Dear Freesurfers,
I know this is a very simple question. I'm just having trouble specifying
the correct directories for rtview based on the example. When I run rtview,
it can't find the image files that really do exist in the directory.
For the following example in the help section: I did what I
Hi Michelle
many of the FS binaries use knowledge of the standard directory tree
under SUBJECTS_DIR to do things like lookup the original coordinates of a
flattened or inflated vertex, which is why you need the --s and --lh.
cheers
Bruce
On
Thu, 13 Oct 2011, Michelle Umali wrote:
Dear Fre
Hi Ping,
it's hard to diagnose from a single slice. If you upload the subject I'll
take a look
cheers
Bruce
On Thu, 13 Oct 2011, Ping-Hong Yeh wrote:
> Hello,
>
> We have a quite a few 3T data got poor result due to the field
> inhomogeneity, especially in the occipital region (see attached).
>
Hi Jodie, I'm still not sure what you are trying to show. If you want to
show each wedge separately, then you will need four contrasts of the
form "-a 1 -c 0", "-a 2 -c 0", etc. If you want to show places where a
voxel responds to *any* of the four, you can use "-a 1 -a 2 -a 3 -a 4
-nosumconds
ZhiLiangLong wrote:
Hi doug
Thanks for your suggestions. I have another two questions:
1: I can't clearly understand that why i should firstly run DODS to
find interaction between my group variables and age,then run DOSS to
obtain difference between groups specified in my contrast files if
Dear Experts,
Does Freesurfer print an automatic log or diary of the manual corrections (to a
brainmask) made in Tkmedit?
Also, is there any way that I can change the color of the edited voxels? It
would be great to view the edited voxels as anything but black and white (eg
dark blue and a bri
I don't know about the rest, but you can change the cursor and surface
colors with View->Configure
Vy Dinh wrote:
> Dear Experts,
>
> Does Freesurfer print an automatic log or diary of the manual
> corrections (to a brainmask) made in Tkmedit?
>
> Also, is there any way that I can change the col
Thanks!
Vy T.U. Dinh
Research Assistant, Neurological Sciences
Rush University Medical Center
Phone: (312) 563-3853
Fax: (312) 563-4660
Email: vy_d...@rush.edu
From: Douglas N Greve [gr...@nmr.mgh.harvard.edu]
Sent: Thursday, October 13, 2011 1:25 PM
To:
We're trying to reconstruct pial and white matter surfaces for cortical
thickness analysis and sections of the gray matter are being excluded,
particularly in the temporal lobes. As far as we can tell, there is no
way to add this back to the pial surface...is there a solution to this
problem?
If there is white matter that is being excluded from the white surface,
then if that is fixed, the pial surface will grow out further and may
include the gray matter originally excluded.
On Thu, 13 Oct 2011, Jordan Pierce wrote:
We're trying to reconstruct pial and white matter surfaces for c
I believe if you go to the View menu you can select "Edited voxels" which
will show what you edited in that session in blue.
If you run:
recon-all -show-edits -s subjid
this will show you white matter and brainmask edits you have made I
belive.
We don't print a log of the manual correections b
We can get that step to work when there's white matter, but there are areas of
only gray matter that are still being excluded.
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The i
Can you send me a snapshot of a few slices where you see this?
On Thu, 13 Oct 2011, Jordan Pierce wrote:
> We can get that step to work when there's white matter, but there are areas
> of only gray matter that are still being excluded.
>
>
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This is very neat. Thank you everyone for your responses!
Vy T.U. Dinh
Research Assistant, Neurological Sciences
Rush University Medical Center
Phone: (312) 563-3853
Fax: (312) 563-4660
Email: vy_d...@rush.edu
From: Allison Player [astev...@nmr.mgh.harvard
can you send us an image or upload the data?
On Thu, 13 Oct 2011, Jordan
Pierce wrote:
We're trying to reconstruct pial and white matter surfaces for cortical
thickness analysis and sections of the gray matter are being excluded,
particularly in the temporal
lobes. As far as we can tell, th
we do however record manual edits in the volumes themselves. Erasing sets
things to 1 (not 0) and editing them on turns them to 255 so you can
always recover edits that you have made
cheers
Bruce
On Thu, 13 Oct 2011, Allison Player
wrote:
> I believe if you go to the View menu you can select "
Dear FreeSurfers,
I'm trying to coregister FA images pre-processed with FSL to Freesurfer,
however i'm having a few problems and was wondering if someone could help me
out.
These are the steps that i carried out:
mri_convert subj_01/mri/brain.mgz brain.nii.gz
fslswapdim brain.nii.gz x z -y brai
Hi Doug,
Thanks for your reply. I tried running the contrast you suggested and
still get the same error as shown below. I'm guessing it's a problem
with my command? What have I done wrong?
Ultimately, I would like to show the response to each wedge as compared
to the others. However, I'm ho
Hi Joana - You can try our in-house tool for within-subject registration,
bbregister, with the --dti option.
a.y
On Thu, 13 Oct 2011, Joana Braga Pereira wrote:
> Dear FreeSurfers,
> I'm trying to coregister FA images pre-processed with FSL to Freesurfer,
> however i'm having a few problems a
Hi Joana,
try bbregister.
cheers
Bruce
On Thu, 13 Oct 2011, Joana Braga Pereira wrote:
> Dear FreeSurfers,
> I'm trying to coregister FA images pre-processed with FSL to Freesurfer,
> however i'm having a few problems and was wondering if someone could help me
> out.
>
> These are the steps t
Hello Experts:
I am new to Freesurfer. Does the SPGR data have to be of axial LPI orientation
in order to run through recon all?
thank you,
cat
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nope
On Thu, 13 Oct 2011, Cat Chong wrote:
>
> Hello Experts:
>
> I am new to Freesurfer. Does the SPGR data have to be of axial LPI
> orientation in order to run through recon all?
>
> thank you,
> cat
>
>
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Hi Cooper, try using the --f option to mri_concat. This takes a text
file in which you can list all the files you want.
doug
On 10/13/11 5:40 PM, Cooper Roddey wrote:
> I think my problem is not with mri_concat after all, but with matlab's
> 'unix' function. In any case, reading a list of input f
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