Hi freesurfer experts,
I've run into a problem of not being able to generate the numerical results
of the analysis I've run through qdec.After I ran the analysis in qdec I
opened the overlay in tksurfer, applied a label, and found a significant
negative correlation between cortical thickness and
How did you create the label ?
On 10/14/16 12:43 PM, Josue Luiz Dalboni Da Rocha wrote:
Dear Doug,
From the curvature file of the ROI (selected portion of surface), we
extract the volume using this 2 command lines:
mri_binarize --i $D_load/lh_masked_all.curv --max -.001 --o
Both contrasts are right. You might want to change the value from 0.5 to
1/6, but that won't affect the actual p-values (only the gamma values).
The 2nd contrast is correct, but it maybe difficult to interpret if the
first contrast has an effect. Technically, you should verify that there
is
You can add --mul 1000 to multiply everything by 1000
On 10/11/16 4:47 PM, Chung, Yoonho wrote:
Hi!
I ran mri_segstats as instructed in the wiki to extract ADC values
from adc.nii. And as you can see below in my output, I think the
decimal digits are truncated and missing the following
It may be the case that the result are not significant. If you have an
apriori region then you can analyze only in that region rather than
doing a whole-brain analysis. That will make the result more significant.
On 10/9/16 4:08 PM, Karamfil Bahchevanov wrote:
Hello Freesurfer experts,
Dear Doug,
From the curvature file of the ROI (selected portion of surface), we extract
the volume using this 2 command lines:
mri_binarize --i $D_load/lh_masked_all.curv --max -.001 --o
$D_load/lh_masked_all_bin.mgh
mri_segstats --seg $D_load/lh_masked_all_bin.mgh --id 1 --i
please send command lines
On 10/14/16 6:36 AM, Damien MARIE wrote:
Hi,
Just adding a word about the e-mail of ma colleague Josue. What he
meant is that he extracted volumes for exactly the same ROI (a merging
of destrieux labels of Hechl’s gyrus, Heschl's sulcus and planum
temporale) using
So the result of step 4 looks ok on the volume but not on the surface?
How are you putting the volume-based ROI back on the surface? This is
tricky because now it will be a 1mm thin label. You should use
mri_vol2surf for this, maybe selecting the --projfrac-max to make sure
that it grabs the
It will not
On 10/13/16 10:34 AM, Eelco van Duinkerken wrote:
Ah sorry for the low level of info. I am aiming to do a simple group
comparison, where I'm comparing thickness between controls and obese
or T2DM patients, regressing out the effect of age, sex and,
hypertension. So I created one
It will be constrained by the group with the smaller number of subjects.
There is not anything wrong with unequal group sizes, but it is less
efficient than if you had split your acquisitions evenly.
On 10/13/16 10:17 AM, Bruce Fischl wrote:
Hi Eelco
it depends on how you setup your GLM.
The entire medial wall has thickness values of 0 because there is no
cortex there. There needs to be a surface in that area because we need a
closed surface.
On 10/12/16 8:10 PM, Taha Abdullah wrote:
Hello All,
Quick question, I ran recon-all with the qcache option and after
converting the
Could be. Can you run dcmunpack instead of unpacksdcmdir? You should be
able to use the same command line. Let me know how it goes.
doug
On 10/13/16 5:25 PM, Marco Loggia wrote:
Hello Doug and Freesurfers,
We are having trouble unpacking DTI data collected in Bay7.
Data are here: cd
The last time I tried, I was using 5.1.0, but the graphics requirements
are very modest and I don't believe they have increased. In the past
there were some issues, with bad drivers on linux (I don't think this is
an issue any longer on linux).
hth
d
On 10/14/16 10:57 AM, Dix Meiberth wrote:
Also, don't use -qcache until after you have run and manually inspected
your analysis
On 10/13/16 3:29 PM, Z K wrote:
> You provided us with very little information to help you solve your
> problem. Please read the "How to describe you problem" section of our wiki:
>
>
Thanks for your reply, did you use the newest release for your analyses?
Best,
DM
-Ursprüngliche Nachricht-
Von: freesurfer-boun...@nmr.mgh.harvard.edu
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] Im Auftrag von dgw
Gesendet: Freitag, 14. Oktober 2016 16:24
An:
The graphics card will not be an issue. I have used much slower
integrated graphics without any problem.
hth
d
On 10/14/16 9:05 AM, Dix Meiberth wrote:
> Dear all,
>
>
>
> I’m thinking about starting a cortical thickness analysis. Therefore I
> would like to buy a new machine, namely an Apple
Dear all,
I'm thinking about starting a cortical thickness analysis. Therefore I would
like to buy a new machine, namely an Apple iMac 21,5"
including: 2,8 GHz Quad-Core Intel Core i5 (Turbo Boost up to 3,3 GHz); 8 GB
1867 MHz LPDDR3 RAM (on-board); Intel Iris Pro Graphics 6200
The Apple
Hi,
Just adding a word about the e-mail of ma colleague Josue. What he meant is
that he extracted volumes for exactly the same ROI (a merging of destrieux
labels of Hechl’s gyrus, Heschl's sulcus and planum temporale) using 1- a .curv
file of this ROI, mri_binarize and mri_segstats or 2- a
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