Hi Jiook,
That is a bit weird. What was the error that you got on the left hemisphere?
In any case, 10 mins sounds about right. Does the output segmentation look ok?
Cheers,
Eugenio
Juan Eugenio Iglesias
Honorary Senior Research Associate
Translational Imaging Group
University College
It seems that mri_robust_register crashed. Martin, any ideas?
The algorithm worked because the rough registration from the previous step was
apparently enough to yield a decent segmentation.
Maybe we should consider stopping the whole process if mri_robust_register
dies...
Juan Eugenio
Thanks, Jacky. Sorry about that mistake.
Juan Eugenio Iglesias
Postdoctoral researcher BCBL
www.jeiglesias.com
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Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer
From: "Jacky Lee"
To: "Eugenio Iglesias"
Cc: "Freesurfer support
heers,
/E
Juan Eugenio Iglesias
Postdoctoral researcher BCBL
www.jeiglesias.com
www.bcbl.eu
Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer
From: "Jacky Lee"
To: "Eugenio Iglesias"
Cc: "Freesurfer support list"
Sent: Thursday, M
My email client is replacing the combination colon + right parenthesis by a
smiley! If the same thing happened to you, please replace the smiley by a colon
and a right parenthesis...
Next time I'll just attach the code.
Sorry for the inconvenience
Juan Eugenio Iglesias
Postdoc
x27;, SCP = '
num2str(SCPvol)]);
end
end
One more thing: if you haven't edited anything around the SCP, I would use the
original estimate for this structure. The reason is that, because the SCP is
very thing, the voxel count is a much poorer approximation for the volume as
brainstem structures using the hard
segmentations. You would simply have to count the number of voxels labeled as
midbrain, pons, SCP and medulla for each subject. You can easily do this e.g.
with Matlab (let me know if you need help with this).
Cheers,
Eugenio
Juan Eugenio Iglesias
Postdoctoral
Dear Haque,
FreeSurfer 6 has not been released yet. But if you want to try the brainstem
segmentation module, you can download the dev version; you will find it in
there.
Cheers,
Eugenio
Juan Eugenio Iglesias
Postdoctoral researcher BCBL
www.jeiglesias.com
www.bcbl.eu
Legal disclaimer
space); please see
the details in the wiki:
https://surfer.nmr.mgh.harvard.edu/fswiki/HippocampalSubfields
If you send me the T2FLAIR and T2STIR images for a sample subject, I can take a
look and give you more accurate answers ;-)
Cheers,
Eugenio
Juan Eugenio Iglesias
Postdoctoral researcher
Dear Maximilià,
first of all, sorry for the late response.
We assume throughout the code that mv a.ext b.ext will overwrite b.ext if it
exists. If this is not the case in your system, maybe you could create an alias
from 'mv' -> 'mv -f' before calling recon-all?
Cheers,
Yes!
Juan Eugenio Iglesias
Postdoctoral researcher BCBL
www.jeiglesias.com
www.bcbl.eu
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- Original Message -
From: "Patrick Sezen"
To: "Freesurfer support list"
Sent: Monday, April 18, 201
hard, and since such results affect the hippocampal
module, reproducing the subfield segmentation would in turn also be hard.
Does this make sense?
Cheers,
/E
Juan Eugenio Iglesias
Postdoctoral researcher BCBL
www.jeiglesias.com
www.bcbl.eu
Legal disclaimer/Aviso legal/Lege-oharra
Hi Tyson,
the hippocampal module shouldn't change between your beta and the FS6 release,
but the main recon-all stream will. Since the latter is used to initialize the
former, the results will be a bit different.
Cheers,
/Eugenio
Juan Eugenio Iglesias
Postdoctoral researcher
Almost correct!
recon-all -all -s subj1_T1 -i subj1_T1/I0001.dcm -hippocampal-subfields-T1T2
subj1_hipp/I0001.dcm T2hipp
Also, this is assuming that you have defined the environment variable
SUBJECTS_DIR. Otherwise, you'd need to add the flag -sd .
Cheers,
/Eugenio
Juan Eugenio Igl
nd me the T1 and T2 scans if you are not sure whether they are
sufficiently well aligned or not.
