Hi,
When I try to register my functional data to anatomical data using
reg-feat2anat --feat feat_directory --subject subject_name
I get the following error message
ERROR: could not read ///example_func.nii.gz as 24
What does this mean? And how can I fix this?
Best wishes
Carolyn
__
Thanks Doug,
I have tried your suggestion and set the command make_average_subject running
again. I has been going for several hours but there is no visible
change/activity on the console, is this unusual?.
Also, there are only 13 subjects, how long would you expect this process to
take
it should not be taking that long. It must be hanging somewhere. Try
re-running it with --debug as the first option. It will print out a
bunch of stuff to the screen, but you should be able to see where it
hangs (if it does).
doug
Furlong, Carolyn wrote:
Thanks Doug,
I have tried your sug
hi,I have some question to ask,
First,now I want to add four parts of the occipital lobe's gray matter
volume(Lateral Occipital,Lingual,Cuneus,Pericalcarine) to evaluate occipital
lobe development,can I do like this?
second, I also want to use the occipital lobe's cortical thickness to
eva
Dear All
I meet a problem when I run the command
mris_wm_volume
to calculate the white matter volume for each hemisphere.
The error message is coplied here
>> mris_wm_volume
>> mris_wm_volume: error while loading shared libraries: libstdc++.so.6:
cannot open shared object file: No such file o
Rhuang,
I'm guessing that you're using our Centos freesurfer distribution (type:
cat $FREESURFER_HOME/build-stamp.txt to find out). You'll want to use
our RedHat 9 freesurfer distribution with Suse9.3.
Nick
On Mon, 2007-05-14 at 17:05 +0200, Ruiwang Huang wrote:
> Dear All
>
> I meet a prob
Dear Nick
Many thanks for your message.
Here is the output after my typing
>> cat $FREESURFER_HOME/build-stamp.txt
>> freesurfer-Linux-rh9-stable-pub-v3.0.3
Do I need update the freesurfer on my PC?
Ruiwang
On Monday 14 May 2007 17:26, you wrote:
> Rhuang,
>
> I'm guessing that you're u
This is the MeasurementName in the .fsgdf file.
On Sun, 2007-05-13 at 23:03 +0100, Morgan Hough wrote:
> Once I have defined a label in tksurfer and I select *Tools -> *Group*
> -> Graph Marked Vertices Avg to open a scatterplot window, how do I
> change the y axis label from the default "extern
This suggests that the number of values in the .mgh file is different
than the number of vertices in the surface. Did you regenerate the
surface after generating the .mgh file?
On Sun, 2007-05-13 at 15:29 -0400, Catherine Hartley wrote:
> Hi,
>
> I'm having a problem with the development version
you can use mri_info on the .mgh file to check (and mris_info on the
surface)
On Mon, 14 May 2007, Kevin Teich wrote:
This suggests that the number of values in the .mgh file is different
than the number of vertices in the surface. Did you regenerate the
surface after generating the .mgh file?
Ruiwang,
It looks like you are already running what I thought would be the
correct version (rh9 is redhat 9). Can you send me the output of this
command?
ldd `which mris_wm_volume`
Nick
On Mon, 2007-05-14 at 17:43 +0200, Ruiwang Huang wrote:
> Dear Nick
>
> Many thanks for your message.
>
Dear Nick
Thanks a lot. Here is the output of ' ldd `which mris_wm_volume`
linux-gate.so.1 => (0xe000)
libjpeg.so.62 => /usr/lib/libjpeg.so.62 (0x40019000)
libtiff.so.3 => /usr/lib/libtiff.so.3 (0x40038000)
libz.so.1 => /lib/libz.so.1 (0x40088000)
lib
Rhuang,
I just realized that mris_wm_volume is not part of the stable release,
so you must have gotten the 'dev' release of it at some point in time,
and probably got the Centos build of mris_wm_volume (which uses libstdc+
+.so.6).
So I have posted the 'rh9' build of mris_wm_volume here:
ftp://s
Dear Nick
Thanks a lot. Here is the output of ' ldd `which mris_wm_volume`
linux-gate.so.1 => (0xe000)
libjpeg.so.62 => /usr/lib/libjpeg.so.62 (0x40019000)
libtiff.so.3 => /usr/lib/libtiff.so.3 (0x40038000)
libz.so.1 => /lib/libz.so.1 (0x40088000)
lib
can you send the log file?
