---

From: Douglas N Greve <greve@nmr.mgh.harvard.edu>
To: Antonella Kis <atorok9@yahoo.com>; freesurfer <freesurfer@nmr.mgh.harvard.edu>
Sent: Wednesday, August 31, 2011 3:00 PM
Subject: Re: [Freesurfer] : Error with dt_recon

If they meet the requirements outlined in the help section (run with
--help).

Antonella Kis wrote:
> Dear Doug,
>
> I can get this values if I convert the dicom files with MRIcron. Can I
> use this values?
>
> Thanks.
> Antonella
>
> PS> Why when I ran the dt_recon I didn't get the fa.nii, adc.nii and
> some more file? Is thsi because I didn't have the bvects and bvals?
>
> ------------------------------------------------------------------------
> *From:* Douglas N Greve <greve@nmr.mgh.harvard.edu>
> *To:* Antonella Kis <atorok9@yahoo.com>; freesurfer
> <freesurfer@nmr.mgh.harvard.edu>
> *Sent:* Wednesday, August 31, 2011 2:35 PM
> *Subject:* Re: [Freesurfer] : Error with dt_recon
>
> It does not always work to extract them from the dicom. You should talk
> to whoever set up your scans to get the bvals and bvects.
> doug
>
> Antonella Kis wrote:
> > Hi Doug,
> >
> > Thanks again. From where I take the bvals and bvects. I was reading
> > that if my DICOM files were acquired using a Siemens scanner, then
> > this information can be extracted from the DICOM headers but I don't
> > know how to do it.
> >
> >
> > Please help.
> >
> > Many thanks.
> > AK
> > ------------------------------------------------------------------------
> > *From:* Douglas N Greve <greve@nmr.mgh.harvard.edu
> <mailto:greve@nmr.mgh.harvard.edu>>
> > *To:* Antonella Kis <atorok9@yahoo.com <mailto:atorok9@yahoo.com>>;
> freesurfer
> > <freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu>>
> > *Sent:* Wednesday, August 31, 2011 2:11 PM
> > *Subject:* Re: [Freesurfer] : Error with dt_recon
> >
> >
> > That's almost right. Just specify the subject name and not the full
> > path. Also, you will need to supply bvals and bvects
> > dt_recon --i DTI_15.nii.gz --s NPI001 --o
> > /usr/local/freesurfer/NPI001/DTI_15
> >
> >
> >
> > Antonella Kis wrote:
> > > Hi Doug,
> > >
> > > Thanks again for helping. So my question is then: I will pass for --i
> > > (the input data) the .nii.gz file from the DTI data  and the it is OK
> > > to use for the --s which defines the file of the structural recon a
> > > file called NPI001 where I have 10 files after recon-all (bem, label,
> > > mri, surf, stats, etc)? In other words if I will set-up:
> > >
> > > setenv FREESURFER_HOME /usr/local/freesurfer
> > > setenv SUBJECTS_DIR $FREESURFER_HOME
> > >
> > > and since my files are in /usr/local/freesurfer/NPI001 I am then
> doing:
> > >
> > > cd /usr/local/freesurfer/NPI001
> > >
> > > Here I have the pre-processed files after recon-all and a file called
> > > DTI_15 with my diffussion data and the DTI_15.nii.gz file so I can
> run:
> > >
> > > dt_recon --i DTI_15.nii.gz --s /usr/local/freesurfer/NPI001 --o
> > > /usr/local/freesurfer/NPI001/DTI_15
> > >
> > > Is this right?
> > >
> > > I will try by the time you answer but please let me know if you have
> > > any objection and/or advise.
> > >
> > > Many thanks,
> > > AK
> > >
> > >
> > >
> > >
> > >
> ------------------------------------------------------------------------
> > > *From:* Douglas N Greve <greve@nmr.mgh.harvard.edu
> <mailto:greve@nmr.mgh.harvard.edu>
> > <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>>
> > > *To:* Antonella Kis <atorok9@yahoo.com <mailto:atorok9@yahoo.com>
> <mailto:atorok9@yahoo.com <mailto:atorok9@yahoo.com>>>;
> > freesurfer
> > > <freesurfer@nmr.mgh.harvard.edu
> <mailto:freesurfer@nmr.mgh.harvard.edu>
> <mailto:freesurfer@nmr.mgh.harvard.edu
> <mailto:freesurfer@nmr.mgh.harvard.edu>>>
> > > *Sent:* Wednesday, August 31, 2011 1:49 PM
> > > *Subject:* Re: [Freesurfer]: Error with dt_recon
> > >
> > > If you pass it dicom, it will try to extract the bvalues, which is
> > > where it is failing.
> > > doug
> > >
> > > Antonella Kis wrote:
> > > > Dear Doug,
> > > >
> > > > Sorry but I still have a question about this error:
> > > > I understood that dt_recon it takes original dicom images as input
> > > and it generates multiple NIFTI volumes that will be used in later
> > > steps.So why I need to use the NIFTI as input?
