Hi Doug,
I tried to run the mri_surf2surf command as follows and got this error:
[b.overs~]$ mri_surf2surf --srcsubject fsaverage --srcsurfval
lh.Yeo2011_7Networks_N1000.annot --trgsubject testsubj --trgsurfval
lh.Yeo2011_7Networks_N1000.annot --hemi lh --save-annot
ERROR: Option --save-annot
Dear list,
I am trying to use mri_glmfit to run statistics on TRACULA outputs (by
tract), as suggested by the wiki (
https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/TraculaStatistics).
I used the following command line:
mri_glmfit --glmdir ilf.glmdir --table ilf.txt --fsgd sociodemo.fsgd --C
Hi All,
I was running freesurfer for a patient case of two time points. Will you
suggest to run it as a group, such as one time point as a template and
followed by longitudinal study, discussing atrophy or run these two time
points separately as two individual, running everything such recon-all,
d
Hi Bruce,
I uploaded the subject dirs (base for TP1_4 and TP2_4, as well as the
cross-sectionally processed time points for TP1, TP2, and TP4). In the
meantime, one of them, template TP1_4 has finished with error. The other one
(base TP2_4) is still running.
What do you suggest in this situati
Hi Doug,
Thanks for the clarification. So in the case of cortical thickness,
qcache, mris_fwhm or mri_surf2surf would all do the same thing and so I
should be getting similar results if everything is entered in the same
fashion. This would be the approriate choice compared to mri_smooth.
For
There is not a difference between mris_fwhm and mri_surf2surf.
mris_smooth smoothes the xyz coordinates of the vertices of a surface
(the others smooth an overlay).
On 05/05/2016 03:53 PM, Ajay Kurani wrote:
> Hi Doug,
>Thanks for the quick reply.
>
> Is there a difference from qcache/mris_
Hi Doug,
Thanks for the quick reply.
Is there a difference from qcache/mris_fwhm with mris_smooth and
mri_surf2surf -fwhm ? If so, which is recommended for cortical thickness
analysis?
Thanks,
Ajay
On Wed, May 4, 2016 at 11:18 PM, Ajay Kurani
wrote:
> Hi Freesurfer Experts,
>Just as
Hi Doug,
Sorry for the confusion. I currently have individual and group mean fcMRI
z-maps from a seed based resting-state analysis (non GLM), but I could also
do a GLM-involved analysis for each subject with the seed's timeseries as a
regressor. My ultimate goal is have a group z-map that is thres
On 05/02/2016 07:39 AM, maaike rive wrote:
> Dear freesurfer experts,
>
>
>
>
> I have a question regarding correction of cortical measures or global
> measures (ICV, total surface area). As I understand from literature
> and the freesurfer wiki, a model for thicknes
I guess I'm unclear as to what you are trying to do. Are you trying to
do a time series analysis of the resting state to extract, eg,
correlation with a seed? Or have you already done your time series
analysis on each subject, reducing each to a single number at each
voxel, and now you are doin
To see whether the final label is correct, load the label in freeview or
tksurfer and see if it looks right.
You can use mris_anatomical_stats to get the volumes, etc, from the
label (-l option). You may want to recombine the lobes into an
annotation with mris_label2annot
doug
On 05/05/2016 1
see if this link answers your question
http://surfer.nmr.mgh.harvard.edu/fswiki/UserContributions/FAQ#Q.Whatgoesintothecalculationofsubcorticalvolume.3FWehavetriedaddingvolumesofindividualsubcorticalareasbutthetotaldoesnotequalthesubcorticalvolumeprovidedbyaseg.Isthesubcorticalvolumecalculationacc
Hi all,
I’m trying to open a couple aseg.mgz labels and color code them. I thought I’d
do this by making my own ColorLUT table, setting the color of my regions, and
then making every other region in the table be completely transparent by
fiddling with the opacity value. I can’t figure out what
Hello Folks,
I used the recon-all -i -all -segmentation for the structural
image. FreeSurfer makes several folder and one of them is "stats". In this
folder, there is aseg.stats that includes volume of different brain
regions. Also, I found "mri_segstats" command line that gives us the volume
of
Thanks, Doug.
I'm still a little unclear about how to set up a timeseries regressor (120
timepoints) in the design matrix while also specifying the # of subjects
(500). Would the design matrix be a 500x120 or 120x500?
I should mention that my ultimate goal is to find a statistically sig.
threshol
Yes. Thank you!
Sent from my iPhone
> On May 5, 2016, at 11:09 AM, Ani Varjabedian wrote:
>
> Hi Sarah,
>
> If you are using 5.1 you only have one button for editing, the head with the
> pencil in it, like you shared in your screenshot. If you click on that it
> will open up a box that is ti
Hi Sarah,
If you are using 5.1 you only have one button for editing, the head with
the pencil in it, like you shared in your screenshot. If you click on
that it will open up a box that is titled "voxel editing", but you
should also see a checkbox at the top of it for "recon editing" (I
attac
Hi Doug, the Choi file is a striatal functional connectivity atlas which we
distribute. It's under the average directory.
Hi Bronwyn,
To transform the Choi's striatal atlas to your individual subject, Here's a
(non-ideal) suggestion I previously suggested to another user:
1) Assuming you are qui
On 5/4/16 11:40 PM, Bronwyn Overs wrote:
Hi Freesurfer Mailing List,
I wish to extract stats for my sample for the Yeo 2011 cortical
parcellations and the Choi 2012 striatal parcellations (7 networks)
that are provided for download on the freesurfer wiki. My questions
are as follows:
1. I
So you have 1 column, but you want 1 column for each vertex? We don't
have anything to do that, but you can do it in matlab, eg,
M = fast_vol2mat(MRIread('lh.yourdata.mgh'));
M will be a 240x127000 matrix
On 5/4/16 8:36 PM, Taha Abdullah wrote:
Hello Doug,
Sorry for the confusing and long emai
Hi Katarina
if you want us to look you need to upload the entire subject dirs (tarred
and gzipped). TO visualize it, look at the inflated.nofix in freeview in 3D
mode and just see what the big defects look like. If you load the
orig.nofix at the same time you can goto a vertex in the big defect
Hi Bronwyn
it depends on the type of stats, but you would either map the Yeo
annotations to your subjects, or map the stats from your subjects to
fsaverage.
cheers
Bruce
On Thu, 5 May 2016, Bronwyn Overs wrote:
> Hi Freesurfer Mailing List,
>
> I wish to extract stats for my sample for the Y
Underneath, they both use the same code, so they should give the same
results. Are you saying they are different? I don't know what SurfFWHM
is doing so I can't comment on what those results mean. Measuring the
FWHM on the surface is quite tricky.
doug
On 5/4/16 6:41 PM, Ajay Kurani wrote:
H
Thank you.
I have uploaded the files (lh.inflated_TP_1_4.nofix and
lh.inflated_TP_2_4.nofix).
What should I do as a next step?
Cheers
Katarina Trojacanec, M.Sc.
Teaching and research assistant
Faculty of Computer Science and Engineering
Ss. Cyril and Methodius University - Skopje, Republic of
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