On Tue, 2010-02-23 at 08:26 -0500, Martin Reuter wrote: > 1. you need to specify -all after recon-all (as Sita said) > 2. recon-all is the program name and needs to be the first command > 3. -force is needed if the directory exist, alternatively you can delete > the subject directory and start fresh again > > recon-all -all -force -i ... -i ...
to be precise: (I forgot the -s for the subject name:) recon-all -all -s subj001 -i ... -i .... -force > > -Martin > > On Tue, 2010-02-23 at 12:42 +0000, Janani Dhinakaran wrote: > > Thank you for your help. It again only ran for a minute. The > > difference this time seemed to be that it asked me to rerun the > > command with -force. > > > > I wrote out > > s0964...@cric-0012:~$ > > SUBJECTS_DIR=~/Desktop/Allimages/MRIscan/janani/CRIC-0014_5679.adb.DICOM > > to start with. > > > > Then I typed out what you sent > > s0964...@cric-0012:~$ recon-all > > -i > > /home/s0964091/Desktop/Allimages/MRIscan/janani/CRIC-0014_5679.adb.DICOM/Dhinakaran^Janani^-0002-0001-00001.dcm > > -i > > /home/s0964091/Desktop/Allimages/MRIscan/janani/CRIC-0014_5679.adb.DICOM/Dhinakaran^Janani^-0004-0001-00001.dcm > > -s subj001 > > ERROR: > > /home/s0964091/Desktop/Allimages/MRIscan/janani/CRIC-0014_5679.adb.DICOM/subj001 > > exists, delete or re-run with -force > > > > > > So I added -force to the beginning which caused an error- > > > > s0964...@cric-0012:~$ -force recon-all > > -i > > /home/s0964091/Desktop/Allimages/MRIscan/janani/CRIC-0014_5679.adb.DICOM/Dhinakaran^Janani^-0002-0001-00001.dcm > > -i > > /home/s0964091/Desktop/Allimages/MRIscan/janani/CRIC-0014_5679.adb.DICOM/Dhinakaran^Janani^-0004-0001-00001.dcm > > -s subj001 > > No command '-force' found, did you mean: > > Command 'zforce' from package 'gzip' (main) > > -force: command not found > > > > I tried adding it in the end and as I said earlier, it ran well but > > only for a minute. It seems to have done mri_convert ans done a run1 > > and 3 without a run2 > > > > s0964...@cric-0012:~$ recon-all > > -i > > /home/s0964091/Desktop/Allimages/MRIscan/janani/CRIC-0014_5679.adb.DICOM/Dhinakaran^Janani^-0002-0001-00001.dcm > > -i > > /home/s0964091/Desktop/Allimages/MRIscan/janani/CRIC-0014_5679.adb.DICOM/Dhinakaran^Janani^-0004-0001-00001.dcm > > -s subj001 -force > > INFO: > > /home/s0964091/Desktop/Allimages/MRIscan/janani/CRIC-0014_5679.adb.DICOM/subj001 > > exists with -i, but -force specified. > > Deleting any previous source volumes > > Subject Stamp: freesurfer-Linux-centos4_x86_64-stable-pub-v4.5.0 > > Current Stamp: freesurfer-Linux-centos4_x86_64-stable-pub-v4.5.0 > > INFO: SUBJECTS_DIR > > is /home/s0964091/Desktop/Allimages/MRIscan/janani/CRIC-0014_5679.adb.DICOM > > Actual FREESURFER_HOME /usr/local/freesurfer > > -rw-rw-r-- 1 s0964091 s0964091 39914 Feb 23 > > 12:28 > > /home/s0964091/Desktop/Allimages/MRIscan/janani/CRIC-0014_5679.adb.DICOM/subj001/scripts/recon-all.log > > Linux CRIC-0012 2.6.31-19-generic #56-Ubuntu SMP Thu Jan 28 02:39:34 > > UTC 2010 x86_64 GNU/Linux > > /home/s0964091/Desktop/Allimages/MRIscan/janani/CRIC-0014_5679.adb.DICOM/subj001 > > > > mri_convert > > /home/s0964091/Desktop/Allimages/MRIscan/janani/CRIC-0014_5679.adb.DICOM/Dhinakaran^Janani^-0002-0001-00001.dcm > > > > /home/s0964091/Desktop/Allimages/MRIscan/janani/CRIC-0014_5679.adb.DICOM/subj001/mri/orig/001.mgz > > > > > > mri_convert > > /home/s0964091/Desktop/Allimages/MRIscan/janani/CRIC-0014_5679.adb.DICOM/Dhinakaran^Janani^-0002-0001-00001.dcm > > > > /home/s0964091/Desktop/Allimages/MRIscan/janani/CRIC-0014_5679.adb.DICOM/subj001/mri/orig/001.mgz > > > > $Id: mri_convert.c,v 1.146.2.5 2009/04/08 18:40:23 nicks Exp $ > > reading > > from > > /home/s0964091/Desktop/Allimages/MRIscan/janani/CRIC-0014_5679.adb.DICOM/Dhinakaran^Janani^-0002-0001-00001.dcm... > > Getting Series No > > INFO: Found 751 files > > in /home/s0964091/Desktop/Allimages/MRIscan/janani/CRIC-0014_5679.adb.DICOM > > INFO: Scanning for Series Number 2 > > Scanning Directory > > INFO: found 176 files in series > > INFO: loading series header info. > > > > RunNo = 1 > > INFO: sorting. > > INFO: (512 512 176), nframes = 1, ismosaic=0 > > PE Dir ROW ROW > > AutoAlign matrix detected > > AutoAlign Matrix --------------------- > > 1.000 0.000 0.000 0.000; > > 0.000 1.000 0.000 0.000; > > 0.000 0.000 1.000 0.000; > > 0.000 0.000 0.000 1.000; > > > > FileName > > > > /home/s0964091/Desktop/Allimages/MRIscan/janani/CRIC-0014_5679.adb.DICOM/Dhinakaran^Janani^-0002-0001-00001.dcm > > Identification > > NumarisVer syngo MR B17 > > ScannerModel Verio > > PatientName Dhinakaran^Janani^ > > Date and time > > StudyDate 20100126 > > StudyTime 141335.671000 > > SeriesTime 142623.875000 > > AcqTime 142155.855000 > > Acquisition parameters > > PulseSeq tfl3d1_ns > > Protocol t1_mpr_ns_sag_p2_iso > > PhEncDir ROW > > EchoNo 1 > > FlipAngle 9 > > EchoTime 2.48 > > InversionTime 900 > > RepetitionTime 1900 > > PhEncFOV 250 > > ReadoutFOV 250 > > Image information > > RunNo 1 > > SeriesNo 2 > > ImageNo 1 > > NImageRows 512 > > NImageCols 512 > > NFrames 1 > > SliceArraylSize 1 > > IsMosaic 0 > > ImgPos 90.3776 114.4676 105.9606 > > VolRes 0.4883 0.4883 1.0000 > > VolDim 512 512 176 > > Vc -0.0244 -0.9997 -0.0000 > > Vr -0.0170 0.0004 -0.9999 > > Vs -0.9996 0.0244 0.0170 > > VolCenter -2.7567 -8.2942 -17.5285 > > TransferSyntaxUID 1.2.840.10008.1.2.1 > > INFO: no Siemens slice order reversal detected (good!). > > TR=1900.00, TE=2.48, TI=900.00, flip angle=9.00 > > i_ras = (-0.0244253, -0.999702, -2.75516e-09) > > j_ras = (-0.0169601, 0.000414383, -0.999856) > > k_ras = (-0.999558, 0.0244218, 0.0169652) > > writing > > to > > /home/s0964091/Desktop/Allimages/MRIscan/janani/CRIC-0014_5679.adb.DICOM/subj001/mri/orig/001.mgz... > > /home/s0964091/Desktop/Allimages/MRIscan/janani/CRIC-0014_5679.adb.DICOM/subj001 > > > > mri_convert > > /home/s0964091/Desktop/Allimages/MRIscan/janani/CRIC-0014_5679.adb.DICOM/Dhinakaran^Janani^-0004-0001-00001.dcm > > > > /home/s0964091/Desktop/Allimages/MRIscan/janani/CRIC-0014_5679.adb.DICOM/subj001/mri/orig/002.mgz > > > > > > mri_convert > > /home/s0964091/Desktop/Allimages/MRIscan/janani/CRIC-0014_5679.adb.DICOM/Dhinakaran^Janani^-0004-0001-00001.dcm > > > > /home/s0964091/Desktop/Allimages/MRIscan/janani/CRIC-0014_5679.adb.DICOM/subj001/mri/orig/002.mgz > > > > $Id: mri_convert.c,v 1.146.2.5 2009/04/08 18:40:23 nicks Exp $ > > reading > > from > > /home/s0964091/Desktop/Allimages/MRIscan/janani/CRIC-0014_5679.adb.DICOM/Dhinakaran^Janani^-0004-0001-00001.dcm... > > Getting Series No > > INFO: Found 751 files > > in /home/s0964091/Desktop/Allimages/MRIscan/janani/CRIC-0014_5679.adb.DICOM > > INFO: Scanning for Series Number 4 > > Scanning Directory > > INFO: found 176 