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Just to add some more info here:
The peak location of regions, X1 and X2, which I found without including
ICV as covariate are very close with the peak locations I found in
Gamma_Without_ICV
(~5.15), whereas Gamma_With_ICV is almost all over the brain (
Hi Doug,
Thank you very much for your reply and my apologies for this belated response.
The two approaches you mentioned were the only ones we could think that might
work for a DV like cortical thickness.
That being said, we were originally thinking of a repeated measures anova.
However, (an
For noise compare the values in the rstd.mgh file, for effect size look
in the gamma.mgh file
On 07/24/2018 12:27 PM, Martin Juneja wrote:
>
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>
> Hi Dr. Greve,
>
> Thanks for your quick reply. Could you please give me more details how
> can I check this whet
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Great, thank you!
On Tue, Jul 24, 2018 at 12:28 PM, Bruce Fischl
wrote:
> no, they should be the same
>
> On Tue, 24 Jul 2018, Rosemary Nicholas wrote:
>
>
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>>
>> Hi Andrew,
>> Thanks!
>>
>> So as long as we set
no, they should be the same
On Tue, 24 Jul 2018, Rosemary Nicholas wrote:
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Hi Andrew,
Thanks!
So as long as we set the seed in mris_ca_label the results should be
consistent, right? Would there be any difference to running it this way
(independe
Hi Sofia
you should be able to "reslice like" the rawavg.mgz:
mri_convert -rl rawavg.mgz brainmask.mgz brainmask.rawavg.mgz
you might also want to specify the interpolation as e.g. nearest with -rt
nearest (trilinear is the default I believe)
On Tue, 24 Jul 2018,
Sofia Rodriguez Penuela wrot
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Hi Dr. Greve,
Thanks for your quick reply. Could you please give me more details how can
I check this whether its because of noise or its because of less CV
difference?
I am not sure what method/way is the best and commonly used to confirm
these factor
Hi Sofia,
Would it be possible to send us the volume and one of the surface files
you loaded?
Best,
Ruopeng
On 07/24/2018 12:08 PM, Sofia Rodriguez Penuela wrote:
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Dear Freesurfer team,
After loading a volume in Freeview, we try to load surfaces, but
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Hi Andrew,
Thanks!
So as long as we set the seed in mris_ca_label the results should be
consistent, right? Would there be any difference to running it this way
(independently) and running it with recon-all?
Thanks,
Rosemary
On Mon, Jul 23, 2018 at
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Hello team,
We have first fixed non-cortex voxels in the pial surface using the
brainmask.mgz volume, and we next corrected pial surfaces that
mistakenly included cerebellum by creating a copy of
'brain.finalsurfs.mgz' named 'brain.finalsurfs.manedit.
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I am using mri_vol2vol --mov L_AIP_mask.nii.gz --targ
$FSLDIR/standard/MNI152_T1_1mm_brain.nii.gz --inv --reg
$FREESURFER_HOME/average/mni152.mni305.subfov1.dat --o L_AIP_MNI152.nii.gz
--interp nearest
(I used mni152.mni305.subfov1.dat in my registr
no idea how to help with the vol2vol problem without a command line and
more description of the problem
On 7/24/18 6:52 AM, Yagmur Ozdemir 19 wrote:
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By copying the matrix that comes up in the terminal, then readjusting
it, if needed, in a different .dat f
your results could have vanished after ICV correction for one of two
reasons: the CV difference became less or the values became noisier (or
a combination). So check in your data which one of those things happened.
On 7/23/18 8:30 PM, Martin Juneja wrote:
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Hi Martin
no, the stats are all from subject-space segmentations and surfaces.
cheers
Bruce
On Tue,
24 Jul 2018, Martin Steppan wrote:
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Dear Freesurfer/s,
Sorry, it might be a stupid question, since I am a newbie in this field.
Is the ?.aparc.sta
The parcellation starts off in fsaverage space. It is mapped through the
surface-based registration into the native subjects surface space.
There, the boundaries are refined to better fit the individual. The
transformation is based on folding patterns which are pretty consistent
across the age
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In --temp /home/zwj/SCH_immune/A00 you seem to be missing the last bit of the
file name, like .mgz or .nii. This option passes the template volume you want
the output volume to match.
For the second question, you can load that annotation and the indi
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Dear experts,
Could you tell us how to convert label to volume? when I run this command
"mri_label2vol --label lh.insular.label --temp /home/zwj/SCH_immune/A001
--identity --o insular.img", errors happened: corRead(): can't open file
/home/zwj/S
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By copying the matrix that comes up in the terminal, then readjusting it, if
needed, in a different .dat file, I can fix the issue. But I would still
appreciate any suggestions on how to use mri_vol2vol with a binarized mask, or
what might be causing
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Dear Freesurfer/s,
Sorry, it might be a stupid question, since I am a newbie in this field.
Is the ?.aparc.stats file somehow based on transformation to fsaverage
space? I am aware that this is the case for -qcache, but is this also true
for the predefi
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Hello freesurfer experts,
I am editing the registration matrix between two volumes (fsaverage's T1 to fit
MNI152 from fsl) using tkregister2, and I cannot save the registration because
I do not have permission to change the .dat file I originally ope
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