try giving it the dicoms directly as input (instead of converting first) 
and make sure you have -all on the recon-all command line and see if that 
works
Bruce
On Fri, 8 Mar 2013, Valtina Pouegue wrote:
 
> Just a dial error. I use the all at the end. 
> I have 4 subjects and a set of dicom for each subjects. I would like to
> convert my dicoms files to be able to make a segmentation with Freesurfer
> ...
> 
> Date: Fri, 8 Mar 2013 14:32:20 -0500
> From: fischl@nmr.mgh.harvard.edu
> To: pvaltti@hotmail.com
> CC: nicks@nmr.mgh.harvard.edu; freesurfer@nmr.mgh.harvard.edu;
> greve@nmr.mgh.harvard.edu
> Subject: Re: [Freesurfer] Time
> 
> what are you trying to do? If run a recon, your first command should have a 
> -all at the end of it
> 
> cheers
> Bruce
>
> 
> On Fri, 8 Mar 2013, Valtina Pouegue wrote:
> 
> > I don't think the disk is  a problem: I have a lot of space. But in resume
> ,
> > here is exactly what i did ( in order):- I created a folder where I saved
> > the dicoms of my subject
> > - I tried the command 
> > 
> > recon-all -i <path-to-first-structural> [-i <path-to-second-structural>] -
> s
> > <subjid>
> > 
> >  like recon-all -i $SUBJECTS_DIR/PatientXX/blablabla.dcm -s XX . 
> > - I got a folder with empty folders excepts orig which got a folder name
> > '001.mgz'.
> > - I thought that the file was .mgz was my dicom in .mgz, so I try opened
> > them with tkmedit , and It didn't work
> > - I also launch just after the recon-all command for segmentation .
> > - Just after I try the mri_convert for my subject like '
> > mri_convert  $SUBJECTS_DIR/PatientXX/blablabla.dcm out.mgz
> > - I got an mgz folder in the /mri/
> > - I opened it with tkmedit and I could see the volume
> > 
> > So, I retry with another subject , an I got the error described in the
> > previous mail. Did I make a mistake somewhere? 
> > VP
> > 
> >  Date: Fri, 8 Mar 2013 14:19:29 -0500
> > > From: fischl@nmr.mgh.harvard.edu
> > > To: pvaltti@hotmail.com
> > > CC: greve@nmr.mgh.harvard.edu; freesurfer@nmr.mgh.harvard.edu;
> > nicks@nmr.mgh.harvard.edu
> > > Subject: RE: [Freesurfer] Time
> > >
> > > looks like you don't have permission to write to that directory (or the
> > > disk is full)
> > >
> > > On Fri, 8 Mar 2013, Valtina Pouegue wrote:
> > >
> > > >
> > > > VP,I try FreeView,, tit<s really nice!
> > > > I dont really know what going on, i try mri-convert with another subje
> ct
> > > > aand i get this:
> > > > --------------------
> > > > [esther@IP132-207-67-224 /]$ mri_convert
> > > > $SUBJECTS_DIR/Patient3B/IM-0007--2095579184-0001.dcm out.mgz
> > > >mri_convert/home/esther/Freesurfer/freesurfer/subjects/Patient3B/IM-000
> 7--2
> > 095579184-0
> > > > 001.dcm out.mgz 
> > > > $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $
> > > > readingfrom/home/esther/Freesurfer/freesurfer/subjects/Patient3B/IM-00
> 07--20955791
> > 84-0
> > > > 001.dcm...
> > > > Starting DICOMRead2()
> > > > dcmfile=/home/esther/Freesurfer/freesurfer/subjects/Patient3B/IM-0007-
> -2095579184-
> > 0
> > > > 001.dcm
> > > > dcmdir = /home/esther/Freesurfer/freesurfer/subjects/Patient3B
> > > > Ref Series No = 9
> > > > Found 22 files, checking for dicoms
> > > > Found 20 dicom files in series.
> > > > First Sorting
> > > > Computing Slice Direction
> > > > Vs: 0.260945 -0.596504 6.96965
> > > > Vs: 0.0372779 -0.0852149 0.995665
> > > > Second Sorting
> > > > Counting frames
> > > > nframes = 1
> > > > nslices = 20
> > > > ndcmfiles = 20
> > > > PE Dir = ROW (dicom read)
> > > > TransferSyntaxUID: --1.2.840.10008.1.2.1--
> > > > Loading pixel data
> > > > TR=466.66, TE=9.00, TI=0.00, flip angle=90.00
> > > > i_ras = (-0.9993, -0, -0.0374158)
> > > > j_ras = (-0.00317395, -0.996363, 0.0851462)
> > > > k_ras = (-0.0372779, 0.0852149, 0.995665)
> > > > writing to out.mgz...
