hey mike,
take a look at:
ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mc-bbr
cheers,
satra
On Mon, Dec 19, 2011 at 2:04 AM, Michael Waskom mwas...@stanford.eduwrote:
Hi Doug,
Is it possible to use the bbregister parameters to resample a functional
image such that it
Hello,
I was hoping someone may know the answer to this. I am using freesurfer
version 5.1.
Using this command unpacksdcmdir -src DICOMS/$1_dicom -targ $1
-fsfast -scanonly $1/scan_$1.txt
where scan_name.txt lists the scan names used in the protocol and $1 is
the subject's ID. I keep getting
hi eveyone
i ru the command recon-all of the 5.1 version of freesurfer
on some subjects using the following arguments : recon-all -i database/ctr/ctr1
-subjid ctr1. it created a directory ctr1 in my SUBJECTS_DIR directory with all
the sub-directories inside, but with no
-i needs to point to the first dicom (or whichever format your scanner
data is in) in the series.
Allison
On Mon, 19 Dec 2011, LAOUCHEDI MAKHLOUF wrote:
hi eveyone
i ru the command recon-all of the 5.1 version of
freesurfer on some subjects using the following arguments :
What scanner did these come from? That tag is the pixel spacing. If that
is not there, then something is really wrong.
doug
dmill...@bu.edu wrote:
Hello,
I was hoping someone may know the answer to this. I am using freesurfer
version 5.1.
Using this command unpacksdcmdir -src
That may or may not do what you want. I think that version keeps the
functional data in the functional space. It would be better to register
each TR to the anat, then simply sample each TR to the anatomical space
(volume or surface) rather than going back into functional space.
doug
Satrajit
Hello,
Recalling these emails:
The methods are somewhat different. For the value in the aseg.stats
table, the method is to compute the total volume inside the pial surface
and subtract the total volume inside the white surface. For
mris_anatomical_stats, the method is to compute the thickness
As you noted, the surfaces bisect the hippocampus and amygdala, so the
small amount of tissue outside the pial surface is not included in the
surface based measures of total GM volume. Compared to the overall
variation in brain size, this should be inconsequential.
cheers,
-MH
On Mon,
Hi,
running bedpostx directly from the command line appears to have worked
bedpostx dmri
Multiple subjects now have the following files and directories within
their bedpostx directory:
bvals mean_ph2samples.nii.gz
bvecs mean_th1samples.nii.gz
Hi all,
We've been trying to use FsFast for functional connectivity analysis using
the left hippocampus as the seed (isolated from aseg). We used the
following command to make the analysis:
mkanalysis-sess -fwhm 0 -fsd bold -mcextreg -polyfit 2 -TR 2.6 -analysis
lhippo_fcfsfast-analysis -nuisreg
Hi Maya, the problem is that the wm.dat file, by default, only has one
column (just the mean of the WM). It is possible to have the top N
principle components in the wm.dat file, but this needs to be set up
when you configure the WM fcseed (it does not really help much). The
same goes for
Hi Satra and Doug,
That script is good to know about. But, from what I can tell, it looks
like it will output a timeseries in the same space as the original template
(each frame gets transformed with a combination of the matrix specifying
its registration to the anatomical and the inverse of the
It will output a register.dat for each frame. You can extract the frame
from the time series (mri_convert --frame ), apply the reg with
mri_vol2vol or mri_vol2surf, then concatenate the results back into a
time series (mri_concat)
doug
Michael Waskom wrote:
Hi Satra and Doug,
That script is
Sorry, I guess it's not clear what I'm hoping to do.
Because I'm going to use this data for mvpa, I don't want to resample into
1x1x1 voxels or go onto the surface. But I have multiple runs that I want
to use, so I need there to be a voxel-to-brain correspondence across the
different runs.
hi michael,
so for each frame of every session you get a bbreg file and the script ends
up aligning the volumes to some reference. all you need to do is propagate
that reference across your sessions. you might for example want this to be
the middle volume of your entire experiment.
cheers,
OK, cool, I'll look into this for the future.
But back to my original question. If I already have data preprocessed with
several runs, each run motion-corrected within-session, and an affine
registration from each run's space to the anatomical determined by
bbregister, is there any way to use
Hi Andreia, I don't think this is a problem for the GM volume (ie, parts
of the amyg or hippo getting counted twice). The thickness should be 0
in those areas, so they should not contribute to GM volume. The
computation of the WM volume is done in a different way (still surface
based) but
Hi Freesurfers,
We are trying to do a resting-state functional connectivity analysis using
freesurfer. Instead of using the aparc+aseg segmentations as seeds, we
would like to use a subject-specific surface label that we have defined a
priori as the seed region.
In the fcseed-config step, what
Hi Donald,
With regards to longitudinal analysis, I am not as familiar with the
issue you are mentioning. Perhaps some other person on the list can
comment.
With regards to your other comments, I think your reading is correct.
However, I should mention that the reported accuracies *really*
ah in that case you need to multiply the affine stored in one session's
bbreg with the inverse of the other bbreg from the target session and then
use mri_vol2vol with the composite transform. note: only nearest or
trilinear interp
cheers,
satra
On Tue, Dec 20, 2011 at 12:07 AM, Michael Waskom
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