Dear Priti, Anastasia,
Thank you for your help, I created bvec and bval files and it went fine.
But now I have another error in preprocessing step.
I attach a log file. Could you please take a look at that?
Thank you,
Tanja.
trac-preproc exited with ERRORS at Fri Feb 10 10:52:37 CET 2012
Hi Jeff,
I think you want to use Doug's tools for this (mri_glm and such). He'll
probably comment in an hour or two
cheers
Bruce
On Mon, 13
Feb 2012, Jeff Sadino wrote:
Hello FreeSurfers,
I want to compare cortical thickness differences between my two groups. Is
this the correct
Hi Jeff, you should use mris_preproc to stack the subjects into one
file, mri_surf2surf to smooth them, and mri_glmfit to analyze them
(including computing the difference between groups and other stats). See
the group tutorial on the web page. You could probably do what you are
suggesting, but
Hi Jeff,
make_average_subject is just if you want to visualize results on a
surface presenting the average of your own subjects, rather than using
the provided 'fsaverage'. It is not necessary (and not related) to
performing group statistical comparisons per se.
You can use the 'qdec' utility
Hi Antonella, what level of detail do you want? I think that most people
are reporting MNI coordinates.
doug
On 2/13/12 2:44 PM, Antonella Kis wrote:
Hi Doug,
I will be very grateful if you give me some directions regarding how I
can get my clusters location ( my output is too general
Hello all,
I'm trying to run mri_volcluster on our third-level functional data
and one of the required flagged arguments is the register.dat file.
Our data preprocessing/registration was done in FSL, not Freesurfer,
so we don't have this particular file. Is there anything we can do to
get around
Dear FreeSurfers,
To get a better view on the pial surface of the Heschl' Gyri I used the
command mri_vol2surf after having created the suitable label with
(label2vol). My goal is to get
My Command was: *mri_vol2surf --src pf_lh_vol.mgz --hemi lh --srcreg
register.dat --out_type paint --o
You need to set the nb0 parameter (number of low-b volumes in the
beginning of your DWI series).
On Tue, 14 Feb 2012, Tetiana Dadakova wrote:
Dear Priti, Anastasia,
Thank you for your help, I created bvec and bval files and it went fine.
But now I have another error in preprocessing step.
PS: The info on what you need to set it here:
https://surfer.nmr.mgh.harvard.edu/fswiki/dmrirc
# Number of low-b images
# Must be specified if inputs are not DICOM
# Default: Read from DICOM header
#
set nb0 = 10
On Tue, 14 Feb 2012, Tetiana Dadakova wrote:
Dear Priti, Anastasia,
Thank
Hi Huiting, you don't need to give it a register.dat. That only gives
you access to label locations of your clusters. If this is something you
want, you can use $FREESURFER_HOME/average/mni152.register.dat.
doug
Huiting Liu wrote:
Hello all,
I'm trying to run mri_volcluster on our
Antonella Kis wrote:
Hi Doug,
1) I would like to report the MNI coordinates and also a more exactly
region I mean if possible tto find exactly where in the
Left-Cerebral-White-Matter and Right-Cerebral-White-Matter my cluster
is located.
What do you me by exactly where? The nearest
Hi,
I am trying to use selxavg3-sess function and getting this error. Below is
the error I get. I actually have this fingertap.par file but freesurfer
somehow does not see it. Any help would be
appreciated.
Thanks!
