2. What result data do you mean?
3. Yes, although I'll leave the details to Doug (since I don't remember how his cluster code works).
4. The significance doesn't depend on the cluster size unless you do multiple comparison corrections (and even then only if you do them a certain way)
cheers Bruce On Thu, 23 Jul 2015, A-reum Min wrote:
HELLO developer
I have some question to you..
1. Every patient is given to the same number of vertex?
2. When i use a Qdec, How can I get the subject result data?
3. Could i get the significant vertex’s number, extent of the
significant area and gray matter volume?
4. Is it significant blue color which how many connected vertex?
2015-05-29 2:03 GMT+09:00 A-reum Min <naniy...@gmail.com>:
hello developer~
reconstruction is well done, so i'm doing on 'qdec' step..
Actually, i don't know how to treat the Design menu exactly..
---------------------------------------------------------------------------
Discrete(fixed factors) : diagnosis
continuous (covariate) : age , Left-Lateral-Ventricle
---------------------------------------------------------------------------
which one click before analyze?
age range is 12years~24years/
all subjects are adolescent.
and no outlier in age range.. so.. age (continuous factor) does not
nasessart?
2015-05-29 1:19 GMT+09:00 A-reum Min <naniy...@gmail.com>:
hello developer~
reconstruction is well done, so i'm doing on 'qdec' step..
Actually, i don't know how to treat the Design menu exactly..
---------------------------------------------------------------------------
Discrete(fixed factors) : diagnosis
continuous (covariate) : age , Left-Lateral-Ventricle
---------------------------------------------------------------------------
which one click before analyze?
2015-04-05 21:41 GMT+09:00 Bruce Fischl
<fis...@nmr.mgh.harvard.edu>:
I'm glad it worked out
Bruce
On Sun, 5 Apr 2015, A-reum Min wrote:
Hello Bruce~
You're right.. my PISA dicom file header
is too short
so, freesurfer didn't read it.
Therefore I use another subjects dicom
file and then freesurfer read it!
thank you for u r adavice to me.
I really appreciate u
2015-04-05 7:08 GMT+09:00 Bruce Fischl
<fis...@nmr.mgh.harvard.edu>:
Hi A-reum
the problem is that newer versions
of scanner software compress
dicoms and the version of FS you
have doesn't know how to read
it. So you need to decompress them
before passing them to
recon-all
cheers
Bruce
On Sun, 5 Apr 2015, A-reum Min
wrote:
Hello developer~
Can you summarize what the
problem is?
==>
my problem is recon-all -i
didn't working...
so, if i type the recon-all
-i~then show up theses
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
ERROR: 32512, see
/tmp/root.tmp.decompressed.dcm.55srMV.dcmdjpeg.out
for
more details
Linux localhost.localdomain
2.6.32-504.el6.x86_64 #1
SMP Wed Oct 15 04:27:16
UTC 2014 x86_64 x86_64
x86_64 GNU/Linux
dcmdjpeg.fs: error while
loading shared libraries:
libijg8.so.3.6: cannot
open shared object file: No
such file or directory
+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
then, i click the
root.tmp.decompressed.dcm.55srMV.dcmdjpeg.out,
show
up
these
dcmdjpeg.fs: error while
loading shared libraries:
libijg8.so.3.6: cannot
open shared object file: No
such file or directory
Are you trying to read
compressed dicom?
==>
Am i trying to read
compressed dicom?
I send my 10071579.dicom(i
use this) to you,
using -i, convert the dicom
file to mgh file. i just
know that dicom file
convert to mgz format using
-i /my data path
Is it right..??
If so, Can you try running
dcmdjpeg on it to create
a new (uncompressed)
series and give that to
recon-all?
==> (actually, i didn't
understand your sentence
means perfectly..)
zeke
tomeaurl(ftp://surfer.nmr.mgh.harvard.edu//pub/dist/freesurfer/dev_binaries/c
en
t
os6_x86_64/dcmdjpeg.fs)
and then, replace my
existing
$FREESURFER_HOME/bin/dcmdjpeg.fs file.
Also, make sure it is set to
executable by typing
the following in a
terminal window:
$> chmod a+x
$FREESURFER_HOME/bin/dcmdjpeg.fs
2015-04-05 2:30 GMT+09:00
Bruce Fischl
<fis...@nmr.mgh.harvard.edu>:
Hi A-reum
sorry, I'm coming into
this late. Can you
summarize what the
problem is? Are you
trying to read compressed
dicom? If so, can
you try running
dcmdjpeg on it to create a new
(uncompressed)
series and give that
to recon-all?
cheers
Bruec
On Sat, 4 Apr 2015,
A-reum Min wrote:
Hello
developers..
i type the
recon-all -i~then show up
theses
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
ERROR: 32512,
see
/tmp/root.tmp.decompressed.dcm.55srMV.dcmdjpeg.out
for
more details
Linux
localhost.localdomain
2.6.32-504.el6.x86_64 #1
SMP Wed Oct 15
04:27:16
UTC 2014 x86_64
x86_64 x86_64 GNU/Linux
dcmdjpeg.fs:
error while loading shared
libraries:
libijg8.so.3.6:
cannot
open shared
object file: No such file or
directory
+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
error is occured
(a little differntly..)
then, i click
the
root.tmp.decompressed.dcm.55srMV.dcmdjpeg.out,
show
up
these
dcmdjpeg.fs:
error while loading shared
libraries:
libijg8.so.3.6:
cannot
open shared
object file: No such file or
directory
i'm so sorry..to
bother you..
