Dear Matt and freesurfers,
I am encounting this old problem, that is, using fsl_sub to launch FreeSurfer
jobs in SGE and get this error message: (standard_in) 2: Error: comparison in
expression
and freesurfer stoped. But running freesurfer without fsl_sub is OK (using
fsl_sub to launch other c
Hi Yue
if you sample them on to the surface with mri_vol2surf you can use the
overlay histogram facility in tksurfer to do what you want. You can also
use mask_label to remove values outside of an ROI if that is what you are
interested in.
cheers
Bruce
On Fri, 1 Nov 2013, ?? wrote:
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Hi Freesurfers!
Has any one got an answer to this query asked sometime ago:
> "Hi list,
> I have a question, probably trivial, on OFFSET in qdec GUI. What's this? And
> what I can do using it?
Hi Bruce,
I'm referring to "offset" in qdec/Display threshold line, near Min/Mid/Max. For
example, I
Hi Bruce,
Thanks for the information. The surface works for me. These histograms
generated from the surfaces, if I understand correctly, are based on the
intensities along the boundaries of one region. Can I also generate histograms
including the whole region? Like Pick putamen or caudate and g
Hi Yue
tksurfer will only display cortical histograms. For subcortical regions
you are probably best off using something like matlab (which would be
pretty trivial)
cheers
Bruce
On Fri, 1 Nov 2013, ?? wrote:
Hi Bruce,
Thanks for the information. The surface works for me. These histograms
g
I think the latest version of FSL has this sorted out (it doesn't change
your machine's POSIXLY_CORRECT setting except briefly in the middle of
fsl_sub).
Peace,
Matt.
From: chenchunhuichina
Date: Friday, November 1, 2013 2:55 AM
To: Matt Glasser
Cc: free surfer
Subject: ERROR: comparison
Dear Freesurfers and experts
Can any one please tell me what the offset box next to the max. box (under
Threshold) in QDEC GUI is for? When I change from e.g 0 to 1 or higher I get
larger significant clusters. How and when is this feature used?
I also notice this very question is on the archive
Hi Bruce,
Thanks for responding so quickly.
Sorry I probably don't describe my question clearly and my examples are bad.
This is really new to me. So please correct me if I say something wrong. Let me
explain again. Hopefully it will make some sense.
What I want to do is first to segment out
Hi Hamza
offset is the zero point of the colorscale. Usualy it is 0 so that atuff
that is <0 is displayed in blue/cyan and stuff that is >0 in yellow/red
cheers
Bruce
On Fri, 1 Nov 2013, Hamza Alshuft
wrote:
Dear Freesurfers and experts
Can any one please tell me what the offset box next
Hi Alex, if you use "-m cespct" it will report the mean percent signal
change within the ROI. Does this work?
doug
On 10/31/2013 02:37 PM, Alexandra Tanner wrote:
> Hi Doug and Freesurfers,
>
> I would like to calculate percent signal change within an anatomical ROI
> for a group of subjects in
Hi Bruce,
Thanks. Is it statistically sound to use e.g offset 1? My between-group
results are not FDR corrected at offset 0, but if I change the offset to 1
results will be larger in size and FDR corrected! Any pitfalls with that?
Cheers
Hamza
On 01/11/2013 15:53, "Bruce Fischl" wrote:
>Hi Ha
Hi Hazma
log-p values are zero-centered by construction so you probably shouldn't be
changing offset.
Bruce
On Fri, 1 Nov 2013, Hamza Alshuft wrote:
> Hi Bruce,
>
> Thanks. Is it statistically sound to use e.g offset 1? My between-group
> results are not FDR corrected at offset 0, but if I cha
the surfaces can be used to sample in many different ways using options to
mri_vol2surf. For example you could average over the ribbon then display
the histogram of that. For subcortical structures the surfaces don't make
sense, so you are better off just doing it in matlab cheers Bruce
On Fr
Got you. I will check out ribbon and read more about mri_vol2surf. Thanks for
your help!
Yue
> Date: Fri, 1 Nov 2013 12:16:48 -0400
> From: fis...@nmr.mgh.harvard.edu
> To: moonblue...@hotmail.com
> CC: freesurfer@nmr.mgh.harvard.edu
> Subject: RE: [Freesurfer] How to generate histograms of inten
Hi Doug,
Thanks, this seems to work!
Quick question -- in the past we've done ROI analyses where we've
functionally constrained our labels. When calculating percent signal
change we would take the output from funcroi-table-sess divide it by the
output of funcroi-table-sess with no -c flag (the ba
It depends on how are you defining "percent contrast". What you are are
slightly different methods.
Using -m cespct is equivalent to computing
100*Sum(contrast_i/baseline_i)/N where i is a voxel in the ROI
Your method is equivalent to computing 100*Sum(contrast_i)/Sum(baseline_i)
So they will
Once the file is in 3-column format:
cat yourfilename | awk '{print $1 -$2 $3}'
On Thu, 31 Oct 2013, Salil Soman wrote:
Hi Anastasia,
Thank you for this code piece. Is there a way to modify it so that set y's
sign gets flipped? (I have a dataset where its is acquired on GE (so the Y
row gets
Great, thanks for the clarification Doug!
Best,
Alex
>
> It depends on how are you defining "percent contrast". What you are are
> slightly different methods.
>
> Using -m cespct is equivalent to computing
> 100*Sum(contrast_i/baseline_i)/N where i is a voxel in the ROI
> Your method is equivalen
Hi Victor
If you upload the subject I'll take a look
Buce
On Nov 1, 2013, at 5:43 PM, Victor Kovac wrote:
> Freesurfer experts,
>
> I have attached the recon-all log from the scan I included an image of in my
> previous email. Any suggestions on how to deal with dilated ventricles when
> th
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