Hi Pablo
 
yes, any single file that is in the correct series should be fine
Bruce
On Fri, 30 
Aug 2013, pablo najt wrote:
 
> Dear FS,
> Following on my question about the initial format of my files for running
> recon -all, I finally managed to get the Dicom files for our images.
> However, as the imaging protocol includes several modalities, (resting
> state, functional, T1, DTI), we had to sort the dicom files. For my
> structural data, on which I intend to run FS. Now I get 163 files which I
> assume are the number of slices. They look like this:
> 
> MR.1.3.12.2.1107.5.2.13.20520.30000006050913395956200007879  MR.1.3.12.2.11
> 07.5.2.13.20520.30000006050913395956200007961
> 
> MR.1.3.12.2.1107.5.2.13.20520.30000006050913395956200007880  MR.1.3.12.2.11
> 07.5.2.13.20520.30000006050913395956200007962
> 
> MR.1.3.12.2.1107.5.2.13.20520.30000006050913395956200007881  MR.1.3.12.2.11
> 07.5.2.13.20520.30000006050913395956200007963
> 
> MR.1.3.12.2.1107.5.2.13.20520.30000006050913395956200007882  MR.1.3.12.2.11
> 07.5.2.13.20520.30000006050913395956200007964
> 
> MR.1.3.12.2.1107.5.2.13.20520.30000006050913395956200007883  MR.1.3.12.2.11
> 07.5.2.13.20520.30000006050913395956200007965
> 
> MR.1.3.12.2.1107.5.2.13.20520.30000006050913395956200007884  MR.1.3.12.2.11
> 07.5.2.13.20520.30000006050913395956200007966
> 
> MR.1.3.12.2.1107.5.2.13.20520.30000006050913395956200007885  MR.1.3.12.2.11
> 07.5.2.13.20520.30000006050913395956200007967
> 
> MR.1.3.12.2.1107.5.2.13.20520.30000006050913395956200007886  MR.1.3.12.2.11
> 07.5.2.13.20520.30000006050913395956200007968
> 
> MR.1.3.12.2.1107.5.2.13.20520.30000006050913395956200007887  MR.1.3.12.2.11
> 07.5.2.13.20520.30000006050913395956200007969
> 
> MR.1.3.12.2.1107.5.2.13.20520.30000006050913395956200007888  MR.1.3.12.2.11
> 07.5.2.13.20520.30000006050913395956200007970
> 
> 
>  
> 
> My question is, for running "recon-all -i john_time1.nii.gz -s
> john_time1" which file should I use in the place of "nii.gz" file? Can I use
> any of the MR.1.3.12.2 .... (listed above)? 
> Many thanks,
> Pablo
> 
> ____________________________________________________________________________
> From: pablonajt@hotmail.com
> To: freesurfer@nmr.mgh.harvard.edu
> Date: Tue, 27 Aug 2013 17:14:04 +0000
> Subject: Re: [Freesurfer] Talairach Failure Detection
> 
> Hi I have one last question. I just noticed that my images are in Philips
> format. Would you recommend to convert to DICOM anyway? Or should I used
> NIFTI?Thanks,
> Pablo
> 
> Date: Tue, 27 Aug 2013 12:31:09 -0400
> From: fischl@nmr.mgh.harvard.edu
> To: pablonajt@hotmail.com
> CC: freesurfer@nmr.mgh.harvard.edu
> Subject: Re: [Freesurfer] Talairach Failure Detection
> 
> yes, definitely. The dicoms are best
> On Tue, 27 Aug 2013, pablo najt wrote:
> 
> > Thank you very much for your input. Yes, I did start with analyze format a
> nd also I have visually inspected the images. Almost all my
> > scans consistently show an extended whole in the prefrontal area (with a f
> ew exception of some scans showing this in posterior
> > locations). 
> > I am assuming the best is to start with either DICOM or NIFTI and avoid an
> alyze format. Is this correct?
> > 
> > Best,
> > Pablo
> >   
> > 
> > Date: Tue, 27 Aug 2013 12:08:22 -0400
> > From: fischl@nmr.mgh.harvard.edu
> > To: pablonajt@hotmail.com
> > CC: freesurfer@nmr.mgh.harvard.edu
> > Subject: Re: [Freesurfer] Talairach Failure Detection
> > 
> > Hi Pablo
> > 
> > have you visually inspected the talairach xform to see if it is indeed 
> > incorrect? What input format did you start with? Most of these occur 
> > because people start with analyze, which doesn't have the direction 
> > cosines, and so the data is oriented incorrectly
> > 
> > cheers
> > Bruce
> >
> > 
> > On Tue, 27 Aug 2013, pablo najt wrote:
> > 
> > > Dear FS experts,I am contacting you to report an error after launching r
> econ -all for one of my subjects (see below). I am using a
> > > macbook pro with snow leopard version 10.6.8. 
> > > 
> > > I would greatly appreciate if you could advise me which step/s should I 
> take to correct this.
> > > Thank you for your attention,
> > > Pablo
> > > 
> > > Error:------------------------------------------------------------------
> -------------------------------------------------------------
> > -
> > > ------------------
> > > #@# Talairach Failure Detection Mon Aug 19 23:01:43 EDT 2013
> > > /Users/pablonajt/subjects/tr5713/mri
> > > \n talairach_afd -T 0.005 -xfm transforms/talairach.xfm \n
> > > ERROR: talairach_afd: Talairach Transform: transforms/talairach.xfm ***F
> AILED*** (p=0.0554, pval=0.0034 < threshold=0.0050)
> > > Manual Talairach alignment may be necessary, or
> > > include the -notal-check flag to skip this test,
> > > making sure the -notal-check flag follows -all
> > > or -autorecon1 in the command string.
> > > See http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Talairach
> > > Darwin Pablo-Najts-MacBook-Pro.local 10.8.0 Darwin Kernel Version 10.8.0
> : Tue Jun  7 16:33:36 PDT 2011;
> > > root:xnu-1504.15.3~1/RELEASE_I386 i386
> > > 
> > > recon-all -s tr5713 exited with ERRORS at Mon Aug 19 23:01:43 EDT 2013
> > > 
> > >
> > 
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> > 
> >
> 
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> in this e-mail is intended only for the person to whom it is addressed. If
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> _______________________________________________ Freesurfer mailing list
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> 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.
> 
>