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, std...@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: zkauf...@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, <std...@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: zkauf...@nmr.mgh.harvard.edu >> Data: 22-mar-2013 20.53 >> A: <std...@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, std...@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 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 > 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 ------------------------------------------------------------------------------------- Juan Eugenio Iglesias, PhD http://www.jeiglesias.com igles...@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
