Dear List Members,
When I try to run the qdec I got following error,
Please tell me how to rectify it.
bmssa-desktop:~/freesurfer/subjects> qdec
qdec.bin: error while loading shared libraries: libXss.so.1: cannot open shared
object file: No such file or directory
Thanks.
Best Regards,
Muhamma
Hi Bruce,
I was able to change the white matter label values to 255 and the rest to 1
however when I ran -autorecon2-wm the new surface looks the same as the old
when I view them both in tksurfer. Should I be running something else with
recon-all to get a fixed segmentation?
Miggy
On Wed, Sep 4
Dear list membes,
Please guide me how to create the qdec.table.dat for my own mri data.
Thank you.
Best Regards,
Muhammad
Naveed Iqbal Qureshi
P please don't print this e-mail unless
you really need to
Hello,
I have run recon-all for my subject, if I want to get more subcortical
segmentation, e.g., globus pallidus, medulla, pons and so on, how can I do?Can
I manually draw these region on the bert image and transfer them to individual
subject, like mri_label2label?
Thanks.
Lisa
I'm not sure you can do that with a linear model. What would your model
look like?
doug
On 9/4/13 9:18 PM, Yang, Daniel wrote:
Hi Freesurfer,
Is it possible to specify only two main effects but no interaction
effect by using mri_glmfit?
If yes, could you provide an example?
Details are
No, that will just smooth the orig surface, it will not cause it to
follow intensity gradients
On 9/4/13 7:56 PM, David Romano wrote:
Thanks, Doug; this helps me to formulate my second question better,
which is:
2) Assuming that no change in intensity is necessary, would the files
lh.whit
sorry, -fthresh
btw, if you type tkmedit and hit return, it will give you all the options
On 9/4/13 8:08 PM, std...@virgilio.it wrote:
> Error: Parsing command line options
> Option -fmin not recognized
> This option was not recognized and ignored.
>
>
> Messaggio originale
> Da: gr...@nm
I ended up fixing the error through symlink.
From: Rongxiang Tang
To: "freesurfer@nmr.mgh.harvard.edu"
Sent: Wednesday, September 4, 2013 8:04 PM
Subject: error during longitudinal -base stream
Hi All,
I found an error during the longitudinal -base stre
Hi Freesurfer,
Is it possible to specify only two main effects but no interaction effect by
using mri_glmfit?
If yes, could you provide an example?
Details are much appreciated!
Thanks!
Daniel
--
Yung-Jui "Daniel" Yang, PhD
Postdoctoral Researcher
Yale Child Study Center
New Haven, CT
(203) 7
Hi All,
I found an error during the longitudinal -base stream:
#@# Ex-vivo Entorhinal Cortex Label lh Wed Sep 4 19:35:00 CDT 2013
mris_spherical_average -erode 1 -orig white -t 0.4 -o 611 label lh.entorhinal
lh sphere.reg lh.EC_average lh.entorhinal_exvivo.label
painting output onto subject
no, the smoothing is done irrespective of the intensity volume (in
mris_smooth). The smoothness constraints in mris_make_surfaces are more
sophisticated (they assume that the surfaces are well-fit by quadratic
patches, not planes) and also move the surface to lie at large intensity
gradients
Error: Parsing command line options Option -fmin not recognized This option was
not recognized and ignored.
Messaggio originale
Da: gr...@nmr.mgh.harvard.edu
Data: 5-set-2013 1.40
A:
Cc:
Ogg: Re: [Freesurfer] R: Re: R: Re: R: Re: R: Re: R: Re: R: R: Re: Mask from
cortical parcellati
Thanks, Doug; this helps me to formulate my second question better, which
is:
2) Assuming that no change in intensity is necessary, would the files
lh.white, lh.area, and lh.curv produced by the mri_make_surfaces command
(in the -white subsection of the -autorecon2 section) be the same as the
file
use
tkmedit Diff01 orig.mgz -overlay frontal_rh.nii.gz -fmin 0.5
On 09/04/2013 07:36 PM, std...@virgilio.it wrote:
> When I use tkmedit Diff01 orig.mgz frontal_rh.nii.gz I have this error.
> Error: Loading Surface frontal_rh.nii.gz
> Couldn't load the surface.
> Tkmedit couldn't read the surfa
I highlighted some difference.
frontal_rh.nii.gz data_type INT32dim1 256dim2 256dim3
256dim4 1datatype 8pixdim11.00pixdim2
1.00pixdim31.00pixdim40.010999cal_max
0.cal_min
The orientation looks right to me, ie, the little letters on the side
that indicate direction are correct. The odd orientation that it is
displayed in is an fslview issue
On 09/04/2013 07:16 PM, std...@virgilio.it wrote:
> If I not change the output orientation the .nii.gz is wrong (please
>
(Sorry -- inadvertently hit a key that triggered the "send" function.
