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: pablon...@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: fis...@nmr.mgh.harvard.edu
To: pablon...@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: fis...@nmr.mgh.harvard.edu
> To: pablon...@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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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.
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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
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