Dear Freesurfer experts,
I have a question about extracting vertex values of VtxMax for each subject
(for surface eara, in this case).
Based on earlier postings, I used the command mri_segstats (--seg
${x}/surf/lh/area.pial --i ${x}/surf/lh/area.pial --vox vertexno 0 0).
First, I'm
Hi,
I have run a correlation in QDEC and I have quite a lot of results, some of
which pass monte simulation correction at p=0.05 and some of which remain at
p=0.0001. Ideally, I'd like a single figure that will display all significant
results regardless of their p-value. However, I would need
HI Jorge,
how do you determine the number of rows(L) in the contrast matrix?
so if we want to test the effect of cannabis usage, which is the third column
in our design matrix : would our contrast matrix be something like:
CM.C = [0 0 1 0 0 0 0]
or
CM.C = [0 0 1 0 0 0 0; 0 0 -1 0 0 0 0; 0
Thanks!
Date: Mon, 5 Jan 2015 14:57:12 -0500
From: gr...@nmr.mgh.harvard.edu
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] Extracting vertexvalues
It is reporting both the value at that vertex and the mean of all the
other vertices. To get only the value for the vertex,
Based on the log file, you ran trac-all -prep -c dmrirc.all. The
configuration that you attached was called dmrirc.all.txt. Are these files
the same?
On Mon, 5 Jan 2015, Katherine Damme wrote:
Sorry I just copied that from remotely accessing my desktop and viewing the doc
in the terminal.
Ciao Giovanni - Based on the commas, I'm guessing that your unix
environment is set to a non-US language setting. You can change this with:
setenv LANG en_US.UTF-8
Actually, if you download the latest update of tracula, you won't have to
transpose your tables and it'll also apply the above
Hello Freesurfer experts,
We have T1 data from a 3T GE 32-channel head coil that exhibits areas of
hyperintense white matter. Specifically there are areas of the wm.mgz on the
periphery with values ranging from 117-121, which lead to
overextending/overestimation of the wm.mgz.
1) Can anyone
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Message: 2
Date: Sun, 04 Jan 2015 21:04:42 -0500
From: Douglas Greve gr...@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] Error message
I think so. The attached one is definitely correct.
On Mon, Jan 5, 2015 at 4:01 PM, Anastasia Yendiki
ayend...@nmr.mgh.harvard.edu wrote:
Based on the log file, you ran trac-all -prep -c dmrirc.all. The
configuration that you attached was called dmrirc.all.txt. Are these files
the same?
Hello Freesurfer Users,
I have been attempting to use the DWI prep steps described under
FS/Diffusion http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Diffusion,
but have gotten the following error.
ERROR: cannot extract sWiPMemBlock.alFree[8] from
We have the same problem using the same coil (GE 750; mainly occipital
pole), so any suggestions for how to correct this would be very helpful.
Thanks!
Anthony
On 1/5/15, 7:05 PM, Douglas Merkitch wrote:
Hello Freesurfer experts,
We have T1 data from a 3T GE 32-channel head coil that
Hi Jennifer - You're very welcome, thank you for trying out TRACULA!
About the eigenvectors: what software are you using to visualize the
lines? Unfortunately freeview in version 5.3 has a bug in the vector
display, so it may show the vectors wrong when they are not.
About those few cases
This can't be the one you used when you got the bvecs error. This
configuration file would give you an error in the very beginning, before
any commands would ever run, because of this line:
set dcmroot = $SUBJECTS_DIR/$subjlist/orig
Have you tried running trac-all with the dmrirc.all.txt
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Message: 2
Date: Sun, 04 Jan 2015 21:04:42 -0500
From: Douglas Greve gr...@nmr.mgh.harvard.edu
Subject: Re
It is reporting both the value at that vertex and the mean of all the
other vertices. To get only the value for the vertex, add --id 1
doug
On 01/05/2015 03:52 AM, maaike rive wrote:
Dear Freesurfer experts,
I have a question about extracting vertex values of VtxMax for each
subject (for
When you run multiple comparisons in qdec, there should be a file the
Analysis Results called something like mc-z.abs.th30.sig.cluster.mgh.
That will be the clusters with the p-value at each vertex replaced by
the cluster-wise p-value (ie, all vertices in a cluster will have the
same value).
FYI
Forwarded Message
Subject:Register Now for OHBM 2015! {Disarmed}
Date: Mon, 05 Jan 2015 11:30:49 -0600
From: i...@humanbrainmapping.org
Reply-To: i...@humanbrainmapping.org
To: gr...@nmr.mgh.harvard.edu
*OHBM 2015 Registration Is Now Open!*
Aloha
Hello,
One of my collaborators has done the automatic cortical parcellation of our
brain data through FreeSurfer, but my advisor would like me to double-check
that the parcellation does not have any errors. I've found the tutorial
discussing about how to run the cortical parcellation, but I am
Hi Liz
we haven't done much editing of parcels, but it can be done in tksurfer.
You would probably need to convert the annotation to a set of labels, edit
the labels then reassemble them as an annotation (if you need them that
way)
cheers
Bruce
On Mon, 5 Jan 2015, Liz Wieland wrote:
Dear all,
I have two questions:
1. I used both version 5.3 and 5.1 to process the same batch of subjects,
the volume stats were quite different. For example, the white matter
hypointensity was 3865 mm3 in Freesurfer 5.1 aseg.stats, then it became
3118.9 mm3 in Freesurfer 5.3 aseg.stats. Other
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