Cheers,
/Eugenio
Juan Eugenio Iglesias
Postdoctoral researcher BCBL
www.jeiglesias.com
www.bcbl.eu
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- Original Message -
Eugenio Iglesias
Postdoctoral researcher BCBL
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- Original Message -
From: "Claudia Testa"
To: "Freesurfer support list"
Sent: Thursday, March 31, 2016 11:03:38 AM
Subj
In the hippocampal subfield segmentation, this happens once every 100-200
subjects. Three for seven is pretty bad. I'll take a look as soon as I can.
Cheers,
/Eugenio
Juan Eugenio Iglesias
Postdoctoral researcher BCBL
www.jeiglesias.com
www.bcbl.eu
Legal disclaimer/Aviso legal/Lege-o
Hi Claudia,
Sorry for the late response.
I am aware of this bug and I'm exploring possible solutions. How often does it
happen in your data (i.e., how many subjects out of how many)?
Cheers,
Eugenio
Juan Eugenio Iglesias
Postdoctoral researcher BCBL
www.jeiglesias.com
www.bcbl.eu
FreeView). If you manually
rotate / translate the T2, make sure that you check the "do not resample" box
when you save the rotated scan in order not to lose information.
Cheers,
/Eugenio
Juan Eugenio Iglesias
Postdoctoral researcher BCBL
www.jeiglesias.com
www.bcbl.eu
Legal disclaimer/A
I only changed some details (e.g., temporary directories) that do not affect
the output.
Juan Eugenio Iglesias
Postdoctoral researcher BCBL
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www.bcbl.eu
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- Original Message -
From: "Bruce F
Hi again,
the brainstem module is at the end of the recon-all stream, and because
recon-all stopped because of the error, the brainstem code never ran.
Juan Eugenio Iglesias
Postdoctoral researcher BCBL
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Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal
Hi Claudia.
Does the recon-all command complete successfully? The error seems to be in
mri_aparc2aseg, right?
Juan Eugenio Iglesias
Postdoctoral researcher BCBL
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www.bcbl.eu
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- Original Message
olume] [ADCvolumeResampled] -rl brainstemSsLabels.v10.mgz -odt
float
and then work with [ADCvolumeResampled] and brainstemSsLabels.v10.mgz
Cheers,
/Eugenio
Juan Eugenio Iglesias
Postdoctoral researcher BCBL
www.jeiglesias.com
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OK now I get it ;-)
You can simply do:
mri_convert T2.FSspace.mgz T2.FSspace.resampled.mgz -odt float -rl
[lr]h.hippoSfLabels-T1-T2.v10.mgz
The rl flag says: "reslice like the following volume"
Cheers,
Eugenio
Juan Eugenio Iglesias
Postdoctoral researcher BCBL
www.jeig
and exactly what you mean. Do you want to deform the segmentations back
to the original T2 space?
Cheers,
Eugenio
Juan Eugenio Iglesias
Postdoctoral researcher BCBL
www.jeiglesias.com
www.bcbl.eu
Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer
From: "Prabesh
Hi Sarah,
It's perfectly fine. Ideally, one would process everything with the same
version so results are more easily reproducible but, since there's no FS 6.0
available yet, this is probably your best option for now, actually.
Cheers,
Eugenio
Juan Eugenio Iglesias
Postdoctoral
Dear Henri,
As of today, there's no plan to add any new labels to the brainstem atlas.
Cheers,
/Eugenio
Juan Eugenio Iglesias
Postdoctoral researcher BCBL
www.jeiglesias.com
www.bcbl.eu
Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer
From: "Henri P
Hi Mohamad,
you might have run out of memory. Could you please try allocating more RAM for
the job?
Cheers,
/Eugenio
Juan Eugenio Iglesias
Postdoctoral researcher BCBL
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- Original Message
Got it! All you need to do is to replace Smoke_e024 by T1, which is the ID of
the analysis:
quantifyHippocampalSubfields.sh T1 Nicotine_HSF.txt
Let me know if it doesn't work!
Cheers,
/Eugenio
Juan Eugenio Iglesias
Postdoctoral researcher BCBL
www.jeiglesias.com
www.bcbl.eu
Hi Alan,
can you please list the files in the mri directory of any of the subjects and
send me the output?