Here's the final version of the previous message:)
Hi everyone,
I've been trying to go through the various steps described on the page:
http://surfer.nmr.mgh.harvard.edu/fswiki/ReconAllDevTable
and I'm trying to understand
lh.orig.nofix is the original tesselation without anything done to it.
To get to lh.white, the defects are automatically corrected to create
lh.orig. lh.orig is then refined with smoothness and intensity
constraints to produce lh.white
doug
On 09/04/2013 07:07 PM, David Romano wrote:
> Hi eve
Don't change the output orientation in mri_convert
On 09/04/2013 07:05 PM, std...@virgilio.it wrote:
> T1.mgz is corrected in tkmedit.
>
> When I added also frontal_rh.nii.gz
>
> tkmedit Diff01 orig.mgz frontal_rh.nii.gz
>
> Error: Loading Surface frontal_rh.nii.gz
> Couldn't load the surface.
> T
Hi everyone,
I've been trying to go through the various steps described on the page:
http://surfer.nmr.mgh.harvard.edu/fswiki/ReconAllDevTable
and I'm trying to understand part of the -autorecon2 section, and in
particular,
1) how the lh.orig.nofix file that is produced by the end of the
-tes
T1.mgz is corrected in tkmedit.
When I added also frontal_rh.nii.gz
tkmedit Diff01 orig.mgz frontal_rh.nii.gz
Error: Loading Surface frontal_rh.nii.gz Couldn't load the surface. Tkmedit
couldn't read the surface you specified. This could be because the file wasn't
a surface type that tkmedit reco
Hi Tara,
You can try with fwhm=0 as Doug suggested, or 5 if it works. I'm still trying
to see whether the level of fwhm could be modified in qdec so that you can
input your own level (e.g. 1 or 2, instead of the specified 0-5-10-15-20-25).
Nick,
Do you know if there is a keyword that can be cha
first, display it in tkmedit and verify that it is incorrect there. If
it is correct, then the problem is in your viewer
If it is incorrect, send me the command lines you used for mri_binarize
and mri_convert
On 09/04/2013 06:46 PM, std...@virgilio.it wrote:
> I have used mri_convert to obtain
I'd like to perform probtrackx (FSL) from seed (subcortical) to target
(cortical) masks.
To this aim, I should trasform all cortical and subcortical masks obtained by
FS on MNI space.
Therefore, firstly, I'd like to overlay the masks that I obtained by
mri_binarize on the structural image to c
use the orig.mgz or any of the other FS volumes
On 09/04/2013 05:48 PM, std...@virgilio.it wrote:
>
> I'd like to perform probtrackx (FSL) from seed (subcortical) to target
> (cortical) masks.
>
> To this aim, I should trasform all cortical and subcortical masks
> obtained by FS on MNI space.
>
Hi Miggy
can you cc the list so that others can answer? The two atlases we provide
are described in:
https://surfer.nmr.mgh.harvard.edu/ftp/articles/fischl04-parcellation.pdf
https://surfer.nmr.mgh.harvard.edu/ftp/articles/desikan06-parcellation.pdf
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC
I don't understand your question. Can you elaborate?
On 09/04/2013 05:27 PM, std...@virgilio.it wrote:
> I mean anatomical.nii.gz with the same spatial features of the masks.
>
> Thanks,
>
>
> Stefano
>
> Messaggio originale
> Da: std...@virgilio.it
> Data: 4-set-2013 23.02
> A: ,
> Ogg: [
I mean anatomical.nii.gz with the same spatial features of the masks.
Thanks,
Stefano
Messaggio originale
Da: std...@virgilio.it
Data: 4-set-2013 23.02
A: ,
Ogg: [Freesurfer] R: Re: Mask from cortical parcellation
Thank you very much.
A last help, please. How is the anatomical
Hi Celine - The path.pd.nii.gz file contains the full probability
distribution without any thresholding. This distribution, as with any
probabilistic tractography method, expresses the amount of uncertainty in
which is the path of most coherent diffusion between the two end regions.
(In tracul
Hi Miggy,
not sure about your first issue as the ribbon is the gray matter and the
wm.mgz is white matter, so how would edits in one change the other?
For the second one, there is a flag in mris_register that allows you to
draw a label on an individual subject and indicate what parcellation u
Thank you very much.
