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 s0964091@CRIC-0012:~$ SUBJECTS_DIR=~/Desktop/Allimages/MRIscan/janani/CRIC-0014_5679.adb.DICOM to start with.
Then I typed out what you sent s0964091@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-
s0964091@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
s0964091@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 xfgavin@gmail.com wrote: On Tue, Feb 23, 2010 at 12:27 AM, Janani Dhinakaran janinthesky@gmail.com wrote: > When I set SUBJECTS_DIR to /Desktop/..... I get this > > s0964091@CRIC-0012:~$ export > SUBJECTS_DIR=~/Desktop/Allimages/MRIscan/janani/CRIC-0014_5679.adb.DICOM/ > s0964091@CRIC-0012:~$ echo $SUBJECTS_DIR > /home/s0964091/Desktop/Allimages/MRIscan/janani/CRIC-0014_5679.adb.DICOM/ > > Which makes it part of home anyway. > > When I add home into the path I get a double- > > s0964091@CRIC-0012:~$ export > SUBJECTS_DIR=~/home/s0964091/Desktop/Allimages/MRIscan/janani/CRIC-0014_5679.adb.DICOM > s0964091@CRIC-0012:~$ echo $SUBJECTS_DIR > /home/s0964091/home/s0964091/Desktop/Allimages/MRIscan/janani/CRIC-0014_5679.adb.DICOM > > And the Recon-all has errors too. > > s0964091@CRIC-0012:~$ 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 <xfgavin@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 >> <janinthesky@gmail.com> wrote: >> > Is this what you meant: >> > >> > First I tried >> > s0964091@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 >> > >> > >> > s0964091@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 <xfgavin@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 >> >> <janinthesky@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. >> >> > >> >> > >> >> > >> >> > >> >> > s0964091@CRIC-0012:~/Desktop/Allimages/MRIscan/janani/CRIC-0014_5679.adb.DICOM$ >> >> > echo $SUBJECTS_DIR >> >> > Desktop/Allimages/MRIscan/janani/CRIC-0014_5679.adb.DICOM >> >> > >> >> > >> >> > s0964091@CRIC-0012:~/Desktop/Allimages/MRIscan/janani/CRIC-0014_5679.adb.DICOM$ >> >> > 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