Cheers,
Eugenio
Juan Eugenio Iglesias
Postdoctoral researcher BCBL
www.jeiglesias.com
www.bcbl.eu
Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer
From
Here it is (open access)
http://www.sciencedirect.com/science/article/pii/S1053811915001895
Juan Eugenio Iglesias
Postdoctoral researcher BCBL
www.jeiglesias.com
www.bcbl.eu
Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer
From: "Mohamad J. Alshikho&
explicitly on the brainstem regions. But Bruce's opinion might be different?
Cheers,
/Eugenio
Juan Eugenio Iglesias
Postdoctoral researcher BCBL
www.jeiglesias.com
www.bcbl.eu
Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer
From: "Mohamad J. Alsh
ation (ideally,
you would position the box in an slightly oblique positions such that the
coronal slices cut the hippocampus perpendicularly to it major axis).
Cheers,
Eugenio
Juan Eugenio Iglesias
Postdoctoral researcher BCBL
www.jeiglesias.com
www.bcbl.eu
Legal disclaimer/Aviso legal
Sorry, it wasn't clear from the previous email whether the left hemi had
completed or not.
Can you please send me the recon-all log file?
Cheers,
/E
Juan Eugenio Iglesias
Postdoctoral researcher BCBL
www.jeiglesias.com
www.bcbl.eu
Legal disclaimer/Aviso legal/Lege-oharra: www.bc
Hi Jiook,
the log file says that the analysis of the left side did complete. Were the
output files written?
Cheers,
Eugenio
Juan Eugenio Iglesias
Postdoctoral researcher BCBL
www.jeiglesias.com
www.bcbl.eu
Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer
From
Hi Alan,
If you only want volumes, you can use quantifyHippocampalSubfields.sh. If you
want to use the segmentations for something else (eg building ROIs for
functional or diffusion), then you need to look into the mgz segmentation files.
Cheers
Eugenio
Juan Eugenio Iglesias
Postdoctoral
ctory directly (Zeke, Nick, what do you think?)
Cheers,
Eugenio
Juan Eugenio Iglesias
Postdoctoral researcher BCBL
www.jeiglesias.com
www.bcbl.eu
Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer
From: "Fengji Geng"
To: "Freesurfer support list"
Dear Andrew,
sorry for the late reply.
Aren't there any error outputs for the two cases?
If not, would you mind uploading the subjects so I can take a look?
Cheers,
Eugenio
Juan Eugenio Iglesias
Postdoctoral researcher BCBL
www.jeiglesias.com
www.bcbl.eu
Legal disclaimer/Aviso
Hi Alan,
the subfield module is not present in 5.3; you'll need to download the
development version (or wait until 6.0 is released, which should be pretty
soon=.
Cheers,
Eugenio
Juan Eugenio Iglesias
Postdoctoral researcher BCBL
www.jeiglesias.com
www.bcbl.eu
Legal disclaimer/
Hi Chris,
at this point, the software does not split the SCP into its left and right
parts.
But, you definitely gave me something to think about. When I have the time,
I'll try to work on this and release a patch.
Cheers,
Eugenio
Juan Eugenio Iglesias
Postdoctoral researcher
Hi Andrew,
it's perfectly possible. It would just make your results a bit harder to
reproduce, but that's about it ;-)
Cheers,
Eugenio
Juan Eugenio Iglesias
Postdoctoral researcher BCBL
www.jeiglesias.com
www.bcbl.eu
Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-
Hi Daniele,
do you think you could send us the subject? norm.mgz, wmparc.mgz and aseg.mgz
should be enough.
Also, have you experienced this problem with other subjects?
Cheers,
Eugenio
Juan Eugenio Iglesias
Postdoctoral researcher BCBL
www.jeiglesias.com
www.bcbl.eu
Legal disclaimer
ot;
Juan Eugenio Iglesias
Postdoctoral researcher BCBL
www.jeiglesias.com
www.bcbl.eu
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From: "Gronenschild Ed (NP)"
To: "Freesurfer support list"
Sent: Tuesday, November 17, 2015 7:09:46 PM
Su
Ciao, Daniele,
the alveus segmentation was very thin and unreliable, so we left it our of the
results (even though it is still used in the model, and influences the fit of
the atlas to the MRI scan).
