Re: [Freesurfer] Hippocampal segmentation doubts

Thu, 05 Jul 2012 02:27:17 -0700

Thank you so much for your answer Koen,

I understand, but now I'm having some trouble when running the command on one subject, hope you can help me.

I have tried to perform the hippocampal subfields segmentation by running:

recon-all -s MySubject -hippo-subfields
 and also:
kvlSegmentHippocampalSubfields.sh MySubject left /root/trabajo/freesurfer/subjects /root/trabajo/freesurfer/subjects/MySubject/tmp/subfieldResults 

But I always get the following error:

maximalDeformation: 75.1793
Transforming mesh
Done transforming mesh
Rasterizing Levenberg-Marquardt...
numberOfEntries: 24131

/root/trabajo/freesurfer/bin/kvlSegmentHippocampalSubfields.sh: line 18: 23175 Segmentation fault      kvlSegmentWithoutGUI configurationFileDeformableRegistration.txt
failed to do kvlSegmentWithoutGUI configurationFileDeformableRegistration.txt
Linux localhost.localdomain 2.6.9-34.ELsmp #1 SMP Thu Mar 9 06:23:23 GMT 2006 x86_64 x86_64 x86_64 GNU/Linux

recon-all -s MySubject exited with ERRORS at Tue Jul  3 15:54:39 CEST 2012

For more details, see the log file /root/trabajo/freesurfer/subjects/MySubject/scripts/recon-all.log
To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting



The recon-all.log says:

#--------------------------------------------
#@# Hippocampal Subfields processing Tue Jul  3 15:48:33 CEST 2012

 mkdir -p /root/trabajo/freesurfer/subjects/MySubject/tmp/subfieldResults

 kvlSegmentHippocampalSubfields.sh MySubject left /root/trabajo/freesurfer/subjects /root/trabajo/freesurfer/subjects/MySubject/tmp/subfieldResults 

Linux localhost.localdomain 2.6.9-34.ELsmp #1 SMP Thu Mar 9 06:23:23 GMT 2006 x86_64 x86_64 x86_64 GNU/Linux

recon-all -s MySubject exited with ERRORS at Tue Jul  3 15:54:39 CEST 2012

To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
 


This error occurres only on this subject and for the left hemisphere, not like this for the right hemisphere, which ends perfectly when running the second command. I'm sending you the configurationFileDeformation for the left hemisphere, in case it may help. Any help will be so appreciated

Best Regards,
Gabriel




El 04/07/12, Koen Van Leemput <k...@nmr.mgh.harvard.edu> escribió:
Hi Gabriel,

1. Using pre-processed data obtained with an older version of
FreeSurfer should be OK, as long as you remember that the obtained
results might/will be different from the ones you'd get if you had run
the whole analysis from scratch.

2. The generic label "hippocampus" is used to denote the tail of the
hippocampus, where no attempt is made to further subdivide between the
different subfields. This is admittedly not a great naming convention
- sorry for the confusion.

3. You should not do any correction on the obtained volumes: "partial
volume" here merely means the effect of voxels containing a mix of
different subfields simultaneously. The "non-partial volume" results
here only indicate that this effect is not explicitly modeled when you
call the hippocampal subfield segmentation routine with its default
settings.

Hope this helps,

Koen


On Thu, Jun 28, 2012 at 5:29 AM, Gabriel Gonzalez Escamilla
<ggon...@upo.es> wrote:
>
> Dear Freesurfer experts
>
> I'm starting to deal with the FS v5.1 hippocampal subfields segmentation,
> and I have a couple doubts...
>
> If I have my subjects segmented from an older FS version, Would be any
> problem when running the -hippo-subfields?
> I'm guessing not, but I wanna be sure. Because, as I've looked the
> -hippo-subfields recon seems to not modify the whole brain segmentation, am
> I right?
>
> second, when I apply the "kvlQuantifyHippocampalSubfieldSegmentations.sh" I
> do obtain two txt files containing such segmentation of the 8 hippocampal
> subfields, but at the beggining it appear a field for the left and right
> hippocampus, but I don't know exactly what does this column represents,
> because if I sum the other colums the subfield sums are so much bigger than
> the hippocampus field; i.e.
> volume_in_number_of_voxels   Left-Hippocampus   left_presubiculum   left_CA1
> left_CA2-3   left_fimbria   left_subiculum   left_CA4-DG
> left_hippocampal_fissure
> c_12_hipo    3789.97    3215.08    2654.65    7705.2    336.857    4841.63
> 4158.49    356.626
>
>
> and last. Do I need to somehow do some partial volume corrections to this
> output volumes? Because the txt file sais nonPartialVolumeStats, and I'd saw
> on the page that the output is "0.5*0.5*0.5mm^3".
>
>
> Many thanks in advanced,
> Gabriel
>
>
>
>
>
> --
> --------------------------
> PhD. student Gabriel González-Escamilla
> Laboratory of Functional Neuroscience
> Department of Physiology, Anatomy, and Cell Biology
> University Pablo de Olavide
> Ctra. de Utrera, Km.1
> 41013 - Seville
> - Spain -
>
> Email: ggon...@upo.es
> http://www.upo.es/neuroaging/es/
>
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--
--------------------------
PhD. student Gabriel González-Escamilla
Laboratory of Functional Neuroscience
Department of Physiology, Anatomy, and Cell Biology
University Pablo de Olavide
Ctra. de Utrera, Km.1
41013 - Seville
- Spain -

Email: ggon...@upo.es
http://www.upo.es/neuroaging/es/
# Configuration for deforming toward aseg
logDirectory: deformableRegistrationLog
imageFileName: aseg_thresholded.mgz
meshCollectionFileName: 
/root/trabajo/freesurfer/data/GEMS/CurrentMeshCollection30.gz
K: 0.01
compressionLookupTableFileName: 
/root/trabajo/freesurfer/data/GEMS/compressionLookupTable_left.txt
boundingFileName: imageDump_coregistered.mgz
sameGaussianParameters: 17 550 552 553 554 555 556 557
sameGaussianParameters: 24 2 3
imageSmoothingSigmas: 0
meshSmoothingSigmas: 3

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