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Hi,
This won't affect the eTIV as that is derived purely from the affine
registration. See Buckner et al. (2004) NeuroImage 23:724-738. for more
details.
-Niels
On Mon, Nov 26, 2018 at 6:46 AM 박경일 wrote:
> External Email - Use Caution
>
> De
Hi Kyung
eTIV is estimated from the determinant of the Talairach transform, so
won't be affected much by bits of things like the chiasm being left
around.
cheers
Bruce
On Mon, 26 Nov 2018, 박경일 wrote:
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Dear experts,When I see the images through
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Dear Qimo,
You do need a T1 volume to run the main recon-all; sorry if the wiki wasn’t
clear enough. It is true that segmenta_T2.sh only uses the intensities of the
FLAIR scan, but a recon-all processed T1 is still necessary.
Cheers,
/E
--
Juan Euge
Hi Andrade
the computational complexity of the topology fixing is square in the
number of vertices in the largest defect (actually in the convex hull of
it). That means that subjects with small defects are process very rapidly,
but large ones can take a long time. Typically if you have a very l
Hi Karin, are you attempting to build or run freesurfer? Your original issue
seems related to fsl, not freesurfer. I suggest consulting their help list to
get FSLVm7_64 running correctly - https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/Support
best,
Andrew
From: on behalf of Karin Markenroth
Bloch
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Dear FS experts,
I was wondering if it is possible to run recon-all (e.g. autorecon2,
autorecon3) on skull-stripped images which have gone through N4
correction.
Would it be okay to run?
recon-all -i sub1.nii.gz -subjid s1 -autorecon1 -sd . -noskulls
Hi Katie
I think that should be ok, but of course the only way to know for sure is
to try!
cheers
Bruce
On Mon, 26 Nov 2018, Kathryn Fitzgerald wrote:
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Dear FS experts,
I was wondering if it is possible to run recon-all (e.g. autorecon2,
autor
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thank you for your quick response - I will!
On Mon, Nov 26, 2018 at 1:12 PM Bruce Fischl
wrote:
> Hi Katie
>
> I think that should be ok, but of course the only way to know for sure is
> to try!
>
> cheers
> Bruce
>
> On Mon, 26 Nov 2018, Kathryn Fit
answers below
On 11/21/2018 01:53 PM, srishti goel wrote:
>
> External Email - Use Caution
>
> Hi Douglas,
>
> Thank you so much for your response. We just want to be extra careful
> about the way we are doing this and so below I have outlined the exact
> pattern of the group descriptor
When you open it in freeview, you have to specify a surface (eg,
fsaverage/surf/lh.white) and then load that file as an overlay to that
surface
On 11/21/2018 05:11 PM, 姜时泽 wrote:
>
> External Email - Use Caution
>
> Dear freesurfer experts,
> I am using freesurfer to analyze my PET data
That looks ok. How did you create the FSGD file? Sometimes it can be a
little finicky about white space, and a file that looks ok might not
work (eg, if you made the file in windows). Can you send the actual FSGD
file as an attachement?
On 11/22/2018 09:09 AM, Larissa Bechtle wrote:
>
>
On 11/23/2018 11:26 AM, C.P.E. Rollins wrote:
> External Email - Use Caution
> Dear Freesurfer Developers,
> I have a 2-part question:
> 1) I was advised to use permutation to control for multiple
> comparisons in an LGI analysis, would you mind elaborating how to do
> this in command line (in
Use csdbase.y.ocn.dat
See
mri_glmfit-sim --help
for more info
On 11/24/2018 09:31 PM, Azeez, Azeezat wrote:
>
> External Email - Use Caution
>
> Hello,
>
> I used FSGD option to run statistical test on 3 fixed factors each
> with 2 contrast levels. (DEVELOPMENT : old vs young, SEX: male
Can you send the fsgd file?
On 11/25/2018 10:44 AM, Damien MARIE wrote:
>
> External Email - Use Caution
>
> Hi,
> I would like to replicate an analysis I did with qdec but regressing out
> thickness at the vertex level. It’s a myelin group difference with age and
> left average myelin a
Try following this tutorial. It is for fmri, but you can probably apply
it to PET
surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/MultiModalFmriGroup_freeview
Also see you PET module:
surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/MultiModalFmriGroup_freeview
On 11/20/2018 06:34 PM, john Anderson wrot
You don't want to be averaging zero voxels, so masking makes sense.
When you click on the voxels inside one of those segmentation regions (e.g. one
of the CC regions) in freeview, are the FA values that you see high?
