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 ... -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
