Don't include them in the FSGD
On 7/12/17 8:45 PM, haidong wang wrote:
Yes. I want to find brain areas of significant thickness difference
among four groups using the atlas of aparc. Without regressing
covariables, the contrast following runs correctly.
1 -1 0 0
1 0 -1 0
1 0 0 -1
How to do th
Yes. I want to find brain areas of significant thickness difference among
four groups using the atlas of aparc. Without regressing covariables, the
contrast following runs correctly.
1 -1 0 0
1 0 -1 0
1 0 0 -1
How to do that with regressing covariables of age and education?
2017-07-13 6:28 GMT+08:
Thanks for the quick responses; I appreciate it. I gather that is exactly
what the message is telling, but It is very odd as I'm positive I was not
doing anything with the files and it showed the same message for each of
the subjects and for each of the tailrace files on X,Y,Z.
In any case, it is r
hmmm, that doesn't sound like it has anything to do with us unless you
were running a recon when you were tarring. That file is mostly irrelevant
in any case
cheers
Bruce
On Wed, 12 Jul 2017, Schumman
Resonance wrote:
> Hi freesurfers,
> I'm compressing FS files for storage, and while runnig
Smoothing in the volume is the single worst thing that is traditionally
done to brain imaging data as far as precision of spatial localization
goes.
Peace,
Matt.
On 7/12/17, 5:46 PM, "Douglas N Greve"
wrote:
>you should definitely not smooth the volume data. Smoothing should be
>limited to t
you should definitely not smooth the volume data. Smoothing should be
limited to the surface.
On 07/10/2017 11:33 AM, Tamara Tavares wrote:
> Hi All,
>
> I was hoping someone can help me with two naive questions I have:
>
> I have read on the Freesufer wiki that you should smooth surface data
>
sounds like the file itself was being changed or edited as you were
creating the tar file.
On 07/12/2017 06:31 PM, Schumman Resonance wrote:
> Hi freesurfers,
>
> I'm compressing FS files for storage, and while runnig TAR I got this
> message for all the files in the directory I'm compressing:
use fscalc, eg,
fscalc file1.mgh sum file2.mgh -o file1+file2.mgh
run fscalc without any options to get the list of operations
On 07/10/2017 03:28 PM, Van Der Deijl, Rosanne wrote:
> Dear Freesurfer team,
>
> Is it possible to add/subtract/compute the average of freesurfer
> surface .mgh files
i think you would still run into the same probem
On 07/11/2017 12:15 PM, Yann Ying Chye wrote:
> Thanks for your reply,
>
> I have a follow up on my first question - if however I was not looking
> for a main effect of gender, but for the main effect of something else
> (e.g. diagnosis), will it
Is this still a problem?
On 07/11/2017 09:51 AM, Paul Glad Mihai wrote:
> Hi Bruce,
>
> Thanks for the quick reply. I've just finished rerunning it with spm,
> fsl and header init and the latter seemed to work if I write out a
> _bbreg.nii file. The former two failed, however. Apparently using the
Hi freesurfers,
I'm compressing FS files for storage, and while runnig TAR I got this
message for all the files in the directory I'm compressing:
"tar: data/sbj001_post_anat.nii.gz/mri/transforms/talairach.m3z.inv.y.mgz:
file changed as we read it"
Any thoughts on whether this message is making
That will compute the main effect of diagnosis. Is that what you want?
On 07/12/2017 10:29 AM, haidong wang wrote:
> Hello FS expert,
> I have four groups and two covariables. The groups are
> MCI_P,MCI_S,MCI_R,NC and the covariables are age and education. I want
> to test the thickness
yes, I figured it out! Thanks for your help!
From: freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of Douglas N Greve
Sent: Wednesday, July 12, 2017 6:16 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] Subject with missing fMRI data {Dis
Yes, it does. Prior to v6, the brain mask was created by the FSL BET
program, which did not depend on the registration. V6 now maps the
brainmask from the FS analysis into the subject space, which does depend
on the registration
On 07/11/2017 02:36 PM, Li Guo wrote:
> Dear freesurfer developer
what is your mri_glmfit command line?
On 07/12/2017 02:32 PM, Bruss, Joel E wrote:
> I have a group of subjects, scans at time1 and time2 that have been
> run through the longitudinal stream. I have a group of ROIs in MNI
> space that I've been able to push up to fsaverage following the
> Vol
On 07/12/2017 05:11 PM, Lu Zhao wrote:
> Dear Douglas,
>
> Thank you for your kind reply and instruction. But I still have a few
> questions:
>
> 1. how can I get the segmentation for BA areas, which have no
> hemisphere bases?
Not so easy because you need to have complete cortical coverage. If
the command and terminal output look ok. You should compare it to the
results without the frame mask (just use the regular mask). They should
be the same in areas where the frame mask and regular mask completely
agree.
On 07/12/2017 01:54 PM, Sadie Marvel wrote:
> The command will run now with
Dear Douglas,
Thank you for your kind reply and instruction. But I still have a few questions:
1. how can I get the segmentation for BA areas, which have no hemisphere bases?
2. when the cortical atlas is changed, should the '--wm-annot’ be changed
accordingly? For instance, use '—wm-annot aparc
I think if you convert the afni's skull stripping to .mgz format and put
it in mri/brainmask.mgz we will recognize that it is different from
brainmask.auto.mgz and use it instead
cheers
Bruce
On Wed, 12 Jul 2017, Michelle
VanTieghem wrote:
Hi, I am just following up on my previous question.