2015-04-04 9:21
GMT+09:00 A-reum Min
<naniy...@gmail.com>:
hello
i type the
recon-all -i~
then show up
theses
+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
+++++++
ERROR: 32256,
see
/tmp/root.tmp.decompressed.dcm.XhbJG3.dcmdjpeg.out
for more details
Linux
localhost.localdomain
2.6.32-504.el6.x86_64 #1
SMP Wed Oct 15
04:27:16 UTC
2014 x86_64 x86_64 x86_64
GNU/Linux
+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
+++++++
the error is
occured (a little
differntly..)
then, i click
the
/tmp/root.tmp.decompressed.dcm.XhbJG3.dcmdjpeg.out,
show iuo these
sh:
/usr/local/freesurfer/bin/dcmdjpeg.fs:
/lib/ld-linux.so.2: bad ELF
interpreter: No
such file or directory
plz help me
2015-04-04 4:12
GMT+09:00
<zkauf...@nmr.mgh.harvard.edu>:
A-reum,
Please
download the following
file:
ftp://surfer.nmr.mgh.harvard.edu//pub/dist/freesurfer/dev_binaries/centos6_
x86_64/dcmdjpeg.fs
And
replace your existing
$FREESURFER_HOME/bin/dcmdjpeg.fs
file with
the
one from
the link above. Also,
make sure it is
set to
executable
by typing
the
following in a terminal
window:
$> chmod
a+x
$FREESURFER_HOME/bin/dcmdjpeg.fs
And then
try again.
-Zeke
> Hi
doug... recon-all dosen't
working..
>
> If i
type the recon-all -i~
> then,
error occured...
>
>++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
+
+
+
++
>
> JPEG
compressed, decompressing
> cd
/usr/local/freesurfer/subjects/PISA_FSPGR/1/subj01
>
dcmdjpeg.fs +te
/usr/local/freesurfer/subjects/PISA_FSPGR/1/I0071579.dcm
>
/tmp/root.tmp.decompressed.dcm.kBIYHL >&
>
/tmp/root.tmp.decompressed.dcm.kBIYHL.dcmdjpeg.out
> ERROR:
32512, see
/tmp/root.tmp.decompressed.dcm.kBIYHL.dcmdjpeg.out
for
> more
details
> Linux
localhost.localdomain
2.6.32-504.el6.x86_64 #1 SMP
Wed Oct 15
> 04:27:16
UTC 2014 x86_64 x86_64
x86_64
GNU/Linux
>
>
recon-all -s subj01 exited with
ERRORS at
Fri Apr 3
10:39:27
PDT 2015
>
> For more
details, see the log
file
>
/usr/local/freesurfer/subjects/PISA_FSPGR/1/subj01/scripts/recon-all.log
> To
report a problem, see
>
http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
>
>++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
+
+
+
+++
>
> I copy
the libdcmjpeg.so.3.6 and
paste in
FREESURFER_HOME/lib
> after
that type the setenv
LD_LIBRARY_PATH
$FREESURFER_HOME/lib
>
> but..
didn't working ..
>
> same
error occured -->
dcmdjpeg.fs: error
while loading
shared
libraries:
>
libdcmjpeg.so.3.6: cannot open
shared object
file: No
such file
or
>
directory
>
> and i
click the
root.tmp.decompressed.dcm.kBIYHL.dcmdjpeg.out
then show up
> these
>
>
dcmdjpeg.fs: error while loading
shared
libraries:
libdcmjpeg.so.3.6:
> cannot
open shared object file:
No such file
or
directory
>
> how can i to
do ㅜㅜ help me doug
>
_______________________________________________
> Freesurfer
mailing list
>
Freesurfer@nmr.mgh.harvard.edu
>
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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The information in this e-mail is
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it is
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e-mail
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contact the Partners Compliance
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http://www.partners.org/complianceline .
If the e-mail was sent to you
in error
but does not contain patient
information, please contact the sender
and properly
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_______________________________________________
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https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the
person to whom it is
addressed. If you believe this e-mail was sent to you in
error and the e-mail
contains patient information, please contact the Partners
Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was
sent to you in error
but does not contain patient information, please contact
the sender and properly
dispose of the e-mail.
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