files in series > > INFO: loading series header info. > > > > RunNo = 3 > > INFO: sorting. > > INFO: (512 512 176), nframes = 1, ismosaic=0 > > PE Dir ROW ROW > > AutoAlign matrix detected > > AutoAlign Matrix --------------------- > > 1.000 0.000 0.000 0.000; > > 0.000 1.000 0.000 0.000; > > 0.000 0.000 1.000 0.000; > > 0.000 0.000 0.000 1.000; > > > > FileName > > > > /home/s0964091/Desktop/Allimages/MRIscan/janani/CRIC-0014_5679.adb.DICOM/Dhinakaran^Janani^-0004-0001-00001.dcm > > Identification > > NumarisVer syngo MR B17 > > ScannerModel Verio > > PatientName Dhinakaran^Janani^ > > Date and time > > StudyDate 20100126 > > StudyTime 141335.671000 > > SeriesTime 144205.640000 > > AcqTime 143536.830000 > > Acquisition parameters > > PulseSeq tfl3d1_ns > > Protocol t1_mpr_ns_sag_p2_iso > > PhEncDir ROW > > EchoNo 1 > > FlipAngle 9 > > EchoTime 2.64 > > InversionTime 900 > > RepetitionTime 1900 > > PhEncFOV 192 > > ReadoutFOV 192 > > Image information > > RunNo 3 > > SeriesNo 4 > > ImageNo 1 > > NImageRows 512 > > NImageCols 512 > > NFrames 1 > > SliceArraylSize 1 > > IsMosaic 0 > > ImgPos 72.1091 90.1873 96.0943 > > VolRes 0.3750 0.3750 0.8000 > > VolDim 512 512 176 > > Vc -0.0244 -0.9997 -0.0000 > > Vr -0.0170 0.0004 -0.9999 > > Vs -0.9996 0.0244 0.0170 > > VolCenter -2.2327 -4.0250 1.3025 > > TransferSyntaxUID 1.2.840.10008.1.2.1 > > INFO: no Siemens slice order reversal detected (good!). > > TR=1900.00, TE=2.64, TI=900.00, flip angle=9.00 > > i_ras = (-0.0244253, -0.999702, -2.75516e-09) > > j_ras = (-0.0169601, 0.000414383, -0.999856) > > k_ras = (-0.999558, 0.0244218, 0.0169652) > > writing > > to > > /home/s0964091/Desktop/Allimages/MRIscan/janani/CRIC-0014_5679.adb.DICOM/subj001/mri/orig/002.mgz... > > > > #------------------------------------------ > > > > recon-all finished without error at Tue Feb 23 12:33:27 GMT 2010 > > done > > > > I'm quite perplexed now as to why it is going wrong. Is it possible at > > all that my data is not suitable for Freesurfer? > > Thanks for your time, > > Jan > > > > On 23 February 2010 09:00, Xue, Feng <xfga...@gmail.com> wrote: > > On Tue, Feb 23, 2010 at 12:27 AM, Janani Dhinakaran > > <janinthe...@gmail.com> wrote: > > > When I set SUBJECTS_DIR to /Desktop/..... I get this > > > > > > s0964...@cric-0012:~$ export > > > > > > > SUBJECTS_DIR=~/Desktop/Allimages/MRIscan/janani/CRIC-0014_5679.adb.DICOM/ > > > s0964...@cric-0012:~$ echo $SUBJECTS_DIR > > > > > /home/s0964091/Desktop/Allimages/MRIscan/janani/CRIC-0014_5679.adb.DICOM/ > > > > > > Which makes it part of home anyway. > > > > > > When I add home into the path I get a double- > > > > > > s0964...@cric-0012:~$ export > > > > > > > SUBJECTS_DIR=~/home/s0964091/Desktop/Allimages/MRIscan/janani/CRIC-0014_5679.adb.DICOM > > > s0964...@cric-0012:~$ echo $SUBJECTS_DIR > > > > > /home/s0964091/home/s0964091/Desktop/Allimages/MRIscan/janani/CRIC-0014_5679.adb.DICOM > > > > > > And the Recon-all has errors too. > > > > > > s0964...