Hi,Freesurfers
I'm practicing freesufer analysis with tutorial data set. I downloaded all data and I adhere to hierarchy. Now I'm in preprocess session. But I get the following message in that shell every few seconds. I'm a beginner of freesurfer,so please tell me about solvent on this problem.
Kenta
[root@localhost fsfast-tut_2]# ls fb1-analysis-study fb1-raw fbph1-101 fbph1-104 fbph1-106 fb1-preproc-study fb1-raw-study fbph1-103 fbph1-105 [root@localhost fsfast-tut_2]# setenv SUBJECTS_DIR $PWD [root@localhost fsfast-tut_2]# ls fb1-analysis-study fb1-raw fbph1-101 fbph1-104 fbph1-106 fb1-preproc-study fb1-raw-study fbph1-103 fbph1-105 [root@localhost fsfast-tut_2]# mkdir -p my-study [root@localhost fsfast-tut_2]# ls fb1-analysis-study fb1-raw fbph1-101 fbph1-104 fbph1-106 fb1-preproc-study fb1-raw-study fbph1-103 fbph1-105 my-study [root@localhost fsfast-tut_2]# cd my-study/ [root@localhost my-study]# ls [root@localhost my-study]# mkdir -p mgh-101.1/bold [root@localhost my-study]# mkdir -p mgh-101.1/bold/003 [root@localhost my-study]# mkdir -p mgh-101.1/bold/005 [root@localhost my-study]# mkdir -p mgh-101.1/bold/007 [root@localhost my-study]# mkdir -p mgh-101.1/bold/010 [root@localhost my-study]# cp ../fb1-raw/f.mgh-101.1-r003. nii mgh-101.1/bold/003/f.nii [root@localhost my-study]# cp ../fb1-raw/f.mgh-101.1-r005.nii mgh-101.1/bold/005/f.nii [root@localhost my-study]# cp ../fb1-raw/f.mgh-101.1-r007.nii mgh-101.1/bold/007/f.nii [root@localhost my-study]# cp ../fb1-raw/f.mgh-101.1-r010.nii mgh-101.1/bold/010/f.nii [root@localhost my-study]# cd $SUBJECTS_DIR/my-study/ [root@localhost my-study]# echo fbph1-101 > mgh-101.1/subjectname [root@localhost my-study]# preproc-sess -s mgh-101.1 -fwhm 5 -------------------------------------------------------------- preproc-sess logfile is log/preproc-sess.log -------------------------------------------------------------- instem f mc 1 f fmc stc 0 fmc sm 1 fmc fmcsm5 mask 1 brain mgh-101.1 MC ----------------------------- 2009年 11月 2日 月曜日 19:54:41 JST /usr/local/freesurfer/fsfast-tut_2/my-study mc-sess -fstem f -fmcstem fmc -s mgh-101.1 -d /usr/local/freesurfer/fsfast-tut_2/my-study -fsd bold -new -update -no-inorm ---------------------------------------- Logfile is /usr/local/freesurfer/fsfast-tut_2/my-study/log/mc-mgh-101.1-bold.log ------------------------------------------- /usr/local/freesurfer/fsfast-tut_2/my-study/mgh-101.1 RunList: 003 005 007 010 Targ Stem is 003/f ------- ************************** ----------- ------- Motion Correcting Run 003 ----------- ------- ************************** ----------- sess = mgh-101.1 2009年 11月 2日 月曜日 19:54:42 JST mc-afni2 --i 003/f.nii --t 003/f.nii --frame 0 --o 003/fmc.nii --mcdat 003/fmc.mcdat /usr/local/freesurfer/fsfast-tut_2/my-study/mgh-101.1/bold mri_info --nframes --o /tmp/mriinfo.7888 003/f.nii log file is 003/fmc.nii.mclog mcdat file is 003/fmc.mcdat tmp dir is 003/tmp.mc-afni2.7888 #@# -------------------------------- /usr/local/freesurfer/fsfast-tut_2/my-study/mgh-101.1/bold mri_convert 003/f.nii 003/tmp.mc-afni2.7888/tempvol.nii.gz --nskip 0 --ndrop 84 -odt float mri_convert 003/f.nii 003/tmp.mc-afni2.7888/tempvol.nii.gz --nskip 0 --ndrop 84 -odt float nskip = 0 ndrop = 84 $Id: mri_convert.c,v 1.146.2.5 2009/04/08 18:40:23 nicks Exp $ reading from 003/f.nii... TR=3000.