hello, experts
I have some question.
I want to use analyze format instead of DICOM file.
So, i type this sentence
recon-all -i /usr/local/freesurfer/subjects/test_han/I0071579.hdr -i
/usr/local/freesurfer/subjects/test_han/I0071579.img -all -s han001
and then error occured....
ERROR: cannot determine file type for
/usr/local/freesurfer/subjects/test_han/I0071579.hdr
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 han001 exited with ERRORS at Wed Sep 16 06:35:02 PDT 2015
For more details, see the log file
/usr/local/freesurfer/subjects/test_han/han001/scripts/recon-all.log
To report a problem, see
http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
How can i to do using analyze format?
2015-08-27 23:55 GMT+09:00 Douglas N Greve <gr...@nmr.mgh.harvard.edu>:
Specify something for --seg. It just needs to be a surface
overlay of
the same size as the input.
On 08/27/2015 01:49 AM, A-reum Min wrote:
> Hello doug
>
> i enter the ' mri_segstats --i y.mgh --vox 33 0 0 --avgwf
out.dat'
> then, error occured --> ERROR: must specify a segmentation
volume
>
>
> 2015-08-27 12:50 GMT+09:00 Douglas Greve
<gr...@nmr.mgh.harvard.edu
> <mailto:gr...@nmr.mgh.harvard.edu>>:
>
> don't use "vertexno", just put the vertex number, eg,
--vox 33 0 0
>
>
> On 8/26/15 9:22 PM, A-reum Min wrote:
>> Hello developer,
>>
>> I have some question to you.
>>
>> How can i get the significant vertices value using Qdec
result?
>>
>> When i enter the 'mri_segstats --i y.mgh --vox vertexno
33 0 0
>> --avgwf out.dat', then error ouccured --> ERROR : Option
out.dat
>> unknown.
>>
>> So, i enter the 'mri_segstats --i y.mgh --vox vertexno 33
0 0
>> --avgwf out.dat', then error occured --> ERROR : Option 0
unkown.
>>
>> How can i fix it?
>>
>>
>>
>>
>>
>>
>>
>> 2015-08-25 23:41 GMT+09:00 Douglas Greve
>> <gr...@nmr.mgh.harvard.edu
<mailto:gr...@nmr.mgh.harvard.edu>>:
>>
>>
>>
>> On 8/25/15 9:35 AM, A-reum Min wrote:
>>> Hello developers
>>>
>>> I have some question to you.
>>>
>>> 1.In fig.png, how many vertices were composed of
cluster at
>>> least?
>> I'm not sure what you mean. it does not look like
there are
>> any clusters there
>>>
>>> 2. How to change Area Threshold(fig.png)?
>> The area is controlled by the clusterwise threshold
(--cwp)
>> to mri_glmfit-sim
>>>
>>> 3. How to change CSD thresh(fig.png)?
>> That is controlled by the threshold when specifying
"--cache
>> threshold sign" to mri_glmfit-sim
>>>
>>> 4. What is the difference between two words(Area
Threshold,
>>> CSD thresh)?
>> One is the cluster-pvalue and the other is the
>> cluster-forming thershold
>>>
>>> 5. What is the exactly mean two words(Area
Threshold, CSD
>>> thresh)?
>> See above
>>
>>>
>>> Thank you
>>>
>>> 2015-08-12 23:23 GMT+09:00 Douglas N Greve
>>> <gr...@nmr.mgh.harvard.edu
<mailto:gr...@nmr.mgh.harvard.edu>>:
>>>
>>>
>>>
>>> On 08/10/2015 10:06 PM, A-reum Min wrote:
>>> > HI expert !
>>> >
>>> > My name is Areum. I have some question to you.
>>> >
>>> > 1. Does FreeSurfer offer a effect size? if
that offer,
>>> how can i use
>>> > effect size?