Cheers,
Eugenio
Juan Eugenio Iglesias
Postdoctoral researcher BCBL
www.jeiglesias.com
little while to combine all the posteriors
into the segmentation.
Cheers,
Eugenio
Juan Eugenio Iglesias
Postdoctoral researcher BCBL
www.jeiglesias.com
www.bcbl.eu
Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer
From: "Danielle Miller"
To: &
/out_v5.3_35-MRIT1-VO-003-T01-avg.long.base_v5.3_35-MRIT1-VO-003/scripts/
Cheers,
Eugenio
Juan Eugenio Iglesias
Postdoctoral researcher BCBL
www.jeiglesias.com
www.bcbl.eu
Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer
From: "Daniele Orlandi"
To: &
3d view",
untick "label volume", and set the lower and upper thresholds to 200 and 226,
respectively.
Cheers,
Eugenio
Juan Eugenio Iglesias
Postdoctoral researcher BCBL
www.jeiglesias.com
www.bcbl.eu
Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer
This is really weird.
Can you please confirm that the file
/Applications/freesurfer/MCRv80/bin/maci64/libmwi18n.dylib
exists?
Cheers,
Eugenio
Juan Eugenio Iglesias
Postdoctoral researcher BCBL
www.jeiglesias.com
www.bcbl.eu
Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer
:
unsetenv DYLD_LIBRARY_PATH
Let us know if this helps
Cheers,
Eugenio
Juan Eugenio Iglesias
Postdoctoral researcher BCBL
www.jeiglesias.com
www.bcbl.eu
Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer
- Original Message -
From: "Aarthi Padmanabhan"
To: &
nd me a capture of a representative coronal slice
in the hippocampal body.
Cheers,
Eugenio
Juan Eugenio Iglesias
Postdoctoral researcher BCBL
www.jeiglesias.com
www.bcbl.eu
Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer
- Original Message -
From: "Carl Pintzka&
Hi Priyanka,
in the mri directory of each subject, you will find a file named:
[lr]h.hippoSfLabels--.v10.1mm.mgz
which stores the discrete segmentation volume in the 1 mm FreeSurfer voxel
space of that subject.
Kind regards,
Eugenio
Juan Eugenio Iglesias
Postdoctoral researcher BCBL
Hi Alexandra,
Thanks for your email. We have identified the problem an it will be fixed for
the next build of our development version.
Cheers,
Eugenio
Juan Eugenio Iglesias
Postdoctoral researcher BCBL
www.jeiglesias.com
www.bcbl.eu
Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal
Hi Alexandra,
that's weird. Where is the symbolic link pointing?
Cheers,
Eugenio
Juan Eugenio Iglesias
Postdoctoral researcher BCBL
www.jeiglesias.com
www.bcbl.eu
Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer
- Original Message -
From: "Alexandra De A
that you'd get in option 1.
Cheers,
Eugenio
Juan Eugenio Iglesias
Postdoctoral researcher BCBL
www.jeiglesias.com
www.bcbl.eu
Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer
- Original Message -
From: "Priyanka Mehta"
To: "Freesurfer suppo
Weird! The up and down arrows should move the current slice up and down,
whereas page up/down should change the slice... You can also click on the other
views to change the current slice.
Cheers,
Eugenio
Juan Eugenio Iglesias
Postdoctoral researcher BCBL
www.jeiglesias.com
www.bcbl.eu
Legal
Page up / page down should work
Juan Eugenio Iglesias
Postdoctoral researcher BCBL
www.jeiglesias.com
www.bcbl.eu
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- Original Message -
From: "Mohamad J. Alshikho"
To: freesurfer@nmr.mgh.harvard.edu
Sent:
Ciao Nicola,
With 5.3, you won't have any problems. I haven't tried with 5.1 but it should
be fine as well.
This all said: ideally you would run everything with the same version for the
sake of reproducibility.
Cheers,
Eugenio
Juan Eugenio Iglesias
Postdoctoral resea
Hi Prabesh (et al),
I installed Ubuntu 15.04 at home and unsetting JAVA_TOOL_OPTIONS solved the
problem (in the end it worked for you, too, right?).
