Thank you for that -- the problem is indeed solved with this newer version of bbregister.

On Apr 22, 2013, at 2:45 PM, Douglas N Greve wrote:

This is a problem that originated with newer versions of tcsh. Try using
the version of bbregister from here:

ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/bbregister


doug

On 04/22/2013 02:28 PM, Winter, Warren wrote:
Hi all,

I also had this same problem with -T2pial, posted on the archives back in March.  I, too, have a log where mri_convert is given an input of "ERROR: could not determine file for ...", and I believe I've traced it back to this early line in bbregister (our copy is dated at 2/23/2013, revision 1.49.2.2): "set fsvol  = brainmask".  In our recon-all script (dated 2/19/2013, revision 1.379.2.65), the T2pial code block runs this command:

bbregister --s $subjid --mov $t2flairraw --lta $mdir/transforms/${t2flair}raw.lta --init-fsl --T2

With init-fsl set to true, bbregister then runs an fslregister command containing "--fslvol $fsvol", which ends up being interpreted as --fsvol $mdir/brainmask and generating an error.  When I manually ran the same bbregister command with --fsvol brainmask.mgz added, mri_convert got the correct input and everything worked.

Is it possible that our versions of recon-all and/or bbregister are not the most up-to-date copies?

Warren

On Apr 22, 2013, at 7:56 AM, Eduard Vilaplana Martinez wrote:

Dear FS experts,

Any idea about that problem? Does anybody has used this pial correction technique?

Thanks in advance

Best regards,

Eduard
________________________________________
De: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] en nom de Eduard Vilaplana  Martinez [EVilaplana@santpau.cat]
Enviat el: dijous, 18 / abril / 2013 11:05
Per a: Charles Malpas; Freesurfer@nmr.mgh.harvard.edu
Tema: Re: [Freesurfer] T2 pial

Dear all,

Here is the output of the mri_info b0_mricron_20120529_152032DTI32DirSENSEs601a1000.nii.The image that I'm using as a T2 is, in fact, the b0 from the DTI. It's is the highest resolution volume I have, so I don't have many alternatives.


Volume information for b0_mricron_20120529_152032DTI32DirSENSEs601a1000.nii
         type: nii
         dimensions: 160 x 160 x 80
         voxel sizes: 1.6000, 1.6000, 2.0000
         type: FLOAT (3)
          fov: 256.000
          dof: 0
       xstart: -128.0, xend: 128.0
       ystart: -128.0, yend: 128.0
       zstart: -80.0, zend: 80.0
           TR: 10800.00 msec, TE: 0.00 msec, TI: 0.00 msec, flip angle: 0.00 degrees
      nframes: 1
      PhEncDir: UNKNOWN
ras xform present
   xform info: x_r =  -0.9968, y_r =   0.0651, z_r =  -0.0464, c_r =     0.3105
             : x_a =   0.0726, y_a =   0.9806, z_a =  -0.1824, c_a =    24.5431
             : x_s =  -0.0336, y_s =   0.1851, z_s =   0.9821, c_s =   -17.0332
Orientation   : LAS
Primary Slice Direction: axial

voxel to ras transform:
              -1.5949   0.1042  -0.0928   123.2741
               0.1161   1.5689  -0.3647   -95.6693
              -0.0538   0.2962   1.9643  -114.9972
               0.0000   0.0000   0.0000     1.0000

voxel-to-ras determinant -5.12001

ras to voxel transform:
              -0.6230   0.0454  -0.0210    78.7222
               0.0407   0.6128   0.1157    66.9172
              -0.0232  -0.0912   0.4911    50.6094
               0.0000   0.0000   0.0000     1.0000

I also attach the "normal" streamline log file and the "pial-refinement" log file.

Thanks in advance!