>>> >
>>> If you're doing a group analysis, you can
compute
>>> fscalc glmdir/contrast/gamma.mgh div
glmdir/rstd.mgh -o
>>> glmdir/contrast/effectsize.mgh
>>> >
>>> > 2. I was wondering about the stats.dat file in
>>> stats_table (in Qdec
>>> > folder).
>>> >
>>> > Stats.dat file’s value mean that each area’s
average
>>> (include whole
>>> > vertex) or each
>>> >
>>> > area’s average (only significant vertex)?
>>> >
>>> what stats.dat? if subject/stats/lh.aparc.stats,
then
>>> the area is the
>>> total area for the ROI
>>> >
>>> > 3. Can I get whole vertex value or significant
vertex
>>> value? Because,
>>> > I want to
>>> >
>>> > compare two groups correlation using SPSS. In
>>> addition, I want to compare
>>> >
>>> > thickness, volume and surface area correlation
within
>>> the one group
>>> > using SPSS.
>>> >
>>> You can extract a given vertex with
>>> mri_segstats --i y.mgh --crs vertexno 0 0
--avgwf
>>> vertexno.dat
>>> vertexno.dat will be a text file with number of
rows
>>> equalt to thge
>>> number of subjects where the value is the data
from the
>>> given (0-based)
>>> vertex no. y.mgh is the input to mri_glmfit
>>> >
>>> > 4. I currently use the default cluster
>>> size(significant area threshold
>>> > is 0mm^2). So, I
>>> >
>>> > want to control cluster size larger than
default
>>> cluster size. How can
>>> > I control the
>>> >
>>> > cluster size?
>>> >
>>> I don't know what you mean.
>>> >
>>> > 5. In FreeSurfer manual, GLM and Qdec have a
same
>>> results. But when I
>>> > use the
>>> >
>>> > both(GLM, Qdec) group analysis program results
are not
>>> same. What is
>>> > differences
>>> >
>>> > between two analysis program? How can I get
same
>>> result while GLM and
>>> > Qdec?
>>> >
>>> No way to know unless you tell us the specifics
of what
>>> you did
>>> >
>>> > 6. How can I get surface area and volume using
>>> GLM(group analysis
>>> > program)?
>>> >
>>> surface area and volume are outputs of
recon-all, not glm
>>> >
>>> >
>>> > plz reply to me
>>> >
>>> >
>>> > 2015-08-10 21:35 GMT+09:00 A-reum Min
>>> <naniy...@gmail.com <mailto:naniy...@gmail.com>
>>> > <mailto:naniy...@gmail.com
<mailto:naniy...@gmail.com>>>:
>>> >
>>> > Hello developer~
>>> >
>>> > I have some questions to you.
>>> >
>>> > 1. Does FreeSurfer offer a effect size? if that
>>> offer, how can i
>>> > use effect size?
>>> >
>>> > 2. I was wondering about the stats.dat file in
>>> stats_table (in
>>> > Qdec folder).
>>> >
>>> > Stats.dat file’s value mean that each area’s
>>> average (include
>>> > whole vertex) or each
>>> >
>>> > area’s average (only significant vertex)?
>>> >
>>> > 3. Can I get whole vertex value or significant
>>> vertex value?
>>> > Because, I want to
>>> >
>>> > compare two groups correlation using SPSS. In
>>> addition, I want to
>>> > compare
>>> >
>>> > thickness, volume and surface area correlation
>>> within the one
>>> > group using SPSS.
>>> >
>>> > 4. I currently use the default cluster
>>> size(significant area
>>> > threshold is 0mm^2). So, I
>>> >
>>> > want to control cluster size larger than default
>>> cluster size. How
>>> > can I control the
>>> >
>>> > cluster size?
>>> >
>>> > 5. In FreeSurfer manual, GLM and Qdec have a
same
>>> results. But
>>> > when I use the
>>> >
>>> > both(GLM, Qdec) group analysis program results
are
>>> not same. What
>>> > is differences
>>> >
>>> > between two analysis program? How can I get same
>>> result while GLM
>>> > and Qdec?
