Hi,
is there any way to overlay only certain regions of interest from the LUT table
and not all of them in freeview or tkmedit over a T1 image? I want to just
display certain areas or ROIs.
thanks,
AJ
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Thanks Doug,
I'll try that.
Tomer
On Apr 12, 2012, at 2:04 PM, Douglas N Greve wrote:
> First, convert the annotation to a segmentation, something like
>
> mri_annotation2label --subject subjectname --hemi lh --seg lh.aparc.mgh
>
> Then binarize the segmentation and mask with your functiona
Hi Cindy
which segmentation? If the aseg, you can start after that. Try running
recon-all -s -make all
cheers
Bruce
On Fri, 13 Apr 2012, Cynthia Elisabeth
Krafft wrote:
> Hello,
>
> Sorry for a newbie question. If we have to edit the segmentation (and all
> that we are interested in investig
Hello,
Sorry for a newbie question. If we have to edit the segmentation (and all that
we are interested in investigating is the volumetric data), what step should I
run after that? Is it necessary to run "recon-all -autorecon2 -autorecon3" or
is there some less time-consuming processing that wi
Dear Experts,
I wonder whether someone could explain to me how the monte-carlo correction
in qdec manages to be instantaneous. I appreciate it uses pre-computed
data, but I am a little confused. I thought that this sort of permutation
based method is based on relabelling of one's own specific dat
Thank you everyone for your great input. After reading through all of the
suggestions and references, I like the idea of using ICV rather than global
averages, at least for this current study. However, I do have one more
question. All the papers normalize on surface area. If we want to present
Thanks Bruce. I used mri_info to verify. And there seems to be a small
mismatch.
I have an original contrast overlay file 'sig.nii', then I used
mri_vol2vol --mov sig.nii --targ $SUBJECTS_DIR/$subj/mri/T1.mgz --reg
register.dat --o sig-aligned.nii
to get a new overlay sig-aligned.nii which is al
Chris,
going forward, yes, i would recommend installing centos6. you can use
the centos4 freesurfer build in the meantime, until the centos6
freesurfer build (the faster one) is ready. you dont have to rerun your
subjects if your happy with the current results. the next release
doesnt have any
Hi Nick,
So would you recommend I install Centos 6 on the new workstation?
In addition, I've run recon-all on a large study group (>100); I take it I'll
have to re-run all of them?
Thanks,
Chris
Chris,
yes, the centos5 build freesurfer 5.1 will work on centos6 (we use it
i
Hi Miranka, why not create a contrast that computes this difference?
When you do this, there will be a gamma.mgh file in the contrast
directory that has this information in it.
doug
On 04/12/2012 02:06 PM, Miranka Wirth wrote:
> Dear freesurfers,
>
> I am trying to create a map that shows the ve
Dear freesurfers,
I am trying to create a map that shows the vertex-wise magnitude of
thinning (f.e.) between two groups, similar to Fig5 in Dickerson et
al., 2009.
I know how to extract the group-average thickness map from the beta.mg
(mri_convert beta.mgh group1.mgh --frame 0 etc.), assuming tha
First, convert the annotation to a segmentation, something like
mri_annotation2label --subject subjectname --hemi lh --seg lh.aparc.mgh
Then binarize the segmentation and mask with your functional:
mri_binarize --i lh.aparc.mgh --match segid --mask sig.mgh --mask-thresh
2 --o seg.masked.mgh
Th
thanks it works now :)
On 04/12/2012 12:48 PM, Douglas N Greve wrote:
> Take the inverse
>
> On 04/12/2012 01:47 PM, Johnson wrote:
>> I do the transformation in Matlab, I found out that the matlab
>> *load_mgh* function returns the vox2ras matrix, where can I find the
>> ras2vox matrix?
>>
>> On 0
Take the inverse
On 04/12/2012 01:47 PM, Johnson wrote:
> I do the transformation in Matlab, I found out that the matlab
> *load_mgh* function returns the vox2ras matrix, where can I find the
> ras2vox matrix?
