I check the recon-all.log. It appears that the cortical region for
caudalanteriorcongulate for this subject is very small..
table columns are:
number of vertices
total surface area (mm^2)
total gray matter volume (mm^3)
average cortical thickness +- standard deviation (mm)
Dear FreeSurfer Experts,
Theoretically, if you have a set of functional ROIs, is it possible to derive
the cortical thickness, white surface area, and gray matter volume of those
functional ROIs in FreeSurfer?
Many thanks!!
Daniel
--
Yung-Jui "Daniel" Yang, PhD
Postdoctoral Researcher
Yale Chi
Hi Alex, are you running it from the project folder? It is looking for a
folder called "log" in the current directory. It should be creating this
folder (bug). So, if you run it from the project folder, the log folder
will be there. Or can create a log folder in your current directory
(mkdir l
The argument to --src_type should be the input file (eg, lh.curv,
lh.sulc, lh.thickness). The --trgsurfval should be the name of the
output file and --trg_type should be curv
doug
On 7/30/13 3:25 AM, fatma zribi wrote:
Dear Bruce,
I try to execute this command to smooth and resample data b
Hello,
I just have a quick question about how to find the group mean of a significant
cluster found in thickness analysis in QDEC. I have run comparison of a number
of clinical groups with healthy controls and found several clusters of
significant thinning. In the stats table generated by QDE
Hi Ella, sorry for the delay. The VRF gets reduced by a factor roughly
equal to TR/dPSD, so 5 in your case. Whether this matters depends on how
you eventually want to analyze the data. If you are going to assume a
shape to the HRF (eg, using SPM or FSL), then it won't make much
difference since
by "everything inside" you mean subcortical white matter and gray
matter? If so, look at ribbon.mgz
doug
On 8/5/13 6:25 PM, pfot...@nmr.mgh.harvard.edu wrote:
> Hi FS Community,
>
> Is there a way to create a binary mask of everything that is inside the
> cortical ribbon of a subject (includin
You should setup contrasts to test the group mean for each group
separately in addition to your contrast of interest. I'm actually not
sure whether QDEC will do this for you or not. Then
cd glmdir/group1contrast
mri_segstats --annot fsaverage lh
../contrast-of-interest/cache.th13.abs.sig.ocn
Hi FS Community,
Is there a way to create a binary mask of everything that is inside the
cortical ribbon of a subject (including the cortical ribbon)?
I ran:
mri_binarize --i aseg.mgz --match 3 --match 42 --o test.mgz which gave me
a binary mask of the cerebral cortex, but I was wondering whether
Hello Sal,
I tried setting my display to :0.0 and was able to get the tkmedit program
to open on my Mac Mountain Lion machine so Im not exactly sure why yours
is having difficulty. Have you installed XQuartz?
http://xquartz.macosforge.org/landing/
If you already have XQuartz installed I would go
Hello,
I just have a quick question about how to find the group mean of a significant
cluster found in thickness analysis in QDEC. I have run comparison of a number
of clinical groups with healthy controls and found several clusters of
significant thinning. In the stats table generated by QDE
There is not an automated tool. I would do it in matlab, loading in the
segmentation, for each seg find the voxels in the segmentation and set
their values equal to your computed value. You can use MRIread.m and
MRIwrite.m
doug
On 8/5/13 6:37 AM, Oscar Sotolongo Grau wrote:
Mapping data in
Something is going wrong. Can you carefully document the key strokes and
mouse clicks you used?
doug
On 8/5/13 1:08 PM, Peter Boulos wrote:
Good afternoon,
I am getting much different results in my QDEC before and after
running monte carlo cluster correction. Upon initially running the
Q
are you looking in the right place? Look in $SUBJECTS_DIR, not the
current directory
doug
On 8/5/13 5:45 PM, Joseph Andreano wrote:
> Hi All,
>
> I'm trying to use recon-all on some structural data, and when I drop the
> command (specifically, recon-all -i
> /cluster/iaslab/SPAR/mri/recon/3dana
Hi Joe
try adding -all to the end. You need to specify a directive for it to
carry out
cheers
Bruce
On Mon, 5 Aug 2013, Joseph Andreano wrote:
> Hi All,
>
> I'm trying to use recon-all on some structural data, and when I drop the
> command (specifically, recon-all -i
> /cluster/iaslab/SPAR/mri/
That is a little strange. Can you look at the wmparc.mgz to see if it is
there? Also look at the aparc+aseg.mgz to see how big the cortical
region for caudalanteriorcingulate is. The wmparc is based on the aparc
part of aparc+aseg.
doug
On 8/5/13 12:49 PM, Yang, Daniel wrote:
Dear FreeSurf
Hi All,
I'm trying to use recon-all on some structural data, and when I drop the
command (specifically, recon-all -i
/cluster/iaslab/SPAR/mri/recon/3danat/003/001.mgz -subjid
SPAR_016_130708), I get this error message:
ERROR: You are trying to re-run an existing subject with (possibly) new
input
Thank you!
