable-v6-beta-20161116-5037eae
INFO: SUBJECTS_DIR is /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T
Actual FREESURFER_HOME /Applications/freesurfer_v6beta_16Nov2016
Darwin glenn-stebbins-computer.local 12.6.0 Darwin Kernel Version 12.6.0: Wed 
Mar 18
16:23:48 PDT 2015; root:xnu-2050.48.19~1/RELEASE_X86_64 x86_64
dyld: DYLD_ environment variables being ignored because main executable 
(/usr/bin/top) is
setuid or setgid
/Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T/1039
\n 
mri_convert/Volumes/JGG_WD_4TB_hard_drive_2/raw_data_UIC_3T/1039/raw_reordered/005-SAG_FSPGR_BRAVO_
PURE/4355-0005-1
/Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T/1039/mri/orig/001.mgz \n
mri_convert.bin/Volumes/JGG_WD_4TB_hard_drive_2/raw_data_UIC_3T/1039/raw_reordered/005-SAG_FSPGR_BRAVO_
PURE/4355-0005-1
/Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T/1039/mri/orig/001.mgz 
$Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $
reading 
from/Volumes/JGG_WD_4TB_hard_drive_2/raw_data_UIC_3T/1039/raw_reordered/005-SAG_FSPGR_BRAVO_
PURE/4355-0005-1...
Starting DICOMRead2()
dcmfile 
=/Volumes/JGG_WD_4TB_hard_drive_2/raw_data_UIC_3T/1039/raw_reordered/005-SAG_FSPGR_BRAVO_
PURE/4355-0005-1
dcmdir 
=/Volumes/JGG_WD_4TB_hard_drive_2/raw_data_UIC_3T/1039/raw_reordered/005-SAG_FSPGR_BRAVO_
PURE
Ref Series No = 5
Found 138 files, checking for dicoms
Found 136 dicom files in series.
First Sorting
Computing Slice Direction
Vs: -1.2 0 0
Vs: -1 0 0
Second Sorting
IsDWI = 0, IsPhilipsDWI = 0
Counting frames
nframes = 1
nslices = 136
ndcmfiles = 136
PE Dir = ROW (dicom read)
Loading pixel data
TR=9.23, TE=3.72, TI=450.00, flip angle=13.00
i_ras = (0, -1, 0)
j_ras = (0, 0, -1)
k_ras = (1, -0, 0)
writing to 
/Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T/1039/mri/orig/001.mgz...
if: Expression Syntax.
===

I did a quick search of the mail archives involving Mac and dyld variables, and 
it seems
like this may be something that you may provide a fix for? 


Thanks,

Doug

Douglas Merkitch
Neurological Sciences
Rush University Medical Center
Phone: (312) 563-3853
Fax: (312) 563-4660
Email: douglas_merki...@rush.edu





On Nov 29, 2016, at 3:36 PM, Z K 
 wrote:

  Hello Douglas,

  Any chance you can upload the two data files
  005-SAG_FSPGR_BRAVO_PURE/4355-0005-1 and 4355-0006-1:

  
https://urldefense.proofpoint.com/v2/url?u=https-3A__surfer.nmr.mgh.harvard.edu_fswiki
_FtpFileExchange&d=DgIBAg&c=XxU8ngzB_WPJXKyiin_6iQ&r=GRn28rC6ssBi3WYtpTHXUZZiKgdhzFrFkzz
7_Ref9iw&m=tZ1yGlSjLRqbYLtgmRPVoSSCpQd1kptkk2pxdtqLxSM&s=t6LIHJ4FymbrNntHP5rjaeG3EwBFHeE
  kINY_hAxr--w&e=

  Ide like to try and reproduce this. Thanks.

  -Zeke




  On 11/29/2016 04:20 PM, Douglas Merkitch wrote:
Hello Doug,

Command line & terminal output:

recon-all -i
/Volumes/JGG_WD_4TB_hard_drive_2/raw_data_UIC_3T/1039/raw_reordered/005-SAG_FSPGR_BRAVO_
PURE/4355-0005-1
-i
/Volumes/JGG_WD_4TB_hard_drive_2/raw_data_UIC_3T/1039/raw_reordered/006-SAG_FSPGR_BRAVO_
PURE_REPEAT/4355-0006-1
-s 1039
ERROR: cannot find

/Applications/freesurfer_v6beta_16Nov2016/average/RB_all_2008-03-26.gca

I do have the following similarly-named files in the v6 beta
average
directory:
RB_all_2008-03-26.mni152.2mm.lta
RB_all_2016-05-10.vc700.gca
RB_all_withskull_2016-05-10.vc700.gca

Thanks for the prompt response!

