Hi Nick,
thanks for your advice - Freesurfer v5.2 has now been installed on our
clusters and I am running the recon_all script again with this version. Is
it necessary to re-run everything from scratch again ('mk subjdirs' and
'mri_convert') using this version or will it be okay to just re-run
Hi Bruce and other users,
I have read the article on EC that you have suggested.
But, I do not understand how I should obtain the EC thickness outcomes
/statistical maps from my analysis.
I have some question, please.
I have already performed recon-all and cortical thickness analysis.
For
it depends on (1) what you want to do with them (e.g. functional analysis
vs. thickness) and (2) the quality of the scans
On Tue, 5 Mar 2013, Schumman
Resonance wrote:
This is a question for the FS community in general,
I gather there is variability around this, but rather than an exact
Sinead,
For subjects you have already processed with a prior version, you can just
run:
recon-all -s subjid -all
and it will retain any edits that were made.
Nick
Hi Nick,
thanks for your advice - Freesurfer v5.2 has now been installed on our
clusters and I am running the recon_all
All,
Any idea how can I sort this error,
Loading data table /Users/chikkuvarghese/subject/qdec/qdec.table.dat...
Number of columns: 4
fsid column:1
Number of factors: 3
Number of subjects: 1
ERROR: QdecDataTable::Load: problem parsing file
Dear Freesurfer experts,
I am interested in a specific brain region that is based on the 2009
atlas. I used Qdec to 'Generate Stats Data Tables' to get the cortical
thickness info for this region and saved them in a file.
Then I used SPSS and did an ANOVA test. The ANOVA test reveals that the
Hi, I'm a new user of Freesurfer.
1) I would like to extract only the cortex cerebrum . So I think I don't need
the complete subcortical segmentation ( 20-40 hours). Do you know a way to
segment only cortex or only ( cortex+ pial ( left/rigt hemispher)?2) I already
try the complete
Hi VP
sorry, the subcortical stuff is needed to automate the cortical surface
modeling, so you need teh whole thing.
We do distribute matlab scripts for reading the surfaces in
(read_surf.m).
cheers
Bruce
On Wed, 6 Mar 2013, Valtina Pouegue
wrote:
Hi, I'm a new user of Freesurfer.
Hi Sean - Thanks for trying out the new version!
From what I've seen, the file $FSLDIR/etc/fslversion exists in FSL 5 as
well. Does it exist in your distribution?
a.y
On Wed, 6 Mar 2013, Sean Hatton wrote:
Hi all,
I have installed FreeSurfer 5.2 to take advantage of improvements in
Thanks for the info, Nick. That is very helpful.
Our install partition has limited size. So the idea is not to get rid of
anything, but rather move these big data files somewhere else with much
larger disk quota. I guess I could move the whole subject away. As long as
SUBJECTS_DIR is set
Hi Chikku-- can you try with a /newline at the end of your .dat file?
shantanu
On Wed, March 6, 2013 10:40 am, Varghese Chikku wrote:
All,
Any idea how can I sort this error,
Loading data table /Users/chikkuvarghese/subject/qdec/qdec.table.dat...
Number of columns: 4
fsid column:1
DJ,
symbolic links would work. for instance:
cd freesurfer
mv average path_to_larg_disk_space/freesurfer_data
ln -s path_to_larg_disk_space/freesurfer_data/average
then you should have a link to average remaining in the freesurfer dir
but the space is consumed elsewhere.
Nick
On Wed,
Hi Sara,
yes, should work, just make sure that all cross are 5.1 (and not mixed)
to remain consistent.
By the way 5.1 can process differently many time points for each
subject. Just not subjects with a single time point only. To include
those you'd need 5.2
Best, Martin
On 03/06/2013 01:32
Sarah,
I'm cc'ing martin reuter on this, but yes, you should be able to use
your cross-sectionally processed scans from v5.1 in a longitudinal
analysis using v5.2.