Eduard


________________________________________
De: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] en nom de Charles Malpas [c.malpas@student.unimelb.edu.au]
Enviat el: dijous, 18 / abril / 2013 02:11
Per a: Freesurfer@nmr.mgh.harvard.edu
Tema: Re: [Freesurfer] T2 pial

Hi All,

I have a similar error, which I traced back (I think!) to bbregister failing to write FLAIRraw.lta. My only solution was to download the subject directories from our linux (RedHat) cluster and run the registration on an OSX binary. This then creates the .lta file and I upload it back to the linux cluster to run -FLAIRpial which creates the FLAIR.mgz volume. Weird, I know!

Kind regards,

- Charles


On 18 April 2013 03:15, Nick Schmansky <nicks@nmr.mgh.harvard.edu<mailto:nicks@nmr.mgh.harvard.edu>> wrote:
Eduard,

Can you send the whole recon-all.log file?  The error show below is a
strange one.  It appears as if the string "ERROR: could not determine
file" is the input to mri_convert, and I'm not sure how that can happen.

Also double check (by viewing in freeview) that T2raw.mgz is a valid
file (ie, looks like a T2-space brain).

and perhaps send output of:

mri_info b0_mricron_20120529_152032DTI32DirSENSEs601a1000.nii

Nick


On Wed, 2013-04-17 at 13:04 +0000, Eduard Vilaplana Martinez wrote:
Dear FreeSurfer experts,

First of all, congrats for this new 5.2 stable version.

My name is Eduard, and I'm trying to perform de T2 pial refinement in a pre-processed subject with the B0 image from a DTI. I used that command:


recon-all -autorecon3 -T2pial -s ACC019/ -T2 /home/linux/Escritorio/COHORTE_T2/b0_mricron_20120529_152032DTI32DirSENSEs601a1000.nii

Being "ACC019" the subject ID and "/home/linux/Escritorio/COHORTE_T2/b0_mricron_20120529_152032DTI32DirSENSEs601a1000.nii" the path to the T2 nifti.

Whatever I do, it always return me the following error. Any suggestions would be greatly appreciated. Thanks in advance.


@# Refine Pial Surfs w/ T2/FLAIR Wed Apr 17 14:37:42 CEST 2013

bbregister --s ACC019 --mov /home/linux/Escritorio/COHORTE_T2/ACC019/mri/orig/T2raw.mgz --lta /home/linux/Escritorio/COHORTE_T2/ACC019/mri/transforms/T2raw.lta --init-fsl --T2

Log file is /home/linux/Escritorio/COHORTE_T2/ACC019/mri/transforms/T2raw.dat.log
Wed Apr 17 14:37:42 CEST 2013

setenv SUBJECTS_DIR /home/linux/Escritorio/COHORTE_T2
cd /home/linux/Escritorio/COHORTE_T2/ACC019/scripts
/usr/local/freesurfer/bin/bbregister --s ACC019 --mov /home/linux/Escritorio/COHORTE_T2/ACC019/mri/orig/T2raw.mgz --lta /home/linux/Escritorio/COHORTE_T2/ACC019/mri/transforms/T2raw.lta --init-fsl --T2