Thanks,

Doug

Douglas Merkitch
Neurological Sciences
Rush University Medical Center
Email: douglas_merki...@rush.edu






On Nov 29, 2016, at 3:12 PM, Douglas N Greve
mailto:gr...@nmr.mgh.harvard.edu>> wrote:

  can you send your command line and full terminal
  output?


  On 11/29/2016 04:10 PM, Douglas Merkitch wrote:
Hello experts,

I was attempting to test out the
freesurfer v6 beta and encountered

Re: [Freesurfer] ERROR: cannot find RB_all_2008-03-26.gca & Now DYLD Variables

2016-11-29 Thread Douglas Merkitch 
Hello again,

I did, in fact, encounter another error that resulted in only the first 
mri/orig/001.mgz and not the mr/orig/002.mgz file to be written. Below is the 
command line and terminal output:


===
recon-all -i 
/Volumes/JGG_WD_4TB_hard_drive_2/raw_data_UIC_3T/1039/raw_reordered/005-SAG_FSPGR_BRAVO_PURE/4355-0005-1
 -i 
/Volumes/JGG_WD_4TB_hard_drive_2/raw_data_UIC_3T/1039/raw_reordered/006-SAG_FSPGR_BRAVO_PURE_REPEAT/4355-0006-1
 -s 1039
Subject Stamp: freesurfer-Darwin-OSX-stable-v6-beta-20161116-5037eae
Current Stamp: freesurfer-Darwin-OSX-stable-v6-beta-20161116-5037eae
INFO: SUBJECTS_DIR is /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T
Actual FREESURFER_HOME /Applications/freesurfer_v6beta_16Nov2016
Darwin glenn-stebbins-computer.local 12.6.0 Darwin Kernel Version 12.6.0: Wed 
Mar 18 16:23:48 PDT 2015; root:xnu-2050.48.19~1/RELEASE_X86_64 x86_64
dyld: DYLD_ environment variables being ignored because main executable 
(/usr/bin/top) is setuid or setgid
/Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T/1039
\n mri_convert 
/Volumes/JGG_WD_4TB_hard_drive_2/raw_data_UIC_3T/1039/raw_reordered/005-SAG_FSPGR_BRAVO_PURE/4355-0005-1
 /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T/1039/mri/orig/001.mgz \n
mri_convert.bin 
/Volumes/JGG_WD_4TB_hard_drive_2/raw_data_UIC_3T/1039/raw_reordered/005-SAG_FSPGR_BRAVO_PURE/4355-0005-1
 /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T/1039/mri/orig/001.mgz
$Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $
reading from 
/Volumes/JGG_WD_4TB_hard_drive_2/raw_data_UIC_3T/1039/raw_reordered/005-SAG_FSPGR_BRAVO_PURE/4355-0005-1...
Starting DICOMRead2()
dcmfile = 
/Volumes/JGG_WD_4TB_hard_drive_2/raw_data_UIC_3T/1039/raw_reordered/005-SAG_FSPGR_BRAVO_PURE/4355-0005-1
dcmdir = 
/Volumes/JGG_WD_4TB_hard_drive_2/raw_data_UIC_3T/1039/raw_reordered/005-SAG_FSPGR_BRAVO_PURE
Ref Series No = 5
Found 138 files, checking for dicoms
Found 136 dicom files in series.
First Sorting
Computing Slice Direction
Vs: -1.2 0 0
Vs: -1 0 0
Second Sorting
IsDWI = 0, IsPhilipsDWI = 0
Counting frames
nframes = 1
nslices = 136
ndcmfiles = 136
PE Dir = ROW (dicom read)
Loading pixel data
TR=9.23, TE=3.72, TI=450.00, flip angle=13.00
i_ras = (0, -1, 0)
j_ras = (0, 0, -1)
k_ras = (1, -0, 0)
writing to 
/Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T/1039/mri/orig/001.mgz...
if: Expression Syntax.
===

I did a quick search of the mail archives involving Mac and dyld variables, and 
it seems like this may be something that you may provide a fix for?


