Re: [Freesurfer] Freesurfer dev version : recon all error mpr2mni305

2018-04-19 Thread Douglas N. Greve 
How does the input image look, ie, orig.mgz?


On 04/19/2018 09:49 AM, Jones, Richard wrote:
>
> I ran the command shown below to do recon-all on DICOM images from a 
> Philips Ingenia scanner using the development version of freesurfer on 
> a Mac running high Sierra.
>
> recon-all -i 
> /Users/Shared/HOPE_SS_Data/HOPE_SS020_Anat/IM-0001-0001.dcm -subject 
> HOPE_SS020 –all
>
> The program crashed with the error “ERROR: mpr2mni305 failed, see 
> transforms/talairach_avi.log”
>
> The talairach_avi.log file is shown below, followed by the log file. 
> As a test I ran the same command, on the same data, using Freesurfer 6 
> and that ran without problems (except that it didn’t handle the 
> diffusion tags in the Philips DICOM header correctly so I had to set 
> FS_LOAD_DWI=0, this was not a problem in the development version). Any 
> suggestions as to what may be causing the problems with the library in 
> the development version?
>
> Thanks,
>
> Richard
>
> /Applications/freesurfer_dev/subjects/HOPE_SS020/mri
>
> /Applications/freesurfer_dev/bin/talairach_avi
>
> --i orig_nu.mgz --xfm transforms/talairach.auto.xfm
>
> $Id: FreeSurferEnv.csh,v 1.89 2016/06/09 14:54:31 zkaufman Exp $
>
> Darwin meshuga.choa.org 17.5.0 Darwin Kernel Version 17.5.0: Mon Mar  
> 5 22:24:32 PST 2018; root:xnu-4570.51.1~1/RELEASE_X86_64 x86_64
>
> Thu Apr 19 08:45:01 EDT 2018
>
> mri_convert.bin orig_nu.mgz talsrcimg.img
>
> $Id: mri_convert.c,v 1.227 2017/02/16 19:15:42 greve Exp $
>
> reading from orig_nu.mgz...
>
> TR=6.98, TE=3.14, TI=0.00, flip angle=8.00
>
> i_ras = (-1, 7.45058e-09, 0)
>
> j_ras = (3.72529e-09, -4.88944e-09, -1)
>
> k_ras = (0, 1, 4.88944e-09)
>
> writing to talsrcimg.img...
>
> Analyze Output Matrix
>
> -1.0   0.0   0.0   128.15305;
>
> 0.0  -0.0   1.0  -116.15433;
>
> 0.0  -1.0   0.0   128.60870;
>
> 0.0   0.0   0.0   1.0;
>
> 
>
> INFO: set hdr.hist.orient to -1
>
> mpr2mni305 talsrcimg
>
> Thu Apr 19 08:45:02 EDT 2018
>
> /Applications/freesurfer_dev/bin/mpr2mni305 talsrcimg
>
> $Id: mpr2mni305,v 1.5 2015/12/18 23:56:21 zkaufman Exp $
>
> target=711-2C_as_mni_average_305
>
> -
>
> analyzeto4dfp talsrcimg -O0 -y
>
> -
>
> $Id: ifh2hdr.c,v 1.3 2007/05/05 10:45:03 nicks Exp $
>
> Thu Apr 19 08:45:02 2018
>
> Writing: talsrcimg.4dfp.hdr
>
> $Id: analyzeto4dfp.c,v 1.2 2007/05/05 00:00:06 nicks Exp $
>
> Reading: talsrcimg.hdr
>
> header size 348 bytes
>
> hdr.dime.datatype offset=70    value=2
>
> hdr.dime.bitpix offset=72    value=8
>
> hdr.hist.orient offset=252  value=-1
>
> dimensionality 4
>
> dimensions   256   256 256 1
>
> Reading: talsrcimg.img
>
> Writing: talsrcimg.4dfp.img
>
> Writing: talsrcimg.4dfp.ifh
>
> ifh2hdr talsrcimg -r0to255
>
> ori=2
>
> -
>
> gauss_4dfp talsrcimg 1.1
>
> -
>
> dyld: Library not loaded: /usr/local/opt/gcc/lib/gcc/7/libgfortran.4.dylib
>
>   Referenced from: /Applications/freesurfer_dev/bin/gauss_4dfp
>
>   Reason: image not found
>
> Abort
>
> ERROR: 'gauss_4dfp talsrcimg 1.1' failed! status=134
>
> ERROR: mpr2mni305 execution aborted
>
> Subject Stamp: freesurfer-darwin-OSX-ElCapitan-dev-20180415-0d56499
>
> Current Stamp: freesurfer-darwin-OSX-ElCapitan-dev-20180415-0d56499
>
> INFO: SUBJECTS_DIR is /Applications/freesurfer_dev/subjects
>
> Actual FREESURFER_HOME /Applications/freesurfer_dev
>
> Darwin meshuga.choa.org 17.5.0 Darwin Kernel Version 17.5.0: Mon Mar  
> 5 22:24:32 PST 2018; root:xnu-4570.51.1~1/RELEASE_X86_64 x86_64
>
> /Applications/freesurfer_dev/subjects/HOPE_SS020
>
> \n mri_convert 
> /Users/Shared/HOPE_SS_Data/HOPE_SS020_Anat/IM-0001-0001.dcm 
> /Applications/freesurfer_dev/subjects/HOPE_SS020/mri/orig/001.mgz \n
>
> mri_convert.bin 
> /Users/Shared/HOPE_SS_Data/HOPE_SS020_Anat/IM-0001-0001.dcm 
> /Applications/freesurfer_dev/subjects/HOPE_SS020/mri/orig/001.mgz
>
> $Id: mri_convert.c,v 1.227 2017/02/16 19:15:42 greve Exp $
>
> reading from 
> /Users/Shared/HOPE_SS_Data/HOPE_SS020_Anat/IM-0001-0001.dcm...
>
> Starting DICOMRead2()
>
> dcmfile = /Users/Shared/HOPE_SS_Data/HOPE_SS020_Anat/IM-0001-0001.dcm
>
> dcmdir = /Users/Shared/HOPE_SS_Data/HOPE_SS020_Anat
>
> Ref Series No = 301
>
> Found 202 files, checking for dicoms
>
> Found 200 dicom files in series.
>
> First Sorting
>
> Computing Slice Direction
>
> Vs: -0.897217 -0.0611658 0.0354633
>
> Vs: -0.996909 -0.0679621 0.0394038
>
> Second Sorting
>
> IsDWI = 0, IsPhilipsDWI = 0
>
> Counting frames
>
> nframes = 1
>
> nslices = 200
>
> ndcmfiles = 200
>
> PE Dir = ROW (dicom read)
>
> Loading pixel data
>
> TR=6.98, TE=3.14, TI=0.00, flip angle=8.00
>
> i_ras = (0.0644896, -0.994415, 0.0835493)
>
> j_ras =