$Id: bbregister,v 1.49.2.2 2013/02/23 01:32:22 mreuter Exp $
Linux linux-To-be-filled-by-O-E-M 3.2.0-40-generic #64-Ubuntu SMP Mon Mar 25 21:22:10 UTC 2013 x86_64 x86_64 x86_64 GNU/Linux
FREESURFER_HOME /usr/local/freesurfer
mri_convert /home/linux/Escritorio/COHORTE_T2/ACC019/mri/orig/T2raw.mgz /home/linux/Escritorio/COHORTE_T2/ACC019/mri/transforms/tmp.bbregister.5969/template.nii
mri_convert /home/linux/Escritorio/COHORTE_T2/ACC019/mri/orig/T2raw.mgz /home/linux/Escritorio/COHORTE_T2/ACC019/mri/transforms/tmp.bbregister.5969/template.nii
$Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $
reading from /home/linux/Escritorio/COHORTE_T2/ACC019/mri/orig/T2raw.mgz...
TR=10800.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-0.996796, 0.0725774, -0.0336276)
j_ras = (0.065149, 0.980551, 0.185135)
k_ras = (-0.0464102, -0.182351, 0.982138)
writing to /home/linux/Escritorio/COHORTE_T2/ACC019/mri/transforms/tmp.bbregister.5969/template.nii...
fslregister --s ACC019 --mov /home/linux/Escritorio/COHORTE_T2/ACC019/mri/transforms/tmp.bbregister.5969/template.nii --reg /home/linux/Escritorio/COHORTE_T2/ACC019/mri/transforms/tmp.bbregister.5969/reg.init.dat --niters 1 --maxangle 90 --nobetmov --tmp /home/linux/Escritorio/COHORTE_T2/ACC019/mri/transforms/tmp.bbregister.5969/fslregister --dof 6 --fsvol brainmask

Log file is /home/linux/Escritorio/COHORTE_T2/ACC019/mri/transforms/tmp.bbregister.5969/reg.init.dat.fslregister.log

Wed Apr 17 14:37:42 CEST 2013
--s ACC019 --mov /home/linux/Escritorio/COHORTE_T2/ACC019/mri/transforms/tmp.bbregister.5969/template.nii --reg /home/linux/Escritorio/COHORTE_T2/ACC019/mri/transforms/tmp.bbregister.5969/reg.init.dat --niters 1 --maxangle 90 --nobetmov --tmp /home/linux/Escritorio/COHORTE_T2/ACC019/mri/transforms/tmp.bbregister.5969/fslregister --dof 6 --fsvol brainmask
$Id: fslregister,v 1.34.2.2 2012/11/08 16:18:56 greve Exp $
linux-To-be-filled-by-O-E-M
Linux linux-To-be-filled-by-O-E-M 3.2.0-40-generic #64-Ubuntu SMP Mon Mar 25 21:22:10 UTC 2013 x86_64 x86_64 x86_64 GNU/Linux
nIters 1
--------------------------------------
/home/linux/Escritorio/COHORTE_T2/ACC019/scripts
mri_convert ERROR: could not determine file for /home/linux/Escritorio/COHORTE_T2/ACC019/mri/ERROR: /home/linux/Escritorio/COHORTE_T2/ACC019/mri/transforms/tmp.bbregister.5969/fslregister/refvol.fslregister.nii
mri_convert ERROR: could not determine file for /home/linux/Escritorio/COHORTE_T2/ACC019/mri/ERROR: /home/linux/Escritorio/COHORTE_T2/ACC019/mri/transforms/tmp.bbregister.5969/fslregister/refvol.fslregister.nii

mri_convert: extra arguments ("not" and following)

