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:
- Download the file "kvl.zip" from this link:
ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/fsdev/zkaufman/
- 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
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------------------------------------------------------------------------------------- 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