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-0.9973, -0.0712038, 0.0179835) j_ras = (0.0625429, -0.951817, -0.300222) k_ras = (0.038494, -0.298286, 0.9537) changing data type from 4 to 3 (noscale = 0)... Dropping last 84 frames writing to 003/tmp.mc-afni2.7888/tempvol.nii.gz... #@# -------------------------------- /usr/local/freesurfer/fsfast-tut_2/my-study/mgh-101.1/bold mri_convert 003/f.nii 003/tmp.mc-afni2.7888/invol.nii.gz -odt float mri_convert 003/f.nii 003/tmp.mc-afni2.7888/invol.nii.gz -odt float $Id: mri_convert.c,v 1.146.2.5 2009/04/08 18:40:23 nicks Exp $ reading from 003/f.nii... TR=3000.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-0.9973, -0.0712038, 0.0179835) j_ras = (0.0625429, -0.951817, -0.300222) k_ras = (0.038494, -0.298286, 0.9537) changing data type from 4 to 3 (noscale = 0)... writing to 003/tmp.mc-afni2.7888/invol.nii.gz... #@# -------------------------------- /usr/local/freesurfer/fsfast-tut_2/my-study/mgh-101.1/bold 3dvolreg -verbose -dfile 003/fmc.mcdat -base 003/tmp.mc-afni2.7888/tempvol.nii.gz -prefix 003/tmp.mc-afni2.7888/outvol.nii.gz 003/tmp.mc-afni2.7888/invol.nii.gz ++ 3dvolreg: AFNI version=AFNI_2008_07_18_1710 (Feb 10 2009) [32-bit] ++ Authored by: RW Cox *+ WARNING: If you are performing spatial transformations on an oblique dset, such as 003/tmp.mc-afni2.7888/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:003/tmp.mc-afni2.7888/tempvol.nii.gz is 17.858507 degrees from plumb. ++ Reading in base dataset 003/tmp.mc-afni2.7888/tempvol.nii.gz ++ Oblique dataset:003/tmp.mc-afni2.7888/invol.nii.gz is 17.858507 degrees from plumb. ++ Reading input dataset 003/tmp.mc-afni2.7888/invol.nii.gz ++ Edging: x=3 y=3 z=2 ++ Creating mask for -maxdisp + Automask has 35321 voxels + 5274 voxels left in -maxdisp mask after erosion ++ Initializing alignment base ++ Starting final pass on 85 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.. ++ CPU time for realignment=3.03 s [=0.0356 s/sub-brick] ++ Min : roll=-0.058 pitch=-0.007 yaw=-0.048 dS=-0.054 dL=-0.105 dP=-0.106 ++ Mean: roll=-0.007 pitch=+0.094 yaw=-0.023 dS=+0.145 dL=-0.029 dP=-0.026 ++ Max : roll=+0.062 pitch=+0.333 yaw=+0.016 dS=+0.318 dL=+0.121 dP=+0.017 ++ Max displacements (mm) for each sub-brick: 0.00 0.06 0.04 0.06 0.08 0.11 0.16 0.15 0.17 0.14 0.23 0.32 0.38 0.44 0.25 0.28 0.37 0.37 0.39 0.28 0.30 0.58 0.18 0.31 0.29 0.29 0.27 0.26 0.25 0.30 0.29 0.27 0.64 0.31 0.17 0.22 0.30 0.31 0.33 0.38 0.38 0.35 0.17 0.17 0.35 0.41 0.39 0.36 0.36 0.41 0.39 0.39 0.39 0.46 0.36 0.42 0.40 0.39 0.38 0.39 0.38 0.41 0.38 0.30 0.33 0.36 0.35 0.37 0.38 0.38 0.39 0.38 0.38 0.38 0.37 0.36 0.34 0.35 0.33 0.34 0.34 0.37 0.36 0.37 0.33 ++ Max displacement in automask = 0.64 (mm) at sub-brick 32 ++ Wrote dataset to disk in 003/tmp.mc-afni2.7888/outvol.nii.gz 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