It is not. -qcache is a preprocessing step prior to doing group analysis
with QDEC. If you use it, you should only do so after you have finished
all the individual analysis (eg, manual edits)
On 4/11/18 10:02 PM, Alexopoulos, Dimitrios wrote:
Is it recommended to use the -qcache flag in the ba
Hi Doug, thanks for the explanation! Also --projfrac-max -.1 1 .1 is a big
improvement, I think it should be good for my purposes. Feeling good about this
now!
Cheers,
DB
___
On 04/11/2018 12:44 PM, David Beeler wrote:
> Hi Doug, thanks for the response! So
Is it recommended to use the -qcache flag in the basic recon-all -all command?
What does it do and what are the advantage of using it?
Jim
The materials in this message are private and may contain Protected Healthcare
Information or other information of a sensit
It would answer the question "if I were a voxel of the forceps major, how
likely would I be to be in any particular location?"
From: freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of Krieger, Donald N.
Sent: Wednesday, April 11, 2018 2:10:50 PM
To: Freesurfe
Are you doing this inside or outside of FSFAST? If outside you would
register your fmri to the anatomical with bbregister, then use
mri_vol2surf to map it to the surface, then surf2surf to map it to
fsaverage, then smooth, then mri_glmfit to test for a differnece between
groups, then mri_glmfit
can you send your command line and terminal output?
On 04/11/2018 05:41 AM, Frauke Beyer wrote:
> Dear experts,
>
> I have an issue with mri_surf2surf (i suspect). I have resampled
> T1-values to the fsaverage template using mri_vol2surf and a --projfrac
> of 0.25 with the default white matter su
The fsfast commands require matlab or octave. I'm not sure how that will
work in the linux shell in windows
On 04/11/2018 03:50 PM, Savio Wong wrote:
> Hi everyone,
>
> I have installed freesurfer on windows 10 linux shell following this link:
>
> http://nuclear-imaging.info/site_content/2016/09
On 04/11/2018 12:44 PM, David Beeler wrote:
> Hi Doug, thanks for the response! So it looks like my initial
> transform from surface label to anatomical volume wasn't working
> because my template.nii.gz and brainmask were in a different space
> than the functional data I was processing. This
X.runflac(1).flac.ev(2).tirf is the time samples (eg, 0 to 30 sec)
X.runflac(1).flac.ev(2).Xirf is the actual HRF
If you are using the spmhrf, you can look at the matlab function
fast_spmhrf
On 04/11/2018 10:56 AM, Sarah Cole wrote:
> Just one clarification, this is for first level analysis (
p.s. you probably want to grab a new freeview also, as it lets you jump
to the voxel coords of each control point so you can see them
On Wed, 11 Apr
2018, Hoopes, Andrew wrote:
Hi Anna,
You can download the new mri_normalize from this link -
https://surfer.nmr.mgh.harvard.edu/pub/dist/fre
Hi Anna,
You can download the new mri_normalize from this link -
https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/dev_binaries/centos6_x86_64/mri_normalize
To get it into your FS installation, first set executable permissions and then
move it into your $FREESURFER_HOME/bin directory (sudo
Hi everyone,
I have installed freesurfer on windows 10 linux shell following this link:
http://nuclear-imaging.info/site_content/2016/09/12/installing-running-freesurfer-windows-10/
Recon-all and freeview run perfectly on the system. However, when I tried
to run mkcontrast, I encountered the fol
Hello Carissa,
There have been some changes to the files related to the “—make all” option.
You can try downloading an updated version of the
recon-all.makefile from the list of files under,
ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/dev_binaries/centos7_x86_64/
and replace the exis
Ok - I have that sum.
For the forceps major, it's 111,685.
If I normalize by that, i.e. divide each voxel value by that, then I certainly
get something that looks like a probability distribution since the sum of the
normalized voxel entries over the entire volume is 1.0 as you had said in an
ear
Hi Don - You would normalize these numbers by their sum, not by their maximum
(i.e., not by 255).
a.y
From: freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of Krieger, Donald N.
Sent: Wednesday, April 11, 2018 1:51:43 PM
To: Freesurfer support list
Subject:
Hi, Anastasia.
Yes, that makes it simpler.
I can see that each of the path.pd.nii.gz has a voxel entry for the same number
of voxels. I'm looking at elmo.2008 for which that number is 1,294,336 which I
presume is the volume of this person's brain as delivered by freesurfer.
