Hi Ye,
can you cc the list so that others can help you? 787 would usually be too many files for an anatomical. Something on the order of 170-256 is more typical. If you visualize them the white matter should be bright, the gray matter darker and the CSF very dark
Bruce
On Wed, 26 Jun 2013, ye tian wrote:
Dear Bruce,
I just confirmed a few hours ago that I indeed have structural MRI data
though. I have attached an example of the last 787 files from my data below.
In fact, I tried to use only those to reconstruct my volumes and surfaces.
Do they serve as inputs to freesurfer?
Thank you very much!
Sincerely,
Ye
On Wed, Jun 26, 2013 at 5:04 PM, Bruce Fischl <fischl@nmr.mgh.harvard.edu>
wrote:
no, once they have been acquired you can't change anything. You
have to hope that they also acquired structural data in addition
to the functional data (which is quite common). You can't change
the way your images were formed posthoc...
On Wed, 26 Jun 2013, ye tian wrote:
Dear Bruce,
If I understand correctly, I should bring these
images back to the scanner
and change some settings. Am I right?
Sincerely,
Ye
On Wed, Jun 26, 2013 at 4:59 PM, Bruce Fischl
<fischl@nmr.mgh.harvard.edu>
wrote:
you need to know what different scan types
were acquired. The
ones you showed were the fMRI time-series and
designed to
hilight changes in blood oxygenation level,
which is an indirect
marker of changes in neural firing, not
anatomy
On Wed, 26 Jun 2013, ye tian wrote:
Dear Bruce,
I inherited the data from a previous
graduate
student. I sent out a message
to learn more information about the
scanner a few
days ago.
What information do I need to know about
the
scanner?
Thank you so much for your time and
effort!
Sincerely,
Ye
On Wed, Jun 26, 2013 at 4:41 PM, Bruce
Fischl
<fischl@nmr.mgh.harvard.edu>
wrote:
Hi Ye
you can't convert it, you have to
acquire it
that way. Where did
you get your data?
Bruce
On Wed, 26 Jun 2013, ye tian
wrote:
Dear Bruce,
Sorry for my lack of
knowledge. I looked
online, but
couldn't find how to
convert MRI data to
T1-weighted
anatomical. Would
you please shine some
light on it?
Thank you very much!
Sincerely,
Ye
On Wed, Jun 26, 2013 at 4:21
PM, Bruce
Fischl
<fischl@nmr.mgh.harvard.edu>
wrote:
Hi Ye
you need to give
recon-all a
T1-weighted
anatomical (e.g.
mprage, SPGR/FLASH,
etc...), not
the fMRI
data.
cheers
Bruce
On Wed, 26 Jun 2013,
ye tian
wrote:
Dear Bruce,
Recon-all exits
with the
following error
ERROR: input(s)
cannot have
multiple
frames!
$SUBJECTS_DIR/Barba50527_2/mri/orig/001.mgz has 439
frames
If I open
001.mgz using
freeview, I
obtain the image
in the
attachment saved
as freeview
001.mgz.png.
In order to make
sure that
my problem
does not come
from further
upstream, I
am including the
major steps
that I took
to get to
this error.
MAJOR STEPS
STEP0:
My inherited
data has names
BARBA50527.MR.MEDITATE_MEDITATION.#.#.year.month.day.#.#.#.#.#.IMA
where each # is
a string of
numbers.
STEP1:
The images can
be grouped
into five
categories,
according to the
numbers in
the names that
occupy the
positions of
the red #:
1.1-1.3,
2.1,
3.1-3.160,
4.1-4.439,
5.1-5.439
[1] Note: Images
from groups
4 & 5 are
very
different from
the images of
groups 1, 2 and
3. A link to
a youtube
video of all
the images can
be seen
in note[1].
STEP2:
recon-all -s
Barba50527_2
-i
/Path_to_data/BARBA50527.MR.MEDITATE_MEDITATION.4.1.2010.07.27.10.52.51
.437500.56148038.IMA
-i
/Path_to_data/BARBA50527.MR.MEDITATE_MEDITATION.5.1.2010.07.27.10.52.51
.437500.56148502.IMA
recon-all
completes without
error.
[2] Note: other
attempts
leads to
different errors.
See note [2] for
details.
STEP3:
recon-all -s
Barba50527_2
-autorecon1
Exits with the
error message
at the
beginning of the
email. The
number 439
seems to come
from the
number of files
in each
group.
USEFUL COMMENTS
http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg23764.html
I will do it for
001.mgz and
002.mgz and
will let
you know how it
goes.
QUESTIONS
1. Do I really
need to
manually parse
the sequence
of images? If
so, how?
2. I don't
really need to
mri_convert my
files into
other formats,
e.g.,
.dcm, do I?
3. Each file
from groups 4
and 5 have
multiple
images. Do I
need to cut
them
into sub-images,
each with
one brain?
Thank you very
much!
Sincerely,
Ye
NOTES:
Note [1]
A video of the
data can be
found at
http://www.youtube.com/watch?v=W8ZFGvGvHVc&list=UUfGdQq3j1gqPAc4z6Spmu2g
On the top left
corner:
the white text
is:
current frame
number / total
frame number
the yellow text
is: the
name of the
frame
Note[2]
recon-all -s
Barba50527_2
-i
/Path_to_data/BARBA50527.MR.MEDITATE_MEDITATION.1.1.2010.07.27.10.52.51
.437500.56141898.IMA
Completes
without error
recon-all -s
Barba50527_2
-autorecon1
Warning: only
one run found
Error:
MRIsample(): source
matrix has
zero
determinant;
matrix is:
EOF
econ-all -s
Barba50527_2
-i
/Path_to_data/BARBA50527.MR.MEDITATE_MEDITATION.1.1.2010.07.27.10.52.51
.437500.56141898.IMA
-i
/Path_to_data/BARBA50527.MR.MEDITATE_MEDITATION.2.1.2010.07.27.10.52.51
.437500.56148502.IMA
-i
/Path_to_data/BARBA50527.MR.MEDITATE_MEDITATION.3.1.2010.07.27.10.52.51
.437500.56148502.IMA
-i
/Path_to_data/BARBA50527.MR.MEDITATE_MEDITATION.4.1.2010.07.27.10.52.51
.437500.56148038.IMA
-i
/Path_to_data/BARBA50527.MR.MEDITATE_MEDITATION.5.1.2010.07.27.10.52.51
.437500.56148502.IMA
error.log:
matrix
dimensionality
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