@cric-0012:~$ recon-all -i > > > > > /home/s0964091/Desktop/Allimages/MRIscan/janani/CRIC-0014_5679.adb.DICOM/Dhinakaran^Janani^-0002-0001-00001.dcm > > > -i > > > > > /home/s0964091/Desktop/Allimages/MRIscan/janani/CRIC-0014_5679.adb.DICOM/Dhinakaran^Janani^-0004-0001-00001.d > > > > here should be .dcm, > > meanwhile, you > > don't need to export SUBJECTS_DIR, because we don't need > > global level > > environment variables. > > please try as below: > > under your shell indicator, type: > > > > > > SUBJECTS_DIR=~/Desktop/Allimages/MRIscan/janani/CRIC-0014_5679.adb.DICOM > > > > > > recon-all > > -i > > /home/s0964091/Desktop/Allimages/MRIscan/janani/CRIC-0014_5679.adb.DICOM/Dhinakaran^Janani^-0002-0001-00001.dcm > > -i > > /home/s0964091/Desktop/Allimages/MRIscan/janani/CRIC-0014_5679.adb.DICOM/Dhinakaran^Janani^-0004-0001-00001.dcm > > -s subj001 > > > > > > Hope this could solve your trouble. > > > > > > > ERROR: cannot find > > > > > /home/s0964091/Desktop/Allimages/MRIscan/janani/CRIC-0014_5679.adb.DICOM/Dhinakaran^Janani^-0004-0001-00001.d > > > Linux CRIC-0012 2.6.31-19-generic #56-Ubuntu SMP Thu Jan 28 > > 02:39:34 UTC > > > 2010 x86_64 GNU/Linux > > > > > > recon-all exited with ERRORS at Mon Feb 22 16:24:46 GMT 2010 > > > > > > > > > It doesn't run recon at all. Unlike the previous command > > which did but > > > incompletely. > > > > > > Jan > > > > > > > > > On 22 February 2010 16:21, Xue, Feng <xfga...@gmail.com> > > wrote: > > >> > > >> It seems that your problem is the recon-all script couldn't > > find your > > >> SUBJECTS_DIR, possibly because you didn't give it full > > path. So I > > >> suggest to try define SUBJECTS_DIR as > > >> > > /home/s0964091/Desktop/Allimages/MRIscan/janani/CRIC-0014_5679.adb.DICOM, > > >> then rerun your recon-all command as before. > > >> > > >> On Mon, Feb 22, 2010 at 10:44 PM, Janani Dhinakaran > > >> <janinthe...@gmail.com> wrote: > > >> > Is this what you meant: > > >> > > > >> > First I tried > > >> > s0964...@cric-0012:~$ recon-all > > >> > > > > > home/s0964091/Desktop/Allimages/MRIscan/janani/CRIC-0014_5679.adb.DICOM > > >> > ERROR: Flag > > >> > > > > > home/s0964091/Desktop/Allimages/MRIscan/janani/CRIC-0014_5679.adb.DICOM > > >> > unrecognized. > > >> > > > > > home/s0964091/Desktop/Allimages/MRIscan/janani/CRIC-0014_5679.adb.DICOM > > >> > Linux CRIC-0012 2.6.31-19-generic #56-Ubuntu SMP Thu Jan > > 28 02:39:34 UTC > > >> > 2010 x86_64 GNU/Linux > > >> > > > >> > recon-all exited with ERRORS at Mon Feb 22 14:39:27 GMT > > 2010 > > >> > > > >> > Then I tried putting full path in front of both file sets > > >> > > > >> > > > >> > s0964...@cric-0012:~$ recon-all -i > > >> > > > >> > > > > > home/s0964091/Desktop/Allimages/MRIscan/janani/CRIC-0014_5679.adb.DICOM/Dhinakaran^Janani^-0002-0001-00001.dcm > > >> > -i > > >> > > > >> > > > > > home/s0964091/Desktop/Allimages/MRIscan/janani/CRIC-0014_5679.adb.DICOM/Dhinakaran^Janani^-0004-0001-00001.dcm > > >> > -s subj001 > > >> > ERROR: cannot find > > >> > > > >> > > > > > home/s0964091/Desktop/Allimages/MRIscan/janani/CRIC-0014_5679.adb.DICOM/Dhinakaran^Janani^-0002-0001-00001.dcm > > >> > Linux CRIC-0012 2.6.31-19-generic #56-Ubuntu SMP Thu Jan > > 28 02:39:34 UTC > > >> > 2010 x86_64 GNU/Linux > > >> > > > >> > recon-all exited with ERRORS at Mon Feb 22 14:41:36 GMT > > 2010 > > >> > > > >> > Jan > > >> > > > >> > > > >> > On 22 February 2010 14:30, Xue, Feng <xfga...@gmail.com> > > wrote: > > >> >> > > >> >> Try with full path, e.g. > > >> >> > > >> > > >> > > /home/s0964091/Desktop/Allimages/MRIscan/janani/CRIC-0014_5679.adb.DICOM > > >> >> > > >> >> On Mon, Feb 22, 2010 at 7:36 PM, Janani Dhinakaran > > >> >> <janinthe...