Thanks,

Doug

Douglas Merkitch
Neurological Sciences
Rush University Medical Center
Phone: (312) 563-3853
Fax: (312) 563-4660
Email: douglas_merki...@rush.edu





On Nov 29, 2016, at 3:36 PM, Z K 
mailto:zkauf...@nmr.mgh.harvard.edu>>
 wrote:

Hello Douglas,

Any chance you can upload the two data files
005-SAG_FSPGR_BRAVO_PURE/4355-0005-1 and 4355-0006-1:

  
https://urldefense.proofpoint.com/v2/url?u=https-3A__surfer.nmr.mgh.harvard.edu_fswiki_FtpFileExchange&d=DgIBAg&c=XxU8ngzB_WPJXKyiin_6iQ&r=GRn28rC6ssBi3WYtpTHXUZZiKgdhzFrFkzz7_Ref9iw&m=tZ1yGlSjLRqbYLtgmRPVoSSCpQd1kptkk2pxdtqLxSM&s=t6LIHJ4FymbrNntHP5rjaeG3EwBFHeEkINY_hAxr--w&e=

Ide like to try and reproduce this. Thanks.

-Zeke




On 11/29/2016 04:20 PM, Douglas Merkitch wrote:
Hello Doug,

Command line & terminal output:

recon-all -i
/Volumes/JGG_WD_4TB_hard_drive_2/raw_data_UIC_3T/1039/raw_reordered/005-SAG_FSPGR_BRAVO_PURE/4355-0005-1
-i
/Volumes/JGG_WD_4TB_hard_drive_2/raw_data_UIC_3T/1039/raw_reordered/006-SAG_FSPGR_BRAVO_PURE_REPEAT/4355-0006-1
-s 1039
ERROR: cannot find
/Applications/freesurfer_v6beta_16Nov2016/average/RB_all_2008-03-26.gca

I do have the following similarly-named files in the v6 beta average
directory:
RB_all_2008-03-26.mni152.2mm.lta
RB_all_2016-05-10.vc700.gca
RB_all_withskull_2016-05-10.vc700.gca

Thanks for the prompt response!

Thanks,

Doug

Douglas Merkitch
Neurological Sciences
Rush University Medical Center
Email: douglas_merki...@rush.edu 






On Nov 29, 2016, at 3:12 PM, Douglas N Greve 
mailto:gr...@nmr.mgh.harvard.edu>
> wrote:

can you send your command line and full terminal output?


On 11/29/2016 04:10 PM, Douglas Merkitch wrote:
Hello experts,

I was attempting to test out the freesurfer v6 beta and encountered
the following error during dicom conversion: "ERROR: cannot find
/Applications/freesurfer_v6beta_16Nov2016/average/RB_all_2008-03-26.gca".

I'm currently
running freesurfer-Darwin-OSX-stable-v6-beta-20161116-5037eae on a Mac
Pro (3.33 GHz 6-Core Intel Xeon) with OS X 10.8.5.

Any help would be greatly appreciated!

Thanks,

Doug

Douglas Merkitch
Neurological Sciences
Rush University Medical Center
Phone: (312) 563-3853 
Fax: (312) 563-4660 
Email: douglas_merki...@rush.edu

Re: [Freesurfer] ERROR: cannot find RB_all_2008-03-26.gca

2016-11-29 Thread Douglas Merkitch 
Hello,

Sorry for the confusion - the problem was that, while I had changed the 
$FREESURFER_HOME variable in the mac terminal, I still had the older freesurfer 
version sourced in my .bashrc file. Once I updated that file, the conversion 
went on without error.

Thanks again for the prompt response and I apologize for my error.

Thanks,

Doug

Douglas Merkitch
Neurological Sciences
Rush University Medical Center
Phone: (312) 563-3853
Fax: (312) 563-4660
Email: douglas_merki...@rush.edu





On Nov 29, 2016, at 3:20 PM, Douglas Merkitch 
mailto:douglas_merki...@rush.edu>> wrote:

Hello Doug,

Command line & terminal output:

recon-all -i 
/Volumes/JGG_WD_4TB_hard_drive_2/raw_data_UIC_3T/1039/raw_reordered/005-SAG_FSPGR_BRAVO_PURE/4355-0005-1
 -i 
/Volumes/JGG_WD_4TB_hard_drive_2/raw_data_UIC_3T/1039/raw_reordered/006-SAG_FSPGR_BRAVO_PURE_REPEAT/4355-0006-1
 -s 1039
ERROR: cannot find 
/Applications/freesurfer_v6beta_16Nov2016/average/RB_all_2008-03-26.gca

I do have the following similarly-named files in the v6 beta average directory:
RB_all_2008-03-26.mni152.2mm.lta
RB_all_2016-05-10.vc700.gca
RB_all_withskull_2016-05-10.vc700.gca

Thanks for the prompt response!

