Hi Everyone,
In order to introduce distortion correction methods in our DTI
processing
pipeline, I wanted to acquire B=0 with A->P to P->A phase encode directions,
as recommended by topup tutorials.
I talked to the MRI operators at our facility, and they were not able
to find out
how to fli
Hi All,
I got introduced to SurfStat through this list, and i have been
using it of late
to try some alternatives to the surface based GLM analysis on my data,
already
processed by freesurfer. The results are a perfect match, except for the
x,y,x coordinates
reported by SurfStat (same data
The max is the -log10(p), bounded below by -log10(CWP) for positive
correlations Hence with an -log10(CWP) of 4, the Max
will be greater than 4, and will specify the maximum -log10(p) value in that
cluster, occuring at VtxMax
Is this right for -log10(p) kind if input? This is how i have been
inte
Hi everyone,
I have a couple of questions regarding the contents of
the summary file
generated by mri_surfcluster, and would be happy to get some help.
1) The Max value column, does it represent the SPM{t} value, SPM{z} value
or -log(p)[base 10].
2) Can the Tal{x,y,z}, if adj
Hi all,
what do the .w files (generated, in my case, by mri_surf2cluster)
contain?
How can i view them/use them?
thanks,
sid.
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Freesurfer@nmr.mgh.harvard.edu
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Hi everyone,
For a cluster spanning multiple labels based on a
specific annotation, is
it possible to automatically generate a list of labels (text) of the regions
it
overlaps with? What command/process should do this? mri_surfcluster is just
providing me with the parcellation wh
Hi everyone,
I would like to get the opinion of the users on this,
regarding
the feasibility of using freesurfer for analyzing mouse imaging data,
provided
that we have at our disposal, a supporting atlas. I know that Caret provided
a fine scale parcellation for this species. Ar
Class ctrl should be followed by marker and color specification (Class ctrl
circle red, for e.g). ditto
for cd .
sid.
On Thu, Mar 12, 2009 at 6:37 PM, Jeff Sadino wrote:
> Hello,
>
> Can someone help me get scatterplots of my data? I am using freesurfer
> 3.0.5. I have ran these commands:
>
Hi everyone,
Is it possible to selectively display a few segmentation
labels over an anatomical, using tkmedit? say i would just like
to see label 4 (browsing by label numbers, and not names)?
I am sure there is a documentation on how to do this somewhere...
tha
Hi david,
I dont know if this will help, and i really do not know the
reason why it should work,
but if you append the tcltktixbli/lib, /usr/lib and /usr/lib64 on 64 bit
version *in this order*, the
tksurfer problems are solved. There will still be some unresolved issues
with spuriou
hat it just gives the entire volume (the
> "masking" routine just looks for 0-valued voxels). I don't think it actually
> uses the mask for anything, though.
>
> glmfit is run because that's what the tensor analysis is.
>
> Siddharth Srivastava wrote:
>
>&
Hi everyone,
I have recently started using the dt_recon processing
pipeline
in freesurfer. I just ran a dataset through it, and had a few questions
about
the methodology
1) How does the script calculate the mask from the DW data set. Is there any
way
to influence the mask calcula
ects who did not
> complete the tasks.
>
> Regards
> Jürgen
>
>
>
> On 28.1.2009 20:46 Uhr, "Siddharth Srivastava" wrote:
>
> Hi everyone,
>I was wondering if it is possible to flag missing
> entries in
> the covariates corresp
Hi everyone,
I was wondering if it is possible to flag missing entries
in
the covariates corresponding to subjects, in the construction of the file
passed
through --fsgd to mri_glmfit ? Not all my subjects completed all the tasks,
and i need to code them in the file, somehow.
I think it's just a
> display problem and won't affect anything else, but if you give us the
> example we'll fix it.
>
> Bruce
>
> On Sat, 24 Jan 2009, Siddharth Srivastava wrote:
>
> Hi everyone,
>> Has anyone faced this problem before? Is
shift the
brain posteriorly.
sid.
On Fri, Jan 23, 2009 at 11:37 AM, Siddharth Srivastava wrote:
> Hi bruce,
> I think the offending command is
> mri_convert /../../orig.mgz /../../orig-subject.mgh --apply_transform
> /../../mri/transforms/talairach.xfm -
?
>
>
> On Fri, 23 Jan 2009, Siddharth Srivastava wrote:
>
> Hi Bruce,
>> please find attached a tiff file generated by mri_concat
>> --mean on the original mprages.
>> Here i can see the full view, and i think no registration has been
>> performed
-- Forwarded message --
From: Siddharth Srivastava
Date: Fri, Jan 23, 2009 at 9:10 AM
Subject: Re: [Freesurfer] cropping of average T1
To: Bruce Fischl
ok.. i will try that and let you know... what other image/logs can i provide
for
localizing the source of the error?
sid.
On
> On Thu, 22 Jan 2009, Siddharth Srivastava wrote:
>
> Hi everyone,
>> I am attaching a tiff file showing the tkmedit view of
>> the average
>> T1 that freesurfer created during make_average_subject. I am a bit
>> concerned
>>
>> about t
Hi group,
I have some questions about the interpretation of my
results based on the contrasts that i have used in my analysis.
It is, i am sure a very basic question, and i would like to check
if my interpretation of the results is correct/valid.
