Hi Zhuangming, please remember to post to the list. Thanks! I don't
understand your question. What do you mean by the exterior, anterior,
posterior, etc, surfaces?
On 3/5/14 11:56 PM, 沈庄明 wrote:
Hi Doug,
Thank you for your prompting response. Do you mean the computation
only calculate exte
On 3/5/14 5:25 PM, Tudor Popescu wrote:
Hello, I have some questions on doing group comparisons with
thickness, area and volume. Many thanks in advance for any help!
1) For a DOSS design with group and gender as categorical factors, I
see that an interaction contrast ("Is there a group-gender
By default, the surface area is computed from the white surface (ie,
boundary between WM and GM). It is possible to compute it from the pial
surface (ie, boundary between GM and background)
doug
On 3/5/14 9:14 PM, ??? wrote:
Hi all,
I need to know how is the SurfArea in ?h.aparc.stats ca
Hi all,
I need to know how is the SurfArea in ?h.aparc.stats calculated by
FreeSurfer? Since each cortical parcellation has its own thickness in 3D space,
does the surface area computation consider both the exterior surface (i.e. the
surface separating the gray matter and the background) and
not sure what you mean, those are not mutually exclusive
On 03/05/2014 06:05 PM, krista kelly wrote:
> Ok thanks!
>
> Also, for the lh.cortex pial_lgi, should I stick to --label-thresh .5
> rather than --slabel?
>
>
> On Wed, Mar 5, 2014 at 5:59 PM, Douglas N Greve
> mailto:gr...@nmr.mgh.harvar
Right, one more thing. add --excludeid 0
On 03/05/2014 05:59 PM, krista kelly wrote:
> Thanks Doug! That fixed it. But now I have two numbers in each file,
> which do I use (see also attached file)?
>
> ColHeadersIndex SegId NVertices Area_mm2StructName
> Mean
> StdD
Thanks Doug! That fixed it. But now I have two numbers in each file, which
do I use (see also attached file)?
ColHeaders Index SegId NVertices Area_mm2 StructName Mean StdDev Min Max
Range 1 0 124241 81007.3 Seg 2.7306 0.6613 1.4985 4.4779 2.9795 2 1
3540 2225.6 Seg0001 2.4966 0.3254 2.0
Hello, I have some questions on doing group comparisons with thickness,
area and volume. Many thanks in advance for any help!
1) For a DOSS design with group and gender as categorical factors, I see
that an interaction contrast ("Is there a group-gender interaction in the
mean thickness?") still e
Sorry, I gave you some bad advice. Only use --label-thresh with labels
that have a statistic that is non-zero (this is the last column of the
label file). Eg, in lh.V1.thresh.label, the stat is always 0 (but it is
non-zero in lh.V1.label). The stat is the probability that the vertex is
in the
Hi Anastasia,
We use SLURM.
I have not personally yet run bedpost off of the cluster, but one of my
colleagues was able to run his data off of our cluster ( the whole pathway
including bedpost) without any problem. However he (Jon Wieser) made an
individual dmrirc configuration file script f
Hi Emily - Which job management system does your cluster run on? Have you
ever tried to run any of the FSL parallelized programs, like bedpostx, on
your cluster?
a.y
On Wed, 5 Mar 2014, ebell...@uwm.edu wrote:
>
> Hello,
>
> I plan on running a batch of subjects (around 80) on a computer clus
Hello,
I plan on running a batch of subjects (around 80) on a computer cluster.
I am assuming that in the dmrirc configuration file, I can enter all of the
subjects in subjlist?
However, do I have to add something to it to make sure that each subject gets
sent to a different processor on the
Thanks Doug! I did that and it worked, but now here's another problem: the
values that I obtained for V1, V2, and cortex for each subject are all the
same. For example, BV20 left hemisphere values for V1, V2, and cortex are
all 2.7241 (same thing happens for the right hemisphere). Maybe I can tell
Hello,
Is there any way to extract a three dimensional coordinate representation of
the different brain regions (i.e., their centroids) that freesurfer is
estimating the cortical thickness of?
Any help is appreciated and apologies if this question has been answered before.
regards,
David
_
use asegstats2table (I know, it's confusing:)
doug
On 03/05/2014 01:42 PM, krista kelly wrote:
> Hi again,
>
> My apologies for the barrage of emails! I was able to do mri_segstats
> on V1 labels for pial_lgi using the following:
>
> mri_segstats --label-thresh .5 --slabel $s lh
> $SUBJECTS_DI
Hi again,
My apologies for the barrage of emails! I was able to do mri_segstats on V1
labels for pial_lgi using the following:
mri_segstats --label-thresh .5 --slabel $s lh
$SUBJECTS_DIR/$s/label/lh.V1.thresh.label --i
$SUBJECTS_DIR/$s/surf/lh.pial_lgi --sum
$SUBJECTS_DIR/$s/stats/lh.V1.thresh.la
Perfect, it works thanks!