Thanks,

Doug

Douglas Merkitch
Neurological Sciences
Rush University Medical Center
Email: douglas_merki...@rush.edu





On Nov 29, 2016, at 3:12 PM, Douglas N Greve 
mailto:gr...@nmr.mgh.harvard.edu>> wrote:

can you send your command line and full terminal output?


On 11/29/2016 04:10 PM, Douglas Merkitch wrote:
Hello experts,

I was attempting to test out the freesurfer v6 beta and encountered
the following error during dicom conversion: "ERROR: cannot find
/Applications/freesurfer_v6beta_16Nov2016/average/RB_all_2008-03-26.gca".

I'm currently
running freesurfer-Darwin-OSX-stable-v6-beta-20161116-5037eae on a Mac
Pro (3.33 GHz 6-Core Intel Xeon) with OS X 10.8.5.

Any help would be greatly appreciated!

Thanks,

Doug

Douglas Merkitch
Neurological Sciences
Rush University Medical Center
Phone: (312) 563-3853 
Fax: (312) 563-4660 
Email: douglas_merki...@rush.edu 








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--
Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: 
https://urldefense.proofpoint.com/v2/url?u=https-3A__gate.nmr.mgh.harvard.edu_filedrop2&d=DgIBAg&c=XxU8ngzB_WPJXKyiin_6iQ&r=GRn28rC6ssBi3WYtpTHXUZZiKgdhzFrFkzz7_Ref9iw&m=RYoN0GgWPi9MuiSoN-_tC7n3EM0X-3w27aQb4YV8g_0&s=5c8BG0jWHPLzpY6NB7Qaxm6jR1KlRb-uxt-ubzqrV9U&e=
www.nmr.mgh.harvard.edu/facility/filedrop/index.html
Outgoing: 
https://urldefense.proofpoint.com/v2/url?u=ftp-3A__surfer.nmr.mgh.harvard.edu_transfer_outgoing_flat_greve_&d=DgIBAg&c=XxU8ngzB_WPJXKyiin_6iQ&r=GRn28rC6ssBi3WYtpTHXUZZiKgdhzFrFkzz7_Ref9iw&m=RYoN0GgWPi9MuiSoN-_tC7n3EM0X-3w27aQb4YV8g_0&s=q36YAeWf40aDIu00LgaqEQKGoZ6iygWUhdUQLvWflDo&e=

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Re: [Freesurfer] ERROR: cannot find RB_all_2008-03-26.gca

2016-11-29 Thread Z K 
Hello Douglas,

Any chance you can upload the two data files 
005-SAG_FSPGR_BRAVO_PURE/4355-0005-1 and 4355-0006-1:

   https://surfer.nmr.mgh.harvard.edu/fswiki/FtpFileExchange

Ide like to try and reproduce this. Thanks.