type mri_convert -u for usage

--------------------------------------
/home/linux/Escritorio/COHORTE_T2/ACC019/scripts
mri_convert /home/linux/Escritorio/COHORTE_T2/ACC019/mri/transforms/tmp.bbregister.5969/template.nii /home/linux/Escritorio/COHORTE_T2/ACC019/mri/transforms/tmp.bbregister.5969/fslregister/movvol.fslregister.nii --frame 0
mri_convert /home/linux/Escritorio/COHORTE_T2/ACC019/mri/transforms/tmp.bbregister.5969/template.nii /home/linux/Escritorio/COHORTE_T2/ACC019/mri/transforms/tmp.bbregister.5969/fslregister/movvol.fslregister.nii --frame 0
$Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $
reading from /home/linux/Escritorio/COHORTE_T2/ACC019/mri/transforms/tmp.bbregister.5969/template.nii...
TR=10800.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-0.996796, 0.0725774, -0.0336276)
j_ras = (0.065149, 0.980551, 0.185135)
k_ras = (-0.0464102, -0.182351, 0.982138)
keeping frame 0
writing to /home/linux/Escritorio/COHORTE_T2/ACC019/mri/transforms/tmp.bbregister.5969/fslregister/movvol.fslregister.nii...
Mov determinant is -5.12001
/home/linux/Escritorio/COHORTE_T2/ACC019/scripts
tkregister2_cmdl --mov /home/linux/Escritorio/COHORTE_T2/ACC019/mri/transforms/tmp.bbregister.5969/fslregister/movvol.fslregister.nii --reg /home/linux/Escritorio/COHORTE_T2/ACC019/mri/transforms/tmp.bbregister.5969/fslregister/reg0.6003.dat --regheader --fslregout /home/linux/Escritorio/COHORTE_T2/ACC019/mri/transforms/tmp.bbregister.5969/reg.init.dat.fsl.mat0 --s ACC019 --noedit
tkregister_tcl /usr/local/freesurfer/tktools/tkregister2.tcl
INFO: no target volume specified, assuming FreeSurfer orig volume.
target  volume orig
movable volume /home/linux/Escritorio/COHORTE_T2/ACC019/mri/transforms/tmp.bbregister.5969/fslregister/movvol.fslregister.nii
reg file       /home/linux/Escritorio/COHORTE_T2/ACC019/mri/transforms/tmp.bbregister.5969/fslregister/reg0.6003.dat
LoadVol        0
ZeroCRAS       0
$Id: tkregister2.c,v 1.121.2.1 2011/03/28 20:25:16 greve Exp $
Diagnostic Level -1
INFO: loading target /home/linux/Escritorio/COHORTE_T2/ACC019/mri/orig.mgz
Ttarg: --------------------
-1.000   0.000   0.000   128.000;
0.000   0.000   1.000  -128.000;
0.000  -1.000   0.000   128.000;
0.000   0.000   0.000   1.000;
INFO: loading movable /home/linux/Escritorio/COHORTE_T2/ACC019/mri/transforms/tmp.bbregister.5969/fslregister/movvol.fslregister.nii
Tmov: --------------------
-1.600   0.000   0.000   128.000;
0.000   0.000   2.000  -80.000;
0.000  -1.600   0.000   128.000;
0.000   0.000   0.000   1.000;
mkheaderreg = 1, float2int = 0
Computing reg from header (and possibly input matrix)
---- Input registration matrix (computed) --------
0.997  -0.073   0.034   0.214;
-0.046  -0.182   0.982  -30.911;
-0.065  -0.981  -0.185   1.512;
0.000   0.000   0.000   1.000;
---------------------------------------
---- Input registration matrix --------
0.997  -0.073   0.034   0.214;
-0.046  -0.182   0.982  -30.911;
-0.065  -0.981  -0.185   1.512;
0.000   0.000   0.000   1.000;
Determinant 1
subject = ACC019
RegMat ---------------------------
0.997  -0.073   0.034   0.214;
-0.046  -0.182   0.982  -30.911;
-0.065  -0.981  -0.185   1.512;
0.000   0.000   0.000   1.000;
FSLOUTPUTTYPE NIFTI
tkreg2FSL: mov det = -5.12001, ref det = -1
Wed Apr 17 14:37:44 CEST 2013
/home/linux/Escritorio/COHORTE_T2/ACC019/scripts