> > > > mghWrite(out.mgz, -1): could not open file
> > > > ERROR: failure writing out.mgz
> > > > [esther@IP132-207-67-224 /]$ 
> > > > ------------------
> > > >
> > > > I thiought that the software automatically created the out.mgz....
> > > >
> > > > > Date: Fri, 8 Mar 2013 13:39:51 -0500
> > > > > From: fischl@nmr.mgh.harvard.edu
> > > > > To: greve@nmr.mgh.harvard.edu
> > > > > CC: pvaltti@hotmail.com; freesurfer@nmr.mgh.harvard.edu;
> > > > nicks@nmr.mgh.harvard.edu
> > > > > Subject: Re: [Freesurfer] Time
> > > > >
> > > > > or even
> > > > >
> > > > > freeview -v /path/to/dicomfile
> > > > > On Fri, 8 Mar 2013, Douglas N Greve wrote:
> > > > >
> > > > > >
> > > > > > No, you can just run tkmedit -f subject/mri/orig/001.mgz
> > > > > > You do not need to run recon-all to get a volume, you can just run
> > > > > > mri_convert, eg
> > > > > > mri_convert /path/to/dicomfile out.mgz
> > > > > > tkmedit -f out.mgz
> > > > > >
> > > > > > doug
> > > > > >
> > > > > > On 03/08/2013 12:54 PM, Valtina Pouegue wrote:
> > > > > >> If i'm right, the command: > recon-all -s 13A -all execute the
> > whole
> > > > > >> segmentation ( between 20-40 hours).
> > > > > >> So , if I just want the see the volume, I have to to the
> > segmentation
> > > > > >> [ absolutely] ?
> > > > > >> VP
> > > > > >>
> > > > > >>> Date: Fri, 8 Mar 2013 12:36:34 -0500
> > > > > >>> From: greve@nmr.mgh.harvard.edu
> > > > > >>> To: pvaltti@hotmail.com
> > > > > >>> CC: freesurfer@nmr.mgh.harvard.edu; nicks@nmr.mgh.harvard.edu
> > > > > >>> Subject: Re: [Freesurfer] Time
> > > > > >>>
> > > > > >>> You will need to run the full processing stream. You can do that
> > from
> > > > > >>> the beginning with
> > > > > >>>
> > > > > >>> recon-all -i $SUBJECTS_DIR/Patient13A/IM-0006--2095457776-0001.d
> cm
> > -s
> > > > > >>> 13A -all
> > > > > >>>
> > > > > >>> but now that you have a file there, you can run
> > > > > >>>
> > > > > >>> recon-all -s 13A -all
> > > > > >>>
> > > > > >>> doug
> > > > > >>>
> > > > > >>>
> > > > > >>> On 03/08/2013 12:31 PM, Valtina Pouegue wrote:
> > > > > >>>> I convert my set of DICOM of the folder 'Patient13A'
> > > > > >>>> ------------
> > > > > >>>> [esther@IP132-207-67-224 ~]$ recon-all -i
> > > > > >>>> $SUBJECTS_DIR/Patient13A/IM-0006--2095457776-0001.dcm -s 13A
> > > > > >>>> Subject Stamp: freesurfer-Linux-centos6_x86_64-stable-pub-v5.2.
> 0
> > > > > >>>> Current Stamp: freesurfer-Linux-centos6_x86_64-stable-pub-v5.2.
> 0
> > > > > >>>> INFO: SUBJECTS_DIR is /home/esther/Freesurfer/freesurfer/subjec
> ts
> > > > > >>>> Actual FREESURFER_HOME /home/esther/Freesurfer/freesurfer
> > > > > >>>> Linux IP132-207-67-224 3.4.6-2.fc17.x86_64 #1 SMP Thu Jul 19
> > 22:54:16
> > > > > >>>> UTC 2012 x86_64 x86_64 x86_64 GNU/Linux
> > > > > >>>> /home/esther/Freesurfer/freesurfer/subjects/13A
> > > > > >>>>
> > > > > >>>> mri_convert
> > > > > >>>>
> > > > >>>/home/esther/Freesurfer/freesurfer/subjects/Patient13A/IM-0006--209
> 545777
> > 6-
> > > > 0001.dcm
> > > > > >>
> > > > > >>>> /home/esther/Freesurfer/freesurfer/subjects/13A/mri/orig/001.mg
> z
> > > > > >>>>
> > > > > >>>> mri_convert
> > > > > >>>>
> > > > >>>/home/esther/Freesurfer/freesurfer/subjects/Patient13A/IM-0006--209
> 545777
> > 6-
> > > > 0001.dcm
> > > > > >>
> > > > > >>>> /home/esther/Freesurfer/freesurfer/subjects/13A/mri/orig/001.mg
> z
> > > > > >>>> $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp 
> $
> > > > > >>>> reading from
> > > > > >>>>
> > > > >>>/home/esther/Freesurfer/freesurfer/subjects/Patient13A/IM-0006--209
> 545777
> > 6-
> > > > 0001.dcm...