> > > >
> > > > Thnak you.
> > > > AK
> > > >
> > > >
> > ------------------------------------------------------------------------
> > > > *From:* Douglas N Greve <greve@nmr.mgh.harvard.edu
> <mailto:greve@nmr.mgh.harvard.edu>
> > <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>
> > > <mailto:greve@nmr.mgh.harvard.edu
> <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu
> <mailto:greve@nmr.mgh.harvard.edu>>>>
> > > > *To:* Antonella Kis <atorok9@yahoo.com
> <mailto:atorok9@yahoo.com> <mailto:atorok9@yahoo.com
> <mailto:atorok9@yahoo.com>>
> > <mailto:atorok9@yahoo.com <mailto:atorok9@yahoo.com>
> <mailto:atorok9@yahoo.com <mailto:atorok9@yahoo.com>>>>
> > > > *Cc:* "fischl@nmr.mgh.harvard.edu
> <mailto:fischl@nmr.mgh.harvard.edu> <mailto:fischl@nmr.mgh.harvard.edu
> <mailto:fischl@nmr.mgh.harvard.edu>>
> > > <mailto:fischl@nmr.mgh.harvard.edu
> <mailto:fischl@nmr.mgh.harvard.edu>
> > <mailto:fischl@nmr.mgh.harvard.edu
> <mailto:fischl@nmr.mgh.harvard.edu>>>" <fischl@nmr.mgh.harvard.edu
> <mailto:fischl@nmr.mgh.harvard.edu>
> > <mailto:fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu>>
> > > <mailto:fischl@nmr.mgh.harvard.edu
> <mailto:fischl@nmr.mgh.harvard.edu>
> > <mailto:fischl@nmr.mgh.harvard.edu
> <mailto:fischl@nmr.mgh.harvard.edu>>>>;
> "freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu>
> > <mailto:freesurfer@nmr.mgh.harvard.edu
> <mailto:freesurfer@nmr.mgh.harvard.edu>>
> > > <mailto:freesurfer@nmr.mgh.harvard.edu
> <mailto:freesurfer@nmr.mgh.harvard.edu>
> > <mailto:freesurfer@nmr.mgh.harvard.edu
> <mailto:freesurfer@nmr.mgh.harvard.edu>>>"
> > > <freesurfer@nmr.mgh.harvard.edu
> <mailto:freesurfer@nmr.mgh.harvard.edu>
> > <mailto:freesurfer@nmr.mgh.harvard.edu
> <mailto:freesurfer@nmr.mgh.harvard.edu>>
> > <mailto:freesurfer@nmr.mgh.harvard.edu
> <mailto:freesurfer@nmr.mgh.harvard.edu>
> > <mailto:freesurfer@nmr.mgh.harvard.edu
> <mailto:freesurfer@nmr.mgh.harvard.edu>>>>
> > > > *Sent:* Tuesday, August 30, 2011 3:51 PM
> > > > *Subject:* Re: [Freesurfer] Fw: Error with dt_recon
> > > >
> > > > It's looking for the values in the dicom file (which apparently does
> > > not have them). Convert the dicom to nifit, then use the nifti as
> > > input, then pass files with bvals and bvects on the command line.
> > > > doug
> > > >
> > > > Antonella Kis wrote:
> > > > >
> > > > >
> > > > > Dear Bruce:
> > > > >
> > > > > I am running the dt_recon:
> > > > > # setenv FREESURFER_HOME /usr/local/freesurfer          # setenv
> > > SUBJECTS_DIR $FREESURFER_HOME
> > > > > # cd /usr/local/freesurfer/NPI001
> > > > > # dt_recon --i
> > >
> >
> /usr/local/freesurfer/NPI001/dti/1.3.46.670589.11.17385.5.0.7524.2009112812454960001.dcm
>
> >
> > > --s /usr/local/freesurfer/NPI001 --o /usr/local/freesurfer/NPI001/dti
> > > > >
> > > > >
> > > > > and I am getting the following error:
> > > > >
> > > > > ERROR: cannot extract sDiffusion.alBValue[1] from
> > > /usr/local/freesurfer/NPI001/dti/dwi-infodump.dat
> > > > >
> > > > > Can you please give me a hint?
> > > > >
> > > > > Thank you.
