Hi Doug,
following up on my problem with preprocessing, here is the line that we ran:
preproc-sess -sf sessid3 -df sessdir -per-run -sliceorder siemens -fsd bold -fwhm 0 -mni305-2mm -surface self lhrh -force
the part that is failing is:
mc-afni2 --i 004/f.nii.gz --t 004/template.nii.gz --o 004/fmcpr.nii.gz --mcdat 004/fmcpr.mcdat
that line calls 3dvolreg.afni, which is the part that is really failing:
3dvolreg.afni -verbose -dfile 004/fmcpr.mcdat -1Dmatrix_save 004/fmcpr.mat -base 004/tmp.mc-afni2.24802/tempvol.nii.gz -prefix 004/tmp.mc-afni2.24802/outvol.nii.gz 004/tmp.mc-afni2.24802/invol.nii.gz
we tried running it without the .afni extenstion, so using the actual afni 3dvolreg and got no error message:
3dvolreg -verbose -dfile 004/fmcpr.mcdat -1Dmatrix_save 004/fmcpr.mat -base 004/tmp.mc-afni2.24802/tempvol.nii.gz -prefix 004/tmp.mc-afni2.24802/outvol.nii.gz 004/tmp.mc-afni2.24802/invol.nii.gz
This is the output for mc-afni2:
mc-afni2 --i 004/f.nii.gz --t 004/template.nii.gz --o 004/fmcpr.nii.gz --mcdat 004/fmcpr.mcdat
/ncf/vcn/Maryam/mri-space/studies/SM_PDM/unpackdata/111206_xu_SM_PDM_05/bold
mri_info --nframes --o /tmp/mriinfo.24802 004/template.nii.gz
log file is 004/fmcpr.nii.gz.mclog
mcdat file is 004/fmcpr.mcdat
tmp dir is 004/tmp.mc-afni2.24802
#@# --------------------------------
/ncf/vcn/Maryam/mri-space/studies/SM_PDM/unpackdata/111206_xu_SM_PDM_05/bold
mri_convert 004/template.nii.gz 004/tmp.mc-afni2.24802/tempvol.nii.gz --nskip 0 --ndrop 0 -odt float
mri_convert 004/template.nii.gz 004/tmp.mc-afni2.24802/tempvol.nii.gz --nskip 0 --ndrop 0 -odt float
nskip = 0
ndrop = 0
$Id: mri_convert.c,v 1.179.2.2 2011/05/16 20:53:47 greve Exp $
reading from 004/template.nii.gz...
TR=2000.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-0.997352, 0.0123936, -0.0716608)
j_ras = (-0.0197242, -0.994536, 0.102512)
k_ras = (-0.0699987, 0.103654, 0.992147)
changing data type from short to float (noscale = 0)...
writing to 004/tmp.mc-afni2.24802/tempvol.nii.gz...
#@# --------------------------------
/ncf/vcn/Maryam/mri-space/studies/SM_PDM/unpackdata/111206_xu_SM_PDM_05/bold
mri_convert 004/f.nii.gz 004/tmp.mc-afni2.24802/invol.nii.gz -odt float
mri_convert 004/f.nii.gz 004/tmp.mc-afni2.24802/invol.nii.gz -odt float
$Id: mri_convert.c,v 1.179.2.2 2011/05/16 20:53:47 greve Exp $
reading from 004/f.nii.gz...
TR=2000.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-0.997352, 0.0123936, -0.0716608)
j_ras = (-0.0197242, -0.994536, 0.102512)
k_ras = (-0.0699987, 0.103654, 0.992147)
changing data type from short to float (noscale = 0)...
writing to 004/tmp.mc-afni2.24802/invol.nii.gz...
#@# --------------------------------
/ncf/vcn/Maryam/mri-space/studies/SM_PDM/unpackdata/111206_xu_SM_PDM_05/bold
3dvolreg.afni -verbose -dfile 004/fmcpr.mcdat -1Dmatrix_save 004/fmcpr.mat -base 004/tmp.mc-afni2.24802/tempvol.nii.gz -prefix 004/tmp.mc-afni2.24802/outvol.nii.gz 004/tmp.mc-afni2.24802/invol.nii.gz
++ 3dvolreg: AFNI version=AFNI_2008_07_18_1710 (Feb 10 2009) [64-bit]
++ Authored by: RW Cox
*+ WARNING: If you are performing spatial transformations on an oblique dset,
such as 004/tmp.mc-afni2.24802/tempvol.nii.gz,
or viewing/combining it with volumes of differing obliquity,
you should consider running:
3dWarp -deoblique
on this and other oblique datasets in the same session.