-Sal
On Mon, Aug 5, 2013 at 2:22 PM, Douglas Greve wrote:
>
> Good question:). It does not look like we are currently creating a stats
> file for the subfields, which means you will have to do it yourself. You
> can do it with something like
>
> cd $SUBJECTS_DIR/subject
> mri_segstat
Good question:). It does not look like we are currently creating a stats
file for the subfields, which means you will have to do it yourself. You
can do it with something like
cd $SUBJECTS_DIR/subject
mri_segstats --seg mri/hippsubfieldseg.mgz --sum stats/hipposub.stats
--pv mri/norm.mgz --e
I see, thanks Bruce!
> Hi Panos,
>
> not unless you want to restrict the registration to be rigid (6 dofs)
>
> cheers
> Bruce
> On
> Mon,
> 5 Aug 2013, pfot...@nmr.mgh.harvard.edu wrote:
>
>> Hi FS Community,
>>
>> Is there a way to control for the size and shape of a ROI when applying
>> co-regis
Hi,
I can run freeview using my current install on Mountain Lion, however when
I run tkmedit or tksurfer I get the following error:
GLUT: Fatal Error in tksurfer.bin: could not open display: :0.0
my /etc/profile has the setting export DISPLAY=:0.0 for a different
program. Is there settings I sh
Hi Alan - The file doesn't need to have an extension, .txt or other. But
you do need to set bvecfile to the full name of the file, including the
extension, if it has one.
a.y
On Mon, 5 Aug 2013, Alan Francis wrote:
Hi Anastasia:
Yes this file does exist but it did not have the *.txt suffi
Dear Doug and Bruce,
Thank you for your emails. I have also run the -hippo-subfields option on
my freesurfer processing. How do I extract those values as tables as well?
Best wishes,
Sal
On Sun, Aug 4, 2013 at 11:10 AM, Bruce Fischl wrote:
> try asegstats2table
>
> cheers
> Bruce
>
> On Sun,
By the way, smoothing can remove the thickening (if there is only a
little and mainly thinning ).
Best, Martin
On 08/05/2013 02:18 PM, Martin Reuter wrote:
> Hi Bastian,
>
> actually (see other mail today) it computes percent thickening per year
> as it is the slope of the linear fit into the me
Hi Bastian,
actually (see other mail today) it computes percent thickening per year
as it is the slope of the linear fit into the measurements (thickness
with respect to age or time). If the slope is negative, there is thinning.
The results (within subject and on fsaverage) have signs so they a
Hi Anastasia:
Yes this file does exist but it did not have the *.txt suffix. Maybe I will
change the suffix and run this again.
thanks,
Alan
On Mon, Aug 5, 2013 at 1:57 PM, Anastasia Yendiki <
ayend...@nmr.mgh.harvard.edu> wrote:
>
> The error says:
> `/autofs/space/dali_003/users/**BW_projec
Hi Vincent,
yes, it is tp2-tp1 / time_delta
so thinning is negative, thickening positive. I'll correct the help
text, the tutorial is right.
It knows about the time point ordering because of the time column.
Best, Martin
On 08/02/2013 09:04 PM, vbrun...@nmr.mgh.harvard.edu wrote:
> Dear Frees
The error says:
`/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons/bvecs.txt':
No such file or directory
Does this file exist?