flirt.fsl -ref /home/linux/Escritorio/COHORTE_T2/ACC019/mri/transforms/tmp.bbregister.5969/fslregister/refvol.fslregister.nii -in /home/linux/Escritorio/COHORTE_T2/ACC019/mri/transforms/tmp.bbregister.5969/fslregister/movvol.fslregister.nii -bins 256 -cost corratio -dof 6 -searchrx -90 90 -searchry -90 90 -searchrz -90 90 -verbose 0 -omat /home/linux/Escritorio/COHORTE_T2/ACC019/mri/transforms/tmp.bbregister.5969/fslregister/fslmat0.trans.mat -schedule /usr/share/fsl/5.0/etc/flirtsch/xyztrans.sch -init /home/linux/Escritorio/COHORTE_T2/ACC019/mri/transforms/tmp.bbregister.5969/reg.init.dat.fsl.mat0
** ERROR (nifti_image_read): failed to find header file for '/home/linux/Escritorio/COHORTE_T2/ACC019/mri/transforms/tmp.bbregister.5969/fslregister/refvol.fslregister'
** ERROR: nifti_image_open(/home/linux/Escritorio/COHORTE_T2/ACC019/mri/transforms/tmp.bbregister.5969/fslregister/refvol.fslregister): bad header info
ERROR: failed to open file /home/linux/Escritorio/COHORTE_T2/ACC019/mri/transforms/tmp.bbregister.5969/fslregister/refvol.fslregister
ERROR: Could not open image /home/linux/Escritorio/COHORTE_T2/ACC019/mri/transforms/tmp.bbregister.5969/fslregister/refvol.fslregister
Image Exception : #22 :: Failed to read volume /home/linux/Escritorio/COHORTE_T2/ACC019/mri/transforms/tmp.bbregister.5969/fslregister/refvol.fslregister.nii
terminate called after throwing an instance of 'RBD_COMMON::BaseException'
Abort (core dumped)
Wed Apr 17 14:37:44 CEST 2013
/home/linux/Escritorio/COHORTE_T2/ACC019/scripts
flirt.fsl -ref /home/linux/Escritorio/COHORTE_T2/ACC019/mri/transforms/tmp.bbregister.5969/fslregister/refvol.fslregister.nii -in /home/linux/Escritorio/COHORTE_T2/ACC019/mri/transforms/tmp.bbregister.5969/fslregister/movvol.fslregister.nii -bins 256 -cost corratio -dof 6 -searchrx -90 90 -searchry -90 90 -searchrz -90 90 -verbose 0 -omat /home/linux/Escritorio/COHORTE_T2/ACC019/mri/transforms/tmp.bbregister.5969/reg.init.dat.fsl.mat -init /home/linux/Escritorio/COHORTE_T2/ACC019/mri/transforms/tmp.bbregister.5969/fslregister/fslmat0.trans.mat -schedule /usr/local/freesurfer/bin/flirt.newdefault.20080811.sch
** ERROR (nifti_image_read): failed to find header file for '/home/linux/Escritorio/COHORTE_T2/ACC019/mri/transforms/tmp.bbregister.5969/fslregister/refvol.fslregister'
** ERROR: nifti_image_open(/home/linux/Escritorio/COHORTE_T2/ACC019/mri/transforms/tmp.bbregister.5969/fslregister/refvol.fslregister): bad header info
ERROR: failed to open file /home/linux/Escritorio/COHORTE_T2/ACC019/mri/transforms/tmp.bbregister.5969/fslregister/refvol.fslregister
ERROR: Could not open image /home/linux/Escritorio/COHORTE_T2/ACC019/mri/transforms/tmp.bbregister.5969/fslregister/refvol.fslregister
Image Exception : #22 :: Failed to read volume /home/linux/Escritorio/COHORTE_T2/ACC019/mri/transforms/tmp.bbregister.5969/fslregister/refvol.fslregister.nii
terminate called after throwing an instance of 'RBD_COMMON::BaseException'
Abort (core dumped)
tkregister2_cmdl --s ACC019 --mov /home/linux/Escritorio/COHORTE_T2/ACC019/mri/transforms/tmp.bbregister.5969/template.nii --reg /home/linux/Escritorio/COHORTE_T2/ACC019/mri/transforms/tmp.bbregister.5969/reg.init.dat --fslreg /home/linux/Escritorio/COHORTE_T2/ACC019/mri/transforms/tmp.bbregister.5969/reg.init.dat.fsl.mat --noedit
tkregister_tcl /usr/local/freesurfer/tktools/tkregister2.tcl
ERROR: cannot open /home/linux/Escritorio/COHORTE_T2/ACC019/mri/transforms/tmp.bbregister.5969/reg.init.dat.fsl.mat
cat: /home/linux/Escritorio/COHORTE_T2/ACC019/mri/transforms/tmp.bbregister.5969/reg.init.dat: No such file or directory
tmp: Subscript out of range.