Cheers,
/Eugenio
Juan Eugenio Iglesias
Postdoctoral researcher BCBL
www.jeiglesias.com
www.bcbl.eu
Legal disclaimer/Aviso legal/Lege-oharra
Sorry, I actually meant:
unset JAVA_TOOL_OPTIONS
Juan Eugenio Iglesias
Postdoctoral researcher BCBL
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www.bcbl.eu
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- Original Message -
From: "Eugenio Iglesias"
To: "Freesurfer supp
IONS
If it doesn't work, I'll install Ubuntu 15 on my laptop this weekiend and do
some more research
Kind regards,
/Eugenio
Juan Eugenio Iglesias
Postdoctoral researcher BCBL
www.jeiglesias.com
www.bcbl.eu
Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer
--
ASEG, the brainstem module has the
advantage that it provides the parcellation into pons, medulla, midbrain and
SCP.
Cheers,
Eugenio
Juan Eugenio Iglesias
Postdoctoral researcher BCBL
www.jeiglesias.com
www.bcbl.eu
Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-discl
Hi Prabesh,
do you get the same error if you try rerunning the module on the same volume?
Also, how much RAM memory does the machine have?
Cheers,
Eugenio
Juan Eugenio Iglesias
Postdoctoral researcher BCBL
www.jeiglesias.com
www.bcbl.eu
Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu
Hi again,
instead of:
mri_extract_label lh.hippoSfLabels-T1.v10.mgz 206 lh.CA1.mgz
your can run:
mri_extract_label lh.hippoSfLabels-T1.v10.mgz 206 lh.CA1.nii
Cheers,
/E
Juan Eugenio Iglesias
Postdoctoral researcher BCBL
www.jeiglesias.com
www.bcbl.eu
Legal disclaimer/Aviso legal/Lege-oharra
Hi Priyanka,
you can use mri_extract_label for that. For example, if you are interested in
CA1 (label 206), you can run:
mri_extract_label lh.hippoSfLabels-T1.v10.mgz 206 lh.CA1.mgz
Cheers,
Eugenio
Juan Eugenio Iglesias
Postdoctoral researcher BCBL
www.jeiglesias.com
www.bcbl.eu
Legal
Hi Alison,
what are your new errors (the ones you get almost immediately)?
Cheers,
Eugenio
Juan Eugenio Iglesias
Postdoctoral researcher BCBL
www.jeiglesias.com
www.bcbl.eu
Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer
- Original Message -
From: "A
Hi Angela,
Of course it is! I'd be thrilled to see what you get out of your analyses;
please keep me posted.
Cheers,
/Eugenio
Juan Eugenio Iglesias
Postdoctoral researcher BCBL
www.jeiglesias.com
www.bcbl.eu
Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer
- Ori
Hi Sampada,
FS 6.0 is not out yet, but you can download the latest dev version from here:
ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/dev/
Using this version, you can run the brainstem module on subjects that have
already been processed with 5.3.
Cheers,
Eugenio
Juan Eugenio Iglesias
Thanks Noah. It doea say on the website that you need the 2012b runtime, but
its definitely buried among too much other, less critical stuff
Cheers
E
Juan Eugenio Iglesias
Postdoctoral researcher BCBL
www.jeiglesias.com
www.bcbl.eu
Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal
Hi Noah,
this error is pretty weird. Can you please send us the exact command you
executed?
Regarding the runtime: your 2014b runtime won't work. You need to follow the
instructions here:
https://surfer.nmr.mgh.harvard.edu/fswiki/MatlabRuntime
Cheers,
Eugenio
Juan Eugenio Iglesias
Postdoc
*.sh
Cheers,
Eugenio
Juan Eugenio Iglesias
Postdoctoral researcher BCBL
www.jeiglesias.com
www.bcbl.eu
Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer
- Original Message -
From: "Xiaowei Zhuang"
To: "Freesurfer support list"
Sent: Wednesday, J
Sorry, I forgot to mention that you should change the permissions of the files.
Please run the following command:
chmod u+x $FREESURFER_HOME/bin/run_segmentSubject*.sh
Cheers,
Eugenio
Juan Eugenio Iglesias
Postdoctoral researcher BCBL
www.jeiglesias.com
www.bcbl.eu
Legal disclaimer/Aviso legal
Hi Angela,
I think this is a problem I fixed in the development version a couple of days
ago. Can you please just try saving the attached 3 files in the directory
$FREESURFER_HOME/bin/ replacing the ones that are there?
