On 11/23/15 10:18 PM, Guido Orlando Pascariello wrote:
Hi FS Expert
I have just looked for this subject a long the list but I haven't
found anything about.
I have been working with FreeSurfer and I could get some segmentation
from my T1 data. I used 'mri_segstats' to quantify volume of som
Other than fsaverage, are there any other files that need to be linked for
recon-all to work?
Thanks
On Mon, Nov 23, 2015 at 4:57 PM, Bruce Fischl
wrote:
> Hi Eric
> No, you can just symlink fsaverage and such
> Cheers
> Bruce
>
> > On Nov 23, 2015, at 9:40 PM, Eric Cunningham wrote:
> >
> > G
Hi FS Expert
I have just looked for this subject a long the list but I haven't found
anything about.
I have been working with FreeSurfer and I could get some segmentation from
my T1 data. I used 'mri_segstats' to quantify volume of some subcortical
region. Also I want to get intensity statistics
P.s. You should use our filedrop which you can find on our website
> On Nov 23, 2015, at 9:43 PM, Annelinde Vandenbroucke
> wrote:
>
> Hi Bruce,
>
> Thank you very much for your quick response.
> Yes I mean that wm.mgz underestimates true white matter. Values are between
> 95 and 108 where it
But is the wm.mgz 'off' (less than 5) there? If the wm.mgz is 95 or something
it means we accurately segmented that voxel. If you upload we will take a look,
but please include specific voxel coords
Cheers
Bruce
> On Nov 23, 2015, at 9:43 PM, Annelinde Vandenbroucke
> wrote:
>
> Hi Bruce,
>
Hi Eric
No, you can just symlink fsaverage and such
Cheers
Bruce
> On Nov 23, 2015, at 9:40 PM, Eric Cunningham wrote:
>
> Greetings Freesurfer experts,
>
> The README file in the $SUBJECTS_DIR says that a different directory can be
> specified by setting the env var SUBJECTS_DIR prior to the
Hi Bruce,
Thank you very much for your quick response.
Yes I mean that wm.mgz underestimates true white matter. Values are between
95 and 108 where it should be 110 or above.
I will upload my subj dir tomorrow. Is there specific place I can upload
to or shall attach it in I reply to you?
Thank y
Greetings Freesurfer experts,
The README file in the $SUBJECTS_DIR says that a different directory can be
specified by setting the env var SUBJECTS_DIR prior to the 'source
$FREESURFER_HOME/FreeSurferEnv.csh' statement.
Do the original contents of SUBJECTS_DIR (such as fsaverage) need to be
moved
Hi Annelinde
when you say a fault wm map, do you mean that the wm.mgz underestimates
the true white matter (that is, there are many voxels that are 0 in the
wm.mgz that are in the white matter)? What is the intensity of the
brain.mgz at those voxels?
If you tar, gzip and upload a subject dir a
Dear all,
I have a faulty wm map (brainmask.mgz) where some regions are not labeled
as white matter where they should. I tried to correct both the wm.mgz map
and add control points (and saved these), afterwards running either
-autorecon2-wm or autorecon2-cp, but neither of these work. I can see th
Hi Lee,
Thank you for your reply. I had read the example tables, but I'm still not sure
how to alter them into my study.May be you could help to check the matrix I
designed and tell me my mistake?
3 classes ( A / B / C group) and 4 variables (gender, age, education, and Moca
test score).
group.
Hi Mike
I agree! It's really hard to detect e.g. the tip of the nose wrapping
into occipital cortex. I was thinking more of the tools that generate
pages of snapshots so you can quickly scan through datasets to find
dramatic failures
cheers
Bruce
On Mon, 23 Nov 2015, Harms, Michael wrote:
>
>
In my experience, none of the quantitative "SNR/CNR" metrics available
through various FS tools (some of which may be part of the QATools)
replace the need to manually inspect the results. Some truly awful data
may show up as "outliers", but you can't count on those values to flag all
the data w
HI Guido
skipping the aseg will mean you need to do a lot more manual intervention
to get good surfaces (e.g. filling ventricles, "spackling" wm inferior to
hippocampus, etc...), so I wouldn't recommend it
sorry
Bruce
On Mon, 23 Nov 2015, Guido
Orlando Pascariello wrote:
Hi FS Experts
I'
Hi FS Experts
I'm using FreeSurfer to process my T1 data in order to get white and pial
surfaces from it.
I have a questions about usages of this file 'aseg.mgz'.
In the 'recon-all' pipeline, there are some steps in which I can use it or
don't use it depend on if I want or don't. I wonder What a
Hi Zeke,
thanks for providing the link, and sorry for not clarifying which version I
am using earlier.
The centos4 version you provided now does not throw the previous errors.
Thanks again, Caspar
2015-11-23 14:54 GMT-05:00 :
> Oh, Sorry about that, I was unaware you were using freesurfer v5.1 o
Oh, Sorry about that, I was unaware you were using freesurfer v5.1 on an
older RedHat system.