> > > > > >>>> Starting DICOMRead2()
> > > > > >>>> dcmfile =
> > > > > >>>>
> > > > >>>/home/esther/Freesurfer/freesurfer/subjects/Patient13A/IM-0006--209
> 545777
> > 6-
> > > > 0001.dcm
> > > > > >>>> dcmdir = /home/esther/Freesurfer/freesurfer/subjects/Patient13A
> > > > > >>>> Ref Series No = 7
> > > > > >>>> Found 23 files, checking for dicoms
> > > > > >>>> Found 21 dicom files in series.
> > > > > >>>> First Sorting
> > > > > >>>> Computing Slice Direction
> > > > > >>>> Vs: -0.598129 1.13977 6.88063
> > > > > >>>> Vs: -0.0854471 0.162824 0.982948
> > > > > >>>> Second Sorting
> > > > > >>>> Counting frames
> > > > > >>>> nframes = 1
> > > > > >>>> nslices = 21
> > > > > >>>> ndcmfiles = 21
> > > > > >>>> PE Dir = ROW (dicom read)
> > > > > >>>> TransferSyntaxUID: --1.2.840.10008.1.2.1--
> > > > > >>>> Loading pixel data
> > > > > >>>> TR=500.00, TE=9.00, TI=0.00, flip angle=90.00
> > > > > >>>> i_ras = (-0.992199, 0.0759614, 0.0988506)
> > > > > >>>> j_ras = (-0.0907614, -0.983726, -0.155063)
> > > > > >>>> k_ras = (0.0854471, -0.162824, 0.982948)
> > > > > >>>> writing to
> > > > > >>>>
> > /home/esther/Freesurfer/freesurfer/subjects/13A/mri/orig/001.mgz...
> > > > > >>>>
> > > > > >>>> #------------------------------------------
> > > > > >>>>
> > > > > >>>> recon-all -s 13A finished without error at Fri Mar 8 11:37:30 E
> ST
> > > > 2013
> > > > > >>>> done
> > > > > >>>> ------------------------------
> > > > > >>>> After i executed the tkmedit..........
> > > > > >>>> VP
> > > > > >>>>> Date: Fri, 8 Mar 2013 12:26:14 -0500
> > > > > >>>>> From: greve@nmr.mgh.harvard.edu
> > > > > >>>>> To: pvaltti@hotmail.com
> > > > > >>>>> CC: freesurfer@nmr.mgh.harvard.edu; nicks@nmr.mgh.harvard.edu
> > > > > >>>>> Subject: Re: [Freesurfer] Time
> > > > > >>>>>
> > > > > >>>>> Does that file exist? What was your command to create the mgz
> > file?
> > > > > >>>>> On 03/08/2013 12:12 PM, Valtina Pouegue wrote:
> > > > > >>>>>> Hi,
> > > > > >>>>>> I convert my files and i get news folders with one file with
> > the
> > > > > >>>>>> extension .mgz in the folder orig. But , when i try to loasd
> > the
> > > > > >>>>>> volume, I get an error
> > > > > >>>>>> -------------
> > > > > >>>>>> [esther@IP132-207-67-224 ~]$ tkmedit 13A orig.mgz
> > > > > >>>>>>
> > > > > >>
> > mghRead(/home/esther/Freesurfer/freesurfer/subjects/13A/mri/orig.mgz,
> > > > > >>>>>> -1): could not open file
> > > > > >>>>>>
> > > > > >>>>>>
> > > > > >>>>>> Error: Loading volume orig.mgz
> > > > > >>>>>>
> > > > > >>>>>> Couldn't read the anatomical volume.
> > > > > >>>>>>
> > > > > >>>>>> Tkmedit couldn't read the volume you specified.
> > > > > >>>>>> This could be because the image format wasn't recognized,
> > > > > >>>>>> or it couldn't find the proper header,
> > > > > >>>>>> or the file(s) were unreadable,
> > > > > >>>>>> or it was the wrong size.
> > > > > >>>>>> -------------------
> > > > > >>>>>>
> > > > > >>>>>> could you please help me ?
