Oh, I see. Thanks very much.
Zonglei Zhen
2008/7/29 Doug Greve <[EMAIL PROTECTED]>
> mkcontrast-sess -a 1 -a 2 -a 3 -a 4 -c 0 -nosumconds
>
> should do it
>
> doug
>
> Zhen Zonglei wrote:
>
> Dear fs/fsfast user:
> Would you please tell me how to do F test in fsfast? For example, I have 4
> co
Mishkin,
That dataset of 27 subjects is used to test the atlas, and is not used
to build the atlas. The 27-subject test set is not available for
download. The 40 subjects used to build the atlas is roughly the same
as that included in the tutorial data set (the 'group analysis'
directory).
Nick
A list of vertices is made from a path by creating a closed curve from
the points along the path and using all the points in the interior of
this closed curve.
A label file (.label) is a text file where the first two lines are
"header" and each line after that is a vertex. The first line has t
Can you elaborate on what you mean by making a label "out of the interior?"
Also, how would you make a label from my list?
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The path is going to try to connect the vertices and make a label out of
the interior. Is that what you want? If you just want a label from your
list, that would be pretty easy to create.
Aaron Shmookler wrote:
Hello,
Here's what I did:
1) mris_convert ?h.inflated file.asc
2) extract vert
Hello,
Here's what I did:
1) mris_convert ?h.inflated file.asc
2) extract vertices of interest into file2.asc
Here is what I want to do:
I want to import the vertices from file2.asc into tksurfer and apply
the *path_new_path_from_marked_vertices
*function so that I can then create a label. How
Hi,
>From what I read here:
https://surfer.nmr.mgh.harvard.edu/fswiki/AsegOptimization
The atlas has is made from 27 data sets (14 GE, 13 SIEMENS). Can you
give a bit more info about the sequences used. ie were they
FLASH-based or MPRAGE.
Are these 27 data sets available for download somewhere?
Hello Doug,
I transformed the aseg_m file to be 3x3x3.
I will try and trouble shot the possible error in that transform-
The AFNI steps I used to transform the freesurfer files to AFNI format, and
than to be 3x3x3 are pasted below.
Liat
-
foreach subj (xxx)
#step1
@SUMA_Make_Spec_FS -sid
Thank you Doug.
I also just got help from the AFNI message board which solved the problem: so
here is a note for AFNI/freesurfer users if they come across this too - if you
run AFNI's @auto_tlrc command use the '-rmode NN' so that it does nearest
neighbor resampling.
- Original Message
Hi Liat-
If you converted directly using mri_convert, you may run into some
problems. If so, I suggest using the program Ziad wrote
(@SUMA_Make_Spec_FS) which takes care of some of the freesurfer/AFNI
conversion problems automatically. See the AFNI posts on this issue.
Anthony
Doug Greve wr
Sorry, don't know anything about those commands. You're probably better
off registering the functional data directly to the anatomical
(fslregister or spmregister) rather than going thru the talairach
transform. You can then use mri_vol2vol to map the functional to the
anatomical, then mri_segs
I'm not sure there is, though the format is pretty simple. You can find
an example in the label directory of one of your subjects. Basically,
the first two lines are header (see example). Then each following line
has 5 numbers:
1. vertex number (0-based)
2. x
3. y
4. z
5. stat
you can just s
mkcontrast-sess -a 1 -a 2 -a 3 -a 4 -c 0 -nosumconds
should do it
doug
Zhen Zonglei wrote:
Dear fs/fsfast user:
Would you please tell me how to do F test in fsfast? For example, I
have 4 conditions, and want to test the 4x4 contrast matrix [1 0 0 0;
0 1 0 0; 0 0 1 0;0 0 0 1] with a F test.
I would suspect that something happened when you converted to afni
format. The aseg starts out at 1mm3, 256^3, but it appears to be 3mm3,
54x64x50. These conversions are quit tricky and easy to get wrong. Also,
did you check the aseg.stats file to assure that the volumes of the amyg
are more-
Hi Doug, I just checked, yes they are.
Liat
PS. I attached the Info files to this message.
- Original Message -
From: Doug Greve <[EMAIL PROTECTED]>
Date: Monday, July 28, 2008 12:16 pm
Subject: Re: [Freesurfer] AFNI /freesurfer aseg files problem
> are you sure that t1rc and pscA ar
Yes, if you spec to use motion correction regressors, then it will look
for mcextreg_000.bfloat. This is created by motion correction. If that
does not exist, then that process might have failed. To see, try
cd /Users/balajigoparaju/Desktop/subjectdata/LD-functional/bold/006
mcparams2extreg -mc
Do you have fsl installed? This is needed for creating the brain masks.
Balaji Goparaju wrote:
Hi Doug and all,
I used the new version of mkbrainmask-sess. It looks like the file is
getting created but it cannot find fslmaths for avmaths.
Is this error something to do with the freesurfer so
are you sure that t1rc and pscA are the same dimension? Remember,
freesurfer resamples everything into 1mm3, 256^3
doug
Liat Levita wrote:
Hello,
I wonder if anyone using AFNI converted freesurfer files has come across this problem (or can tell me if I making an error somewhere that I am ju
Hi Jenifer,
we actually don't use any anatomical landmarks in the automated
segmentation, although it is based on the CMA manual segmentation, so we
will inherit its properties. Dave: can you elaborate?
cheers,
Bruce
On Mon, 28 Jul 2008, Juranek, Jenifer wrote:
Hi,
Is any documentation
Hello,
I wonder if anyone using AFNI converted freesurfer files has come across this
problem (or can tell me if I making an error somewhere that I am just not
seeing right now). I posted the same question on the AFNI board but haven't
gotten feedback as yet.
Here is the problem:
After using f
Hi Doug and all,
There is a problem when i try the individual statistics,
I use the command
selxavg3-sess -analysis LD-analysis -s LD-functional
and i am getting an error:
ERROR: cannot find volume matching
/Users/balajigoparaju/Desktop/subjectdata/LD-functional/bold/006/mcextreg
ERROR: loadin
Hi Doug and all,
I used the new version of mkbrainmask-sess. It looks like the file is
getting created but it cannot find fslmaths for avmaths.
Is this error something to do with the freesurfer software itself, or is
there anything I can do about it?
Thu Jul 24 09:15:51 EDT 2008
/Users/balajigop
Hi,
Is any documentation available for describing the anatomical landmarks
for demarcation of amygdala and hippocampus used by aseg?
Many Thanks,
Jenifer
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Hi Rudolph,
This step is the talairach failure detection, and it's telling you that the
talairach transformation has failed. I don't really know why it failed, but
you should take a look at the transform and see if you can fix it. If it's
happening systematically on your subjects, check the qual
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