Dear Doug and FS experts,
I am trying to use Xhemi tool to study asymmetry in the brain. I have done
the exact procedure you mentioned in WiKi for a group of 40 controls.
1) Is lh.lh-rh.thickness.sm00.mgh the stack of voxel-wise cortical
thickness difference between left and right hemisphere of eac
It looks as though selxavg3-sess generates the contrast analyses at the same
time as the beta weights. Would it be possible to run selxavg3-sess once to
obtain the beta weights, modify the beta.nii.gz file, and then rerun
selxavg3-sess to obtain the contrast statistics using the modified beta w
Dear Prof. Greve
I have additional (and probably silly) questions.
1) Is there much difference between result of monte-carlo null-z simulation
(QDEC GUI) analysis and that of clusterwise correction for multiple
comparisons using 1 permutations? I'm guessing similar results between
both method
Hi,
What type of registration file do you have representing the diff2anat
transformation? With mri_vol2vol you can use many different types of
transformations, if you switch the --reg flag to --xfm, --fsl or --lta,
for example.
Lilla
On Mon, 8 Jul 2013, Hoptman, Matthew wrote:
Hi all,
Hello Pascal,
What exactly are you trying to achieve?
If you would like to make 001.mgz, then use recon-all -i IM-0001-0001.dcm
-s bert.
If you would like to reconstruct the surfaces and the volumes (after doing
the first step), try recon-all -s subject -all.
As far as I am concerned, freesurfer
Hi Freesurfer users,
I am new to Freesurfer and have run into difficulty with running the recon-all
command in terminal on osx. When I type in the command bellow
recon-all –i IM-0001-0001.dcm –subject bert –all
I receive
ERROR: Flag i unrecognized.
Also the usage info on recon-all does no
I tried correlations and the 2nd derivative is definitely not orthogonal.
>> corrcoef([X(1:207,4) X(1:207,5) X(1:207,6)])
ans =
1. -0. -0.5427
-0.1. -0.0298
-0.5427 -0.02981.
I looked at the regressors that SPM generates for the same data:
ans =
Dear Bruce,
Thank you very much!
Sincerely,
Ye
On Tue, Jul 9, 2013 at 3:33 PM, Bruce Fischl wrote:
> No, the wm.mgz is just a means to initialize the surface deformation, and
> the final white surface can be inside or outside of it.
>
> cheers
> Bruce
>
> On Tue, 9 Jul 2013, ye tian wrote:
>
>
No, the wm.mgz is just a means to initialize the surface deformation, and
the final white surface can be inside or outside of it.
cheers
Bruce
On Tue, 9 Jul 2013,
ye tian wrote:
> Dear Freesurfers,
> I have carefully gone through the tutorial data "good_output", and find that
> wm.mgz lies insi
Hi Michael,
I think you should be fine with option 1. Just make sure that all cross are run
with the same version (5.1). It is a little more complicated to keep track of
things, but there should be no bias. That way you don't have to worry about
edits.
If you only have very few edits, I would
Dear Freesurfers,
I have carefully gone through the tutorial data "good_output", and find
that wm.mgz lies inside the boundary of the white matter almost all the
time, with fewer than 10 slices of exception. Whenever there is an
exception, the affected area is relatively small. Therefore, I am won
Thanks for the quick response! So if I wanted to use the Calhoun 2004
approach, I should be able to use the Steffener 2010 correction to address the
violation of the assumption that the regressors were standardized and generate
a new beta.nii.gz file where the primary beta values have been repl
Hi Jon,
I am also confused about this whole discussion. It seems from what you said
earlier that at some point you have been able to run freesurfer on your images.
You did not use the -i flag back then, but somehow managed to get from the
original dicom (via nifti, via some mri_convert command)
Hi,
I have a question about how mkcontrast-sess works. I ran an analysis using
the mkanalysis-sess option spmhrf 2 so there are three regressors for each
predictor, the primary, the latency, and the dispersion. When specifying the
contrast weights for mkcontrast-sess, the documentation indi
There is not a set number as it depends on the size of your effect. If
your effect size is 0, then no number of subjects is enough. To answer
this question, you need a power analysis. Having said that, people often
shoot for 20 because you get to the knee of the DOF-vs-p-value curve on
a t-tes
Why not include it as a condition in your paradigm file?
doug
On 07/09/2013 03:47 PM, Nicholas Paul Denisuk wrote:
> Dear Freesurfer Users,
>
> I am trying to regress out the activity associated with button presses
> in my GLM analysis. How do I generate a nuisance regressor file
> analogous to a
On 07/09/2013 04:11 PM, Joseph Dien wrote:
> Hi,
>I have a question about how mkcontrast-sess works. I ran an
> analysis using the mkanalysis-sess option spmhrf 2 so there are three
> regressors for each predictor, the primary, the latency, and the
> dispersion. When specifying the contra
Dear Freesurfer Users,
I am trying to regress out the activity associated with button presses
in my GLM analysis. How do I generate a nuisance regressor file
analogous to a white matter regressor generated in functional
connectivity (a one column time course file)?
Thanks you,
Nick
_
Dear Freesurfer group
I am interested to do group analysis on my data. If I want to do
inter-individual group analysis, what is the minimum number of subjects I
need to have?
Also if I want to do intra-individual analysis, what is the best way in FS?
I appreciate your time and your help.
Thanks a
Hi guys,
We have some longitudinal scans in which the time1 (T1) scans were processed with FS 5.1, and the T2/T3 scans haven't been processed yet.
I'm trying to assess whether the differences between FS 5.1 and 5.3 warrant us re-running the T1 scans under FS 5.3.
