Thank you very much Eugenio, you are very kind!
Stefano
----Messaggio originale----
Da: iglesias@nmr.mgh.harvard.edu
Data: 26-mar-2013 17.00
A: <stdp82@virgilio.it>
Cc: <zkaufman@nmr.mgh.harvard.edu>, "freesurfer@nmr.mgh.harvard.edu"<freesurfer@nmr.mgh.harvard.edu>
Ogg: Re: R: Re: [Freesurfer] R: Re: R: Re: hippo subfield
I would say intracranial volume from the aseg.stat table
Cheers,
/Eugenio
On Tue, 2013-03-26 at 16:49 +0100, stdp82@virgilio.it wrote:
> Thank you very much Eugenio.
>
>
> I have a last question: Who is the best way to normalize
> the HippocampalSubfieldSegmentation volume results?
>
>
> Stefano
>
> ----Messaggio originale----
> Da: iglesias@nmr.mgh.harvard.edu
> Data: 26-mar-2013 14.37
> A: <stdp82@virgilio.it>
> Cc: <zkaufman@nmr.mgh.harvard.edu>,
> "freesurfer@nmr.mgh.harvard.edu"<freesurfer@nmr.mgh.harvard.edu>
> Ogg: Re: [Freesurfer] R: Re: R: Re: hippo subfield
>
> Ciao, Stefano
>
> to compute subfield volumes, you need to use the script
> kvlQuantifyHippocampalSubfieldSegmentations.sh. The instructions are
> here:
>
> http://surfer.nmr.mgh.harvard.edu/fswiki/HippocampalSubfieldSegmentation
>
> In the wiki page you'll also find instructions to visualize the
> output.
>
> Cheers,
>
> /Eugenio
>
>
> On Tue, March 26, 2013 4:40 am, stdp82@virgilio.it wrote:
> > Hi Zeke and other users,
> > I have finished the Hippocampal Subfields parcellation. New
> files .mgz are
> > located in $SUBJECTS_DIR/mri.
> > Now, I do not understand as I can calculate for each region the
> thickness
> > and volume.
> > Can you help me, please?
> >
> > Stefano
> >
> >
> >
> >
> > ----Messaggio originale----
> > Da: zkaufman@nmr.mgh.harvard.edu
> > Data: 23-mar-2013 20.13
> > A: "freesurfer@nmr.mgh.harvard.edu"<freesurfer@nmr.mgh.harvard.edu>
> > Ogg: Re: [Freesurfer] R: Re: hippo subfield
> >
> > It's not enough to simply put the zip file in the
> > /Applications/freesurfer/bin directory,,, you must extract its
> contents to
> > that directory.
> >
> > Just extract the zip file (anywhere on your machine will do). Then
> copy
> > and paste the extracted files to /Application/freesurfer/bin
> >
> > -Zeke
> >
> > On Mar 22, 2013, at 7:00 PM, <stdp82@virgilio.it> wrote:
> >
> >> Hi Zeke,
> >>
> >> as you explain I have download the kvl.zip and put it in
> >> /Application/freesurfer/bin.
> >>
> >> After rerunning I have:
> >>
> >> [iMac-di-Stefano:freesurfer/subjects/subject_prova] Stefano%
> recon-all
> >> -s Diff01 -hippo-subfields
> >> Subject Stamp: freesurfer-Darwin-lion-stable-pub-v5.2.0
> >> Current Stamp: freesurfer-Darwin-lion-stable-pub-v5.2.0
> >> INFO: SUBJECTS_DIR
> is /Applications/freesurfer/subjects/subject_prova
> >> Actual FREESURFER_HOME /Applications/freesurfer
> >> -rw-rw-r-- 1 Stefano wheel 697785 Mar 22 23:56
> >> /Applications/freesurfer/subjects/subject_prova/Diff01/scripts/recon-all.log
> >> Darwin iMac-di-Stefano.local 12.3.0 Darwin Kernel Version 12.3.0:
> Sun
> >> Jan 6 22:37:10 PST 2013; root:xnu-2050.22.13~1/RELEASE_X86_64
> x86_64
> >> #--------------------------------------------
> >> #@# Hippocampal Subfields processing Fri Mar 22 23:56:49 CET 2013
> >> \n mkdir -p
> >> /Applications/freesurfer/subjects/subject_prova/Diff01/tmp/subfieldResults
> >> \n kvlSegmentHippocampalSubfields.sh Diff01 left
> >> /Applications/freesurfer/subjects/subject_prova
> >> /Applications/freesurfer/subjects/subject_prova/Diff01/tmp/subfieldResults
> >> \n
> >> Doing left side
> >> meshFileName:
> >> /Applications/freesurfer/data/GEMS/CurrentMeshCollection30.gz
> >> compressionLookupTableFileName:
> >> /Applications/freesurfer/data/GEMS/compressionLookupTable_left.txt
> >>
> boundingBoxFileName: /Applications/freesurfer/data/GEMS/imageDump.mgz
> >> subjectName: Diff01
> >> side: left
> >> inputDirectory: /Applications/freesurfer/subjects/subject_prova
> >> outputDirectory:
> >> /Applications/freesurfer/subjects/subject_prova/Diff01/tmp/subfieldResults
> >> directory
> >> /Applications/freesurfer/subjects/subject_prova/Diff01/tmp/subfieldResults/Diff01
> >> already exists
> >> directory
> >> /Applications/freesurfer/subjects/subject_prova/Diff01/tmp/subfieldResults/Diff01/left
> >> already exists
> >> cd
> >> /Applications/freesurfer/subjects/subject_prova/Diff01/tmp/subfieldResults/Diff01/left
> >> cp
> -f /Applications/freesurfer/subjects/subject_prova/Diff01/mri/nu.mgz
> >> .