Cheers,
Eugenio
Juan Eugenio Iglesias
Postdoctoral researcher BCBL
.
Cheers,
Eugenio
Juan Eugenio Iglesias
Postdoctoral researcher BCBL
www.jeiglesias.com
www.bcbl.eu
Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer
- Original Message -
From: "Noah Markowitz"
To: freesurfer@nmr.mgh.harvard.edu
Sent: Thursday, June 25, 2015
everything should work
Cheers,
/Eugenio
Juan Eugenio Iglesias
Postdoctoral researcher BCBL
www.jeiglesias.com
www.bcbl.eu
Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer
- Original Message -
From: "Carl Anderson"
To: "Freesurfer support list"
Sent
Thanks for pinpointing the problem, Elijah. We are working on a solution.
Cheers,
/Eugenio
Juan Eugenio Iglesias
Postdoctoral researcher BCBL
www.jeiglesias.com
www.bcbl.eu
Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer
- Original Message -
From: "Elija
output last week - sorry
about that! We believe that the changes made the module easier to use. Please
see the updated instructions here:
https://surfer.nmr.mgh.harvard.edu/fswiki/HippocampalSubfields
Cheers,
/Eugenio
Juan Eugenio Iglesias
Postdoctoral researcher BCBL
www.jeiglesias.com
Hi again,
The software requires approximately 10GB of RAM
Cheers
Eugenio
Juan Eugenio Iglesias
Postdoctoral researcher BCBL
www.jeiglesias.com
www.bcbl.eu
Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer
- Original Message -
From: Erik O'Hanlon
To: Frees
Hi Angela,
It will work with subjects processed with the previous version; however, I
would recommend (if possible) to run everything with the same version, for the
sake of reproducibility.
Cheers,
/Eugenio
Juan Eugenio Iglesias
Postdoctoral researcher BCBL
www.jeiglesias.com
www.bcbl.eu
Legal
Hi Erik,
I guess your process was killed by the kernel. Maybe you ran out of RAM memory?
How much RAM do you have?
Cheers,
/Eugenio
Juan Eugenio Iglesias
Postdoctoral researcher BCBL
www.jeiglesias.com
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tiny bit better when it comes to separating
AD from controls based solely on hippocampal volume, though.
Cheers,
/Eugenio
Juan Eugenio Iglesias
Postdoctoral researcher BCBL
www.jeiglesias.com
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- Original Me
Hola Cecilio,
Right-Hippocampus and Left-Hippocampus are generic labels for the hippocampal
regions that were not labeled as subiculum, CA, or fimbria in the atlas. In
practice, they correspond to the hippocampal tails.
Cheers,
/Eugenio
Juan Eugenio Iglesias
Postdoctoral researcher BCBL
masks for cortical structures
from the aseg+aparc volume.
/Eugenio
Juan Eugenio Iglesias
Postdoctoral researcher BCBL
www.jeiglesias.com
www.bcbl.eu
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- Original Message -
From: std...@virgilio.it
To:
Hi Josh,
the module is already in the development version of FS, and will be released
along with FS6 hopefully very soon.
Cheers,
/Eugenio
Juan Eugenio Iglesias
Postdoctoral researcher BCBL
www.jeiglesias.com
www.bcbl.eu
Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer
Hi once more,
there is no specific longitudinal subfield module, BUT you can run the subfield
code on the longitudinally processed subjects (i.e., those with
.long. added to their name).
Cheers,
/Eugenio
Juan Eugenio Iglesias
Postdoctoral researcher BCBL
www.jeiglesias.com
www.bcbl.eu
Legal
Hi again,
FS6 is not out yet, but hopefully soon.
The instructions for the new hippocampal subfield module are here:
http://surfer.nmr.mgh.harvard.edu/fswiki/HippocampalSubfields
Cheers,
/Eugenio
Juan Eugenio Iglesias
Postdoctoral researcher BCBL
www.jeiglesias.com
www.bcbl.eu
Legal disclaimer
Hi Erik,
the 6.0 subfield code won't overwrite your 5.3 results, so if you run the 6.0
module on data analyzed with 5.3, both results will co-exist in the MRI
directory of each subject.
