Dear Freesurfer Experts,
I am a senior, and I am going to finish my graduation thesis which is about
the use of freesurfer.So I need some written materials,such as the development
history of Freesurfer, the achievement of Freesurfer and so on. But I don't
know. Can you help me? Or give me
Dear Freesurfers,
I'm going to run 1-way anova, followed by post hoc pairwise comparison. My
factor-of-interest has 4 levels and, in addition, I would like to regress out
the effects of 3 continious variables.
I have attached my *fsgd-file. Therefore, my first *mtx-file should contain the
Dear FreeSurfer experts,
I am trying to recon-all T1 images with the command recon-all -s subjectname
-i /path/to/subject/directory/subject.nii.gz. This command used to work with
several images, but one of my images is always exiting with errrors, in my
opinion without a reason. Any
you need to call mris_make_surfaces directly. It's a bit complicated as you
need to intensity normalize and register the hires volume to the surfaces
first. I have an example script if anyone is interested, but no one has
used it yet but me I don't think (unless Matt Glasser has gotten his
Hi Bobo
try this:
http://www.ncbi.nlm.nih.gov/pubmed/22248573
cheers
Bruce
On Tue, 15 May 2012,
bowan...@mail.ustc.edu.cn wrote:
Dear Freesurfer Experts,
I am a senior, and I am going to finish my graduation thesis which is about
the use of freesurfer.So I need some written
Hi Julia
I don't see any error messages. If you upload the dataset we'll take a
look. Make sure you have enough ram in the machine (2G) and free disk
space.
cheers
Bruce
On Tue, 15 May 2012, Richter, Julia wrote:
Dear FreeSurfer experts,
I am trying to recon-all T1 images with the
Yes, I have a modified script working. For the white surface, the
essentials are the same as Bruce's script but it has some additional stuff
(e.g register T2w to T1w), and I call it in the middle of the recon-all
rather than at the end. For the pial surface, I have done some more
complicated
Hi Martin,
I think this is what you're looking for. If not, let me know.
recon-all -base 137_S_0158_template -tp
/Applications/freesurfer/subjects/corinna/ADNI/BL/137_S_0158/mri/norm.mgz
-tp
/Applications/freesurfer/subjects/corinna/ADNI/12mos/137_S_0158/mri/norm.mgz
-tp
Morning all,
I ran the recon yesterday, and it says it ran without error. I am now running
tkregister2, but for some reason when i compare the coronal view, things look
okay on the mri, but it looks like the axial view for the CT. I'm not sure in
which step this happened?
Thanks,
Mia
Dear all,
I am comparing a group of patients with controls. I extracted:
cortical volume, surface area, cortical thickness and gyrification
index for each subject's lobe.
Comparisons between this variables with Total Intracranial Volume as a
covariate indicated a difference in frontal and
Hi Corinna,
you need a single folder with all subjects and all time point:
so the subjects directory will look like:
me1
me2
me3
you1
you2
...
You can create such a folder and insert symbolic links to the original
subject folders if you want to keep your structure.
Then create the base in
(1) Version: optseq2.c,v 2.21.2.1
(2) Computer operating system: Mac OS X Version 10.7.3
(3) Command line: optseq2 --ntp 230 --tr 1.5 --psdwin 0 24 0.5 --ev go 7 36
--ev nogo 7 12 --nkeep 4 --o gonogo --nsearch 1000
(4) Description of the problem: This is in reference to a go/no-go
paradigm. I
Hi,
Thank you so much for your reply. I am going to read the paper.
However, if the increase in head size obscures the lGI, why this is
not an overall variation? Meaning, why is only for the frontal and
temporal lobes?
thank you
ines
On Tue, May 15, 2012 at 4:30 PM, j janssen
You're getting very low VRFs because of the sub-TR estimation (TR=1.5,
but TER=0.5), so you reduce your power to about 1/3. This is not a
problem unless you analyze your data using an FIR. If you assume a
shape, then the power will come back.
doug
On 05/15/2012 11:41 AM, Andrew Valdespino
That will be fine. We are working on tools to perform mixed effects
analysis on longitudinal, but they are not ready yet. I think Martin has
some tools to exploit the fact that they are longitudinal (eg, computing
a slope normalizing by the first time point or the average of the time
points).
Hi Alexander, what you have there looks like an interaction test for a
2x2 ANOVA. If you are looking for an effect of level, then you will need
something like
1 -1 0 0
1 0 -1 0
1 0 0 -1
Plus 12 zeros on each line for the covariates. I would also first test
for an interaction in the covariates.
Hi Mia, you'll have to give us more information, eg, what was your
command line for tkregister2?
