Dear Bruce,
the two subject dirs are here
https://www.dropbox.com/sh/k1z5o0e6sq90qq0/AABx38QxKvxDhUe2lV9imaa9a.The
original subject is s50 and the rotated one is rs50.
Thank you very much for your help.
Alessia Giuliano
Date: Thu, 5 Jun 2014 16:27:58 -0400
From: fis...@nmr.mgh.harvard.edu
To: fr
yes, it will be automatically excluded
Bruce
On Thu, 5 Jun 2014, Kev wrote:
> Thanks!
> The aseg tells me it is hippocampus; so just to be sure, when you say
> "freeze" you mean that this hippocampus is NOT going to be computed as
> cortical thickness?
> Cheers,
> Kev
>
>
> On Jun 5, 2014, at 4:
Thanks!
The aseg tells me it is hippocampus; so just to be sure, when you say "freeze"
you mean that this hippocampus is NOT going to be computed as cortical
thickness?
Cheers,
Kev
On Jun 5, 2014, at 4:07 PM, Bruce Fischl wrote:
> Hi Kev
>
> I'm not sure from the snapshots, but it looks like
Hi Kev
I'm not sure from the snapshots, but it looks like the region you are
talking about is non-cortical. Check the aseg and see what the labels are
adjacent to the white/pial surface there. It looks like it is part of the
surface that we "freeze" because it is not cortex.
cheers
Bruce
On Th
Hi Freesurfer,
I ran into the following error when running make_average_subject. The
following output is shown after make_average_surface is done.
/Volumes/fMRI/Scanner_Data
setenv SUBJECTS_DIR /Volumes/fMRI/Scanner_Data/
sdout /Volumes/fMRI/Scanner_Data/
mri_convert /Volumes/fMRI/Scanner_Data//P
Thank you so much for your help Paul! I was wondering if I could get a little
more specific help with the .ctab file. Would I just add my ROI to the existing
FreesurferColorLUT.txt (named something different of course) or would I start a
new one from scratch?
Thanks again!
Tara
- Original
hmmm, that is puzzling. Can you upload the two subject dirs with the
rotated direction cosines and I'll take a look?
thanks
Bruce
On Thu, 5 Jun 2014, Alessia
Giuliano wrote:
Dear Bruce,
when I say "the image was rotated" in 2 I mean that I have changed the image
header to reflect a new orie
Hello Martin and FreeSurfer experts,
I've checked the recon-all.log from the 2nd tp of one of the longitudinal
subject directories (1004_1.long.1004_base) and found the following 4 lines
using your search criteria:
1. \n mri_mask -transfer 255 -keep_mask_deletion_edits brainmask.auto.mgz
brain
Dear Bruce,
when I say "the image was rotated" in 2 I mean that I have changed the image
header to reflect a new orientation, instead in 3 there was an additional image
interpolation, therefore a blurring.As you said, I can understand that in the
latter case things change, but how can be explain
Hi Tara,
I do this regularly, though I don't define my Freesurfer ROIs/labels in
QDEC.
*The following will do the process into individual subject space*
*First*:
*mri_label2label *--srclabel path_to_label/label.label --trgsubject {$subj}
--regmethod surface --hemi hemisphere
Do this for as many
Dear Freesurfer team,
what is the best measure for neocortical gray matter from the FS output?
Thank you so much,
best,
Elisabetta
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Th
Hi all,
I am wondering if any one has any experience with converting a freesurfer
surface based ROI created in QDEC into a format I could use on functional data
in afni.
Thank you,
Tara
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Well, if you can't run any AFNI program, then that is the problem.
doug
On 6/5/14 11:37 AM, Nitenson, Adam wrote:
Hi Doug,
Unfortunately that did not seem to work. I am normally able to run
other AFNI programs on this computer (it's what I've been normally
performing my data analyses with)
Hi Doug,
Unfortunately that did not seem to work. I am normally able to run other
AFNI programs on this computer (it's what I've been normally performing my
data analyses with).
Best,
Adam
On Wed, Jun 4, 2014 at 12:02 PM, Douglas N Greve
wrote:
>
> Do the other programs in AFNI work on that c
Hi Christian,
you are interested in the longitudinal change in your study group. The
problem of course is that you are missing a longitudinal control group.
Control groups are so important.
With your data you can analyze if there is change in your study group
(using the 2 stage model, since
I second this approach. Much easier than including a blank slice
Bruce
On Thu, 5 Jun 2014, Jürgen Hänggi wrote:
Dear Sami
Instead of manual editing the FreeSurfer processed data (e.g. adding control
points for white matter), one might try to manipulate the raw T1-w. image.
Maybe removing the i
Hi Alessia
when you say "the image was rotated" do you mean you actually transformed
the image, or you simply changed the image header to reflect a new
orientation? I wouldn't think the latter would have a big effect, but the
former will involve an additional image interpolation (blurring) a
Hi everyone,
I was wondering if someone could comment on which portion of the precentral
gyrus is used to produce subcortical volume stats? Is it just medial or
lateral the whole gyrus?
Many thanks and all the best,
Hugh
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Dear Sami
Instead of manual editing the FreeSurfer processed data (e.g. adding control
points for white matter), one might try to manipulate the raw T1-w. image.
Maybe removing the incomplete slice and interpolating the signal of the
neighboring slices into the missing slice help.
Then the surfa
Problem solved!
took some effort trying everything out, but finally found a simple
solution by transforming everything into MNI
Here's how to convert from surface RAS to mni305
mni305ras = X*S*inv(K)*ras
X = talairach.xfm
S = scanner vox2ras (mri_info --vox2ras orig.mgz)
K = tkreg vox2ras (mri_i
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