Thanks for getting back.
The patched mri_segstats works.
Here are the results of our benchmark runs.
Each result comes from a single run so the precision is questionable.
But it seems clear that 8 processors makes little difference compared with 4.
And parallelizing by side also makes little
Hi Sarah
it's really hard to tell what's going on from a single slice. If you upload
the data and send us the specific coordinates you are talking about we will
take a look
cheers
Bruce
On Mon, 4 May
2015, Sarah Hirsiger wrote:
Dear FreeSurfer experts,
I encounter some erroneous
I think it may be the sagittal sinus that is labelled as grey matter.
Best wishes
Kasper
2015-05-04 14:26 GMT+02:00 Bruce Fischl fis...@nmr.mgh.harvard.edu:
Hi Sarah
it's really hard to tell what's going on from a single slice. If you upload
the data and send us the specific coordinates you
Thank you for answer Douglas.
I have indeed tried to run the analysis by demeaning our covariate, but
unfortunately I get the same error (matrix is ill-conditioned or badly scaled,
condno = 1e+08.).
Any other ways I could deal with this error/
Thank you.
Best, Sanne
-Oorspronkelijk
Thanks
Xiaomin
On Sun, May 3, 2015 at 8:55 AM -0700, Douglas Greve
gr...@nmr.mgh.harvard.edu wrote:
If you just want to exclude those time points then you can use a time
point exclude file. To do this, create a text file with the time in
seconds of the time points you want to exclude (t=0 is
Thanks for your suggestion. That doesn't work.
Xiaomin
On Sun, May 3, 2015 at 8:50 AM -0700, Arman Eshaghi arman.esha...@gmail.com
wrote:
Does this happen with all parts your analysis (lh, rh, and mni305)? or only
mni305 volumetric analysis? Because if it happens with only the volumetric
Hi Ani,
I finished running this person through the pipeline (autorecon2 and autorecon3)
and the cerebellum is still incompletely segmented just as before. Do you
possibly have any other ideas?
Thanks!
Jessica
From: freesurfer-boun...@nmr.mgh.harvard.edu
I am having another problem with mkanalysis-sess, here is my command:
mkanalysis-sess -funcstem fmc.so.sm2 -analysis volanalysis -native -paradigm
human_curv.par -event-related -gammafit 2.25 1.25 -refeventdur 16 -polyfit 2
-TR 2 -nconditions 8 -fsd bold -per-run -tpexclude xy_tpexclude.
it
Hello all,
After running a set of subjects through the automatic recon process, a few
subjects seem to have more space between the gyri than one would expect.
Some of these issues were intensity normalization errors, and were fixed
easily enough by edits to the white matter or using control
Hi FS experts,
I had a couple quick questions about interpreting glmfit-sim results. For
context, I'm interesting in analyzing surface-based morphology differences
(cortical thickness, volume, surface area) between two groups. I ran a simple
t-test contrast (1 -1) using glmfit on two groups
Greetings Freesurfer experts,
although this seemed well address on the wiki, I just wanted to clarify
that if I have already run recon-all on all my subjects, but without the
-qcache flag, once I get to the stage of assembling the data, I would just
need to run:
recon-all -s subjid -qcache
and
yes, that is correct
On 05/04/2015 03:19 PM, Paul Dhami wrote:
Greetings Freesurfer experts,
although this seemed well address on the wiki, I just wanted to
clarify that if I have already run recon-all on all my subjects, but
without the -qcache flag, once I get to the stage of assembling
Francesca,
I looked at the files you sent and replicated the problem. It is due to
creating your lh.EKppa.annot file using FreeSurferColorLUT.txt as the
colortable file. You should create your own colortable file, which is
simple to do, and create a new .annot file using that colortable (ie,
Hello,
I am trying to establish contrast for direct statistical analysis in FS.
if I have for example three subject and I want to correlate thickness with
age
the fsgd file is set
GroupDescriptorFile 1
Title G1V2
Class Patient
Variables age
Input 002 Patient 9
Input 003 Patient 10
Input 004
Hi Doug,
I wanted to run FSFAST without using the paradigm file in the analysis using
the following command lines:
1. preproc-sess -s ${i} -fwhm 5 -surface fsaverage lhrh -mni305-1mm -fsd
bold -per-run
2. fcseed-config -segid 1024 -fcname L_Precentralgyrus.dat -fsd bold -mean
-cfg
Hi Skyler,
(I added the freesurfer list in copy, please post all your questions through
the mailing list, thanks!)
If the number of vertices does no match, it might be that you processed the LGI
before you reprocessed the final version of the surfaces for which you
completed the registration
Dear FreeSurfer team, We are having some (relatively new) problems with the
correction of theFreeSurfer outputs. We suppose that it may be due to unknown
differences thatoccurred in our system than with FreeSurfer, but we wanted to
check with you ifyou have heard of any similar issues before.
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