You only have one subject in sexfemale-groupG2. You can't compute an
offset and slope from one data point.
doug
On 5/6/15 2:29 AM, Sanne Oostermeijer wrote:
> Hi Doug,
>
> Here is the file that you needed.
>
> fsgd file and contrast file
>
> Best, Sanne
>
> Dit e-mailbericht is alleen bestemd voo
Thanks Martin. The concern I have with using -autorecon2-cp -autorecon3 after
-surfsegedit is that, new surfaces are created during -autorecon2-cp
-autorecon3 so that aseg and the surfaces are always out of step with each
other.
Any suggestions on how I could test the validity of the method des
Dear all,
I need to specify this matrix as my F contrast [1 -1 0; 0 1 -1] ,
however I'm not sure how I can do this. Usually for a matrix like [1 0
0; 0 1 0] i use
mkcontrast-sess -analysis analysis-name -contrast ftest -a 1 -a 2 -nosumconds
I can use -c for -1 in the contrast, but using nosumco
Hi,
I have a question about the utility of the make_average_subject command.
I have a schizophrenia study with 115 subjects and am worried about using the
Freesurfer average brain, given that scz patients have distinct morphological
aspects to their brains. I am therefore considering making
Hi FS Experts,
Kindly, I want to inquire if there is any tool in FreeSurfer that can help to
extract or isolate " Free water map" from Diffusion Weighted Imaging (DWI) data.
Thanks
Mohamad
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
htt
Dear all,
I would like to project a volume of statistical values (ang.nii) to the
surface. At the moment I do it as in this example:
mri_vol2surf --src ang.nii --srcreg register.dat --hemi lh --projfrac 0.5
--out ./ang-lh.w --out_type paint
However, what I would like to get is the average val
Hi Mia
if they are ROIs in the Destrieux just load the ?h.aparc.a2009s.annot file
in tksurfer and visualize it that way
cheers
Bruce
On Tue, 5 May 2015,
Mia Ellis wrote:
Dear FS experts,
For my research proposal, I would like to visualize my 5 ROIs (e.g.,
superior temporal cortex, medi
Hi Jane
we don't really see much blurring of folding patterns with the
high-dimensional spherical warp so you might as well use them all
(although there might be issues with memory - perhaps Doug can comment if
this is still true).
cheers
Bruce
On Wed, 6 May 2015, Jane
Garrison wrote:
>
>
Thanks so much Bruce. I also posted yesterday asking about whether it was
possible to get LGI values for a spherical ROI based on a particular mni
coordinate (I’ve been using Qdec so far for group analysis but can’t work out
how to draw the ROI nor how to pull the LGI values. Would you have an
Hi Patrik
vol2surf is very flexible about this. If you look at the help you will see:
Options for projecting along the surface normal:
--projfrac frac : (0->1)fractional projection along normal
--projfrac-avg min max del : average along normal
--projfrac-max min max del : max along
no, sorry. I'll leave that for Doug and Marie
Bruce
On Wed, 6 May 2015, Jane
Garrison wrote:
Thanks so much Bruce. I also posted yesterday asking about whether it was
possible to get LGI values for a spherical ROI based on a particular mni
coordinate (I’ve been using Qdec so far for group a
Hi Matt, I can answer only partially to your question. SUMA/afni in
general supports GIFTI format but I don't know if is it possible to
directly convert from GIFTI to .dset.
Usually I convert my annot file to .niml.roi with FSread_annot and
.niml.roi to .1D.dset with ROI2dataset.
Best
Francesca
Hi Ziad, yes, it's related to that. Thank you for the help!
Best
Francesca
2015-05-06 16:25 GMT+03:00 Ziad Saad :
> Hello folks,
>
> I am ccing all those on the thread because I am not sure my reply to the
> support list will get through.
>
> GIFTI is the way to go as Matt suggested and all of A
Can you please provide me with the "Processor" and "Graphics" hardware
specs of the machine listed under Apple -> About This Mac.
Ive only ever seen this error on old mac minis and its usually indicative
of an incompatible graphics card.