>>> >
>>> > 6. How can I get surface area and volume using
>>> GLM(group analysis
>>> > program)?
>>> >
>>> >
>>> > thanks for your help
>>> >
>>> >
>>> > 2015-07-27 14:28 GMT+09:00 A-reum Min
>>> <naniy...@gmail.com <mailto:naniy...@gmail.com>
>>> > <mailto:naniy...@gmail.com
>>> <mailto:naniy...@gmail.com>>>:
>>> >
>>> > Hello bruce
>>> >
>>> > I solve this problem(12.png)
>>> >
>>> > Thank you
>>> >
>>> > 2015-07-27 13:03 GMT+09:00 dgw
>>> <dgwake...@gmail.com <mailto:dgwake...@gmail.com>
>>> > <mailto:dgwake...@gmail.com
>>> <mailto:dgwake...@gmail.com>>>:
>>> >
>>> > Hi A-reum,
>>> >
>>> > I think you may be able to get a faster
>>> response if you
>>> > include some
>>> > details about your setup: I would start
>>> with the following:
>>> >
>>> >
http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
>>> > and run bugr.
>>> >
>>> > hth
>>> > D
>>> >
>>> > On 7/26/15 5:17 PM, A-reum Min wrote:
>>> > > Hi, Bruce
>>> > >
>>> > > When i use a Qdec, this
message(12.png)
>>> show up..
>>> > > How can i solve this problem?
>>> > >
>>> > > 2015-07-23 22:57 GMT+09:00 Bruce
Fischl
>>> > <fis...@nmr.mgh.harvard.edu
>>> <mailto:fis...@nmr.mgh.harvard.edu>
>>> > <mailto:fis...@nmr.mgh.harvard.edu
>>> <mailto:fis...@nmr.mgh.harvard.edu>>
>>> > > <mailto:fis...@nmr.mgh.harvard.edu
>>> <mailto:fis...@nmr.mgh.harvard.edu>
>>> > <mailto:fis...@nmr.mgh.harvard.edu
>>> <mailto:fis...@nmr.mgh.harvard.edu>>>>:
>>> > >
>>> > > 1. No, each subject has a
different
>>> #. You can map
>>> > to fsaverage
>>> > > (this is what -qcache does if you
>>> specify it for
>>> > recon-all), then
>>> > > they will have the same #.
>>> > >
>>> > > 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
>>> <mailto:naniy...@gmail.com> <mailto:naniy...@gmail.com
>>> <mailto:naniy...@gmail.com>>
>>> > > <mailto:naniy...@gmail.com
>>> <mailto:naniy...@gmail.com>
>>> > <mailto:naniy...@gmail.com
<mailto: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
>>> <mailto:naniy...@gmail.com> <mailto:naniy...@gmail.com
>>> <mailto:naniy...@gmail.com>>
>>> > > <mailto:naniy...@gmail.com
>>> <mailto:naniy...@gmail.com>
>>> > <mailto:naniy...@gmail.com
<mailto: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
>>> <mailto:fis...@nmr.mgh.harvard.edu>
>>> > <mailto:fis...@nmr.mgh.harvard.edu
>>> <mailto:fis...@nmr.mgh.harvard.edu>>
>>> > <mailto:fis...@nmr.mgh.harvard.edu
>>> <mailto:fis...@nmr.mgh.harvard.edu>
>>> > <mailto:fis...@nmr.mgh.harvard.edu
>>> <mailto: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
>>> <mailto:fis...@nmr.mgh.harvard.edu>
>>> > <mailto:fis...@nmr.mgh.harvard.edu
>>> <mailto:fis...@nmr.mgh.harvard.edu>>
>>> > > <mailto:fis...@nmr.mgh.harvard.edu
>>> <mailto:fis...@nmr.mgh.harvard.edu>
>>> > <mailto:fis...@nmr.mgh.harvard.edu
>>> <mailto: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_binarie