On Mon, 5 Aug 2013, Alan Francis wrote:
Hi All:
When I ran trac-preproc I got an error that read s as follows:
trac-preproc exited
Oh, I see. It checks against zero to see if things are specified. I'll
fix that, but in the meantime why don't yo uset everything to 1 instead
of 0
On Mon, 5 Aug 2013, Mark Plantz wrote:
Command and output:
dhcp-165-124-23-213:Desktop IngvalsonLab$ mri_modify -tr 0 -te 0 -ti 0 -fa 0
seg.mgz
Hi All:
When I ran trac-preproc I got an error that read s as follows:
trac-preproc exited with ERRORS at Mon Aug 5 13:12:53 EDT 2013. I do have
a bvec.txt and bval file in each directory.
thanks for your help,
Alan
The following are the messages:
csh::alanf@cerebro[/autofs/space/dali_003/u
It is stored as a label, see fsaverage/label/?h.cortex.label
doug
On 8/5/13 1:14 PM, John Richey wrote:
Dear freesurfer experts,
I was wondering whether there is an existing mask for the left and
right hemispheres for fsaverage. I can't seem to find any
documentation of this, but perhaps I a
Dear freesurfer experts,
I was wondering whether there is an existing mask for the left and right
hemispheres for fsaverage. I can't seem to find any documentation of this, but
perhaps I am missing something?
Thanks in advance,
John.
___
Frees
Good afternoon,
I am getting much different results in my QDEC before and after running
monte carlo cluster correction. Upon initially running the QDEC I have what
appears to be a significant group difference in the prefrontal region that
does not show up after I run the Monte Carlo but at the sam
Command and output:
dhcp-165-124-23-213:Desktop IngvalsonLab$ mri_modify -tr 0 -te 0 -ti 0 -fa
0 seg.mgz seg_new.mgz
Input volume is : seg.mgz
Output volume is : seg_new.mgz
dhcp-165-124-23-213:Desktop IngvalsonLab$
Then, I checked the mri_info for each of the files (input and output)
- *in
Dear FreeSurfer Experts,
I'm looking at stats/wmparc.stats, and there are some inconsistencies between
subjects. I am wondering what might be the cause.
For one subject (say subject 1), part of the information appears to be:
# NRows 66
# NTableCols 10
# ColHeaders Index SegId NVoxels Volume_mm
can you send us the full command line and screen output of what you ran?
On
Mon, 5 Aug 2013, Mark Plantz wrote:
For some reason, when I run that command, I get the following output:
Input volume is : seg_mov
Output volume is : seg_mov_2
There are no errors, but when I check "mri_info" of the
For some reason, when I run that command, I get the following output:
Input volume is : seg_mov
Output volume is : seg_mov_2
There are no errors, but when I check "mri_info" of the output file, the
TR, TE, etc. values are still non-zero. Any ideas what could cause that to
happen?
Thanks!
MP
-- Forwarded message --
From: Mark Plantz
Date: Mon, Aug 5, 2013 at 11:32 AM
Subject: Re: [Freesurfer] TR,TE,TI,FA variability w/ mri_ca_train
To: Bruce Fischl
thank you. Would the command simply be something like this: mri_modify -tr
0 -te 0 -ti 0 -fa 0 ?
On Thu, Aug 1, 201
Hi Panos,
not unless you want to restrict the registration to be rigid (6 dofs)
cheers
Bruce
On
Mon,
5 Aug 2013, pfot...@nmr.mgh.harvard.edu wrote:
> Hi FS Community,
>
> Is there a way to control for the size and shape of a ROI when applying
> co-registration? For instance, I drew a ROI in a
Hi Alan - On the tutorial page you need to follow the directions under "If
you are not at an organized course", and $TUTORIAL_DATA is whatever
directory you have downloaded the tutorial data in.
Please address questions to the list and not to me personally, as other
people may have the same
Hi FS Community,
Is there a way to control for the size and shape of a ROI when applying
co-registration? For instance, I drew a ROI in a scan through freesurfer,
and then when I coregistered that ROI to another scan, the resulting ROI
had a different shape and number of voxels compared to the ori
Hi Yunxin
the surface lives in a continuum and is 2D. Do you mean filling the space
between the ?h.white and ?h.pial surfaces? We do that as part of
recon-all and create ribbon volumes in the mri dir
cheers
Bruce
On Mon, 5 Aug 2013, Yunxin Wang wrote:
Hi dear all,
I'm new here and I've a s
Hi Freesurfers,
I had run Freesurfer over a set of MRIs, extracted the volumes for
different ROIs and correlated with another biomarkers using R. Now I
want to represent the obtained correlations for the segmented ROIs into
a brain template.
Is there some automated way to do that with Freesurfe
Hi dear all,
I'm new here and I've a simple question that how could I transfer the
reconstructed pial surface file(like lh.pial) into a 256*256*256 matlab
matrix used in later fast marching process?
Any suggestion will be appreciated!
Thank guys.
Best,
Yunxin Wang
___
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