Started at Wed Apr 17 14:37:42 CEST 2013
Ended   at Wed Apr 17 14:37:44 CEST 2013

fslregister Done

To check results, run:
tkregister2 --mov /home/linux/Escritorio/COHORTE_T2/ACC019/mri/transforms/tmp.bbregister.5969/template.nii --reg /home/linux/Escritorio/COHORTE_T2/ACC019/mri/transforms/tmp.bbregister.5969/reg.init.dat --surf orig

mri_segreg --mov /home/linux/Escritorio/COHORTE_T2/ACC019/mri/transforms/tmp.bbregister.5969/template.nii --init-reg /home/linux/Escritorio/COHORTE_T2/ACC019/mri/transforms/tmp.bbregister.5969/reg.init.dat --out-reg /home/linux/Escritorio/COHORTE_T2/ACC019/mri/transforms/tmp.bbregister.5969/bbr.pass1.dat --subsamp-brute 100 --subsamp 100 --tol 1e-4 --tol1d 1e-3 --brute -4 4 4 --surf white --gm-proj-frac 0.5 --gm-gt-wm 0.5
regio_read_register(): No such file or directory
Could not open /home/linux/Escritorio/COHORTE_T2/ACC019/mri/transforms/tmp.bbregister.5969/reg.init.dat
mri_segreg --mov /home/linux/Escritorio/COHORTE_T2/ACC019/mri/transforms/tmp.bbregister.5969/template.nii --init-reg /home/linux/Escritorio/COHORTE_T2/ACC019/mri/transforms/tmp.bbregister.5969/bbr.pass1.dat --out-reg /home/linux/Escritorio/COHORTE_T2/ACC019/mri/transforms/T2raw.dat --brute -0.1 0.1 0.1 --interp trilinear --wm-proj-abs 2 --tol 1e-8 --tol1d 1e-3 --c0 0 --mincost /home/linux/Escritorio/COHORTE_T2/ACC019/mri/transforms/T2raw.dat.mincost --dof 6 --nmax 36 --param /home/linux/Escritorio/COHORTE_T2/ACC019/mri/transforms/T2raw.dat.param --surf white --cur-reg /home/linux/Escritorio/COHORTE_T2/ACC019/mri/transforms/tmp.bbregister.5969/reg.curopt.dat --gm-proj-frac 0.5 --nsub 1 --gm-gt-wm 0.5
regio_read_register(): No such file or directory
Could not open /home/linux/Escritorio/COHORTE_T2/ACC019/mri/transforms/tmp.bbregister.5969/bbr.pass1.dat
tkregister2_cmdl --mov /home/linux/Escritorio/COHORTE_T2/ACC019/mri/orig/T2raw.mgz --reg /home/linux/Escritorio/COHORTE_T2/ACC019/mri/transforms/T2raw.dat --noedit --ltaout /home/linux/Escritorio/COHORTE_T2/ACC019/mri/transforms/T2raw.lta
regio_read_register(): No such file or directory
Could not open /home/linux/Escritorio/COHORTE_T2/ACC019/mri/transforms/T2raw.dat
tkregister_tcl /usr/local/freesurfer/tktools/tkregister2.tcl
INFO: no target volume specified, assuming FreeSurfer orig volume.
target  volume orig
movable volume /home/linux/Escritorio/COHORTE_T2/ACC019/mri/orig/T2raw.mgz
reg file       /home/linux/Escritorio/COHORTE_T2/ACC019/mri/transforms/T2raw.dat
LoadVol        0
ZeroCRAS       0
$Id: tkregister2.c,v 1.121.2.1 2011/03/28 20:25:16 greve Exp $
Diagnostic Level -1
ERROR: reading /home/linux/Escritorio/COHORTE_T2/ACC019/mri/transforms/T2raw.dat
Cleaning up