See 3dWarp -help for details.
++ Oblique dataset:004/tmp.mc-afni2.24802/tempvol.nii.gz is 7.185125 degrees from plumb.
++ Reading in base dataset 004/tmp.mc-afni2.24802/tempvol.nii.gz
++ Oblique dataset:004/tmp.mc-afni2.24802/invol.nii.gz is 7.185125 degrees from plumb.
++ Reading input dataset 004/tmp.mc-afni2.24802/invol.nii.gz
++ Edging: x=4 y=4 z=2
++ Creating mask for -maxdisp
+ Automask has 37793 voxels
+ 5984 voxels left in -maxdisp mask after erosion
++ Initializing alignment base
++ Starting final pass on 192 sub-bricks: 0..1..2..3..4..5..6..7..8..9..10..11..12..13..14..15..16..17..18..19..20..21..22..23..24..25..26..27..28..29..30..31..32..33..34..35..36..37..38..39..40..41..42..43..44..45..46..47..48..49..50..51..52..53..54..55..56..57..58..59..60..61..62..63..64..65..66..67..68..69..70..71..72..73..74..75..76..77..78..79..80..81..82..83..84..85..86..87..88..89..90..91..92..93..94..95..96..97..98..99..100..101..102..103..104..105..106..107..108..109..110..111..112..113..114..115..116..117..118..119..120..121..122..123..124..125..126..127..128..129..130..131..132..133..134..135..136..137..138..139..140..141..142..143..144..145..146..147..148..149..150..151..152..153..154..155..156..157..158..159..160..161..162..163..164..165..166..167..168..169..170..171..172..173..174..175..176..177..178..179..180..181..182..183..184..185..186..187..188..189..190..191..
++ CPU time for realignment=12.2 s [=0.0634 s/sub-brick]
++ Min : roll=-0.043 pitch=-0.422 yaw=-0.218 dS=-0.084 dL=-0.077 dP=-0.160
++ Mean: roll=+0.044 pitch=+0.020 yaw=-0.018 dS=-0.014 dL=-0.020 dP=+0.024
++ Max : roll=+0.151 pitch=+0.373 yaw=+0.107 dS=+0.130 dL=+0.037 dP=+0.166
++ Max displacements (mm) for each sub-brick:
0.72 0.79 0.72 0.79 0.72 0.71 0.71 0.71 0.72 0.66 0.72 0.67 0.72 0.66 0.70 0.68 0.65 0.70 0.62 0.69 0.63 0.67 0.60 0.68 0.58 0.64 0.58 0.60 0.55 0.58 0.51 0.61 0.51 0.54 0.49 0.57 0.46 0.55 0.44 0.46 0.41 0.46 0.41 0.40 0.41 0.42 0.41 0.37 0.40 0.36 0.32 0.23 0.20 0.18 0.17 0.17 0.15 0.16 0.18 0.20 0.19 0.17 0.22 0.17 0.15 0.18 0.11 0.12 0.15 0.10 0.21 0.38 0.23 0.20 0.19 0.18 0.15 0.14 0.20 0.13 0.17 0.13 0.11 0.06 0.09 0.04 0.10 0.12 0.13 0.04 0.11 0.03 0.05 0.06 0.05 0.04 0.00 0.03 0.04 0.10 0.09 0.10 0.07 0.12 0.11 0.12 0.19 0.10 0.21 0.16 0.31 0.24 0.28 0.26 0.39 0.26 0.42 0.32 0.40 0.29 0.34 0.32 0.26 0.35 0.32 0.36 0.36 0.31 0.35 0.36 0.39 0.48 0.40 0.55 0.41 0.50 0.41 0.47 0.40 0.49 0.47 0.37 0.56 0.45 0.49 0.50 0.47 0.33 0.60 0.48 0.43 0.35 0.51 0.46 0.45 0.32 0.46 0.39 0.46 0.32 0.49 0.39 0.46 0.36 0.49 0.41 0.46 0.51 0.45 0.47 0.42 0.44 0.47 0.42 0.52 0.47 0.49 0.57 0.52 0.59 0.64 0.62 0.54 0.64 0.62 0.57 0.66 0.57 0.64 0.63 0.53 0.65