-Zeke




On 11/29/2016 04:20 PM, Douglas Merkitch wrote:
> Hello Doug,
>
> Command line & terminal output:
>
> recon-all -i
> /Volumes/JGG_WD_4TB_hard_drive_2/raw_data_UIC_3T/1039/raw_reordered/005-SAG_FSPGR_BRAVO_PURE/4355-0005-1
> -i
> /Volumes/JGG_WD_4TB_hard_drive_2/raw_data_UIC_3T/1039/raw_reordered/006-SAG_FSPGR_BRAVO_PURE_REPEAT/4355-0006-1
> -s 1039
> ERROR: cannot find
> /Applications/freesurfer_v6beta_16Nov2016/average/RB_all_2008-03-26.gca
>
> I do have the following similarly-named files in the v6 beta average
> directory:
> RB_all_2008-03-26.mni152.2mm.lta
> RB_all_2016-05-10.vc700.gca
> RB_all_withskull_2016-05-10.vc700.gca
>
> Thanks for the prompt response!
>
> Thanks,
>
> Doug
>
> Douglas Merkitch
> Neurological Sciences
> Rush University Medical Center
> Email: douglas_merki...@rush.edu 
>
>
>
>
>
> On Nov 29, 2016, at 3:12 PM, Douglas N Greve  > wrote:
>
>> can you send your command line and full terminal output?
>>
>>
>> On 11/29/2016 04:10 PM, Douglas Merkitch wrote:
>>> Hello experts,
>>>
>>> I was attempting to test out the freesurfer v6 beta and encountered
>>> the following error during dicom conversion: "ERROR: cannot find
>>> /Applications/freesurfer_v6beta_16Nov2016/average/RB_all_2008-03-26.gca".
>>>
>>> I'm currently
>>> running freesurfer-Darwin-OSX-stable-v6-beta-20161116-5037eae on a Mac
>>> Pro (3.33 GHz 6-Core Intel Xeon) with OS X 10.8.5.
>>>
>>> Any help would be greatly appreciated!
>>>
>>> Thanks,
>>>
>>> Doug
>>>
>>> Douglas Merkitch
>>> Neurological Sciences
>>> Rush University Medical Center
>>> Phone: (312) 563-3853 
>>> Fax: (312) 563-4660 
>>> Email: douglas_merki...@rush.edu 
>>> 
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>> ___
>>> Freesurfer mailing list
>>> Freesurfer@nmr.mgh.harvard.edu 
>>> https://urldefense.proofpoint.com/v2/url?u=https-3A__mail.nmr.mgh.harvard.edu_mailman_listinfo_freesurfer&d=DgIBAg&c=XxU8ngzB_WPJXKyiin_6iQ&r=GRn28rC6ssBi3WYtpTHXUZZiKgdhzFrFkzz7_Ref9iw&m=RYoN0GgWPi9MuiSoN-_tC7n3EM0X-3w27aQb4YV8g_0&s=waImhwQq0O8LHAlIun2v95CPShQ-yUCVzQzvOhsqD9s&e=
>>>
>>
>> --
>> Douglas N. Greve, Ph.D.
>> MGH-NMR Center
>> gr...@nmr.mgh.harvard.edu 
>> Phone Number: 617-724-2358
>> Fax: 617-726-7422
>>
>> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
>> FileDrop:
>> https://urldefense.proofpoint.com/v2/url?u=https-3A__gate.nmr.mgh.harvard.edu_filedrop2&d=DgIBAg&c=XxU8ngzB_WPJXKyiin_6iQ&r=GRn28rC6ssBi3WYtpTHXUZZiKgdhzFrFkzz7_Ref9iw&m=RYoN0GgWPi9MuiSoN-_tC7n3EM0X-3w27aQb4YV8g_0&s=5c8BG0jWHPLzpY6NB7Qaxm6jR1KlRb-uxt-ubzqrV9U&e=
>>
>> www.nmr.mgh.harvard.edu/facility/filedrop/index.html
>> Outgoing:
>> https://urldefense.proofpoint.com/v2/url?u=ftp-3A__surfer.nmr.mgh.harvard.edu_transfer_outgoing_flat_greve_&d=DgIBAg&c=XxU8ngzB_WPJXKyiin_6iQ&r=GRn28rC6ssBi3WYtpTHXUZZiKgdhzFrFkzz7_Ref9iw&m=RYoN0GgWPi9MuiSoN-_tC7n3EM0X-3w27aQb4YV8g_0&s=q36YAeWf40aDIu00LgaqEQKGoZ6iygWUhdUQLvWflDo&e=
>>
>>
>> ___
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>>
>>
>>
>> The information in this e-mail is intended only for the person to whom
>> it is
>> addressed. If you believe this e-mail was sent to you in error and the
>> e-mail
>> contains patient information, please contact the Partners Compliance
>> HelpLine at
>> https://urldefense.proofpoint.com/v2/url?u=http-3A__www.partners.org_complianceline&d=DgIBAg&c=XxU8ngzB_WPJXKyiin_6iQ&r=GRn28rC6ssBi3WYtpTHXUZZiKgdhzFrFkzz7_Ref9iw&m=RYoN0GgWPi9MuiSoN-_tC7n3EM0X-3w27aQb4YV8g_0&s=l884SPU9n9FO1VCPEZEhUM1DdT4D5SDBf9KDe5zMylY&e=
>>  . If the e-mail was sent to you in error
>> but does not contain patient information, please contact the sender
>> and properly
>> dispose of the e-mail.
>>
>
>
>
> ___
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Re: [Freesurfer] ERROR: cannot find RB_all_2008-03-26.gca

2016-11-29 Thread Douglas N Greve 
can you send your command line and full terminal output?