I have 2 groups, and 1 variable, and
a symlink from $FREESURFER_HOME/subjects/fsaverage to
> your SUBJECTS_DIRS, to spare having to copy the data.
>
> Nick
>
>
> On Sun, 2008-12-28 at 12:01 -0800, Siddharth Srivastava wrote:
> > Hi Nick,
> > Thanks, It was my mistake. It works exactly as you say.
&g
ove subject data around to other directories
> without any problems. Does tksurfer really halt after that 'not in
> scripts dir' message? That is a common message and not an error. Can
> you open tksurfer for the sample bert subject?
>
> Nick
>
>
>
> On Sat, 2008-1
n the color options available). people change the thresholds
> to get the nice pictures.
>
> Nick
>
>
>
>
> On Thu, 2008-12-04 at 19:50 -0800, Siddharth Srivastava wrote:
> > Hi everyone,
> >while the machine is busy crunching through our
>
t does simple open/close/erode/dilate.
>
> cheers,
> Bruce
>
>
>
> On Fri, 19 Dec 2008, Siddharth Srivastava wrote:
>
> Hi everyone,
>> what is the difference in functionality between the mri_*
>> commands and the mris_*
>> commands?
>&
Hi everyone,
what is the difference in functionality between the mri_*
commands and the mris_*
commands?
How does the mris_fill command maintain the distinction
between the left and the
right hemisphere? I see only one filled.mgz having 2 labels? does it write
spm_*.img --o 4d.img
>
> you can also do it with mri_convert, but I don't think it buys you
> anything over using mri_concat.
>
> doug
>
> Siddharth Srivastava wrote:
>
> hi everyone,
>is it possible to combine, using mri_convert, a set of
&g
hi everyone,
is it possible to combine, using mri_convert, a set of
3D spm/analyze files into a 4D analyze file ? can anyone help
me out with the syntax, if possible?
thanks,
sid.
___
Freesurfer
but apparently libvtkHybrid.so.5.2 and
> libvtkRendering.so.5.2 use it (as discovered by running ldd upon all the
> mris_volmask.bin lib dependencies).
>
> What platform are you running? Probably VTK would need to be built on
> that.
>
> Nick
>
> On Thu, 2008-12-11 at 16:27 -0800, S
Hi surfers,
I am trying to understand the source of the following errors. I know it was
not able to locate libXss, but why
should mris_volmask need libXss ? I have been told it is a library used by X
sceensaver
mris_volmask --label_left_whit
Hi all,
1) which steps of the freesurfer processing pipeline depend on/ use
matlab for
execution? I am trying to find out if we have to have matlab installed on
all the
computing nodes on our cluster here, or, if there is just one step, we can
process it
locally, and submit the downstream
Hi everyone,
while the machine is busy crunching through our data set,
i would
like to prepare myself from the next step of the analysis, which is a
region-wise
analysis of the computed metrics by the freesurfer pipeline. Being a
complete
novice in the use of this software, i wou
Hi Prapti,
I think you have to modify the $LD_LIBRARY_PATH shell variable.
first find where libtiff.so.3 is. Usually "locate libtiff.so.3" will tell
you
where the file is at. On my machine, it is in /usr/lib/ and /usr/lib64/
then
LD_LIBRARY_PATH = $LD_LIBRARY_PATH:/usr/lib64/
export LD_LIBRARY_PATH
-with relevant subject-- sorry for multiple sends.
On Mon, Nov 24, 2008 at 8:43 PM, Siddharth Srivastava <[EMAIL PROTECTED]>wrote:
> Hi everyone,
>Any recommendations on how to set up a proper colorscale
> for
> visualization? My data do not have negative
Hi everyone,
Any recommendations on how to set up a proper colorscale
for
visualization? My data do not have negative values (lgi, but a large range,
1 - 15, and i would like to
use the entire range of blue-green etc. maps. I have been playing around
with
the color-scale window i
econ-all with just the flags used for the stages covering
> the parts that have not completed.
>
> In your case:
>
> recon-all -autorecon2-pial -autorecon3 -subjid subj
>
> would be appropriate, as that starts with the finalsurfs stage.
>
> Nick
>
>
> O
Hi again, everyone,
Apologies for another newbie question, but i
was wondering what is the best thing
to be done in case the program crashes in midflight, during the recon-all
invocation. As of now, i have
identified that the processing crashed sometime during mris_mak
Hi Volkmar,
we also had an exception thrown relating to libexpat (what
does it do, anyway?), but we solved it
by creating a soft link between so.1 and so.0 in the same directory (can be
dome with ln -s command on unix/linux,
link what you already have, with what the software wants
on my previously-broken
> system after I installed those files:
>
> libnvidia-tls.so.1 => /usr/lib/tls/libnvidia-tls.so.1
>
> mjp
>
>
>
>
>
>
> On Nov 18, 2008, at 9:35 PM, Bruce Fischl wrote:
>
> Hi Sid,
>>
>> this is a known problem. It ac
Hi !
I am a relatively new user of freesurfer, and currently i have 2
instances
of the same -stable 64bit Linux versions installed, one on my local machine,
and the
other on a cluster, accessible over the network. I have been able to get
freesurfer
running without any problems on my local mach
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