> >> cp -f
> >> /Applications/freesurfer/subjects/subject_prova/Diff01/mri/aseg.mgz .
> >> cp -f
> >> /Applications/freesurfer/subjects/subject_prova/Diff01/mri/transforms/talairach.xfm
> >> .
> >> cp /Applications/freesurfer/data/GEMS/imageDump.mgz .
> >> kvlApplyTransform imageDump.mgz -0.9991 -0.0328 0.0258 144.0010
> -0.0330
> >> 0.9994 -0.0086 2.6560 0.0255 0.0094 0.9996 -3.1939
> >> dyld: Library not loaded: libITKCommon.3.16.dylib
> >> Referenced from: /Applications/freesurfer/bin/kvlApplyTransform
> >> Reason: image not found
> >> /Applications/freesurfer/bin/kvlSegmentHippocampalSubfields.sh:
> line 18:
> >> 5481 Trace/BPT trap: 5 kvlApplyTransform imageDump.mgz
> -0.9991
> >> -0.0328 0.0258 144.0010 -0.0330 0.9994 -0.0086 2.6560 0.0255 0.0094
> >> 0.9996 -3.1939
> >> failed to do kvlApplyTransform imageDump.mgz
> >> -0.9991 -0.0328 0.0258 144.0010
> >> -0.0330 0.9994 -0.0086 2.6560
> >> 0.0255 0.0094 0.9996 -3.1939
> >> Darwin iMac-di-Stefano.local 12.3.0 Darwin Kernel Version 12.3.0:
> Sun
> >> Jan 6 22:37:10 PST 2013; root:xnu-2050.22.13~1/RELEASE_X86_64
> x86_64
> >>
> >> recon-all -s Diff01 exited with ERRORS at Fri Mar 22 23:56:49 CET
> 2013
> >>
> >> For more details, see the log file
> >> /Applications/freesurfer/subjects/subject_prova/Diff01/scripts/recon-all.log
> >> To report a problem, see
> >> http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
> >>
> >>
> >>
> >> ----Messaggio originale----
> >> Da: zkaufman@nmr.mgh.harvard.edu
> >> Data: 22-mar-2013 20.53
> >> A: <stdp82@virgilio.it>, <freesurfer@nmr.mgh.harvard.edu>
> >> Ogg: Re: [Freesurfer] hippo subfield
> >>
> >> Stefano,
> >>
> >> In order to fix this issue please follow these instruction exactly:
> >>
> >> 1) Download the file "kvl.zip" from this link:
> >> ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/fsdev/zkaufman/
> >>
> >> 2) Overwrite the existing kvl files in /Application/freesurfer/bin
> with
> >> the files in kvl.zip
> >>
> >> I was able to replicate your issue and solve it using the steps
> above.
> >> If these steps do not solve the issue for you, please respond with
> a the
> >> exact error you receive.
> >>
> >> Hope this helps.
> >>
> >> -Zeke
> >>
> >>
> >>
> >>
> >>
> >> On 03/22/2013 12:00 PM, stdp82@virgilio.it wrote:
> >> > I'm running:
> >> >
> >> > recon-all -s Diff02 -hippo-subfields
> >> >
> >> > with the following error.
> >> >
> >> > Thanks.