On Nov 25, 2018 8:42 AM, "Winkelbeiner, Stephanie A"
wrote:
External
When total gray is computed, the cerebellum GM volumes are computed by
simply summing up all the voxels whereas the values that are reported in
the aseg.stats file include partial volume correction, which is slightly
different.
On 11/20/2018 02:04 PM, Song, Da-Yea wrote:
>
> External
Hi Batuhan,
I'm trying to access the files now. What is the name of the files/directory
you uploaded? I'm not sure they transferred.
Thanks,
Bram
Bram R. Diamond, BSc
Research Technician II
Laboratory for Computational Neuroimaging
Martinos Center for Biomedical Imaging
Massachusetts Gener
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Thank You for the response.
I'm trying to understand a result I have,
The interaction effect of DEVxSEXxDIA shows decrease in cortical
thickness at a specific cluster.
Can this be interpreted to be "the localized cortical thickness decrease
seen at
I'm not sure I would refer to an interaction as a "decrease" per se
On 11/26/2018 02:44 PM, Azeez, Azeezat wrote:
>
> External Email - Use Caution
>
> Thank You for the response.
> I'm trying to understand a result I have,
> The interaction effect of DEVxSEXxDIA shows decrease in cortica
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Dear freesurfer experts,
I am using freesurfer to analyze some fMRI data collected on two monkeys.
My runs have a partial field of view, since just the posterior part of the
brain was scanned. Unfortunately, no full-head EPI was collected. The
registra
Do you have any scan that was acquired at the same time that is whole
head? Any scan will do. If so, you can run register-sess using the
-bbr-int option (or bbregister directly). Eg, if the anatomical was
acquired at the same time, then, to use register-sess, create a folder
in the session fold
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Thanks for the fast reply!
Unfortunately, I have only 3 mprage scans that were collected in another
day but no whole-head functional data.
Il giorno lun 26 nov 2018 alle ore 22:07 Greve, Douglas N.,Ph.D. <
dgr...@mgh.harvard.edu> ha scritto:
> Do you
And you only have partial field of view fmri data on that day? No whole
brain localizer? Really, any whole-brain volume will do. If you do not,
then you'll have to initialize the bbr registration by hand, which is a
bit of a pain. You'd run something like
tkregisterfv --mov template.nii.gz --ini
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Can it be inferred that "at the cluster there exist significant changes to
cortical thickness due to the interactions of DEVxSEXxDIA"
would that be a better wording ?
On Mon, Nov 26, 2018 at 2:57 PM Greve, Douglas N.,Ph.D. <
dgr...@mgh.harvard.edu> wro
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So, I initially did that with the all_FA_skeletonised and got values around 0.6
for the Cc as expected. Interestingly enough though, when I do the same with
the individual FA_skeletons that I obtained with the tbss_deproject command the
values are ar
In that case, it seems that the low values are introduced when transforming the
skeleton from template space to individual space. If this is so, it has nothing
to do with using the freesurfer segmentation per se. I would ask on the FSL
list.
On Nov 26, 2018 3:41 PM, "Winkelbeiner, Stephanie A"
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Hello Bruce,
Thank you for the quick response.
I unchecked "do not draw on voxels in the range of" in the "Recon Edit"
window, and I was able to get the clone to work nicely.
Thank you for your time!
David
On Mon, Nov 19, 2018 at 1:38 PM David S Le
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Thanks for your interest in my problem and your help, Anastasia! I will do that!
From: freesurfer-boun...@nmr.mgh.harvard.edu
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Yendiki, Anastasia
Sent: Monday, November 26, 2018 3:51 PM
To: F
glad to hear it worked out
Bruce
On Mon, 26 Nov 2018, David S Lee wrote:
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Hello Bruce,
Thank you for the quick response.
I unchecked "do not draw on voxels in the range of" in the "Recon Edit" window,
and I was able to
get the clone to work nicel
Sample the voxel-wise data onto the surface. Then use the --pvr
(per-vertex regressor) option in mri_glmfit. Search the mail archives
for more info.
On 11/20/2018 04:23 AM, Carola Mayer wrote:
>
> External Email - Use Caution
>
> Hello Freesurfer Developers,
>
> I have a general question
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Dear Juan Eugenio Iglesias:
Thanks for the response.
I have a question about T1 and T2 data, whether they must be scanned by
the same patient?
Because I have no T1 sequence data. If i want to get the hippocampal
subfields of T
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