Meryem Yucel
PMI Lab
Extension format = nii.gz
ERROR: opening
Dear all,
We have performed a cluster analysis in Qdec and found a significant
vertex-cluster after correction for multiple testing using the Monte
Carlo simulation. Now, we would like to extract the (unique) identifiers
of all vertices that form the significant cluster. We then would like to
I see, thank you :)
On Tue, Feb 14, 2012 at 6:50 PM, Anastasia Yendiki
ayend...@nmr.mgh.harvard.edu wrote:
PS: The info on what you need to set it here:
https://surfer.nmr.mgh.harvard.edu/fswiki/dmrirc
# Number of low-b images
# Must be specified if inputs are not DICOM
# Default: Read
Hi Meryem, it looks like it is looking for fingertap not
fingertap.par. Could that be the problem?
doug
Meryem Ayse Yucel wrote:
Hi,
I am trying to use selxavg3-sess function and getting this error. Below is
the error I get. I actually have this fingertap.par file but freesurfer
somehow
Hi Florian, you can save the cluster as a label. This is a text file
with xyz values for each vertex. The xyz values are in mni305 space.
doug
Florsek wrote:
Dear all,
We have performed a cluster analysis in Qdec and found a significant
vertex-cluster after correction for multiple testing
Dear Doug,
Can I run the mri_volcluter without --reg ?
I am asking this because when I run:
mri_glmfit-sim \
--glmdir GroupAnalysis_ADC.glmdir \
--grf 3 neg \
--cwpvalthresh .05 \
--overwrite
gives me the following error (I also attached the log file):
Also, does neg
You can do it in tksurfer using the Tools-CustomFill, then select fill
to threshold (or something like that). I think there's a way to do it in
QDEC too. Try looking at the tutorial.
doug
Florsek wrote:
Hi Doug,
do I have to manually draw the new label or can I somehow custom fill
the
Hi,
Now it seems to be working with the par file but I am getting this error.
Any help will be appreciated. Thanks,
Meryem
Computing compensation for resdual AR1 bias
1 -0.5 -0.473129(t=0.192235)
2 -0.25 -0.238292(t=1.09283)
3 0 -0.00411884(t=1.27811)
4 0.25 0.228971
The mask used to compute the global mean does not have any voxels in it
because the field of view is so small. Try running
mkbrainmask-sess -s session -nero 1 -fsd bold
Then run selxavg again. The above mkbrainmask command tells it to only
erode the mask by one voxel (the default in preproc-sess
I tried this. It is still giving the same error. Should I check my mask
files?
Thanks.
The mask used to compute the global mean does not have any voxels in it
because the field of view is so small. Try running
mkbrainmask-sess -s session -nero 1 -fsd bold
Then run selxavg again. The above
Dear experts,
The hippocampal-subfield are expressed as probability maps. For each
subfield, each voxel is assigned a probability of inclusion on a scale of
[0-255]=[0-1]. However, If I were to select only voxels from each
subfield's probability map corresponding to a 50% chance (i.e.
Ha nevermind. While true, I can just mask the masks with each other and
drop the over lapped regions.
-
Josh
On Tue, Feb 14, 2012 at 3:59 PM, Joshua Lee jki...@ucdavis.edu wrote:
Dear experts,
The hippocampal-subfield are expressed as probability maps. For each
subfield, each voxel is
Hello,
I have run into an error while trying to make an average subject using 200
scans.
When I ran this command I got an error:
*make_average_subject --xform talairach.xfm --out 200avgsub --subjects*
The error:
Allocing output
mri_concat(40491) malloc: *** mmap(size=262144) failed (error
Hello Tracula Developer User,
I found a few subjects have pathstat.overall.txt information but with
blank voxel information in pathstats.byvoxel.txt. For such tracts,
they usually len_min = len_max = len_avg. Anyone know what happened
for the fiber tracking? Is it possible to extract the byvoxel
That is, I can use fslmaths from fsl suite to subtract my binarized
subfield rois.
-
Josh
On Tue, Feb 14, 2012 at 4:58 PM, Joshua Lee jki...@ucdavis.edu wrote:
Ha nevermind. While true, I can just mask the masks with each other and
drop the over lapped regions.
-
Josh
On Tue, Feb 14,
Hello, Freesurfers,
I got an error message when I trying to use recon-all function in
freesurfer
on the XUbuntu system installed on the VirtualBox on a Windows 7 machine.
I searched the e-mailing list but I can't find any answers.
My problem is related to the nu_correct and
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