++ Max displacement in automask = 0.79 (mm) at sub-brick 3
Can't connect? tcp_connect[connect]: Connection timed out
++ Wrote dataset to disk in 004/tmp.mc-afni2.24802/outvol.nii.gz
** Warning: overwriting file 004/fmcpr.mcdat
Can't connect? tcp_connect[connect]: Connection timed out
Can't connect? tcp_connect[connect]: Connection timed out
Can't connect? tcp_connect[connect]: Connection timed out
Can't connect? tcp_connect[connect]: Connection timed out
Can't connect? tcp_connect[connect]: Connection timed out
goes on forever......but did create an output vol:
-rw-r--r-- 1 mvpashkam vcn 111254803 Dec 13 12:47 outvol.nii.gz
output from afni's 3dvolreg:
3dvolreg -verbose -dfile 004/fmcpr.mcdat -1Dmatrix_save 004/fmcpr.mat -base 004/tmp.mc-afni2.24802/tempvol.nii.gz -prefix 004/tmp.mc-afni2.24802/outvol.nii.gz 004/tmp.mc-afni2.24802/invol.nii.gz
++ 3dvolreg: AFNI version=AFNI_2011_05_26_1457 (Aug 17 2011) [64-bit]
++ Authored by: RW Cox
*+ WARNING: If you are performing spatial transformations on an oblique dset,
such as 004/tmp.mc-afni2.24802/tempvol.nii.gz,
or viewing/combining it with volumes of differing obliquity,
you should consider running:
3dWarp -deoblique
on this and other oblique datasets in the same session.
See 3dWarp -help for details.
++ Oblique dataset:004/tmp.mc-afni2.24802/tempvol.nii.gz is 7.185125 degrees from plumb.
++ Reading in base dataset 004/tmp.mc-afni2.24802/tempvol.nii.gz
++ Oblique dataset:004/tmp.mc-afni2.24802/invol.nii.gz is 7.185125 degrees from plumb.
++ Reading input dataset 004/tmp.mc-afni2.24802/invol.nii.gz
++ Edging: x=4 y=4 z=2
++ Creating mask for -maxdisp
+ Automask has 37791 voxels
+ 5976 voxels left in -maxdisp mask after erosion
++ Initializing alignment base
++ Starting final pass on 192 sub-bricks: 0..1..2..3..4..5..6..7..8..9..10..11..12..13..14..15..16..17..18..19..20..21..22..23..24..25..26..27..28..29..30..31..32..33..34..35..36..37..38..39..40..41..42..43..44..45..46..47..48..49..50..51..52..53..54..55..56..57..58..59..60..61..62..63..64..65..66..67..68..69..70..71..72..73..74..75..76..77..78..79..80..81..82..83..84..85..86..87..88..89..90..91..92..93..94..95..96..97..98..99..100..101..102..103..104..105..106..107..108..109..110..111..112..113..114..115..116..117..118..119..120..121..122..123..124..125..126..127..128..129..130..131..132..133..134..135..136..137..138..139..140..141..142..143..144..145..146..147..148..149..150..151..152..153..154..155..156..157..158..159..160..161..162..163..164..165..166..167..168..169..170..171..172..173..174..175..176..177..178..179..180..181..182..183..184..185..186..187..188..189..190..191..
