Hello again,
Thanks for your quick response. In addition to my previous question, I
would also like to learn what the default analysis in Qdec is actually
doing.
For example, as I said previously, I have only one patient and a group of
control participants. In that case, in my data table I'm givin
This topic has been discussed previously without a conclusive answer. After
some www inquests I realized that it is easily possible to process nii-images
using spm functions for matlab.
The functions for loading and saving images are:
V = spm_vol(angio_corrected_marked);
Hi all,
I'm looking to create a mask for the hypothalamus on individual subjects. I've
had a good look at the literature, and at the moment, am I right in thinking
the automatic segmentation in Freesurfer doesn't currently include the
hypothalamus?
thanks in advance
Ella
Ella,
My understanding is the same. I've made my own ROI by hand drawing on the
average subject and using various commands to map onto individual subjects. If
you're doing resting analysis then you can check your general whole brain
correlation results against the literature to see if your ROI
Hi Yufeng
perhaps we should take a step back - what are you trying to achieve?
cheers
Bruce
On
Tue, 18 Mar 2014, yufeng huang wrote:
Dear Bruce,
I am a new user of freesurfer. I just followed the process on the
webside(https://surfer.nmr.mgh.harvard.edu/fswiki/SurfaceRegAndTemplates) to
do
Hi Ella
yes, it does not
cheers
Bruce
On Tue, 18 Mar 2014, Ella wrote:
> Hi all,
>
> I'm looking to create a mask for the hypothalamus on individual subjects.
> I've had a good look at the literature, and at the moment, am I right in
> thinking the automatic segmentation in Freesurfer doesn't
Hi Ella,
There are a number of options:
You can draw manual segmentations on individual subjects, though the time and
cost required for this labor-intensive process of manual tracing has become
prohibitive.
Paul's suggestion would be a better one, maybe one of our protocols described
in e.g. h
Tanks doug,
Is it ok like this: mri_glmfit-sim --glmdir qdec/Untitled --cache 1.3 neg ?
Best regards,
Amirhossein Manzouri
On Mon, Mar 17, 2014 at 8:25 PM, Douglas N Greve
wrote:
>
> you will have to run the correction for multiple comparisons with
> mri_glmfit-sim (ie, you can't do it in q
yes
On 3/18/14 9:14 AM, amirhossein manzouri wrote:
Tanks doug,
Is it ok like this: mri_glmfit-sim --glmdir qdec/Untitled --cache 1.3
neg ?
Best regards,
Amirhossein Manzouri
On Mon, Mar 17, 2014 at 8:25 PM, Douglas N Greve
mailto:gr...@nmr.mgh.harvard.edu>> wrote:
you will have
OK, thanks!
Francesco
On 17 March 2014 17:50, Douglas N Greve wrote:
>
> Hi Francesco, please remember to post to the list. Thanks! The baseline is
> a regressor with all ones, so it is measured throughout the scan, not just
> during the rests. This makes the other regression coefficients relat
It is constructing a GLM with design matrix with 2 columns and N rows
where each row is a subject. The row of your patient gets 1 0 and the
rows for the other subjects gets 0 1. When you set up a contrast with [1
-1], you are comparing the value of the subject against the mean of the
others
Can you verify that the label does actually have label points in it?
Just open it in a text editor or cat it to a terminal. If it does have
points, send it to me. Also let me know which version of FS you are running.
doug
On 3/17/14 5:35 PM, Rupa Sabbineni wrote:
muen223-105-dhcp:subjects
Dear FreeSurfer experts,
I am trying to find the surface ROIs for (volumetric) parcellation ROIs,
as mentioned in:
Frye, RE et al. 2010. Surface Area Accounts for the Relation of Gray
Matter Volume to Reading-Related Skills and History of Dyslexia.
Cerebral Cortex 20:2625-2635.
I have run all
These already exist on the surface in the form of annotation, so you can
view them with something like
tksurfer subject lh inflated -annot aparc.annot
there are also stat summaries in the stats folder
doug
On 03/18/2014 10:10 AM, Danielle Sliva wrote:
> Dear FreeSurfer experts,
>
> I am tryi
Hi all,
just two quick questions: to what FS version is this related? And what
is wrong to do if one does not have the fix? Using what
stats/procedures?
Thanks,
Andreia
Quoting Douglas N Greve :
>>> why would one control for total brain volume in doing vertex-based
> analyses when the vert
Dear Anastasia,
Hello, many thanks for your quick reply, sorry for the delay.
I have switched to 3-column format and that does indeed get the process a
little further, so many thanks for that. Unfortunately however I get this new
error during the trac-all -bedp stage:
An exception has been thr
Hi,
When I run selxavg3-sess, I face this error:
ERROR: cannot find volume matching
/autofs/cluster/tootell/pitcairn/1/shahin/ColorPrj/7T/Sbj/myla2/bold_Color/013/mcextreg
ERROR: loading nonpar reg
/autofs/cluster/tootell/pitcairn/1/shahin/ColorPrj/7T/Sbj/myla2/bold_Color/013/mcextreg
-
Hi Colm - Yes, it's fine to run bedpostx directly, with the path to the
dmri directory as its argument.
Since you're using 5.2, note that although there were no issues with
tracula in that version, it is not advisable to use freesurfer recons
produced with 5.2. There was a bug in that versio
Hello all,
I think this is a fairly simple question, but I could not find an existing
answer online. If I close out the terminal window while recon is running, will
the process end? I've had the issue in the past where my computer has gone to
sleep and the process ends up exiting with error.
A
>> why would one control for total brain volume in doing vertex-based
analyses when the vertex-based measures are computed in standard space?
>The vertex-based measures are computed in individual space, not standard
>space
>doug
Many thanks Doug,
Best wishes,
Narly.
_
Hello FreeSurfer experts,
I have a question regarding DTI analysis.
I understand that FA values ranges 0-1, and the values are often thresholded by
0.2.
Now I am asked to report ADC, RD, AD values in my ROIs, and wondering what
would be the most reasonable way.
[1] Do not apply thresholds, jus
Hi Yuko - Option 3, using the same FA threshold to create a mask for all
measures makes sense.
a.y
On Wed, 19 Mar 2014, Yuko Yotsumoto wrote:
> Hello FreeSurfer experts,
>
> I have a question regarding DTI analysis.
>
> I understand that FA values ranges 0-1, and the values are often threshold
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