> > > > > AK
> > > > >
> > > > >
> > > > > _______________________________________________
> > > > > Freesurfer mailing list
> > > > > Freesurfer@nmr.mgh.harvard.edu
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> > <mailto:Freesurfer@nmr.mgh.harvard.edu
> <mailto:Freesurfer@nmr.mgh.harvard.edu>>
> > > <mailto:Freesurfer@nmr.mgh.harvard.edu
> <mailto:Freesurfer@nmr.mgh.harvard.edu>
> > <mailto:Freesurfer@nmr.mgh.harvard.edu
> <mailto:Freesurfer@nmr.mgh.harvard.edu>>>
> > > <mailto:Freesurfer@nmr.mgh.harvard.edu
> <mailto:Freesurfer@nmr.mgh.harvard.edu>
> > <mailto:Freesurfer@nmr.mgh.harvard.edu
> <mailto:Freesurfer@nmr.mgh.harvard.edu>>
> > > <mailto:Freesurfer@nmr.mgh.harvard.edu
> <mailto:Freesurfer@nmr.mgh.harvard.edu>
> > <mailto:Freesurfer@nmr.mgh.harvard.edu
> <mailto:Freesurfer@nmr.mgh.harvard.edu>>>>
> > > <mailto:Freesurfer@nmr.mgh.harvard.edu
> <mailto:Freesurfer@nmr.mgh.harvard.edu>
> > <mailto:Freesurfer@nmr.mgh.harvard.edu
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> <mailto:Freesurfer@nmr.mgh.harvard.edu>
> > <mailto:Freesurfer@nmr.mgh.harvard.edu
> <mailto:Freesurfer@nmr.mgh.harvard.edu>>>
> > > <mailto:Freesurfer@nmr.mgh.harvard.edu
> <mailto:Freesurfer@nmr.mgh.harvard.edu>
> > <mailto:Freesurfer@nmr.mgh.harvard.edu
> <mailto:Freesurfer@nmr.mgh.harvard.edu>>
> > > <mailto:Freesurfer@nmr.mgh.harvard.edu
> <mailto:Freesurfer@nmr.mgh.harvard.edu>
> > <mailto: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 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
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> > > > >
> > > > >
> > > > >
> > >
> ------------------------------------------------------------------------
> > > > >
> > > > > _______________________________________________
> > > > > Freesurfer mailing list
> > > > > Freesurfer@nmr.mgh.harvard.edu
> <mailto:Freesurfer@nmr.mgh.harvard.edu>
> > <mailto:Freesurfer@nmr.mgh.harvard.edu
> <mailto:Freesurfer@nmr.mgh.harvard.edu>>
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> <mailto:Freesurfer@nmr.mgh.harvard.edu>
> > <mailto:Freesurfer@nmr.mgh.harvard.edu
> <mailto:Freesurfer@nmr.mgh.harvard.edu>>>
> > > <mailto:Freesurfer@nmr.mgh.harvard.edu
> <mailto:Freesurfer@nmr.mgh.harvard.edu>
> > <mailto:Freesurfer@nmr.mgh.harvard.edu
> <mailto:Freesurfer@nmr.mgh.harvard.edu>>
> > > <mailto:Freesurfer@nmr.mgh.harvard.edu
> <mailto:Freesurfer@nmr.mgh.harvard.edu>
> > <mailto: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 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.
> > > > >
> > >
> ------------------------------------------------------------------------
> > > > >
> > > > > _______________________________________________
> > > > > Freesurfer mailing list
> > > > > Freesurfer@nmr.mgh.harvard.edu
> <mailto:Freesurfer@nmr.mgh.harvard.edu>
> > <mailto:Freesurfer@nmr.mgh.harvard.edu
> <mailto:Freesurfer@nmr.mgh.harvard.edu>>
> > > <mailto:Freesurfer@nmr.mgh.harvard.edu
> <mailto:Freesurfer@nmr.mgh.harvard.edu>
> > <mailto:Freesurfer@nmr.mgh.harvard.edu
> <mailto:Freesurfer@nmr.mgh.harvard.edu>>>
> > > <mailto:Freesurfer@nmr.mgh.harvard.edu
> <mailto:Freesurfer@nmr.mgh.harvard.edu>
> > <mailto:Freesurfer@nmr.mgh.harvard.edu
> <mailto:Freesurfer@nmr.mgh.harvard.edu>>
> > > <mailto:Freesurfer@nmr.mgh.harvard.edu
> <mailto:Freesurfer@nmr.mgh.harvard.edu>
> > <mailto:Freesurfer@nmr.mgh.harvard.edu
> <mailto: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 <mailto:greve@nmr.mgh.harvard.edu>
> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>
> > <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>
> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>>
> > > <mailto:greve@nmr.mgh.harvard.edu
> <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu
> <mailto:greve@nmr.mgh.harvard.edu>>
> > <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>
> <mailto: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.html
> > > >
> > > >
> > > >
> > >
> > > -- Douglas N. Greve, Ph.D.
> > > MGH-NMR Center
> > > greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>
> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>
> > <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>
> <mailto: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.html
> > >
> > >
> > >
> >
> > --
> > Douglas N. Greve, Ph.D.
> > MGH-NMR Center
> > greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>
> <mailto: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.html
> >
> > _______________________________________________
> > Freesurfer mailing list
> > Freesurfer@nmr.mgh.harvard.edu
> <mailto:Freesurfer@nmr.mgh.harvard.edu>
> <mailto:Freesurfer@nmr.mgh.harvard.edu
> <mailto: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 <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.html
>
> _______________________________________________
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu <mailto: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

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