> >> >
> >> >
> >> > Stefano
> >> >
> >> > Subject Stamp: freesurfer-Darwin-lion-stable-pub-v5.2.0
> >> > Current Stamp: freesurfer-Darwin-lion-stable-pub-v5.2.0
> >> > INFO: SUBJECTS_DIR is
> >> /Applications/freesurfer/subjects/subject_prova/Diff02
> >> > Actual FREESURFER_HOME /Applications/freesurfer
> >> > -rw-rw-r-- 1 Stefano wheel 499999 Mar 22 16:53
> >>
> > /Applications/freesurfer/subjects/subject_prova/Diff02/Diff02/scripts/recon-all.log
> >> > Darwin iMac-di-Stefano.local 12.3.0 Darwin Kernel Version 12.3.0:
> Sun
> >> > Jan 6 22:37:10 PST 2013; root:xnu-2050.22.13~1/RELEASE_X86_64
> x86_64
> >> > #--------------------------------------------
> >> > #@# Hippocampal Subfields processing Fri Mar 22 16:56:31 CET 2013
> >> > \n mkdir -p
> >>
> > /Applications/freesurfer/subjects/subject_prova/Diff02/Diff02/tmp/subfieldResults
> >> > \n kvlSegmentHippocampalSubfields.sh Diff02 left
> >> > /Applications/freesurfer/subjects/subject_prova/Diff02
> >>
> > /Applications/freesurfer/subjects/subject_prova/Diff02/Diff02/tmp/subfieldResults
> >> > \n
> >> > Doing left side
> >> > meshFileName:
> >> /Applications/freesurfer/data/GEMS/CurrentMeshCollection30.gz
> >> > compressionLookupTableFileName:
> >>
> > /Applications/freesurfer/data/GEMS/compressionLookupTable_left.txt
> >> >
> boundingBoxFileName: /Applications/freesurfer/data/GEMS/imageDump.mgz
> >> > subjectName: Diff02
> >> > side: left
> >> >
> inputDirectory: /Applications/freesurfer/subjects/subject_prova/Diff02
> >> > outputDirectory:
> >>
> > /Applications/freesurfer/subjects/subject_prova/Diff02/Diff02/tmp/subfieldResults
> >> > directory
> >>
> > /Applications/freesurfer/subjects/subject_prova/Diff02/Diff02/tmp/subfieldResults/Diff02
> >> > already exists
> >> > directory
> >>
> > /Applications/freesurfer/subjects/subject_prova/Diff02/Diff02/tmp/subfieldResults/Diff02/left
> >> > already exists
> >> > cd
> >>
> > /Applications/freesurfer/subjects/subject_prova/Diff02/Diff02/tmp/subfieldResults/Diff02/left
> >> > cp -f
> >>
> > /Applications/freesurfer/subjects/subject_prova/Diff02/Diff02/mri/nu.mgz
> >> .
> >> > cp -f
> >>
> > /Applications/freesurfer/subjects/subject_prova/Diff02/Diff02/mri/aseg.mgz
> >> .
> >> > cp -f
> >>
> > /Applications/freesurfer/subjects/subject_prova/Diff02/Diff02/mri/transforms/talairach.xfm
> >> > .
> >> > cp /Applications/freesurfer/data/GEMS/imageDump.mgz .
> >> > kvlApplyTransform imageDump.mgz -0.9991 -0.0328 0.0258 144.0010
> >> -0.0330
> >> > 0.9994 -0.0086 2.6560 0.0255 0.0094 0.9996 -3.1939
> >> > dyld: Library not loaded: libITKCommon.3.16.dylib
> >> > Referenced
> from: /Applications/freesurfer/bin/kvlApplyTransform
> >> > Reason: image not found
> >> > /Applications/freesurfer/bin/kvlSegmentHippocampalSubfields.sh:
> line
> >> 18:
> >> > 77530 Trace/BPT trap: 5 kvlApplyTransform imageDump.mgz
> -0.9991
> >> > -0.0328 0.0258 144.0010 -0.0330 0.9994 -0.0086 2.6560 0.0255
> 0.0094
> >> > 0.9996 -3.1939
> >> > *failed to do kvlApplyTransform imageDump.mgz
> >> > -0.9991 -0.0328 0.0258 144.0010
> >> > -0.0330 0.9994 -0.0086 2.6560
> >> > 0.0255 0.0094 0.9996 -3.1939*
> >> > *Darwin iMac-di-Stefano.local 12.3.0 Darwin Kernel Version
> 12.3.0: Sun
> >> > Jan 6 22:37:10 PST 2013; root:xnu-2050.22.13~1/RELEASE_X86_64
> x86_64*
> >> > *
> >> > *
> >> > *recon-all -s Diff02 exited with ERRORS at Fri Mar 22 16:56:31
> CET
> >> 2013*
> >> >
> >> > For more details, see the log file
> >>
> > /Applications/freesurfer/subjects/subject_prova/Diff02/Diff02/scripts/recon-all.log
> >> > To report a problem, see
> >> > http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
> >> >
> >> >
> >> > _______________________________________________
> >> > 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
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> >
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> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
> -------------------------------------------------------------------------------------
> Juan Eugenio Iglesias, PhD
> http://www.jeiglesias.com
> iglesias@nmr.mgh.harvard.edu
> Athinoula A. Martinos Center for Biomedical Imaging
> 149 Thirteenth Street, Suite 2301
> Charlestown, Massachusetts 2129
> U.S.A.
> _______________________________________________
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
>
--
-------------------------------------------------------------------------------------
Juan Eugenio Iglesias, PhD
http://www.jeiglesias.com
iglesias@nmr.mgh.harvard.edu
Athinoula A. Martinos Center for Biomedical Imaging
Department of Radiology, MGH, Harvard Medical School
149 Thirteenth Street, Suite 2301
Charlestown, Massachusetts 2129
U.S.A.