Nick
On Wed, 2013-03-06 at 05:46 +, Sarah Whittle wrote:
Hi,
RE the below post, we have longitudinal data from three time
Dear Experts,
I am setup fs 5.2 and have successfully run freesurfer processing on a SPGR
dataset. However, when I attempt to run Tracula on that dataset, I keep
getting a corRead(): can't open file /path/to/ducks/COR-.info (where to
path to ducks is the patch to where my subjects are located),
Hi Salil - Can you send your trac-all.log and dmrirc files? Thanks!
a.y
On Wed, 6 Mar 2013, Salil Soman wrote:
Dear Experts,
I am setup fs 5.2 and have successfully run freesurfer processing on a SPGR
dataset. However, when I attempt to run Tracula on that
dataset, I keep getting a
Hi Salil - The problem is that you've set dob0 = 1 but you haven't
set b0mlist and b0plist, so it doesn't know where to find your field maps
to do the B0 unwarping.
a.y
On Wed, 6 Mar 2013, Salil Soman wrote:
Thank you.
Please see attached.
-S
On Wed, Mar 6, 2013 at 12:40 PM,
Hi all,
Congrats on the new version! I've been excited to see how the use of data from
T2 images could help pial surface estimation, but I'm encountering a problem
with getting that to work. It seems to be failing to properly execute the
bbregister command built into this part of the new
Hi freesurfers,
I have an event-related design experiment which outputs a file with a line
corresponding to every TR.
i.e. for TR = 1 the first 3 columns of the file look like:
0 0 1
1 0 1
2 0 1
3 0 1
4 0 1
5 1 1
6 1 1
7 1 1
8 1 1
9 1 1
Assuming I have 5 seconds of fixation followed by
Hi again,
We have had some suboptimal results from FreeSurfer's skullstripping algorithm,
even after iteratively trying different watershed thresholds and after checking
the quality of Talairach registration. The results are pretty good, but often
leave some dura matter and bits of neck
you can use
mri_convert -rl ...
to reslice the output of bet so that it has the same geometry as the rest
of our stream
cheers
Bruce
On Wed, 6 Mar 2013, Winter, Warren wrote:
Hi again,
We have had some suboptimal results from FreeSurfer's skullstripping algorithm,
even after iteratively
Thanks Martin and Nick,
We have a number of subjects with single time points too, so I think 5.2 is the
best way to go.
Is there a way to specify which subjects have data at what time points. For
example, if one subject has data at Time 1 and Time 3, and another has data at
Time 2 and Time
Hi Sean - This works on our redhat centos 4 and centos 6. I can dig around
some more, but it'll have to wait for Monday b/c I'll be out of the office
the next couple of days.
As for your other question, the symlink part has been moved to the -prep
step, specifically to make it easier to then
Can you send the terminal output?
doug
On 03/06/2013 04:33 PM, Meryem Ayse Yucel wrote:
Hi all,
I am running:
preproc-sess -s sess01 -fsd bold -fwhm 5 -stc up -per-run
However at the end it did not create an output like fmcsm. I only have
fmc.nii, fmc.up.nii and fmcpr.up.nii. Am I doing
Hi Sarah
The linear mixed effects (LME) estimation procedure deals with missing data and
variable timing across subjects by specifying the time interval since baseline
for each scan. You will have a different number of rows for each subject in
your design matrix depending on how many time
Hi Sarah,
you deal with the time during post-processing (statistical analysis).
Yes, you have differently many rows for each subject.
Years could be time from baseline, or time from start of study (e.g.
start of drug treatment). It may be the same, but if some subjects are
missing the baseline
Dear Freesurfer Team,
when I am trying to set control points in tkmedit (FS 5.1 or 4.5) or to see
control points in Freeview (FS 5.1), I run into a strange problem when I
connect to our server through X11.
Namely, I cannot see the control points, although they are being set when I
place them (they
I would check the mri_em_register registrations of the step that
immediately precedes mri_watershed (and produces
talairach_with_skull.lta). We found that most of the variability and
failures occurred in this step, and mri_watershed itself is a very robust
brain extraction algorithm when it is
Thanks very much!
From: Martin Reuter [mreu...@nmr.mgh.harvard.edu]
Sent: Thursday, 7 March 2013 10:22 AM
To: Sarah Whittle
Cc: Nick Schmansky; freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] Longitudinal analysis of one timepoint
Hi Sarah,
you
The new Freesurfer has an optional flag to adjust NU intensity correction
parameters for images acquired on 3T scanners. There exists also a flag
for MPRage sequences.
I use 3T MPRages. What is the recommended use in this case?
Thanks
Josh
___
Josh,
The new -3T flag affects the nu correction stage, and specifies a 3T-based
target for the talairach alignment, and the existing -mprage flag affects
mri_normalize and mri_segment, so you can use both.
Nick
The new Freesurfer has an optional flag to adjust NU intensity correction
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