Dear FreeSurfer-User,
some of my questions are mentioned in some older postings, but I still struggle
with some basic questions. We are planning to use the new hippocampal subfield
segmentation of FS 5.1 with 3 T Siemens TRIO with 32 channel head coil. Still,
I do not fully understand how
Dear list,
I try to run TRACULA pre-processing step and I get the following
error: /dmri/bvecs: No such file or directory.
I have a folder with reconstructed T1 data and a folder with raw dicom
DTI data. When I start trac-all -prep, it creates directory /dmri/,
but it doesn't create the bvecs fil
Hi Tanja,
It is supposed to be created automatically. Can you send your
configuration file and log file for us to see what's going on?
Thanks,
Priti
> Dear list,
>
> I try to run TRACULA pre-processing step and I get the following
> error: /dmri/bvecs: No such file or directory.
>
> I have a fol
Dear All,
How I can get the FA values in a table after running the GLM group analysis for
my FA data. I have GroupAnalysis-FA-MASKED.ANAT+CVS-to-avg35.mgz and the gmldir.
Thank you.
Antonella
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h
Dear Freesurfer experts,
Can freesurfer do multiple comparison correction in part of the brain (not
the whole brain)? How can it do?
Thank you very much in advance.
Mingxia
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Hi Mingxia, when you run mri_glmfit specify a label of the area that you
want to constrain you analysis to. Then run mri_glmfit-sim and perform
the simulation (use the --sim flag, not the --cache flag).
doug
zhang mingxia wrote:
> Dear Freesurfer experts,
>
> Can freesurfer do multiple compariso
Hello folks,
We are in the processing of writing a paper on cortical thickness. The
cluster-wise simulation that we use is it similar to alphasim monte-carlo
simulation by afni? Do you have any paper on it?
Best Regards,
Manish Dalwani
Instructor
Dept. of Psychiatry
Univ. of CO
You can site this Hagler paper
ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/hagler.2006.ni.surfcluster.pdf
Dalwani, Manish wrote:
> Hello folks,
>
> We are in the processing of writing a paper on cortical thickness. The
> cluster-wise simulation that we use is it similar to alpha
Hi Nick,
Why does mri_compile_edits (-showedits flag) report edits to
brainmask.mgz (both in the edits.mgz volume and its text output) if no
manual edits were actually performed -- i.e, if brainmask.mgz and
brainmask.auto.mgz are identical?
thanks,
-MH
--
Michael Harms, Ph.D.
Dear all,
I use dt_recon to process my DTI data and get my fa.nii for the individual
subjects. I wonder if the FA values can be greater that one since for all my
subjects I got the FA max value graeter than one. Is something wrong with my
data or this is acceptable? I saw in most of the paper
Hi Freesurfer users,
I ran a QDEC analysis and loaded annotation. Is there a way to click on the
activated cluster and print the region with co-ordinates?
Thanks,
Manish Dalwani
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Ok I figured that it is ctrl and mouse click on the co-ordinate of interest.
How can I get the cluster size out?
Thanks,
Manish
On 2/2/12 2:47 PM, "Manish Dalwani" wrote:
Hi Freesurfer users,
I ran a QDEC analysis and loaded annotation. Is there a way to click on the
activated cluster and p
Nevermind, I figured out both my questions! I just have to read the
instructions carefully :)
Manish
On 2/2/12 3:02 PM, "Manish Dalwani" wrote:
Ok I figured that it is ctrl and mouse click on the co-ordinate of interest.
How can I get the cluster size out?
Thanks,
Manish
On 2/2/12 2:47 PM
Hi there - First of all, let me clarify that the new and old trac-all have
no differences in terms of usage, so all of this applies to both.
1. Yes, we did come across the issue of jot not being part of some
platforms. It'll be fixed in the next release. If you're getting this
error, you
Hi Tanja - The file is supposed to be created under
$dtroot/$subjectname/dmri/bvecs. If it's trying to create it as
/dmri/bvecs, this means that something wasn't defined correctly. What is
the exact trac-all command line that you're using? And your configuration
file if you're using one?
a.y
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