A last help, please. How is the anatomical file that I can use to overlay the
masks. I'm noting that masks are characterized by:data_type INT32dim1
256dim2 256dim3 256dim4 1datatype
8pixdim11.00pixdim2
Hi Marie:
I fixed it. It was a pathway error. Thanks again for your help,
best,
Alan
On Wed, Sep 4, 2013 at 2:36 PM, Alan Francis wrote:
> Hi Marie:
>
> It puzzles me too. I checked a few of the aparc_lgi.stats with a regular
> aparc.stats file and they all look exactly the same to me. Extrac
Hi Marie:
It puzzles me too. I checked a few of the aparc_lgi.stats with a regular
aparc.stats file and they all look exactly the same to me. Extracting the
values from the aparc.stats has never run into problems. Even the file size
of 5.7kb is the same. I will keep trying variations in the script
Hi all,
I'm trying to make a group average of a set of subjects that we've
collected various functional data on and use anatomical landmarks of the
group average surface to predict the locations of functional areas that
we've found to be correlated to the anatomy of the ventral cortex. As such,
we
Hi Alan,
I never had this error. Do you get the same error if you use aparcstats2table
with other stats files? Did you check one of those aparc_lgi.stats file to see
whether they look similar to another aparc.stats file in term of structure
(except that the values will be different)?
Marie
Hi Stefano,
Take a look at the lobe mapping section on this wiki page. Example
commands near the end.
https://surfer.nmr.mgh.harvard.edu/fswiki/CorticalParcellation
-Louis
On Wed, 4 Sep 2013, std...@virgilio.it wrote:
> Hi list,
> I need to create a mask of frontal, parietal, temporal and occ
Hi Sinead,
In short, it is most likely a bug. I think the current version of the QA
tools scripts expects a 5.1 recon-all stream, so the output order of files
being slightly different in 5.2/5.3 causes this error/warning to appear.
In the future you should just run QA tools with the -snaps-onl
Dear experts,
I read some previous answers about the thresholding of the paths obtained
after tracula process, but I am not completely sure I had the right
answer.
I will need to get an roi from a path for example the cortico-spinal tract
that will be consistent amongst patients. I will further use
Hi Martin,
Thanks for the information. I have another question which I just noticed:
so if all my individual data were processed and edited in the v 5.0, will it be
problematic if I run the -base and -long in the v5.3 ? I noticed that in the
tutorial, there was a line about:
Important Note!
Hi Marie:
Thanks so much. I used your command and got the average LGI values for each
region for each subject. However when ran the second script, I get the
following message:
csh::alanf@cerebro [/media/Alan_WORK/WORK/De_LISI_Final/LGI_HSF] :
aparcstats2table --subjects HM0403 /HM0503 /HM0603 /HM
Hi Catherine,
1. the -clean flag is only necessary if you used 5.0 or earlier for the
full longitudinal stream. You only used it for the first step (the cross
sectional processing).
2. yes, it's a bad idea to process different subjects with different
version. It's OK to use 5.0 for cross and a
Hi Tara, The problem is that the lGI is already very smooth and then it
gets smoothed again. This causes the total smoothness level to go beyond
what has been done for the simulation. Try using fwhm=0.
doug
On 09/04/2013 09:48 AM, Tara Ann Miskovich wrote:
> Hello,
>
> I am conducting group a
you can use mri_binarize on aparc+aseg, eg, something like
mri_binarize --i aparc+aseg.mgz --match 1003 1012 1014 1032 --o
frontal.nii.gz
those numbers come from $FREESURFER_HOME/FreeSurferColorLUT.txt
That table has a lot of ROIs in it, and not all will be in the
aparc+aseg. You'll be inter
Hi Freesurfers,
I am running recon-all -autorecon1 and I have an error like this:
/libdisk/tmp_EMM/subj/mri
/libdisk/freesurfer/bin/mri_nu_correct.mni
--n 1 --proto-iters 1000 --distance 50 --no-rescale --i orig.mgz --o
orig_nu.mgz
nIters 1
$Id: mri_nu_correct.mni,v 1.18.2.1 2013/01/09 21:23:42 n
Hello,
I am conducting group analyses with LGI data in qdec, and I am having an issue
with the monte carlo simulation I am hoping to get help with.
Under design I leave the Smoothing (FWHM) at 10, and when I try to run the
monte carlo simulation after running the analysis I get this error: Err
Dear all,
I have preprocessed my data using Freesurfer v5.2. I have checked the the
recon-all.log for each subject to make sure that the process completed
without error and that all the appropriate files were created. I have also
visually inspected each image. However, when I run recon checker (fr
recon-all \
-sd \
-s \
-i < path to *one* file in a T1-weighted dicom series or nifti file> \
-all
cheers
Bruce
On Wed, 4 Sep
2013, swathy p.s wrote:
once freesurfer is installed ,how do i run it every time?
___
Hi Anupa
5.2 is a deprecated version and you should definitely upgrade to 5.3.
What was your recon-all command line? You probably did generate the
cortical stats,and they are in a different file (e.g. aparc.stats).
cheers
Bruce
On Tue,
3 Sep 2013, Anupa AV wrote:
Dear FS experts,
I'm us
Hi list,
I need to create a mask of frontal, parietal, temporal and occipital lobes in a
subject by using cortical parcellation output.
Is it possible? Eventually, how can I transform these masks file to mii.gz (to
import them in FSL analysis).
Thank you very much.
Regards,
Stefano
once freesurfer is installed ,how do i run it every time?
___
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