Kind regards,
/Eugenio
Juan Eugenio Iglesias
Postdoctoral researcher BCBL
www.jeiglesias.com
www.bc
Hi Zih-Kai,
the subfield and main FreeSurfer streams are different and therefore give
different results. On average, the volumes estimated by the subfield stream
will be lower, but very highly correlated with those from the main FreeSurfer
stream.
I hope this helps!
/Eugenio
Juan Eugenio
Hi Andreia,
Nothing will prevent you from running FS6's hippocampal subfields on
5.3-processed subjects, even though I'd recommend processing everything with
the same version for the sake of reproducibility.
Cheers,
/Eugenio
Juan Eugenio Iglesias
Postdoctoral researcher BCBL
www.jeig
, and discuss these issues
in the submission.
Kind regards,
/Eugenio
Juan Eugenio Iglesias
Postdoctoral researcher BCBL
www.jeiglesias.com
www.bcbl.eu
Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer
- Original Message -
From: "Erik O'Hanlon"
Juan Eugenio Iglesias
Postdoctoral researcher BCBL
www.jeiglesias.com
www.bcbl.eu
Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer
- Original Message -
From: "Georg Ferdinand Anto von Polier"
To: "Freesurfer support list"
Sent: Tuesday, De
.nii.gz -s )
Cheers,
/Eugenio
Juan Eugenio Iglesias
Postdoctoral researcher BCBL
www.jeiglesias.com
www.bcbl.eu
Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer
- Original Message -
From: "Gunjan Gautam"
To: "Freesurfer support list"
Sent: Mo
Hi Stefano,
we are working on an algorithm to segment the nuclei, but unfortunately I do
not think it is going to be released any time soon.
Kind regards,
/Eugenio
Juan Eugenio Iglesias
Postdoctoral researcher BCBL
www.jeiglesias.com
www.bcbl.eu
Legal disclaimer/Aviso legal/Lege-oharra
Hi Erik,
did you experience the same problem with any other cases?
Also, do you think you could send us the log file
[subjectdir]/scripts/hippo-subfields.log, as well as the contents of
[subjectdir]/tmp/subrieldResults?
Cheers,
/Eugenio
Juan Eugenio Iglesias
Postdoctoral researcher BCBL
Thanks! Unfortunately it won't help; I need specific versions with specific
compilation options etc :-(
Juan Eugenio Iglesias
Postdoctoral researcher BCBL
www.jeiglesias.com
www.bcbl.eu
Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer
- Original Message -
se classes at random.
Cheers,
/Eugenio
Juan Eugenio Iglesias
Postdoctoral researcher BCBL
www.jeiglesias.com
www.bcbl.eu
Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer
- Original Message -
From: "Luigi Antelmi"
To: "e iglesias" , frees
across the image - which can be
very different from the volume stemming from counting the voxels in the
discrete MAP segmentation.
Cheers,
/Eugenio
Juan Eugenio Iglesias
Postdoctoral researcher BCBL
www.jeiglesias.com
www.bcbl.eu
Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal
subjects directory $subject.
Regarding the partial volume segmentation, it's not fully implemented / tested
yet.
Cheers,
/Eugenio
Juan Eugenio Iglesias
Postdoctoral researcher BCBL
www.jeiglesias.com
www.bcbl.eu
Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer
- Ori
?). If you do it both with both
autorecon2 and autorecon3, I believe that the code will be run twice.
Cheers,
/Eugenio
Juan Eugenio Iglesias
Postdoctoral researcher BCBL
www.jeiglesias.com
www.bcbl.eu
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- Original Message
Hi Kev,
1. It will able to use only the T1, only the T2, or both simultaneously.
2. The algorithm is relatively robust against these parameters. However, the
higher the resolution and the lower the noise the better (as usual).
Cheers,
/Eugenio
Juan Eugenio Iglesias
Postdoctoral researcher BCBL
Hi Joshua,
the measurements are in voxels, so you need to multiply them by 0.125 (which is
0.5^3) to obtain values in mm3.
Cheers,
/Eugenio
Juan Eugenio Iglesias
Postdoctoral researcher BCBL
www.jeiglesias.com
www.bcbl.eu
Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer
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