Started at Wed Apr 17 14:37:42 CEST 2013
Ended   at Wed Apr 17 14:37:45 CEST 2013
BBR-Run-Time-Sec 3

bbregister Done
To check results, run:
tkregister2 --mov /home/linux/Escritorio/COHORTE_T2/ACC019/mri/orig/T2raw.mgz --reg /home/linux/Escritorio/COHORTE_T2/ACC019/mri/transforms/T2raw.dat --surf


mri_convert -at /home/linux/Escritorio/COHORTE_T2/ACC019/mri/transforms/T2raw.lta -rl /home/linux/Escritorio/COHORTE_T2/ACC019/mri/orig.mgz /home/linux/Escritorio/COHORTE_T2/ACC019/mri/orig/T2raw.mgz /home/linux/Escritorio/COHORTE_T2/ACC019/mri/T2.mgz

mri_convert -at /home/linux/Escritorio/COHORTE_T2/ACC019/mri/transforms/T2raw.lta -rl /home/linux/Escritorio/COHORTE_T2/ACC019/mri/orig.mgz /home/linux/Escritorio/COHORTE_T2/ACC019/mri/orig/T2raw.mgz /home/linux/Escritorio/COHORTE_T2/ACC019/mri/T2.mgz
ltaReadFile(/home/linux/Escritorio/COHORTE_T2/ACC019/mri/transforms/T2raw.lta): can't open file
$Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $
reading from /home/linux/Escritorio/COHORTE_T2/ACC019/mri/orig/T2raw.mgz...
TR=10800.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-0.996796, 0.0725774, -0.0336276)
j_ras = (0.065149, 0.980551, 0.185135)
k_ras = (-0.0464102, -0.182351, 0.982138)
INFO: Reading transformation from file /home/linux/Escritorio/COHORTE_T2/ACC019/mri/transforms/T2raw.lta...
Reading transform with LTAreadEx()
No such file or directory
ERROR: Reading transform from file /home/linux/Escritorio/COHORTE_T2/ACC019/mri/transforms/T2raw.lta
Linux linux-To-be-filled-by-O-E-M 3.2.0-40-generic #64-Ubuntu SMP Mon Mar 25 21:22:10 UTC 2013 x86_64 x86_64 x86_64 GNU/Linux

recon-all -s ACC019 exited with ERRORS at Wed Apr 17 14:37:45 CEST 2013

For more details, see the log file /home/linux/Escritorio/COHORTE_T2/ACC019/scripts/recon-all.log
To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu>
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer



_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu>
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


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.




--
Charles Malpas
Master of Psychology (Clinical Neuropsychology) / PhD Candidate
Melbourne School of Psychological Sciences & Department of Medicine (RMH)
The University of Melbourne 3010

Melbourne Brain Centre @ RMH
Neuropsychiatry Research Group
Level 4, Main Building, Royal Melbourne Hospital
Phone: 0451 116 434
Email: c.malpas@student.unimelb.edu.au<mailto:c.malpas@student.unimelb.edu.au>
Skype: charles.malpas

_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

--
Warren Winter
Research Coordinator
Boston Children's Hospital
Sheridan Laboratory of Cognitive Neuroscience
Division of Developmental Medicine
1 Autumn Street, AU 650
Boston, MA 02215
857-218-5224


_______________________________________________
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
greve@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/

_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


--
Warren Winter
Research Coordinator
Boston Children's Hospital
Sheridan Laboratory of Cognitive Neuroscience
Division of Developmental Medicine
1 Autumn Street, AU 650
Boston, MA 02215
857-218-5224