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.