Dear FreeSurfer expects,
I ran a cortical thickness analysis that revealed many significant
clusters, but half of them are pretty small. Is there a possibility in qdec
to display only clusters with a certain clustersize on the inflated
surface?
Thank you very much for your help,
best wishes, Mar
Hi, freesurfer experts,
I have a question about how to convert a segmented hippocampal subfield
file into a ROI.
After -hippo-subfields processing using recon-all command, I have got
several files named posterior_left/right_**.mgz. And the segmented volume
just coverd a small area in subject's wh
Hi Freesurfer community,
A quick question, how long takes to run the hippocampal subfield
segmentation for a subject that has already run the typical recon-all
pipeline?
Thank you,
--
--
*Carolina Valencia M
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When I run subfield segmentation for some of the subject, I get segmentation
error. Is there any known workaround these problems as recon-all is ran on a
cluster? I usually get this error Rasterizing
Levenberg-Marquardt.../global/apps/freesurfer/5.1.0/bin/kvlSegmentHippocampalSubfields.sh:
line
Hi,I have looked into cortical surface volume and cortical
jacobian_whitematter. Can I use these measure a in similar way as cortical
thickness? Do jacobian_whitematter represent the whitematter thickness in the
cortex? How reliable are cortical volumes compared to cortical thickness?Best
regar
I want to be able to use a mask in some of the cortical thickness studies so as
to reduce the number of comparisons being conducted as well as to be more
hypothesis driven. Can anyone provide some guidance on whether or not this can
be accomplished?
Thanks,
David
_
Hi Lijie (cc to mailing list),
I wrote a script to do just this in July. Here is a link to a tar file. It
requires knowledge of matlab and bash, but is pretty straight forward. It
https://www.dropbox.com/s/s1f78j2ozv1gw8q/subfield_to_ROI.tar.gz
a) transforms the subfield probabilities to nu.mgz
So our lab is running a couple analyses and we are getting different
results based on whether we use Brain Voyager or Freesurfer that we think
is due to different ROI selection across the two platforms. Is there
anyway to load a BrainVoyager ROI into freesurfer? The BV data has been
talairach tra
Hi Freesurfer community:
I run hippocampal subfields command succesfully
recon-all -s CORBIC_vol15 finished without error at Thu Aug 30 11:29:16 COT
2012
done
but when I run kvlQuantifyHippocampalSubfieldSegmentations.sh
the terminal shows some errors:
resultsDirectory /home/cvalencia/freesu
Hi
kvlQuantifyHippocampalSubfieldSegmentations.sh "expected that the
"-hippo-subfields" flag has been used for each subject in $SUBJECTS_DIR;
if this is not the case the
"kvlQuantifyHippocampalSubfieldSegmentations.sh" script will fail and no
(or incomplete) output files will be generated". f
what is the best way to convert a .vtk surface mesh (with labels as
scalars) to freesurfer .annot format? i am currently converting the vtk
file to freesurfer .label files, then using freesurfer to consolidate these
into an .annot file, which is slow, roundabout, and generates a lot of
files.
che
hello carolina
to me it took about 5-6 hours.
greets,
lorenzo
Da: Carolina Valencia
A: Freesurfer Mailing List
Inviato: Giovedì 30 Agosto 2012 20:37
Oggetto: [Freesurfer] hippocampal subfield segmentation
Hi Freesurfer community,
A quick question,
Hi Freesurfer experts,
I'm very sorry to bother you, but I am very confused with the following
questions:
My experimental design includes 3 discrete factors: diagnosis with two levels
(A, B); genotype with two levels (G, T); gender (F, M), and two covariates.
So I can get 8 classes: AGF, AGM, A
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