R: Re: R: Re: R: Re: hippo subfield - Freesurfer

26 Mar 2013

      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.
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