Hi Doug,
Thanks for pointing me back to that; I had forgotten how much depth it goes
into! I have 2 remaining questions:
1) Why is the tkr vox2ras transform sometimes dramatically different from the
one in the volume header? For instance, in one of the functional volumes I'm
talking about, "
Hello Freesurfer's
I want to set up (thanks to Nick's advice) a model with 2 covariates and one
nuisance variable in QDEC. I am using the Freesurfer Version 4.5 but the QDEC
version I am running is 1.2. I did not see any option for nuisance variables in
it? I therefore went to this link
ftp:/
Hi,
After running QDEC, I would like to output in a table the thickness values
within each clusters. I know this is a dependent variable and I can see the
values on the plot but is there a way that I can get this values in a table?
Thanks,
Antonella
From:
I see. We usually have 2mm isotropic diffusion voxels and an order of
magnitude fewer voxels in the mask. So the high memory requirement here
has to do with the high resolution of your data. These bedpost output
files that it's trying to read in have 50 frames each, so you have to
multiply tha
Hi - The voxel dimensions are 1.0156 x 1.0156 x 2.6 mm in the merged_f1 bedpost
output and the total number of voxels in the nodif_brain_mask is 3,276,800.
Ammar
From: Anastasia Yendiki [ayend...@nmr.mgh.harvard.edu]
Sent: Friday, September 23, 2011 11:41
Hi Ammar - Can you check the voxel dimensions of one of the merged_* files
in the bedpost directory, and also how many voxels are included in the
mask that was used for bedpost? It seems to be failing when loading the
bedpost outputs, which is before it reads any tracula-specific inputs.
a.y
mris_volume returns the volume interior to the entire surface (whichever
surface is provided as input), which in the case of Xh.white as input
will include subcortical gray matter, ventricles, etc.
mris_wm_volume subtracts out the volume of non-wm voxels based on the
aseg.
Here is the usage stat
Hi Ri - Tracula reconstructs 18 specific tracts, listed in step 14 here:
https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Tracula
Just like you cannot use freesurfer to find a region that's not included
in the freesurfer atlas, you canot use tracula to find a tract that's not
included in th
Hi Anastasia,
These are both linux ubuntu 10.04 lts machines. The DICOM images are 1300
slices each 140 KB.
Thanks,
Ammar
From: Anastasia Yendiki [ayend...@nmr.mgh.harvard.edu]
Sent: Friday, September 23, 2011 10:30 AM
To: Moiyadi, Ammar
Cc: freesurfer@n
Hi Doug,
Many thanks for the valuable answer and help.
I would appreciate a lot if you can advise me how I can get in a table from
QDEC the clusters after I find the clusters and also the mean value for the
cortical thickness within this clusters. I know in GLM the files are coming as
an
Dear FreeSurfer Expert,
i am trying to generate the total wm volume using mris_wm_volume
,but this value is different from what i get using mirs_volume ?h.white,
could you explain the differences between these two commands. and which is the
best representation of the surface based total wm vo
Hello All,
I am a total newbee in dt-recon and tracula. So sorry if this is a very basic
question.
>From what I gathered so far-
TRACULA uses the aparc+aseg.mgz from the FreeSurfer recon (T1-weighted volume)
as ROIs to construct the tracts and also constructs a few tracts by default.
Is ther
Hi Ammar - Are these macos or linux machines and what is the size of your
diffusion images?
a.y
On Fri, 23 Sep 2011, Moiyadi, Ammar wrote:
> Hi Freesurfers,
>
> I've been getting a memory allocation error (below) when running trac
> prep and trac paths on my computer with 6 gb ram. Since I wa
Hi Freesurfers,
I've been getting a memory allocation error (below) when running trac prep and
trac paths on my computer with 6 gb ram. Since I was able to run these steps on
a computer with 16 gb, I want to know, what is the minimum memory requirement
for running tracula? Is the memory alloca
Hi Joana,
actually it is possible, when using long_mris_slopes after running your
longitudinal data (I think that is what you did).
I cannot judge if your table is correct. You did create that table from
the longitudinal qdec table as described on the wiki (longitudinal
tutorial) right?
So each
Hi Judit - It's hard to know where the problem occurs without knowing what
was going on right before it. Does this happen in the very beginning
before any other output? Can you send your dmrirc and trac-all.log?
Thanks,
a.y
On Fri, 23 Sep 2011, Judit Haasz wrote:
> Hi,
>
> I have been runnin
The "value" is the dependent variable (eg, thickness).
doug
Bruce Fischl wrote:
> Hi Carolina
>
> I'll leave the 2nd question for Doug and Nick. The first one, I think
> you mean "ventral DC", which is short for "ventral diencephalon". It's
> a grab bag of a bunch of stuff that we can't resolve.
The aseg.stats file is created with 1mm3 input with partial volume
correction.
doug
Adil Javed wrote:
> Hi,
> After running dti_recon and recon_all, I noticed that they produce different
> volumes of various structures for the same brain. Just trying to understand
> why that is?
>
> best,
> A
This is actually something that you cannot currently do in QDEC. Try
doing a search for "paired" on our wiki for instructions on how to do
this type of analysis.
doug
Joana Braga Pereira wrote:
> Dear Freesurfers,
>
> I'm doing a longitudinal analysis of cortical thickness using the
> newest ve
Hi Daniel,
Both of the cases you sent us had a fair amount of neck/spine remaining
after the skullstrip step which caused mris_fix_topology to fail. I
processed both cases again using the following command and recon-all
finished without errors:
recon-all -skullstrip -autorecon2 -autorecon3 -s
Dear Freesurfers,
I'm doing a longitudinal analysis of cortical thickness using the newest
version of Freesurfer and there is something i would like to ask you all.
I have two time points and only one group of patients.
I've finished the pre-processing and am now searching for differences
betwee
Hi,
I have been running tracula on a Linux machine, without a problem. Now I
am trying to run tracula on a Mac-Pro machine (running Mac OS X version
10.7.1 - Lion). I followed the tutorial and set up the requested
structure and configuration file.
When I try running the preprocessing step (tra
Hi Carolina
I'll leave the 2nd question for Doug and Nick. The first one, I think you
mean "ventral DC", which is short for "ventral diencephalon". It's a grab
bag of a bunch of stuff that we can't resolve. You would need to check with
someone like Dave Kennedy (ccd) to get the exact descripti
Hello, all,I have 2 questions:- Does anybody know which structure is represented or correspond to "left ventral IDC" in aseg segmentation?- In QDEC analysis, when we obtatin the significant clusters and see the linear regression or correlation curve, what does it mean the "value" of the curve? Is
Hi AJ,
dti_recon just reconstructs tensors. Why do you think it has anything to do
with computing the volumes of structures?
cheers
Bruce
On Thu, 22 Sep 2011, Adil Javed wrote:
> Hi,
> After running dti_recon and recon_all, I noticed that they produce different
> volumes of various structures
Hi Martin,
Thanks for the cope-snippet. A small C program based on that revealed that
it is a problem with popen (gzip is installed and working
properly, and exchanging gzip with other programs produced the same
error).
Error code 38 (ENOSYS) means "Function not implemented". So the
problem
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