Furlong, Carolyn wrote:
Hi,
When I try to register my functional data to anatomical data using
reg-feat2anat --feat feat_directory --subject subject_name
I get the following error message
ERROR: could not read ///example_func.nii.gz as 24
What does this mean? And
Dear Nick
Thanks a lot. It works.
Have a very nice day
Rhuang
On Monday 14 May 2007 18:23, you wrote:
> Rhuang,
>
> I just realized that mris_wm_volume is not part of the stable release,
> so you must have gotten the 'dev' release of it at some point in time,
> and probably got the Centos build
Hi,
I was able to use surf-sess command (modified in our group) to take pictures
(rgb) of the brain; however, several days ago, I was kept getting errors (even
errors with commands that worked fine before). it keep saying tksurfer.new:
Command not found., then quit. Would you help me out?
Mach
Hi,
I can't seem to get the syntax right for mri_info or mris_info to
work, but i did not regenerate the surfaces after generating the .mgh
file, so the number of vertices should be the same. Any other
possibilities? Should I just rerun the mri_glmfit that generated the
sig.mgh file?
Hi Cate,
there's not much syntax to get write. They take either a volume or a
surface file, with the full path.
Bruce
On Mon, 14 May 2007, Catherine Hartley
wrote:
Hi,
I can't seem to get the syntax right for mri_info or mris_info to work, but i
did not regenerate the surfaces after gen
Hi, I just ran mri_aparc2aseg on a group of subjects, and a couple of them
failed to produce an output file despite lacking any apparent error messages.
The command I ran was (with subj name replaced):
mri_aparc2aseg --s ## --o aparc_cor+aseg.mgz --ribbon --annot final
These are subjects wh
Okay, never mind. It turned out there were a couple nodes without labels
that'd been screwing things up.
Thanks,
-Aaron-
-Original Message-
From: Goldman, Aaron (NIH/NIMH) [C]
Sent: Monday, May 14, 2007 4:27 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] Failure of mri_apar
Hi Doug & others,
I am trying to use reg-feat2anat as it is described on the FSL web page:
http://www.fmrib.ox.ac.uk/fsl/freesurfer/index.html
However, I always seem t get a very bad registration. I tried using different
values for --maxangle --cost mutualinfo --bins, but maintained
can you send the information described in
surfer.nmr.mgh.harvard.edu/fswiki/BugReporting?
doug
[EMAIL PROTECTED] wrote:
Hi Doug & others,
I am trying to use reg-feat2anat as it is described on the FSL web page:
http://www.fmrib.ox.ac.uk/fsl/freesurfer/index.html
However, I always seem t
I'm interested in parsing aseg.mgz into separate binary mask files for
each aseg label. Is this possible? The closest topic I found was located
at the following URL:
http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/MapSegmentationsToFu
nctionalSpace
2.0 Creating binary masks
The segmenta
Hi Jenifer,
yes, you could do that for each label defined in the aseg.stats file (or
the FreeSurferColorLUT.txt, but that will contain labels that don't exist
in that volume).
what else are you trying to do that you need help with?
Bruce
On Mon, 14 May 2007, Juranek, Jenifer wrote:
I'm i
You can also use mri_binarize (it takes any format as input). We don't
have anything that will automatically generate a separate volume for
each label.
Bruce Fischl wrote:
Hi Jenifer,
yes, you could do that for each label defined in the aseg.stats file
(or the FreeSurferColorLUT.txt, but th
On May 14, 2007, at 6:28 PM, Juranek, Jenifer wrote:
I’m interested in parsing aseg.mgz into separate binary mask files
for each aseg label. Is this possible? The closest topic I found
was located at the following URL:
...
I checked the following for additional help…but still need some help
Dear Freesurfer users
Is there any rule of thumb with respect to the size of topological defects?
Sometimes large defects (involving more than 1 or 2 vertices) occur
and the topological correction for these defects runs more than 48 hours and
sometimes failed to correct them. How long shou
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