s/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
>>> <mailto:fis...@nmr.mgh.harvard.edu>
>>> > <mailto:fis...@nmr.mgh.harvard.edu
>>> <mailto:fis...@nmr.mgh.harvard.edu>>
>>> > > <mailto:fis...@nmr.mgh.harvard.edu
>>> <mailto:fis...@nmr.mgh.harvard.edu>
>>> > <mailto:fis...@nmr.mgh.harvard.edu
>>> <mailto: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
>>> <mailto:naniy...@gmail.com>
>>> > <mailto:naniy...@gmail.com
>>> <mailto:naniy...@gmail.com>>
<mailto:naniy...@gmail.com
>>> <mailto:naniy...@gmail.com>
>>> > <mailto:naniy...@gmail.com
>>> <mailto: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
>>> <mailto:zkauf...@nmr.mgh.harvard.edu>
>>> > <mailto:zkauf...@nmr.mgh.harvard.edu
>>> <mailto:zkauf...@nmr.mgh.harvard.edu>>
>>> > > <mailto:zkauf...@nmr.mgh.harvard.edu
>>> <mailto:zkauf...@nmr.mgh.harvard.edu>
>>> > <mailto:zkauf...@nmr.mgh.harvard.edu
>>> <mailto: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
>>> <mailto:Freesurfer@nmr.mgh.harvard.edu>
>>> > <mailto:Freesurfer@nmr.mgh.harvard.edu
>>> <mailto:Freesurfer@nmr.mgh.harvard.edu>>
>>> > >
<mailto:Freesurfer@nmr.mgh.harvard.edu
>>> <mailto:Freesurfer@nmr.mgh.harvard.edu>
>>> > <mailto:Freesurfer@nmr.mgh.harvard.edu
>>> <mailto:Freesurfer@nmr.mgh.harvard.edu>>>
>>> > > >
>>> > >
>>> > >
>>> > >
>>>
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>> > >
>>> > >
>>> > >
>>> > >
>>> _______________________________________________
>>> > > Freesurfer
>>> > > mailing list
>>> > >
>>> > > Freesurfer@nmr.mgh.harvard.edu
>>> <mailto:Freesurfer@nmr.mgh.harvard.edu>
>>> > <mailto:Freesurfer@nmr.mgh.harvard.edu
>>> <mailto:Freesurfer@nmr.mgh.harvard.edu>>
>>> > >
<mailto:Freesurfer@nmr.mgh.harvard.edu
>>> <mailto:Freesurfer@nmr.mgh.harvard.edu>
>>> > <mailto:Freesurfer@nmr.mgh.harvard.edu
>>> <mailto: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.
>>> > >
>>> > >
>>> > >
>>> > >
>>> > >
>>> > >
>>> > >
>>> _______________________________________________
>>> > > Freesurfer mailing list
>>> > >
>>> > > Freesurfer@nmr.mgh.harvard.edu
>>> <mailto:Freesurfer@nmr.mgh.harvard.edu>
>>> > <mailto:Freesurfer@nmr.mgh.harvard.edu
>>> <mailto:Freesurfer@nmr.mgh.harvard.edu>>
>>> > >
<mailto:Freesurfer@nmr.mgh.harvard.edu
>>> <mailto:Freesurfer@nmr.mgh.harvard.edu>
>>> > <mailto:Freesurfer@nmr.mgh.harvard.edu
>>> <mailto: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.
>>> > >
>>> > >
>>> > >
>>> > >
>>> > >
>>> _______________________________________________
>>> > > Freesurfer mailing list
>>> > > Freesurfer@nmr.mgh.harvard.edu
>>> <mailto:Freesurfer@nmr.mgh.harvard.edu>
>>> > <mailto:Freesurfer@nmr.mgh.harvard.edu
>>> <mailto:Freesurfer@nmr.mgh.harvard.edu>>
>>> > >
<mailto:Freesurfer@nmr.mgh.harvard.edu
>>> <mailto:Freesurfer@nmr.mgh.harvard.edu>
>>> > <mailto:Freesurfer@nmr.mgh.harvard.edu
>>> <mailto: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.