Re: [Freesurfer] Freesurfer dev version : recon all error mpr2mni305

2018-04-19 Thread Hoopes, Andrew 
Hi Richard, thanks for pointing this out – I’ll take a look into it.

best
Andrew

From:  on behalf of "Jones, Richard" 

Reply-To: FS Help 
Date: Thursday, April 19, 2018 at 9:49 AM
To: FS Help 
Subject: [Freesurfer] Freesurfer dev version : recon all error mpr2mni305

I ran the command shown below to do recon-all on DICOM images from a Philips 
Ingenia scanner using the development version of freesurfer on a Mac running 
high Sierra.

recon-all -i /Users/Shared/HOPE_SS_Data/HOPE_SS020_Anat/IM-0001-0001.dcm 
-subject HOPE_SS020 –all

The program crashed with the error “ERROR: mpr2mni305 failed, see 
transforms/talairach_avi.log”

The talairach_avi.log file is shown below, followed by the log file. As a test 
I ran the same command, on the same data, using Freesurfer 6 and that ran 
without problems (except that it didn’t handle the diffusion tags in the 
Philips DICOM header correctly so I had to set FS_LOAD_DWI=0, this was not a 
problem in the development version). Any suggestions as to what may be causing 
the problems with the library in the development version?

Thanks,

Richard

/Applications/freesurfer_dev/subjects/HOPE_SS020/mri
/Applications/freesurfer_dev/bin/talairach_avi
--i orig_nu.mgz --xfm transforms/talairach.auto.xfm
$Id: FreeSurferEnv.csh,v 1.89 2016/06/09 14:54:31 zkaufman Exp $
Darwin meshuga.choa.org 17.5.0 Darwin Kernel Version 17.5.0: Mon Mar  5 
22:24:32 PST 2018; root:xnu-4570.51.1~1/RELEASE_X86_64 x86_64
Thu Apr 19 08:45:01 EDT 2018
mri_convert.bin orig_nu.mgz talsrcimg.img
$Id: mri_convert.c,v 1.227 2017/02/16 19:15:42 greve Exp $
reading from orig_nu.mgz...
TR=6.98, TE=3.14, TI=0.00, flip angle=8.00
i_ras = (-1, 7.45058e-09, 0)
j_ras = (3.72529e-09, -4.88944e-09, -1)
k_ras = (0, 1, 4.88944e-09)
writing to talsrcimg.img...
Analyze Output Matrix
-1.0   0.0   0.0   128.15305;
0.0  -0.0   1.0  -116.15433;
0.0  -1.0   0.0   128.60870;
0.0   0.0   0.0   1.0;

