Hi Martin
Thanks a lot for your reply! Is there any reference that the longitudinal
processing would fail if the difference in head size exceeded any certain
value?
Best, Dong
发件人: freesurfer-boun...@nmr.mgh.harvard.edu
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] 代表 Martin Reut
Hello,
New to freesurfer using Linux (successfully reconstructed several images on a
mac) - can you help me determine how to correct the error in this attached
attempt at a recon?
Many thanks,
Linette
Tue Feb 14 22:56:38 EST 2017
/home/cnslab/Desktop/freesurfer/subjects/5098Post
/home/cnslab/D
Hi Emma,
I recommend that you follow the mri_surf2surf and mri_label2vol route.
As recommended in the other emails, you should probably load the
resulting parcellations and make sure they look ok.
As far as I know, "mris_ca_train" and "mris_ca_label" are not quite so
applicable here because they
Hi Martin,
Sorry for the slow reply. Antonin is right about the mri_segstats.
To map the surface parcellation from fsaverage to your individual
subject's anatomical space, you can do the following:
# Transform from fsaverage to subject's surface
>> mri_surf2surf --srcsubject fsaverage --trgsubje
Hi Katarina,
if your run it regularly, and then run it including the —generic-time, and get
the same result twice, we can conclude that the —generic-time has not effect.
You should be fine.
Best, Martin
> On 14 Feb 2017, at 19:38, Katarina Trojacanec
> wrote:
>
> Hi Martin,
>
> Thanks fo
Hi,
I'm sorry for what seems like a trivial question. I couldn't find this
answer in the tutorials or old archive.
I have statistical data in the surface that I have thresholded and
binarized to form a mask. I can load the mask as an overlay in
tksurfer. My understanding is that you need to tur
Hi Adarsh – What operating system are you running this on? It runs fine for me
with this input file when I test it on both a mac and a linux computer.
a.y
From:
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
on behalf of Adarsh Nellore
mailto:adarsh.nellore...@gmail.com>>
Reply-To: Freesurfe
Hello,
I'm preparing to do resting state analyses and I'd like to use the Yeo 2011
network atlas for the cortical parcellations. Looking through the archive, I
know that mri_surf2surf with the -sval-annot flag can be used to convert the
fsaverage from the Yeo et al 2011 study to an individual s
Hi Abby – It looks like the first subject was run before installing the 2014
TRACULA update, and the second subject was run after installing that update.
Can you try running the first subject from scratch (in a new output directory)
now that the update has been installed? This will tell us if it
It is looking for a folder called motion.sm3.lh in the current
directory. This would have been created when you ran mkanalysis-sess.
Does that exist? and does the analysis.info file exist inside it?
On 02/11/2017 02:41 PM, Fatemeh.Molaei-Vaneghi wrote:
> Dear FreeSurfers,
>
> I'm trying to perfo
Hi,
I have a very simple question.
I have cortical volume maps (averaged over 30 subjects). I can view those
in FreeView using lh.pial overlaid with lh.mean.volume.mgh file. In overlay
> configure option, I had to set the min as 0 and max as 4 to display the
average volume. Now the color bar is s
Hi Anastasia,
The file I have seems very similar to the file in that link. I've pasted my
file below:
# Title Pathway Statistics
#
# generating_program /usr/local/freesurfer/bin/dmri_pathstats
# cvs_version
# cmdline /usr/local/freesurfer/bin/dmri_pathstats --intrc
/usr/local/freesurfer/subjects/
Hi Adarsh – The command works fine with our data. When you open your input
file, does it look like the example in the tutorial below?
http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/TraculaStatistics#Anisotropyanddiffusivityaveragedoveranentirepathway
Thanks,
a.y
From:
mailto:freesurfer-bo
Hi Anastasia,
This was the full command:
tractstats2table --inputs
/usr/local/freesurfer/subjects/control_data/diffusion_tracs/Control200/dpath/lh.slft_PP_avg33_mni_flt/pathstats.overall.txt
--overall --tablefile
/usr/local/freesurfer/subjects/control_data/diffusion_tracs/Control200/dpath/lh.slft
Hi Experts!
Quick question: is it possible to re-scale intensities relative to the full
brain atlas?
Details:
Per step 3 of the following tutorial:
https://surfer.nmr.mgh.harvard.edu/fswiki/PetSurfer
I wanted to re-scale the the intensities relative to the full brain atlas. The
command:
Thank you very much!
Kindly, I have one follow up question:
I have VOI 20X20X20 mm have been created during an MR spectroscopy session. This VOI was placed in specific loacation on the T1 image. I have created this VOI using the command "mri_volsynth" and I want to move it from native space (
Hi Dong,
it can work, if time points are close to each other (so not much head growth).
Feel free to try, but make sure you are carefully looking at the surfaces, that
no gray matter is clipped in later time points.
The alternative is to only do cross sectional processing.
Best, Martin
> On
Hi Martin,
Thanks for your reply. I removed the time column from the qdec table (below is
some sample content of the new qdec table):
fsid fsid-base age weight diagnosis gender Glob_CDR NPI-Q_TotScr MMSE_TotScr
FAQ_TotScr visit1_2_3_4
ADNI_sub1_sc ADNI_base1 81.3 y AD M x x x x sc
ADNI_sub1_m
Hi there,
I generated tractographies using the TRACULA pipeline and I'm not trying to
generate the necessary statistics for them using tractstats2table. This is
the command I'm using:
tractstats2table --inputs /usr/local/freesurfer/subjects/control_data/
diffusion_tracs/Control200/dpath/lh.slft_P
I will have to inspect our Mac test results for parallel processing, but
generally speaking we do not see much performance increase in terms of
run times after using 4 threads.
On 02/13/2017 06:13 PM, Francis Tyson Thomas wrote:
> I did provide the execution times in my first email. I have copie
Dear FreeSurfer Experts,
I compared 2 groups in QDEC in spc (from pre to post) and found a cluster that
survives Monte Carlo correction. Now I would like to extract the data for each
participant and each time point from that cluster so that I can plot the change.
How could I do this? I tried th
Hello.
We are looking to save the interim subject files generated when creating an
fsaverage. These seem to be automatically deleted at the end of the process so
we were wondering if there is a flag or script that would save these for us?
Thanks for your help.
John D. West, M.S.
Principal Sys
Hi Andrea
1. the control points don't need to go into locations that are
misclassified, just ones that the intensity is signifantly different from
(and usually less than) 110. They can be correctly segmented as WM.
2. Each control point changes things in a region so they can have a global
ef
Hi FreeSurfer experts,
I have some questions (maybe trivial) about Control Points editing.
1) Following the guide in your website and exploring your tutorial subject
"cp_before" I understood that a Control Point has to be placed in a region
that is definitely white matter but the standard recon-all
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