Dear DTI experts:
I am wondering if anyone knows a solution to this tracula script error:
dmri_pathstats --intrc START_610/dpath/lh.cst_AS_avg33_mni_bbr --dtbase
START_610/dmri/dtifit --path lh.cst --subj START_610 --out
START_610/dpath/lh.cst_AS_avg33_mni_bbr/pathstats.overall.txt --outvox
STA
Dear DTI experts:
I am wondering if anyone could help find the solution for this tracula script
error:
RuntimeError: Command:
dmri_pathstats --intrc START_610/dpath/lh.cst_AS_avg33_mni_bbr --dtbase
START_610/dmri/dtifit --path lh.cst --subj START_610 --out
START_610/dpath/lh.cst_AS_avg33_mni_bbr
I have a group of subjects, scans at time1 and time2 that have been run through
the longitudinal stream. I have a group of ROIs in MNI space that I've been
able to push up to fsaverage following the VolumeRoiCorticalThickness tutorial:
https://surfer.nmr.mgh.harvard.edu/fswiki/VolumeRoiCortical
Hi,
I am just following up on my previous question.
The -gcut does not appear to make any difference on our skull stripping. I
also saw that you can change flags for watershed option. Do you recommend
this? If so, how would you implement this on freesurfer output that was
already run?
We achieve
The command will run now without --wls, but I'm still not sure the output is
correct.
Here is my entire output:
cwd /Freiwald/smarvel/cooked/mygroup4/a_FOB.sm05.lh
cmdline mri_glmfit.bin --y c1_2/ces.nii --osgm --no-prune --frame-mask
masks.nii --surface fsaverage lh --glmdir c1_2/my-glm2.wls --
What did you use to conver to gifti? If you used mris_convert, try it
with either --to-scanner or --to-tkr
On 07/04/2017 03:32 AM, Torben Lund wrote:
> Hello FreeSurfer Developers
>
> I'm attempting to evaluate a segmentation result from CAT12, (sorry)
> with the Freeview program. For version 1
There are several layers of difficulty here:
1. If you just wanted to use a different cortical segmentation, say,
aparc.a2009s or aparc.DKTatlas, then you can run gtmseg with --ctx-annot
aparc.a2009s 11100 12100 or --ctx-annot aparc.DKTatlas 1000 2000. The
numbers are the base numbers in $FREE
Can you send the command line, your key strokes and button presses, and
the terminal output leading up to the error message?
On 07/06/2017 12:27 AM, AYUSHI SHUKLA wrote:
> Hi,
>
> Thank you for your response.
>
> Yes, I checked, and I do have the permission to read the file.
>
> Warm Regards
>
>
Not sure what the problem is, but it might be something specific to your
site (looks like it cannot find the proper libraries to import). Can you
run it at all. Eg, if just run the script without any arguments, do you
get the same thing? What about if you run it with -h ?
On 07/06/2017 03:33 A
sorry, I don't know anything about .tlrc files (or much about AFNI). If
the transform is linear, then you should be able to map between the
spaces with mri_vol2vol or mri_label2vol, but you will need to get the
transform into a FS-compatible format.
On 07/06/2017 01:50 PM, Lauren Stephanie Hop
it might not be possible to use the frame mask with wls. Does it work
without it?
On 07/09/2017 04:46 PM, Sadie Marvel wrote:
> So now that I am using --no-prune, I'm getting this error:
> group wrfx error: MRInormWeights: value less than or eq to 0.
> I found another thread in the mailing list
Is this for a volume analysis? If so, then you'll need to use the --grf
option instead of using the mcz simulations (those are just for surface)
On 07/08/2017 01:03 PM, Aly Negreira wrote:
> Hi Doug!
>
> Thank you for the reply! Re-ran w/ --debug as first option. Below is
> the output. Not sur
Hi Clara,
thanks for the additional information, this is helpful!
If you are calling the scripts with
[lhRgs,lhRgMeans] = lme_mass_RgGrow(lhsphere, lhRe, lhTh0, lhcortex, 2, 95);
then 'lhcortex' will contain the analysis mask, i.e. indices for those vertices
for which the analysis will be perf
Hello freesurfer experts:
I am doing the following steps in the script below:
(1) Use recon -all to calculate the freesurfer T1 anatomical which requires a
single DICOM file to be calculated from each subject.
(2) Use the functional Bold time series data originally derived from DICOM
files f
Hello FS expert,
I have four groups and two covariables. The groups are
MCI_P,MCI_S,MCI_R,NC and the covariables are age and education. I want to
test the thickness differences of the groups regressing out age and
education.My group.effect.mtx is as following with the feedback of error.
1
Dear Peter,
I haven't tried myself, but have a look at:
https://github.com/stnava/ANTsR/wiki/Installing-ANTsR-in-Windows-10-(along-with-FSL,-Rstudio,-Freesurfer,-etc).
It gives an overview of several neuroscientific tools to be installed using
the Windows 10 bash.
Best,
Falk
Von: freesurfer-
Dear all,
I'm looking to set up FreeSurfer on a Windows 10, 64-bit OS. Has anyone tried
this using the Linux BASH shell on the latest (anniversary) version of Windows
10? If so, any tricks to to watch out for?
Best, Peter
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