INFO: set hdr.hist.orient to -1
mpr2mni305 talsrcimg
Thu Apr 19 08:45:02 EDT 2018
/Applications/freesurfer_dev/bin/mpr2mni305 talsrcimg
$Id: mpr2mni305,v 1.5 2015/12/18 23:56:21 zkaufman Exp $
target=711-2C_as_mni_average_305

-
analyzeto4dfp talsrcimg -O0 -y
-

$Id: ifh2hdr.c,v 1.3 2007/05/05 10:45:03 nicks Exp $
Thu Apr 19 08:45:02 2018
Writing: talsrcimg.4dfp.hdr
$Id: analyzeto4dfp.c,v 1.2 2007/05/05 00:00:06 nicks Exp $
Reading: talsrcimg.hdr
header size 348 bytes
hdr.dime.datatype  offset=70value=2
hdr.dime.bitpix offset=72value=8
hdr.hist.orient   offset=252  value=-1
dimensionality 4
dimensions   256   256   256 1
Reading: talsrcimg.img
Writing: talsrcimg.4dfp.img
Writing: talsrcimg.4dfp.ifh
ifh2hdr talsrcimg -r0to255
ori=2

-
gauss_4dfp talsrcimg 1.1
-

dyld: Library not loaded: /usr/local/opt/gcc/lib/gcc/7/libgfortran.4.dylib
  Referenced from: /Applications/freesurfer_dev/bin/gauss_4dfp
  Reason: image not found
Abort
ERROR: 'gauss_4dfp talsrcimg 1.1' failed! status=134
ERROR: mpr2mni305 execution aborted


Subject Stamp: freesurfer-darwin-OSX-ElCapitan-dev-20180415-0d56499
Current Stamp: freesurfer-darwin-OSX-ElCapitan-dev-20180415-0d56499
INFO: SUBJECTS_DIR is /Applications/freesurfer_dev/subjects
Actual FREESURFER_HOME /Applications/freesurfer_dev
Darwin meshuga.choa.org 17.5.0 Darwin Kernel Version 17.5.0: Mon Mar  5 
22:24:32 PST 2018; root:xnu-4570.51.1~1/RELEASE_X86_64 x86_64
/Applications/freesurfer_dev/subjects/HOPE_SS020
\n mri_convert /Users/Shared/HOPE_SS_Data/HOPE_SS020_Anat/IM-0001-0001.dcm 
/Applications/freesurfer_dev/subjects/HOPE_SS020/mri/orig/001.mgz \n
mri_convert.bin /Users/Shared/HOPE_SS_Data/HOPE_SS020_Anat/IM-0001-0001.dcm 
/Applications/freesurfer_dev/subjects/HOPE_SS020/mri/orig/001.mgz
$Id: mri_convert.c,v 1.227 2017/02/16 19:15:42 greve Exp $
reading from /Users/Shared/HOPE_SS_Data/HOPE_SS020_Anat/IM-0001-0001.dcm...
Starting DICOMRead2()
dcmfile = /Users/Shared/HOPE_SS_Data/HOPE_SS020_Anat/IM-0001-0001.dcm
dcmdir = /Users/Shared/HOPE_SS_Data/HOPE_SS020_Anat
Ref Series No = 301
Found 202 files, checking for dicoms
Found 200 dicom files in series.
First Sorting
Computing Slice Direction
Vs: -0.897217 -0.0611658 0.0354633
Vs: -0.996909 -0.0679621 0.0394038
Second Sorting
IsDWI = 0, IsPhilipsDWI = 0
Counting frames
nframes = 1
nslices = 200
ndcmfiles = 200
PE Dir = ROW (dicom read)
Loading pixel data
TR=6.98, TE=3.14, TI=0.00, flip angle=8.00
i_ras = (0.0644896, -0.994415, 0.0835493)
j_ras = (0.0448617, -0.08075, -0.995724)
k_ras =