Freesurfer v5.1 was released quite awhile ago and its entirely possible
that the newest development version of the freesurfer binaries are not
compatible with it. But here is a link to our centos4 build w
Red Hat Enterprise Linux Server release 5.9 (Tikanga)
freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0
Caspar
2015-11-23 14:37 GMT-05:00 :
> What system are you running on? Also, what are the contents of your
> build-stamp.txt file (in your FREESURFER_HOME directory)?
>
> -Zeke
>
>
> > Hi Zeke
Hi Zeke,
I tried the is new version. Now I am getting:
mri_coreg: /lib64/libuuid.so.1: no version information available (required
by mri_coreg)
mri_coreg: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.11' not found
(required by mri_coreg)
mri_coreg: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.
There were some recent changes in the build that eliminated the necessity
for that library. Casper, can you try using this most recent version and
let me know if it works?
ftp://surfer.nmr.mgh.harvard.edu//pub/dist/freesurfer/dev_binaries/centos6_x86_64/mri_coreg
Thanks,
-Zeke
> Zeke, is th
Zeke, is this a new library that we need for v6?
doug
On 11/20/2015 09:42 AM, Caspar M. Schwiedrzik wrote:
> Hi Doug,
> when I try to execute mri_coreg, I get the following error message:
>
> error while loading shared libraries: libnetcdf.so.6: cannot open
> shared object file: no such file or d
You can mask it with the mri.2mm/aseg.mgz ventricle definitions.
However, there is a flaw in your understanding. What you see as
ventricle or WM may be GM in several/many subjects. The 12DOF
registration is not so good that it get all these things lined up properly.
On 11/23/2015 03:16 AM, std.
not that I know of (Ruopeng can chime in). You can use mri_convert to
change the voxel size using the -ois, -ojs, or -oks flags. You'll have
to experiment to see which done and what the value needs to be
On 11/22/2015 04:59 PM, Borzello, Mia wrote:
> Is there a way to change the scale in freevie
Hi Genevieve
I just tracked this down and it is a bug in mri_cc. If you tell Zeke your
hardware/software environment he can get you a new version that should work
cheers
Bruce
On Mon, 23 Nov 2015,
UQAM wrote:
Hi Bruce,
Please find the two files attached.
Genevieve
On Mon, Nov 23, 2015
Hi Elissa
I would create the ROI on the fsaverage surface using either freeview or
tksurfer. You can then use mri_label2label to map it to any subject, and
mris_anatomical_stats -l ... to compute thickness within
the ROI
cheers
Bruce
On Mon, 23 Nov 2015, Elissa Ash wrote:
Dear list,
I am
Dear list,
I am resending a message that I sent on Friday. Any help would be most
sincerely appreciated.
Dear Freesurfers,
I am new to freesurfer and I am trying to understand how to best perform a
cortical thickness analysis for an ROI that is not pre-defined in
freesurfer, such as the IFJ or
Hi all,
I am starting to use QAtools in Freesurfer.
The scripts are working well, but I have two problems:
1. the interpretation of output is the first. Are there ranges of
normality for SNR and intensity? Could you please give me some reference
or link about how to interpret these data? Or do I
Hi Li,
You can find some example FSGD tables here, which you can alter to fit your
analyses.
https://surfer.nmr.mgh.harvard.edu/fswiki/FsgdExamples
Best,
Lee
On Sun, 22 Nov 2015, nellie wrote:
Hi Freesurfer Experts,
I’m a new user of Freesurfer, and I learn how to use this software mainl
Hi Michael
have you visualize the Talairach alignment to see if it indeed incorrect?
Also, can you verify that the direction cosines from your data are properly
read? That is, when you view the orig.mgz in freeview does what it thinks
is inferior/superior etc... correspond to the true (visuall
We are getting an error with recon-all at the stage of Talairach slignment. The
error is the one described on the known issues: Can't locate shellwords.pl in
@INC. We are running perl5.18, so I downloaded and installed perl5.12 and
changed the first line of mritotal as indicated on the ReleaseNo
I was hoping someone could help with this issue...
Michael Amlung, Ph.D.
Assistant Professor
Department of Psychiatry and Behavioural Neurosciences
DeGroote School of Medicine
McMaster University
Peter Boris Centre for Addictions Research
100 West
Hi Neda
how did you copy and past them? Make sure you didn't introduce any extra
carriage return/line feeds and such.
cheers
Bruce
On Sun, 22 Nov 2015, Neda Mohammadi wrote:
>
> Dear FreeSurfer experts,
>
> I have downloaded and installed FreeSurfer. I am trying to run the installat
> ion t
Hi Geneviève
if you send us the $SUBJECTS_DIR/CColorLUT.txt and
$SUBJECTS_DIR/e0070/mri/aseg.12segmentsCC.mgz and we will take a look
cheers
Bruce
On Mon,
23 Nov 2015, UQAM wrote:
Hi,
This a a "re-posting" of a question I've raised last week ; )
I would like to segment the corpus callosum
Hi list,I'm performing fcMRI-seed based by FS-FAST.After group comparison and
Monte Carlo correction I obtained cortical and subcortical clusters in pos and
neg maps.On subcortiacal maps, significant clusters at
grf.th1.3.pos.sig.cluster.nii.gz showed some voxels on ventricle or white
matter. A
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