On Wed, Mar 5, 2014 at 11:35 AM, Douglas N Greve
wrote:
> sorry, it is --slabel
> btw, there is documentation. If you run it without options it gives you a
> list of arguments as well as examples
> doug
>
> On 03/05/2014 11:32 AM, krista kelly wrote:
>
>> Thanks Doug, b
Allright, it works if I use those commands:
UpdateBrushInfo { inBrush inLow inHigh inNewValue inMode inCloneSource }
SetEditBrushConfiguration
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*I would use BrainSegNotVent* found in aseg.stats. You can get more info
here
http://surfer.nmr.mgh.harvard.edu/fswiki/MorphometryStats
doug
On 03/04/2014 10:57 AM, Hugh Pemberton wrote:
> Hi guys, just wondering what you'd say is the best measure for whole
> brain volume? Cortex volume.. Cort
sorry, it is --slabel
btw, there is documentation. If you run it without options it gives you
a list of arguments as well as examples
doug
On 03/05/2014 11:32 AM, krista kelly wrote:
> Thanks Doug, but when I try this I get the following error: Option
> --label unknown
>
>
> On Wed, Mar 5, 2014 a
Thanks Doug, but when I try this I get the following error: Option --label
unknown
On Wed, Mar 5, 2014 at 11:21 AM, Douglas N Greve
wrote:
>
> try
> mri_segstats --label-thresh .5 --label BV20 lh V1.thresh.label --i
> $SUBJECTS_DIR/BV20/surf/lh.pial_lgi --sum lh.V1.thresh.label.stats
>
> On 03/0
It contains the volumes of the white matter parcellation. You can make a
table with asegstats2table and specifying --stats=wmparc.stats
doug
On 03/05/2014 11:16 AM, Victor Kovac wrote:
> So, I assume the aseg.mgz contains the values represented in the
> asegstats2table, but what values does the
try
mri_segstats --label-thresh .5 --label BV20 lh V1.thresh.label --i
$SUBJECTS_DIR/BV20/surf/lh.pial_lgi --sum lh.V1.thresh.label.stats
On 03/05/2014 11:15 AM, krista kelly wrote:
> Hello,
>
> I would like to extract the pial_lgi data from Freesurfer's V1.thresh
> labels but can't quite figur
Hello,
I would like to extract the pial_lgi data from Freesurfer's V1.thresh
labels but can't quite figure it out. I've tried adapting the commands from
the LGI Freesurfer tutorial as such:
mri_segstats --label-thresh BV20 lh V1.thresh.label --i
$SUBJECTS_DIR/BV20/surf/lh.pial_lgi --sum lh.V1.thr
Hello,
if I have selected a voxel in a volume with tkmedit with a tcl script, how can
I set the voxel value to 0.
Sincerely yours pfannmoe
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Hi Claudia, I don't know of anyone using it for rodents. In general, it
is highly tuned to the parameters of the primate (mostly human) brain,
and I think it would be quite difficult to adapt it to rodents. I'm
cc'ing the FS list in case someone else has anything to add.
doug
On 03/05/2014 03:
Micheal,
Im sorry but I sent you conflicting information.
The Centos4 build does NOT have openmp built into it. Our Centos4 builds
use gcc version 3.4.6. It wasnt till gcc 4.2 that the gcc compiler
implement openmp (v2.5)
Our CentOS6 build uses gcc 4.4.7 and does have openmp built into it.
So
Hi Buse, I think this is a two-sample t-test where the 2nd sample is
your individual. You should be able to this in qdec
doug
On 03/05/2014 07:52 AM, Buse Merve Ürgen wrote:
> Hello,
>
> I would like to learn whether we can conduct one-sample t-test using
> Qdec.
> I'm working on a single-case st
Hi Marie,
It appears that the problem was the program that I was using to create the
. Qdecrc file. I was using Text Wrangler. I switched to TextMate and the
problem has been resolved.
Thanks so much for your help!
Krista
On Tue, Mar 4, 2014 at 8:27 PM, Marie Schaer wrote:
>
> Hi Krista,
>
>
Thank you for the information, I wasn't sure if the centos4 build had mp
built into it. I will try this and forward the information on to the
researcher to see how their runs can be improved.
Regards
Michael weiner
-Original Message-
From: Z K [mailto:zkauf...@nmr.mgh.harvard.edu]
Sent
Dear experts,
I have Freesurfer running quite well on Ubuntu for some time. But today when I
tried to run the command ‘qdec’, I got the following error:
Qdec.bin: error while loading shared libraries: libXss.so.1: cannot open shared
object file: No such file or directory
How do I fix this? Th
Hi Karl
why is there any difference in either geometry or pixel values after
converting back and forth? Can you send us your mri_convert command lines
and screen output?
cheers
Bruce
On Wed, 5 Mar 2014, Koschutnig, Karl
(karl.koschut...@uni-graz.at) wrote:
Dear experts,
our group decided
I am wondering if there is a preferred direction for acquiring T1 structural
scan? sagittal or axial? and what is the rational?
Thanks
Carmela
This e-mail may contain confidential and/or privileged information for the sole
use of the intended recipient.
Any review or distribution by anyone ot
Hi Carmela
are all controls scanned with one protocol and all patients with another?
If so, combining them and interpreting the results is going to be
difficult.
sorry
Bruce
On Wed, 5 Mar 2014, Tartaglia, Carmela wrote:
> I have patients and controls scanned on the same scanner but their data
I have patients and controls scanned on the same scanner but their data was
acquired in different orientations. One group is sagittal and the other is
axial. The sizes are 1X1X1 vs 1X1X1.2. Is it possible to combine these images
for freesurfer analysis?
Thanks
carmela
This e-mail may cont
Hello,
I would like to learn whether we can conduct one-sample t-test using Qdec.
I'm working on a single-case study, and I want to compare a single
subject's data with a group of controls (to see how this specific subject
is different from the group) in terms of volume, thickness and
meancurvatur
Hi,
I am getting tzhe following an error if I use the following command in a
tcl-script:
SetBrushInfo 3 1 2000 1
The error is:
"Error: Parsing script file
This error was encountered while running the script specified with the -tcl
option. "
What is wrong?
Sincerely yours pfannmoe
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