> > > > > >>>>>>
> > > > > >>>>>> VP
> > > > > >>>>>>
> > > > > >>>>>>
> > > > > >>>>
> > > > > >>
> > > > ----------------------------------------------------------------------
> --
> > > > > >>>>>> From: nicks@nmr.mgh.harvard.edu
> > > > > >>>>>> Date: Thu, 7 Mar 2013 21:11:31 -0500
> > > > > >>>>>> To: pvaltti@hotmail.com
> > > > > >>>>>> CC: freesurfer@nmr.mgh.harvard.edu; greve@nmr.mgh.harvard.edu
> > > > > >>>>>> Subject: Re: [Freesurfer] Time
> > > > > >>>>>>
> > > > > >>>>>> yes, if you give it the filename of the first .dcm in the
> > > > > >> series, the
> > > > > >>>>>> software will find the other slices and create the .mgz.
> > > > > >>>>>>
> > > > > >>>>>>
> > > > > >>>>>>
> > > > > >>>>>> On Mar 7, 2013, at 9:02 PM, Valtina Pouegue
> > <pvaltti@hotmail.com
> > > > > >>>>>> <mailto:pvaltti@hotmail.com>> wrote:
> > > > > >>>>>>
> > > > > >>>>>> Oh yes. It's my mistake. But should I give the adress of the
> > first
> > > > > >>>>>> file of my set for having the result in .mgz.
> > > > > >>>>>> Thanks.
> > > > > >>>>>>
> > > > > >>>>>>
> > > > > >>>>>>> Date: Thu, 7 Mar 2013 16:00:53 -0500
> > > > > >>>>>>> From: greve@nmr.mgh.harvard.edu
> > > > > >> <mailto:greve@nmr.mgh.harvard.edu>
> > > > > >>>>>>> To: pvaltti@hotmail.com <mailto:pvaltti@hotmail.com>;
> > > > > >>>>>> Freesurfer@nmr.mgh.harvard.edu
> > > > > >> <mailto:Freesurfer@nmr.mgh.harvard.edu>
> > > > > >>>>>>> Subject: Re: [Freesurfer] Time
> > > > > >>>>>>>
> > > > > >>>>>>> You cannot give recon-all a folder as input. It must be an
> > image
> > > > > >>>>>> file.
> > > > > >>>>>>> If you have multiple files, you need multiple -i flags.
> > > > > >>>>>>> doug
> > > > > >>>>>>>
> > > > > >>>>>>>
> > > > > >>>>>>> On 03/07/2013 03:48 PM, Valtina Pouegue wrote:
> > > > > >>>>>>>> Hi,
> > > > > >>>>>>>> Here it is
> > > > > >>>>>>>> [esther@IP132-207-67-224 ~]$ recon-all -i
> > > > > >>>>>>>> /home/esther/Freesurfer/freesurfer/subjects/Patient13B -s 1
> 3B
> > > > > >>>>>>>> Subject Stamp:
> > > > > >> freesurfer-Linux-centos6_x86_64-stable-pub-v5.2.0
> > > > > >>>>>>>> Current Stamp:
> > > > > >> freesurfer-Linux-centos6_x86_64-stable-pub-v5.2.0
> > > > > >>>>>>>> INFO: SUBJECTS_DIR is
> > > > > >> /home/esther/Freesurfer/freesurfer/subjects
> > > > > >>>>>>>> Actual FREESURFER_HOME /home/esther/Freesurfer/freesurfer
> > > > > >>>>>>>> Linux IP132-207-67-224 3.4.6-2.fc17.x86_64 #1 SMP Thu Jul 1
> 9
> > > > > >>>>>> 22:54:16
> > > > > >>>>>>>> UTC 2012 x86_64 x86_64 x86_64 GNU/Linux
> > > > > >>>>>>>> /home/esther/Freesurfer/freesurfer/subjects/13B
> > > > > >>>>>>>>
> > > > > >>>>>>>> mri_convert
> > > > > >>>>>> /home/esther/Freesurfer/freesurfer/subjects/Patient13B
> > > > > >>>>>>>>
> > > > > >> /home/esther/Freesurfer/freesurfer/subjects/13B/mri/orig/001.mgz
> > > > > >>>>>>>>
> > > > > >>>>>>>> mri_convert
> > > > > >>>>>> /home/esther/Freesurfer/freesurfer/subjects/Patient13B
> > > > > >>>>>>>>
> > > > > >> /home/esther/Freesurfer/freesurfer/subjects/13B/mri/orig/001.mgz
> > > > > >>>>>>>> corRead(): can't open file
> > > > > >>>>>>>>
> > > > > >> /home/esther/Freesurfer/freesurfer/subjects/Patient13B/COR-.info
> > > > > >>>>>>>> $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter
> > > > > >> Exp $
> > > > > >>>>>>>> reading from
> > > > > >>>>>> /home/esther/Freesurfer/freesurfer/subjects/Patient13B...