On 11/29/2016 04:10 PM, Douglas Merkitch wrote:
> Hello experts,
>
> I was attempting to test out the freesurfer v6 beta and encountered 
> the following error during dicom conversion: "ERROR: cannot find 
> /Applications/freesurfer_v6beta_16Nov2016/average/RB_all_2008-03-26.gca".
>
> I'm currently 
> running freesurfer-Darwin-OSX-stable-v6-beta-20161116-5037eae on a Mac 
> Pro (3.33 GHz 6-Core Intel Xeon) with OS X 10.8.5.
>
> Any help would be greatly appreciated!
>
> Thanks,
>
> Doug
>
> Douglas Merkitch
> Neurological Sciences
> Rush University Medical Center
> Phone: (312) 563-3853 
> Fax: (312) 563-4660 
> Email: douglas_merki...@rush.edu 
>
>
>
>
>
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

-- 
Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
www.nmr.mgh.harvard.edu/facility/filedrop/index.html
Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

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The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

Re: [Freesurfer] ERROR: cannot find RB_all_2008-03-26.gca

2016-11-29 Thread Douglas Merkitch 
Hello Doug,

Command line & terminal output:

recon-all -i 
/Volumes/JGG_WD_4TB_hard_drive_2/raw_data_UIC_3T/1039/raw_reordered/005-SAG_FSPGR_BRAVO_PURE/4355-0005-1
 -i 
/Volumes/JGG_WD_4TB_hard_drive_2/raw_data_UIC_3T/1039/raw_reordered/006-SAG_FSPGR_BRAVO_PURE_REPEAT/4355-0006-1
 -s 1039
ERROR: cannot find 
/Applications/freesurfer_v6beta_16Nov2016/average/RB_all_2008-03-26.gca

I do have the following similarly-named files in the v6 beta average directory:
RB_all_2008-03-26.mni152.2mm.lta
RB_all_2016-05-10.vc700.gca
RB_all_withskull_2016-05-10.vc700.gca

Thanks for the prompt response!

Thanks,

Doug

Douglas Merkitch
Neurological Sciences
Rush University Medical Center
Email: douglas_merki...@rush.edu





On Nov 29, 2016, at 3:12 PM, Douglas N Greve 
mailto:gr...@nmr.mgh.harvard.edu>> wrote:

can you send your command line and full terminal output?


On 11/29/2016 04:10 PM, Douglas Merkitch wrote:
Hello experts,

I was attempting to test out the freesurfer v6 beta and encountered
the following error during dicom conversion: "ERROR: cannot find
/Applications/freesurfer_v6beta_16Nov2016/average/RB_all_2008-03-26.gca".

I'm currently
running freesurfer-Darwin-OSX-stable-v6-beta-20161116-5037eae on a Mac
Pro (3.33 GHz 6-Core Intel Xeon) with OS X 10.8.5.

Any help would be greatly appreciated!

Thanks,

Doug

Douglas Merkitch
Neurological Sciences
Rush University Medical Center
Phone: (312) 563-3853 
Fax: (312) 563-4660 
Email: douglas_merki...@rush.edu 








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--
Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
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[Freesurfer] ERROR: cannot find RB_all_2008-03-26.gca

2016-11-29 Thread Douglas Merkitch 
Hello experts,

I was attempting to test out the freesurfer v6 beta and encountered the 
following error during dicom conversion: "ERROR: cannot find 
/Applications/freesurfer_v6beta_16Nov2016/average/RB_all_2008-03-26.gca".

I'm currently running freesurfer-Darwin-OSX-stable-v6-beta-20161116-5037eae on 
a Mac Pro (3.33 GHz 6-Core Intel Xeon) with OS X 10.8.5.

Any help would be greatly appreciated!

Thanks,

Doug

Douglas Merkitch
Neurological Sciences
Rush University Medical Center
Phone: (312) 563-3853
Fax: (312) 563-4660
Email: douglas_merki...@rush.edu





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