>>> > >
>>> > >
>>> > >
>>> > >
>>> > >
>>> _______________________________________________
>>> > > Freesurfer mailing list
>>> > > Freesurfer@nmr.mgh.harvard.edu
>>> <mailto:Freesurfer@nmr.mgh.harvard.edu>
>>> > <mailto:Freesurfer@nmr.mgh.harvard.edu
>>> <mailto:Freesurfer@nmr.mgh.harvard.edu>>
>>> > >
<mailto:Freesurfer@nmr.mgh.harvard.edu
>>> <mailto:Freesurfer@nmr.mgh.harvard.edu>
>>> > <mailto:Freesurfer@nmr.mgh.harvard.edu
>>> <mailto: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.
>>> > >
>>> > >
>>> > >
>>> > >
>>> > >
>>> > >
>>> > >
>>> _______________________________________________
>>> > > Freesurfer mailing list
>>> > > Freesurfer@nmr.mgh.harvard.edu
>>> <mailto:Freesurfer@nmr.mgh.harvard.edu>
>>> > <mailto:Freesurfer@nmr.mgh.harvard.edu
>>> <mailto:Freesurfer@nmr.mgh.harvard.edu>>
>>> > <mailto:Freesurfer@nmr.mgh.harvard.edu
>>> <mailto:Freesurfer@nmr.mgh.harvard.edu>
>>> > <mailto:Freesurfer@nmr.mgh.harvard.edu
>>> <mailto: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.
>>> > >
>>> > >
>>> > >
>>> > >
>>> > >
>>> _______________________________________________
>>> > > Freesurfer mailing list
>>> > > Freesurfer@nmr.mgh.harvard.edu
>>> <mailto:Freesurfer@nmr.mgh.harvard.edu>
>>> > <mailto:Freesurfer@nmr.mgh.harvard.edu
>>> <mailto: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.
>>> > >
>>> > _______________________________________________
>>> > Freesurfer mailing list
>>> > Freesurfer@nmr.mgh.harvard.edu
>>> <mailto:Freesurfer@nmr.mgh.harvard.edu>
>>> > <mailto:Freesurfer@nmr.mgh.harvard.edu
>>> <mailto:Freesurfer@nmr.mgh.harvard.edu>>
>>> >
>>>
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>> >
>>> >
>>> >
>>> >
>>> >
>>> >
>>> > _______________________________________________
>>> > Freesurfer mailing list
>>> > Freesurfer@nmr.mgh.harvard.edu
>>> <mailto:Freesurfer@nmr.mgh.harvard.edu>
>>> >
>>>
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>>
>>> --
>>> Douglas N. Greve, Ph.D.
>>> MGH-NMR Center
>>> gr...@nmr.mgh.harvard.edu
<mailto:gr...@nmr.mgh.harvard.edu>
>>> Phone Number: 617-724-2358
>>> Fax: 617-726-7422
>>>
>>> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
>>>
<http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting>
>>> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
>>> www.nmr.mgh.harvard.edu/facility/filedrop/index.html
>>>
<http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html>
>>> Outgoing:
>>>
ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
>>>
>>> _______________________________________________
>>> Freesurfer mailing list
>>> Freesurfer@nmr.mgh.harvard.edu
>>> <mailto:Freesurfer@nmr.mgh.harvard.edu>
>>>
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>>
>>>
>>>
>>>
>>> _______________________________________________
>>> Freesurfer mailing list
>>> Freesurfer@nmr.mgh.harvard.edu
<mailto:Freesurfer@nmr.mgh.harvard.edu>
>>>
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>
>>
>> _______________________________________________
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu
>> <mailto: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.
>>
>>
>>
>>
>> _______________________________________________
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu
<mailto:Freesurfer@nmr.mgh.harvard.edu>
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
> _______________________________________________
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
<mailto: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.
>
>
>
>
> _______________________________________________
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
--
Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
www.nmr.mgh.harvard.edu/facility/filedrop/index.html
Outgoing:
ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
