Hi everyone,
After running -hippo-subfields, I converted the voxel output of
-hippo-subfields to mm^3 based on the instructions given here:
https://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/2013-June/031188.html.
Then I summed the volumes for all of the subfields (assuming that this would
Hi all,
A couple questions regarding post-surgery scans.
1. Is there a way to run scans of post-surgical brains that takes resections
into account and gives more accurate results than "recon-all -all"?
2. Is it possible to obtain resection volumes with FreeSurfer? I tried to do
this indirectly
Hi Sierra,
the hippocampal subfield segmentation is computed using a separate
model, so it doesn't agree perfectly with the hippocampal mask in
aseg.mgz. In fact, the volume estimates tend to be a bit smaller (but
highly correlated).
Cheers,
/Eugenio
On 09/30/2013 10:42 AM, Germeyan, Sierra (NI
Hi,
I would like to verify (as a sanity check and to make sure that I'm on the
right track in my analysis) that preproc-sess runs with -no-subcort-mask by
default in freesurfer-Darwin-lion-stable-pub-v5.2.0, but with -no-subcort-mask
turned off by default in stablev5.3.0 on snowleopard.
I firs
Hi, quick question
I'm just going to rerun these without the -T2 stuff for now so I can get
going on analysis.
What stages of recon-all do I have to run to fix everything the -T2pial
mishap broke? The process flow tables on the website seem a bit out of date.
mw
On Sat, Sep 28, 2013 at 3:24 PM
Hi again,
Sorry, I didn't list all the commands I have been using:
preproc-sess -s $subj -fsd bold -sliceorder odd -surface fsaverage lhrh -mni305
-fwhm 3 -per-run -force (and with -no-subcort-mask in v5.3.0 on snowleopard)
mkanalysis-sess -fsd bold -stc odd -mni305 2 -fwhm 3 -paradigm para.pa
Freesurfer experts,
I'm attempting to utilize an archived e-mail's contents to resample data in
MNI152 to 305.
The script I'm using is as follows:
*mri_vol2vol \*
*--mov
/extern/research/tools/freesurfer-5.3.0/subjects/fsaverage/mri.2mm/mni305.cor.mgz
\*
*--targ FSL_MNI152_FreeSurferConformed_1mm
1. sorry, not easily that I can think of
2. I guess you could try mri_robust_register on the brain.mgz, output the
halfway volumes, then count ones that are 0 in the post and not 0 in the
pre (and probably are brain in the aseg of the pre)
cheers
Bruce
On Mon, 30 Sep 2013, Germeyan, Sierra (NI
Hi Experts,
I am trying to figure out the total surface area of a hemisphere. I
found out 3 ways to read the area data:
1. Read the lh.area file directly [A, f]=read_curv('lh.area');
Total surface area: sum(A) = 86905.15mm^2
2. Read from the ~/stats/lh.curv.stats (generated by
They do have the same default. Note that if you run preproc-sess with
-no-subcort-mask and then run it again without -no-subcort-mask it will
not generate a new file. Could that have happened?
doug
On 09/30/2013 01:21 PM, Leila Reddy wrote:
> Hi,
>
> I would like to verify (as a sanity check
what do you mean the frontal lobe is pointing straight up?
On 09/30/2013 02:32 PM, Paul Beach wrote:
> Freesurfer experts,
>
> I'm attempting to utilize an archived e-mail's contents to resample
> data in MNI152 to 305.
>
> The script I'm using is as follows:
> /mri_vol2vol \/
> /--mov
> /ext
There are a couple of things happening.
The lh.area has the vertices in the medial wall zeroed so #1 below does
not include all of the unknown area. Here the "medial wall" is defined
as anything outside of lh.cortex.label
The mris_anatomical_stats (#3 ) command below does include the medial wa
Hi FS Community,
I was wondering whether there is a way to get a binary mask of the pons.
Thanks in advance,
Panos
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Hi Wen, are you using version 5.3? If so, then you will already have all
the programs and atlases
doug
ps. Please remember to post to the list. thanks!
On 09/29/2013 06:08 AM, wen.zhang55 wrote:
> Dear Doug:
> Sorry to bother you, but i have a trouble to download the programs
> acoording to
Hi Daniel, I 'm not sure what your question is ...
doug
On 09/29/2013 08:30 AM, Daniel Klein wrote:
> Dear FreeSurfer experts,
>
> thanks a lot for your solution.
> It works fine.
> I have some further questions to polynomial fitting with qdec, to
> prevent misunderstandings from my point of v
Is this in tkmedit?
On 09/30/2013 06:59 PM, Paul Beach wrote:
> Hi Doug,
>
> Sorry, I should have been more specific. I meant for when one looks at
> the resulting transformation in a sagittal view.
>
> More specifically...
> Instead of this:
> Inline image 1
>
> It looks more like this (though m
View it in tkmedit to see if it is really a problem with your vol2vol
command.
doug
On 09/30/2013 07:33 PM, Paul Beach wrote:
> No. That was just a general example of how the image looks - from a
> stock google image of an FSL brain (I'm not in the lab and so cannot
> put up actual images
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