@gmail.com> wrote: > > >> >> > Hello, > > >> >> > I ran recon-all on Friday. It ran for around a minute > > instead of > > >> >> > 30-48 > > >> >> > hours. Unfortunately, when I try tkmedit and other > > such commands, the > > >> >> > pictures don't visualise. > > >> >> > So today I first confirmed that the SUBJECTS_DIR was > > in Desktop path. > > >> >> > (Because over the weekend it had gone back to > > usr/local... path and > > >> >> > so I > > >> >> > re-exported it just now.) > > >> >> > Then I tried running recon-all again. > > >> >> > > > >> >> > > > >> >> > > > >> >> > > > >> >> > > > > > s0964...@cric-0012:~/Desktop/Allimages/MRIscan/janani/CRIC-0014_5679.adb.DICOM$ > > >> >> > echo $SUBJECTS_DIR > > >> >> > > > Desktop/Allimages/MRIscan/janani/CRIC-0014_5679.adb.DICOM > > >> >> > > > >> >> > > > >> >> > > > > > s0964...@cric-0012:~/Desktop/Allimages/MRIscan/janani/CRIC-0014_5679.adb.DICOM$ > > >> >> > recon-all -i Dhinakaran^Janani^-0002-0001-00001.dcm -i > > >> >> > Dhinakaran^Janani^-0004-0001-00001.dcm -s subj001 > > >> >> > ERROR: SUBJECTS_DIR > > >> >> > > > Desktop/Allimages/MRIscan/janani/CRIC-0014_5679.adb.DICOM does > > not > > >> >> > exist. > > >> >> > > > >> >> > Can anyone help me understand what I can do? > > >> >> > Thanks > > >> >> > Jan > > >> >> > -- > > >> >> > I am the Sun, I know no darkness. > > >> >> > > > >> >> > _______________________________________________ > > >> >> > Freesurfer mailing list > > >> >> > Freesurfer@nmr.mgh.harvard.edu > > >> >> > > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > >> >> > > > >> >> > > >> >> > > >> >> > > >> >> -- > > >> >> Best Regards > > >> >> > > >> >> Xue, Feng Phd. candidate > > >> >> Major in Developmental Cognitive Neuroscience > > >> >> > > >> >> National Key Laboratory of Cognitive Neuroscience and > > Learning > > >> >> Beijing Normal University > > >> >> Beijing, China. 100875 > > >> >> Tel: +86-13810154455 > > >> >> web: http://psychbrain.bnu.edu.cn > > >> >> ============================================== > > >> >> Welcome to MuDuo JinSheng BBS @ Beijing Normal > > University > > >> >> telnet://bbs.mdjs.org > > >> >> http://bbs.mdjs.org > > >> > > > >> > > > >> > > > >> > -- > > >> > I am the Sun, I know no darkness. > > >> > > > >> > > >> > > >> > > >> -- > > >> Best Regards > > >> > > >> Xue, Feng Phd. candidate > > >> Major in Developmental Cognitive Neuroscience > > >> > > >> National Key Laboratory of Cognitive Neuroscience and > > Learning > > >> Beijing Normal University > > >> Beijing, China. 100875 > > >> Tel: +86-13810154455 > > >> web: http://psychbrain.bnu.edu.cn > > >> ============================================== > > >> Welcome to MuDuo JinSheng BBS @ Beijing Normal University > > >> telnet://bbs.mdjs.org > > >> http://bbs.mdjs.org > > > > > > > > > > > > -- > > > I am the Sun, I know no darkness. > > > > > > > > > > > > > -- > > > > Best Regards > > > > Xue, Feng Phd. candidate > > Major in Developmental Cognitive Neuroscience > > > > National Key Laboratory of Cognitive Neuroscience and Learning > > Beijing Normal University > > Beijing, China. 100875 > > Tel: +86-13810154455 > > web: http://psychbrain.bnu.edu.cn > > ============================================== > > Welcome to MuDuo JinSheng BBS @ Beijing Normal University > > telnet://bbs.mdjs.org > > http://bbs.mdjs.org > > > > > > > > > > -- > > I am the Sun, I know no darkness. > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