> Dear freesurfer,
>
> I tried using kvlThresholdImage on a
Hi Marie:
I installed the Image Processing Toolbox on Matlab 2015a and proceeded with
the analysis of brain that underwent the recon- all processing. However, it
gave me another error message which is as follows. Could you please help me.
thank you,
Alan
Hi Marie:
I just had another problem wi
Hi Bruce,
Thanks a lot for your answer! This is exactly what I was looking for.
I looked at the https://surfer.nmr.mgh.harvard.edu/fswiki/mri_vol2surf website
that did not specify these options.
Thanks again!
Patrik
___
Freesurfer mailing list
Freesur
Dear FreeSurfers,
I wrote the last week asking for some help with this.
I would like to run the reconstruction process starting from segmentations
(grey, white and deep grey matter) obtained with a different software. The
ultimate goal is to measure the cortical thickness in correspondence of t
you can try running the commands with --help and see what they tell you
(or sometimes -h). That's where this came from
cheers
Bruce
On Wed, 6 May 2015, Andersson, Jonas Patrik wrote:
> Hi Bruce,
>
> Thanks a lot for your answer! This is exactly what I was looking for.
> I looked at the https:/
did you see the email I sent last night about you having one group with
only one subject?
On 05/06/2015 08:50 AM, Verfaillie, Sander wrote:
>
> Dear Douglasor colleague,
>
> Currently I am working on one of the last steps of freesurfer
> analyses; the mri_glmdir.
>
> However, trying multiple FSG
memory should not be a problem
On 05/06/2015 08:33 AM, Bruce Fischl wrote:
> Hi Jane
>
> we don't really see much blurring of folding patterns with the
> high-dimensional spherical warp so you might as well use them all
> (although there might be issues with memory - perhaps Doug can comment if
>
> On 6 May 2015, at 16:49, Douglas N Greve wrote:
>
> memory should not be a problem
>
> On 05/06/2015 08:33 AM, Bruce Fischl wrote:
>> Hi Jane
>>
>> we don't really see much blurring of folding patterns with the
>> high-dimensional spherical warp so you might as well use them all
>> (although
Hello,
I am able to reproduce the error reported below and I am working on
creating an updated version of the kvlThresholdImage binary. I will
inform you and the list when it is available, probably sometime in the
next day or so.
-Zeke
On 05/05/2015 03:43 PM, Fábio Dalprá wrote:
> Dear freesu
wow, I don't know what is going on here. When I run
mkanalysis-sess -mni305 1
It responds as it should:
ERROR: must specify either -per-run or -per-session
you probably want to use -per-run unless you used
-per-session when you ran preproc-sess
However, when I cut and paste the "
Hi Freesurfer experts
I am planing to do a voxelwise group analysis from images acquired at 7T,
and I wanted to use the mri_cvs_register script, which gives very nice
normalization outputs. I was wondering how to adapt the script to images
that we have with 0.33mm isotropic resolution, and which ar
Hi Doug,
Thank you very much for your support. It seems to me that the typos in the
command lines are related to the auto correction property in Outlook So I am
attaching a text file including all the command lines that I used in the
analysis:
I ran the analysis successfuly for the spaces lh a
Hi Celine,
The m3z morph encodes a sptial transformation between two particular
coordinate systems. When you use mri_vol2vol below, the original space is
not the same as for your input volume used to be and that is why the
volumes are not in correspondence.
Could you compute the registration
Thank you Lilla for the suggestion.
You mean that I should run mri_cvs_register on the high res volume, is
that correct? In that case, how can I specify the input volume? I did not
find in the --help a way to specify manually the file to be registered,
just the subject id.
Thank you again
Celine
>
Hi Doug,
Sorry to interrupt you again with this topic. Don't you think, to
regress out my unwanted event (eletric shock), I need to convolv this event
with the hrf model and then use the outcome as my regressor?
Regards
On Fri, May 1, 2015 at 12:23 PM, Douglas Greve
wrote:
> I don't necess
28 matches
Mail list logo
