Thank you Bruce, this works great.
This is just for the records:
$ mris_expand -thickness surf/lh.white 0.35 surf/lh.white_outer0.35GM
using distance as a % of thickness
expanding surface surf/lh.white by 35.0% of thickness and writing it to
surf/lh.white_outer0.35GM
$ mris_expand
Hello all,
How do I get aparc stats (area) using the pial surface, please?
Thanks,
Andreia
- Mensagem encaminhada de _andre...@sapo.pt -
Data: Thu, 27 Mar 2014 11:31:13 +
De: _andre...@sapo.pt
Responder Para: Freesurfer support list
Hi Clint
you can do this with mris_anatomical_stats -l label name ...
cheers
Bruce
p.s. and you can use mri_label2label to map the label from one subject to
others
On Thu, 27
Mar 2014, Clint Johns wrote:
Hi,
We are having some trouble extracting ROI (thickness) information using a
label
glad it worked out
Bruce
On Fri, 28 Mar 2014, Markus Gschwind wrote:
Thank you Bruce, this works great.
This is just for the records:
$ mris_expand -thickness surf/lh.white 0.35
surf/lh.white_outer0.35GM
using distance as a % of thickness
expanding surface surf/lh.white
Hi Meng
can you send us the contents of .xdebug_tkmedit? You'll need to start
tkmedit from a directory that you have write access to
cheers
Bruce
On Fri, 28 Mar 2014, limengsecret wrote:
Hi freesurfer，
I installed the package of freesurfer according to the intruction of
freesurfer
Hi Freesurfers,
I have some questions about ROI analyses.
1. I use the mni305 and fsaverage flags during preprocessing. Does this mean
that when I run funcroi-config, funcroi-sess, etc, the analysis is being done
for each subject in mni305 space, as opposed to native space? Meaning, If I
I tested the license file you sent out to the list and it worked for me.
But in the future please refrain from sending the contents of the
license file in a public forum like this.
I suppose its possible your file was currupted in some way so Im going
to resend you the license file offline and
On 03/28/2014 08:51 AM, Emily Boeke wrote:
Hi Freesurfers,
I have some questions about ROI analyses.
1. I use the mni305 and fsaverage flags during preprocessing. Does this mean
that when I run funcroi-config, funcroi-sess, etc, the analysis is being
done for each subject in mni305
Look at the wiki for our group analysis tutorial
On 03/28/2014 09:41 AM, Linda Xu wrote:
Dear Douglas,
What should I do next? I do not know how to use the freesurfer to
calculate the correlation different of two group. So could you give me
some advice?
Yours Linda
2014-03-27 19:18
try this
mris_anatomical_stats -mgz -cortex ../label/lh.cortex.label -f
../stats/lh.aparc.pial.stats -b -a ../label/lh.aparc.annot -c
../label/aparc.annot.ctab vrfp-oct11-anat lh pial
On 03/28/2014 06:31 AM, _andre...@sapo.pt wrote:
Hello all,
How do I get aparc stats (area) using the pial
On 03/28/2014 12:04 PM, Emily Boeke wrote:
Hi Doug,
Thanks for the response.
Regarding #1, I am still confused. if the ROI boundaries computed in native
space are mapped to fsaverage/mni305 space, doesn't that mean the actual
computing of the averages is done in fsaverage/mni305 space?
Dear Sir,
My experiment design is let the two group of subjects watch a movie and
calculate the correlation between two condition.
Now I get the correlation result from AFNI. I want to calculate the
correlation different between the two group by using freesurfer.
However the group analysis in
Hi there,
After conducting a DODS analysis (One group, four factors, one
covariate), we were able to identify a region (LH pars opercularis)
whose mean thickness differed when two of the four factors interacted.
In order to further investigate the interaction, we obtained each
participant's mean
Are you sure your R design matrix and contrasts are consistent with FS?
Also, something could have gone wrong in the transfer to each subject. I
would recommend extracting the data directly out of the input file
(y.mgh) using mri_segstats with --slabel, especially if the label is small.
On
I'm not sure I understand your paradigm or what you are trying to do.
You would have had to have given afni the same information to do a
task-based analysis
doug
On 03/28/2014 12:19 PM, Linda Xu wrote:
Dear Sir,
My experiment design is let the two group of subjects watch a movie
and
Jorge, do you output the FWHM?
doug
On 03/27/2014 03:14 PM, jorge luis wrote:
Hi Pedro
Sorry, right now the only multiple comparisons corrections implemented
in lme are the original Benjamini and Hochberg (1995) FDR procedure
(lme_mass_FDR) and a more recent and powerful two-stage FDR
Hi Doug,
Thanks for the response.
Regarding #1, I am still confused. if the ROI boundaries computed in native
space are mapped to fsaverage/mni305 space, doesn't that mean the actual
computing of the averages is done in fsaverage/mni305 space? Why would mapping
to fsaverage/mni305 space be
Hi Doug,
Thank you very much! It did the trick!
However, I've noticed that the surface area obtained from the pial
surface is bigger than the one obtained from white surface in 3 labels:
Example of a control subject:Bankssts(WM=1161; pial=1026),
pericalcarine(WM=1614, pial=1412) and
I tried to do surfer reconstruction (version 5.3) collected in SIEMENS 7T, with
error: imgreg_4dfp /opt/freesurfer-530/average/711-2C_as_mni_average_305
/opt/freesurfer-530/average/711-2B_as_mni_average_305_mask talsrcimg_g11 none
talsrcimg_to_711-2C_as_mni_average_305_t4 1283' failed!
We are reasonably certain that the R design matrix matches but I will
certainly double check and report back.
I also wondered about the transfer of the label to each subject, and
wanted to use mri_segstats... but since we didn't use qdec, we don't
seem to have a y.mgh input file, and I'm not sure
If you used mri_glmfit, just use whatever you passed as --y
doug
On 03/28/2014 02:06 PM, Clint Johns wrote:
We are reasonably certain that the R design matrix matches but I will
certainly double check and report back.
I also wondered about the transfer of the label to each subject, and
Dear Douglas,
What should I do next? I do not know how to use the freesurfer to
calculate the correlation different of two group. So could you give me some
advice?
Yours Linda
2014-03-27 19:18 GMT-04:00 Linda Xu lynda@gmail.com:
Dear Douglas,
OK, I will figure it out. And my next
Dear Sir,
My experiment design is let the two group of subjects watch a movie and
calculate the correlation between two condition. Now I get the correlation
result from AFNI. I want to calculate the correlation different between the
two group by using freesurfer.
I try to do it by using
There is not such a script. You can do a different check though by
computing the mean area on the crown and in the fundus in the native
subject space, then comparing these numbers across subjects to see if
the effect holds. This test gets around the problems of sampling areal
measures into a
Hi FS community,
I am using FS 5.3 to do a longitudinal analysis on some data of mine. I
have manually edited some of the reconstructed scans (i.e. addition of
control points and white voxels) where the reconstruction was not as
precise:
1) Is the base template created from the recon-all -base
between what two conditions? Please don't be shy about giving us more
than a few sentences explaining what you are doing. I'm sure it is clear
to you, but it is easy to lose someone who knows nothing about your paradigm
doug
On 03/28/2014 02:52 PM, Linda Xu wrote:
Dear Sir,
My experiment
Hi,
I think there is something wrong with mris_make_face_parcellation to read
the license, because I tried it on other computers, on which all other
freesurfer codes we usually use, work fine, but not this one.
On Thu, Mar 27, 2014 at 3:39 PM, Mahshid Najafi mhs...@gmail.com wrote:
The output
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