We don't have those number available, but you can generate them with
something like:
#1 Convert the annotation to a set of labels. This is for the Desikan
atlas, but you can spec the destrieux instead
mri_annotation2label --subject fsaverage --hemi lh --outdir ~/tmp/aparc
# For each label,
Hi Robert, both of those are correct. The 2nd will give you
OldAgeSlope-YoungAgeSlope correcting for Gender and BEH
doug
On 7/23/13 10:40 AM, Robert Schulz wrote:
Dear all,
I have 2 short questions regarding a correlation analysis I'd like to
perform with mri_glmfit (surface-based DTI data
What is your command line? This is surely an initialization error. Try
running tkregister2 with --regheader to see where it starts. If that is
close, then use --init-header on bbregister
doug
On 7/23/13 4:13 PM, Smian wrote:
Thank you for your reponse. The registration has turned out quite
Hi Cesar, when you say that it is on the left hemi, do you mean the left
side of the image or the right side of the image. tkmedit displays in
radiological convention, so a right hemi label should show up on the
left side.
doug
On 7/23/13 4:45 PM, Cesar Echavarria wrote:
Hello freesurfe
You can try using bbregister. Normally, you don't use bbregister on a
segmentation, but the segmentation index numbers just happen to be
"T1-weighted".
doug
ps. Please remember to copy the list when responding. thanks!
On 7/23/13 9:51 AM, Mark Plantz wrote:
Hi Doug,
Sorry about that vag
Hello freesurfers
I want to convert a surface-defined label to an auxiliary volume file. I've
created my label on the right hemisphere. I then enter the following
command to convert this label into a volume
mri_label2vol --label
/cluster/tootell/pitcairn/1/users/Cesar/good_subjects_anat/abir_anat
Hi Mark
have you tried using a transform? Usually with more than one subject we
require that they be registered. I haven't looked at that code in a long
time, so I am not positive that it would fix this problem, but it might.
In any case if they aren't registered it won't generate a useful at
Thank you for your reponse. The registration has turned out quite
strangely (please see attached). I checked the first value in the
mincost file and it is quite high (~0.95). I'm assuming that means that
the initialization was bad. I tried changing the initialization from fsl
to spm and header,
Hi Yi-Ping
try using the -i switch to mris_sphere.
cheers
Bruce
On Tue, 23 Jul 2013, Lo, Yiping
wrote:
>
>
> Hi Freesurfer,
>
> I am tring to inflate pial surface until the sphere. I have tried
> mris_inflate and set the number of iteration to be large. However, it seems
> to inflate the brai
you can use bbregister to register your T2* volumes to the surface, then
mri_vol2surf to sample and display it.
cheers
Bruce
On Tue, 23 Jul 2013, Smian wrote:
> Hi everyone,
>
> To put things into context, I am trying to follow the four step
> methodology outlined in this paper (Cohen-Adad, 2013
Hello freesurfers,
I recently ran into a problem with mri_ca_train, a function that
creates a .gca atlas from a manually segmented volume and input volume(s).
My command line is:
mri_ca_train -T1 T1.mgz CMH-11460 CMH-11461 ~/Desktop/atlas.gca
The results:
processing subject CMH-11461, 1
Hi
i am using corticals parcels (destrieux) as nodes in a connectivity study
using the NBS (Network Based Statistics) tool; i want to assign MNI coordinates
for these nodes. is there any MNI coordinates in freesurfer for each component
of this parcellation (not for every vertex in those comp
Hi, I'm sorry for sending a duplicate request, but I am still really
confused about the discrepancy between group-level findings in qdec (ROIs
that are different across my 2 groups) and lack of a difference on the
extracted thickness measures for those same custom ROIs. More info is
below. Please l
Hi everyone,
To put things into context, I am trying to follow the four step
methodology outlined in this paper (Cohen-Adad, 2013)
http://www.sciencedirect.com/science/article/pii/S1053811913000700
I have already performed recon-all on MPRAGE data. I have also carried
out the following steps:
Dear all,
I have 2 short questions regarding a correlation analysis I'd like to perform
with mri_glmfit (surface-based DTI data are correctly preprocessed and
concatenated into mgh file, statistics are performed on fsaverage space).
1) I'd like to look for correlation between the surface-data
Dear all,
I have 2 short questions regarding a correlation analysis I'd like to perform
with mri_glmfit (surface-based DTI data are correctly preprocessed and
concatenated into mgh file, statistics are performed on fsaverage space).
1) I'd like to look for correlation between the surface-data
Hi Freesurfer,
I am tring to inflate pial surface until the sphere. I have tried mris_inflate
and set the number of iteration to be large. However, it seems to inflate the
brain to a limit and no further inflation. I have also tried mris_sphere, but
it seems not what I want. It more likely to
Hi Doug,
Thanks for your reply. Yes, it does work with a longer -refeventdur. In
fact, I had tried that yesterday before posting my original message but
I'd forgotten to make the corresponding changes to the 3rd column of the
paradigm file and so kept getting the error message.
The shortest I
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