I see two possible optio
Hello,
I would like to verify something regarding subcortical volume estimation in
Freesurfer before we move forward with our analyses. From what I've read on
the wiki and listserv, it seems the subcortical and cortical processing
streams are largely independent. If one were only interested in sub
Hi Anastasia,
For one of my subjects, I am noticing that the right uncinate fasciculus
is very diffuse and more importantly, erroneously crosses from the frontal
to the temporal lobe. I looked at the original endpoint ROI generated by
trac-all -prior (rh.unc_AS_avg33_mni_bbr_end1.nii.gz) and the
Dear Jon,
Thank you very much!
Yes, it is the same area. I set the cursor in one place and clicked the C,
H and C buttons in tkmedit tools.
Sincerely,
Ye
On Tue, Jul 9, 2013 at 10:20 AM, Jonathan Holt wrote:
> Ye,
>
> personally I edit once I see an issue in any view, and I continue to look
Ye,
personally I edit once I see an issue in any view, and I continue to look
for problems in all 3 views. In those images it seems like the issue with
the cb is less drastic this time around. Is it the same area? In any case I
would make minor edits in the images you provided, very minor. The ima
you can have two discrete variables (two levels each) and two continuous
variables. If you want more than that, you will need to run mri_glmfit
instead.
doug
On 07/09/2013 02:30 AM, Jiang Jiyang wrote:
> Dear all,
>
> I am using qdec to do a shape analysis with 16 control variables. I
> was wo
Thank you for your email. Yes that v is what freesurfer home is set to.
Somehow that GCA file (SMS numerous others) were missing from the averages
folder. I manually chopped them from a different 5.3 install, but am not
sure v why they are missing (I am the only person using this machine and
did no
Hi Lilla,
thanks for the advice, I'll just upgrade my RAM to 24 GB (maybe it will
help FSFAST too ;-)). I used the --m3d flag as a blind guess about the
possible cause of the aforementioned error, thank you for clearing that up,
I'll skip it next time.
Best regards,
Marcel
2013/7/9 Lilla Zolle
Hi Marcel, You would ned at least twice as much. Also, is there a
specific reason for you to use the --m3d flag? That will result in writing
out uncompressed morph files which will take up a lot of space.
Lilla
On Tue, 9 Jul 2013, Marcel Falkiewicz wrote:
Dear FreeSurfers,
I'm trying to us
Hi Peter, no it is not. You will have to use mri_glmfit.
doug
On 7/9/13 9:29 AM, Peter Bohn wrote:
Dear Freesurfer experts,
is it already possible to define more than two possible factors for
discrete variables in the latest qdec version or is that option still
limited to 2 possible variab
Ye,
Since no one's replied, I'll say it does look like the cb is infringing on
the pial surface. It's easier to tell the boundary toward the center of the
brain than it is toward the lower portion. It's easier to tell, in my
opinion, in the coronal view. Toggling the surface off may help as well.
Helo all,
I was finally able to figure out my configuration file problem. But when I run
the first step of pre-processing I receive an error about freesurfer being
unable to read a certain dwi_frame file.
ln -sf /Users/WayneFeng/Desktop/JG005/JG005/JG005/freesurfer/dmri/dwi.nii.gz
/Users/Wayn
Hi Fatma
don't use the -1 flag if you are regtering to a template, only if you are
registering individual surfaces to each other. You probably want the output
to be named lh.sphere_reg and go in the s000/surf dir.
cheers
Bruce
On Tue, 9 Jul 2013, fatma
zribi wrote:
Dear Mr,
When I exec
Dear Mr,
When I execute mris_register to register one subject to a template., I have
this message of error:
mris_register -1 s000/surf/lh.sphere
avg_all_subjects_SD/lh.reg.template.tif sphere_reg
treating target as a single subject's surface...
$Id: mris_register.c,v 1.59 2011/03/02 00:04:33 nic
Hi Salil
what is FREESURFER_HOME set to? Is it /usr/local/freesurfer? Does
/usr/local/freesurfer/average/RB_all_2008-03-26.gca exist?
cheers
Bruce
On Mon, 8 Jul
2013, Salil Soman wrote:
Hi,
Am running this command:
$FREESURFER_HOME/bin/recon-all -i 3DSPGR.nii.gz -s WCA_248_T1Q_FS
-nuint
Dear
Freesurfer experts,
is it already possible to define more than two possible factors for discrete
variables
in the latest qdec version or is that option still limited to 2 possible
variables?
Thanks for your help!
Best regards
Peter
__
Hi Cararina,
sorry, I don't think we have anything to do this in matlab. You could
write a tcl script to do it automatically in tksurfer and call that from
inside matlab I guess.
cheers
Bruce
On Tue, 9 Jul 2013, Catarina Rua wrote:
>
> Dear freesurfer admin,
>
> I'm writing a piece of code in
Thanks for clarifying this Doug!
Please let me know if anyone has suggestions about my other questions
below, re skull stripping.
Cheers!
T
On 8 July 2013 18:01, Douglas N Greve wrote:
>
> 001.mgz -> raw.mgz -> orig.mgz -> nu.mgz -> T1.mgz
>
> If you only have one run, then 001 and raw are the
Dear freesurfer admin,
I'm writing a piece of code in matlab based on freesurfer reconstructed brains
generating series of labels to an annotation file.
However, I wanted to include a process similar to the existing in tksurfer
options in the 'custom fill' where you can fill in all vertices up
Dear FreeSurfers,
I'm trying to use mri_cvs_register, however the process can't complete and
I get the following error:
[...]
loading transform id string =
data size = 18728074
uilen = 6
loading transform id string =
data size = 19845421
uilen = 6
loading transform id string =
data size = 1
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