++ CPU time for realignment=0 s [=0 s/sub-brick]
++ Min : roll=-0.043 pitch=-0.422 yaw=-0.218 dS=-0.084 dL=-0.077 dP=-0.160
++ Mean: roll=+0.044 pitch=+0.020 yaw=-0.018 dS=-0.014 dL=-0.020 dP=+0.024
++ Max : roll=+0.151 pitch=+0.373 yaw=+0.107 dS=+0.130 dL=+0.037 dP=+0.166
++ Max displacements (mm) for each sub-brick:
0.72 0.79 0.72 0.79 0.72 0.71 0.71 0.71 0.72 0.66 0.72 0.67 0.72 0.66 0.70 0.68 0.65 0.70 0.62 0.69 0.63 0.67 0.60 0.68 0.58 0.64 0.58 0.60 0.55 0.58 0.51 0.61 0.51 0.54 0.49 0.57 0.46 0.55 0.44 0.46 0.41 0.46 0.41 0.40 0.41 0.42 0.41 0.37 0.40 0.36 0.32 0.23 0.21 0.18 0.17 0.17 0.15 0.16 0.18 0.20 0.19 0.17 0.22 0.17 0.15 0.18 0.11 0.12 0.15 0.10 0.21 0.38 0.23 0.20 0.19 0.18 0.15 0.14 0.20 0.13 0.17 0.13 0.11 0.06 0.09 0.04 0.10 0.12 0.13 0.04 0.11 0.03 0.05 0.06 0.05 0.04 0.00 0.03 0.04 0.10 0.09 0.10 0.07 0.12 0.11 0.12 0.19 0.10 0.21 0.16 0.31 0.24 0.28 0.26 0.39 0.26 0.42 0.32 0.40 0.29 0.34 0.32 0.26 0.35 0.32 0.36 0.36 0.31 0.35 0.36 0.39 0.48 0.40 0.55 0.41 0.50 0.41 0.47 0.40 0.49 0.47 0.37 0.56 0.45 0.49 0.50 0.47 0.33 0.60 0.48 0.43 0.35 0.51 0.46 0.45 0.32 0.46 0.39 0.46 0.32 0.49 0.39 0.46 0.36 0.49 0.41 0.46 0.51 0.45 0.47 0.42 0.44 0.47 0.42 0.52 0.47 0.49 0.57 0.52 0.59 0.64 0.62 0.54 0.64 0.62 0.57 0.66 0.57 0.64 0.63 0.53 0.65
++ Max displacement in automask = 0.79 (mm) at sub-brick 3
++ Wrote dataset to disk in 004/tmp.mc-afni2.24802/outvol.nii.gz
** Warning: overwriting file 004/fmcpr.mcdat
created an output vol: -rw-r--r-- 1 mvpashkam vcn 111260685 Dec 13 13:01 outvol.nii.gz
Any idea where the problem might be?
Thanks,
Maryam
On Mon, Dec 12, 2011 at 12:00 PM, freesurfer-request@nmr.mgh.harvard.eduwrote:
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Today's Topics:
- preprocessing error (Maryam Vaziri Pashkam)
- Re: preprocessing error (Douglas Greve)
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- References/materials for interaction analysis in freesurfer (Bhavani Shankara Bagepally)
- Re: dt_recon error (Yuko Yotsumoto)
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- Re: run preproc-sess with -nomc (Thunell Evelina)
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Message: 1 Date: Sun, 11 Dec 2011 14:34:05 -0500 From: Maryam Vaziri Pashkam mvaziri.p@gmail.com Subject: [Freesurfer] preprocessing error To: freesurfer@nmr.mgh.harvard.edu Message-ID: <CAEEXA4cePaYDO8EPMpma7ThADfnd1qcYfg2HnnHz+7sVrVBTjw@mail.gmail.com
Content-Type: text/plain; charset="iso-8859-1"
Hi,
I am running preprocessing on my data using freesurfer 5.1, fsl 4.1.7, and matlab R2009a (I also tried it with matlab 2007a) on Harvard cluster and I am receiving an error. I connect to the cluster using terminal and SSH connection in mac.
the preprocessing is stalled in the middle with this error:
++ Max displacement in automask = 0.79 (mm) at sub-brick 3 Can't connect? tcp_connect[connect]: Connection timed out ++ Wrote dataset to disk in 004/tmp.mc-afni2.20850/outvol.nii.gz ** Warning: overwriting file 004/fmcpr.mcdat Can't connect? tcp_connect[connect]: Connection timed out Can't connect? tcp_connect[connect]: Connection timed out Can't connect? tcp_connect[connect]: Connection timed out
It does not stop running and output an error. But rather keeps printing the last line and does not move forward. Any idea where the problem might be?
Thanks, Maryam