> > > > > >>>>>>>>
> > > > > >>>>>>>> VP
> > > > > >>>>>>>
> > > > > >>>>>>> --
> > > > > >>>>>>> Douglas N. Greve, Ph.D.
> > > > > >>>>>>> MGH-NMR Center
> > > > > >>>>>>> greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>
> > > > > >>>>>>> Phone Number: 617-724-2358
> > > > > >>>>>>> Fax: 617-726-7422
> > > > > >>>>>>>
> > > > > >>>>>>> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
> > > > > >>>>>>> FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.ht
> ml
> > > > > >>>>>> <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html>
> > > > > >>>>>>> Outgoing:
> > > > > >>>>>> ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve
> /
> > > > > >>>>>>>
> > > > > >>>>>>> _______________________________________________
> > > > > >>>>>>> Freesurfer mailing list
> > > > > >>>>>>> Freesurfer@nmr.mgh.harvard.edu
> > > > > >>>>>> <mailto:Freesurfer@nmr.mgh.harvard.edu>
> > > > > >>>>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> > > > > >>>>>>>
> > > > > >>>>>>>
> > > > > >>>>>>> The information in this e-mail is intended only for the pers
> on
> > > > > >>>>>> to whom it is
> > > > > >>>>>>> addressed. If you believe this e-mail was sent to you in err
> or
> > > > > >>>>>> and the e-mail
> > > > > >>>>>>> contains patient information, please contact the Partners
> > > > > >>>>>> Compliance HelpLine at
> > > > > >>>>>>> http://www.partners.org/complianceline . If the e-mail was
> > sent
> > > > > >>>>>> to you in error
> > > > > >>>>>>> but does not contain patient information, please contact the
> > > > > >>>>>> sender and properly
> > > > > >>>>>>> dispose of the e-mail.
> > > > > >>>>>>>
> > > > > >>>>>>
> > > > > >>>>>> _______________________________________________
> > > > > >>>>>> Freesurfer mailing list
> > > > > >>>>>> Freesurfer@nmr.mgh.harvard.edu
> > > > > >> <mailto: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
> > The
> > > > > >>>>>> information in this e-mail is intended only for the person to
> > > > > >> whom it
> > > > > >>>>>> is addressed. If you believe this e-mail was sent to you in
> > > > > >> error and
> > > > > >>>>>> the e-mail contains patient information, please contact the
> > > > > >> Partners
> > > > > >>>>>> Compliance HelpLine at http://www.partners.org/complianceline
> > > > > >> . If
> > > > > >>>> the
> > > > > >>>>>> e-mail was sent to you in error but does not contain patient
> > > > > >>>>>> information, please contact the sender and properly dispose o
> f
> > > > > >> the
> > > > > >>>> e-mail.
> > > > > >>>>>
> > > > > >>>>> --
> > > > > >>>>> Douglas N. Greve, Ph.D.
> > > > > >>>>> MGH-NMR Center
> > > > > >>>>> greve@nmr.mgh.harvard.edu
> > > > > >>>>> Phone Number: 617-724-2358
> > > > > >>>>> Fax: 617-726-7422
> > > > > >>>>>
> > > > > >>>>> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
> > > > > >>>>> FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html
> > > > > >>>>> Outgoing:
> > > > > >> ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
> > > > > >>>>>
> > > > > >>>>> _______________________________________________
> > > > > >>>>> Freesurfer mailing list
> > > > > >>>>> Freesurfer@nmr.mgh.harvard.edu
> > > > > >>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> > > > > >>>
> > > > > >>> --
> > > > > >>> Douglas N. Greve, Ph.D.
> > > > > >>> MGH-NMR Center
> > > > > >>> greve@nmr.mgh.harvard.edu
> > > > > >>> Phone Number: 617-724-2358
> > > > > >>> Fax: 617-726-7422
> > > > > >>>
> > > > > >>> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
> > > > > >>> FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html
> > > > > >>> Outgoing:
> > > > ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
> > > > > >>>
> > > > > >
> > > > > >
> > > > > _______________________________________________
> > > > > 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 The information
> in this e-mail is intended only for the person to whom it is addressed. If
> you believe this e-mail was sent to you in error and the e-mail contains
> patient information, please contact the Partners Compliance HelpLine at
> http://www.partners.org/complianceline . If the e-mail was sent to you in
> error but does not contain patient information, please contact the sender
> and properly dispose of the e-mail.
> 
>