On 05/15/2012 09:56 AM, Borzello, Mia wrote:
Morning all,
I ran the recon yesterday, and it says it ran without error. I am now running
tkregister2, but for some reason when i compare the
Dear All,
I would like to know if there is a way to eliminate from my significant
clusters (grf.th3.pos.sig.cluster.mgh) obtained after running mri_glmfit-sim
with grf option and using mri_volcluster the clusters with a size smaller than
50 mm^3 or in other words to keep only clusters with a
Keep changing the --cwpvalthresh until all clusters smaller than 50 are
gone.
doug
On 05/15/2012 12:43 PM, Antonella Kis wrote:
Dear All,
I would like to know if there is a way to eliminate from my
significant clusters (grf.th3.pos.sig.cluster.mgh) obtained after
running mri_glmfit-sim
Dear all,
I'm trying to use the new script for the inter-hemisphere analysis, in
Fs version 5.0. I have downloaded the files as suggested
(http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg21706.html).
Surfreg seems to be running fine (surfreg --s subject --t fsaverage_sym
--lh), but
Hi Irene, can you send the log file for the command that is failing?
doug
On 05/15/2012 01:28 PM, Irene Altarelli wrote:
Dear all,
I'm trying to use the new script for the inter-hemisphere analysis, in
Fs version 5.0. I have downloaded the files as suggested
Hi Bruce and Michael,
That would be very nice. Do I just email you the hi-res
*whole-brain*mprages, or is their another way to get the images to
you?
On the other hand, I'm a fair hand at scripting. I'd be willing to
experiment with any scripts that you might provide.
Last, and on an unrelated
Dear all,
How can I obtain an average lGI for each subject's hemipshere?
I've tried:
mris_anatomical_stats -mgz -f
lh.lgi.stats -b -a ../label/lh.aparc.annot -c ../label/
lgi.annot.ctab -t pial_lgi
$SUBJECT lh
but I had the following error:
ERROR: stating file .../label/lh.aparc.annot
It
Dear all,
For a longitudinal analysis I need to have within subject templates. After
some preprocessing that included FSL's BET, and linear registration of all
time points to time-point 1, I fed images to mri_robust_template:
mri_robust_template --mov tp1 tp2 tp3 --template template_address
That looks right. You can also run something like:
mri_segstats --slabel subject lh ../label/lh.cortex.label --in
lh.thickness --sum sum.dat --id 1
The output is sum.dat
doug
On 05/15/2012 02:14 PM, Inês Violante wrote:
I think I got it, but it would be great if someone could tell me if
Dear Freesurfer Folks,
I have returned to the problem of trying to extract T2 values from a T2-map
using aseg mri_segstats.
When I attempt mri_segstats it only returns a small subset of the regions
from aseg (see attached file).
I would like to attach the T2 map but the file exceeds the 25mb
Hi Carl,
you can ftp it or filedrop it (both are detailed on the fs wiki site)
cheers
Bruce
On
Tue, 15 May 2012, Carl Anderson wrote:
Dear Freesurfer Folks,
I have returned to the problem of trying to extract T2 values from a T2-map
using aseg mri_segstats.
When I attempt mri_segstats it
p.s. what format is the attachment? It doesn't have an extension
On Tue,
15 May 2012, Carl Anderson wrote:
Dear Freesurfer Folks,
I have returned to the problem of trying to extract T2 values from a T2-map
using aseg mri_segstats.
When I attempt mri_segstats it only returns a small
Hi Carl, those are all that are in the aseg.mgz. What more did you expect?
doug
On 05/15/2012 03:44 PM, Carl Anderson wrote:
Dear Freesurfer Folks,
I have returned to the problem of trying to extract T2 values from a
T2-map using aseg mri_segstats.
When I attempt mri_segstats it only
Hi Freesurfer experts,
A newbie question regarding working with QDEC. When I try to upload
the qdec.table.dat file (attached) an error messages pops up Error
loading the data table.
To the best of my knowledge I've followed the guidelines on the
tutorial in terms of formatting. What would
The last line does not end in a new line. Open it in your text editor,
go to the last line, hit return, save it, and try again.
doug
On 05/15/2012 05:15 PM, Fidel Vila wrote:
Hi Freesurfer experts,
A newbie question regarding working with QDEC. When I try to upload
the qdec.table.dat file
Hello,
I am trying to get the asegmentation information after the recon-all run in
the table form, but I am continuously getting the following error
asegstats2table --subjects AA262.G1 AA267.G2 AA304.G1 --meas volume --tablefile
asegstats.txt
SUBJECTS_DIR : /opt/freesurfer/subjects
Parsing the
Do those files exist? Do they have content in them?
doug
On 05/15/2012 05:51 PM, Rashmi Singh wrote:
Hello,
I am trying to get the asegmentation information after the recon-all
run in the table form, but I am continuously getting the following error
asegstats2table --subjects AA262.G1
Dear Freesurfer experts,
I have fMRI data that are processed in AFNI that I would like to examine the
relationship with cortical thickness measures. In particular, I am interested
in vertex-wise correlation of thickness and BOLD % signal change.
The problem is I am new to Freesurfer. So far I
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