Most of those voxel
Also, I'm using Freesurfer 5.3
On Wed, Apr 11, 2018 at 1:50 PM, Connor Garris wrote:
> Hello,
>
> I'm running into a problem when subparcellating my regions of interest
> where after subparcellating there are some sublcusters that are labelled
> identically by freesurfer even though they are dis
Hello,
I'm running into a problem when subparcellating my regions of interest
where after subparcellating there are some sublcusters that are labelled
identically by freesurfer even though they are distinct subclusters. More
specifically, I ran one iteration of mris_divide_parcellation passing it
Thanks, Anastasia.
I'll think about this and get back if I can't figure it out.
Best - Don
From: freesurfer-boun...@nmr.mgh.harvard.edu
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Yendiki, Anastasia
Sent: Wednesday, April 11, 2018 12:46 PM
To: Freesurfer support list
Subject:
The probability maps are independent for each tract. Each one just tells you
how likely this one tract is to go through any given voxel, but it tells you
nothing about other tracts. Does this make sense?
On Apr 11, 2018 12:00 PM, "Krieger, Donald N." wrote:
Thanks for getting back, Anastasia.
Hi Doug, thanks for the response!
So it looks like my initial transform from surface label to anatomical volume
wasn't working because my template.nii.gz and brainmask were in a different
space than the functional data I was processing. This happened because I was
taking the raw f.nii.gz, doing
Thanks for getting back, Anastasia.
I'm not suggesting that it should be done differently than it is.
I'm just trying to understand how the voxel values map to probability. That's
why I described the wrong headed way I was thinking about it ... so you could
tell me where I'm going wrong.
Fro
This wouldn't work because these 18 tracts do not include all tracts in the
brain.
On Apr 11, 2018 11:19 AM, "Krieger, Donald N." wrote:
I was thinking that for a single voxel, the total of the values assigned to the
voxel over all the tracts would have a maximum of 255 and that 255 would
corr
Hello,
I am running recon-all for several subjects’ 7T data using Freesurfer version
6.0 and currently trying to ensure appropriate skull stripping and pial/wm
surface generation. For a few participants that needed some control points
added and for which I reran them through the –autorecon2-cp
Hi Karin,
This tutorial will explain how to find your dicom input file:
http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Practice
Best,
Emma
From: freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of Karin Westin
Sent: Wednesday, April 11, 2018 9:29:37
I was thinking that for a single voxel, the total of the values assigned to the
voxel over all the tracts would have a maximum of 255 and that 255 would
correspond to a probability of 1.0.
I can see is likely wrong but for sure it's too simple since each voxel could
contain crossing fibers from
Just one clarification, this is for first level analysis (individual
subjects).
Thanks
On Wed, Apr 11, 2018 at 9:54 AM, Sarah Cole wrote:
> Hi Doug,
>
> At the end of my FSFAST analysis, I would like to plot the Canonical HRF
> shape generated by FSFAST for my events. I have found this thread:
Hi Doug,
At the end of my FSFAST analysis, I would like to plot the Canonical HRF
shape generated by FSFAST for my events. I have found this thread:
https://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/2013-July/031902.html
but I am not sure if I understand this line:
"plot(X.runflac(1).flac.ev(
The volume would have to be normalized to a total sum of 1 for the voxel values
to represent an actual distribution.
From: freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of Krieger, Donald N.
Sent: Wednesday, April 11, 2018 10:43:11 AM
To: Freesurfer support
Great - thanks - that's what I need.
I can use the probability for each pixel as a weight for the neuroelectric
current count for that pixel to quantify the activity for the tract.
I assume that each voxel value maps directly to its probability, i.e. 0-255 -->
0.0 - 1.0
Thanks again - best - Do
Hi Don - No, dlabel/ contains files that are used in the pathway
reconstruction, but the output of the reconstruction is saved in dpath/.
There's a subdirectory in there for each pathway, and it contains a volume
called path.pd.nii.gz. This is the probability that each voxel belongs to this
pat
Hi everybody!
I'm very new to freesurfer and I'm trying to perform a reconstruction using
recon-all. My problem is I don't see how I can access a single file to
input to recon-all. I've run dcmunpack -src
but the only output I get is
Found 2 unique series: 4 401
Subject (name of subject)
Date (
Thanks for the additional information, Anastasia.
I will look for those files.
What I am after is a list of xyz coordinates for each of the 18 tracts. I see
masks in the trctrain/trc0xy/dlabel/mni directories which appear to be what I'm
looking for. They have names like
_AS_..nii.gz
where str1 =
Dear experts,
I have an issue with mri_surf2surf (i suspect). I have resampled
T1-values to the fsaverage template using mri_vol2surf and a --projfrac
of 0.25 with the default white matter surface. Then I loaded these
values in Matlab using MRIread, inverted them and saved them back into a
file us
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