>
> On 04/12/2012 12:11 PM, Bruce Fischl wrote:
>> yes
>> On Thu, 12 Apr 2012, Johnson
I do the transformation in Matlab, I found out that the matlab
*load_mgh* function returns the vox2ras matrix, where can I find the
ras2vox matrix?
On 04/12/2012 12:11 PM, Bruce Fischl wrote:
yes
On Thu, 12 Apr 2012, Johnson wrote:
The vector coordinates will be in the voxel space
On 04/12/
sorry. meant to sent to the list, too.
L
> Hi Bruce,
>
> Yes that's what I wanted! The --fstarg flag uses the
> $SUBJECTS_DIR/$subj/mri/orig.mgz as the targ so in my case it would be the
> same as using --targ $SUBJECTS_DIR/$subj/mri/T1.mgz.
>
> So I guessed it had worked from the beginning but I
Try loading it in tkmedit, something like:
tkmedit sub01 orig.mgz -overlay sig_2subj01_volumetric.nii
doug
On 04/12/2012 03:46 AM, René Besseling wrote:
> Hi Doug,
> Sorry, missed your reply. I assumed the --identity argument was used
> for looking up the surface-to-volume mapping somewhere in
Hi Zhang, there should be a file named something like
"cache.th13.abs.y.ocn.dat" that is output as part of the correction for
multiple comparisons. This will have a column for each significant
cluster in the order that the clusters are in. Each row is a subject. So
you can take the mean over th
Hi Lingqiang, first run
reg-mni305.2mm --s subject --reg regfile.dat
to get a registration. Then run
mri_vol2vol --mov sig.nii --reg regfile.dat --fstarg --o sig_high.nii
doug
On 04/12/2012 12:06 PM, Lingqiang Kong wrote:
> Hi Surfers,
>
> I am trying to resample a GLM analysis contrast o
Hi Ellen, you can create a contrast to do this, something like:
mkcontrast-sess -a 1 -c 0 -sumdelays -setwdelay
-sumdelays will sum across the different time points
-setwdelay will cause it to prompt you for a list of weights, one for
each time point. You should give the timpoints in the fir win
yes
On Thu, 12 Apr 2012, Johnson wrote:
> The vector coordinates will be in the voxel space
>
> On 04/12/2012 11:54 AM, Bruce Fischl wrote:
>> Hi Johnson
>>
>> it depends whether you are using the ras2vox or vox2ras. It should be:
>>
>> V_rawavg = M_ras2vox_rawavg * inv(M_ras2vox_aseg) * V_aseg
The vector coordinates will be in the voxel space
On 04/12/2012 11:54 AM, Bruce Fischl wrote:
> Hi Johnson
>
> it depends whether you are using the ras2vox or vox2ras. It should be:
>
> V_rawavg = M_ras2vox_rawavg * inv(M_ras2vox_aseg) * V_aseg
>
> Where the V_* are 4x1 homogenous vectors.
>
> ch
Hi Steve,
they are very much subject specific! The stats in the aseg.stats are
partial-volume corrected using the aseg.mgz and the norm.mgz
cheers
Bruce
On Thu, 12 Apr 2012, Steven Thomas Korycinski wrote:
> Freesurfer users,
>
> Can anyone tell me if the subcortical segmentation shown in TkM
Hi Johnson
it depends whether you are using the ras2vox or vox2ras. It should be:
V_rawavg = M_ras2vox_rawavg * inv(M_ras2vox_aseg) * V_aseg
Where the V_* are 4x1 homogenous vectors.
cheers
Bruce
On Thu, 12 Apr
2012, Johnson wrote:
> so to be clear about it, suppose T1 is the matrix in aseg
Hi Lingqiang
do you mean in voxel register with the anatomy, with the same voxel
dimensions, etc...? If so I think you can specify --targ \
$SUBJECTS_DIR/$subject/mri/T1.mgz
or you mri_convert with -rl
cheers
Bruce
On Thu, 12 Apr 2012, Lingqiang Kong wrote:
> Hi Surfers,
>
> I am trying t
or change it to float if they are bigger than 255
On Thu, 12 Apr 2012,
Douglas N Greve wrote:
> You can do it with mri_convert
> mri_convert seg_edited.mgz seg_edited.mgz -odt uchar --no_scale 1
> Note that your segmentation ids should all be between 0 and 255
> doug
>
>
> On 04/12/2012 11:49 AM,
Hi,
We ran a first-level FIR analysis on our functional data with selxavg3-sess,
which outputs a single ces.nii file for each subject containing the contrast
images for all timepoints. Now we would like to create an image representing
the sum of a subset of these images in a time-window of inte
so to be clear about it, suppose T1 is the matrix in aseg and T2 is the
one in rawavg,
to transform from aseg to rawavg I will apply invert(T1)*T2 is that
correct?
On 4/11/2012 8:12 PM, Bruce Fischl wrote:
>> Invert one and compose it with the other
>>
>>
>>
>> On Apr 11, 2012, at 7:48 PM, John
You can do it with mri_convert
mri_convert seg_edited.mgz seg_edited.mgz -odt uchar --no_scale 1
Note that your segmentation ids should all be between 0 and 255
doug
On 04/12/2012 11:49 AM, Anthony Dick wrote:
> Hello,
>
> I am running the rebuild_gca_atlas.csh program and got the following
> err
Hi Surfers,
I am trying to resample a GLM analysis contrast overalay ('sig.nii') back
to individual subject anatomical space (T1.mgz). The functional scans and
the anatomical scans were acquired on two different days and were
co-registered with register.dat. The T1.mgz has high resolution and the
Hello,
I am running the rebuild_gca_atlas.csh program and got the following
error for seg_edited.mgz, which is the manually defined file imported
from a different program outside of freesurfer.
mri_ca_train: segmentation file /seg_edited.mgz is not type UCHAR
or FLOAT
Is there a way to redefi
what is your command line? Make you you use -f before the surface name so
it knows you are loading a surface. Also, please send us the info we need
to help you! Command line, operating system, terminal output, FS version,
etc
cheers
Bruce
On Thu, 12 Apr 2012, Domenico M.
Mezzapesa wrote:
What version of freesurfer are you running? Would it be possible to send
us the surface file that crashed it?
Ruopeng
On 4/12/12 5:12 AM, Domenico M. Mezzapesa wrote:
> Dear FreeSurfer experts,
>
> I have a problem using FreeView: it can load
> volume without problems, but when I try to load sur
Hi haochuanxi
there are lots and lots of binaries in FreeSurfer. You can look at the
help for each one if you want, but are you sure you need to? It may be
that the recon-all script is most of what you need.
cheers
Bruce
On Thu, 12 Apr 2012, ??
wrote:
Dear FS experts
I could not underst
Dear FreeSurfer experts,
I have a problem using FreeView: it can load
volume without problems, but when I try to load surface it crash.
The
error is:
MatrixMultiply: m2 is null!
No such file or directory
Best
regards
Domenico M Mezzapesa
Invita i tuoi amici e Tiscali ti premia! Il consi
Hi Doug,
Sorry, missed your reply. I assumed the --identity argument was used for
looking up the surface-to-volume mapping somewhere in the predefined folder
structure of this subject. Anyhow, my last command was
mri_surf2vol --surfval sig_2subj01.mgh --hemi rh --fillribbon --identity
sub01 --tem
Dear FS experts
I could not understand fully the Program Name: tkregister2_cmdl and Program
Name: mri_make_uchar and Program Name: mri_ca_label and
Program Name: mri_gcut and Program Name: mri_concatenate_lta and Program Name:
mri_normalize_tp2 and Program Name: mris_topo_fixer and Prog
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