Hi all
i am developping an application for neuronavigation, and i want to use
freesurfer cortical parcellation and sub-cortical segmentation, is there any
freesurfer command to convert surface files to vtk files ?
Thanks
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areas exist ?
Thanks
De : Bruce Fischl
À : LAOUCHEDI MAKHLOUF
Cc : "freesurfer@nmr.mgh.harvard.edu"
Envoyé le : Vendredi 26 juillet 2013 15h33
Objet : Re: [Freesurfer] correspondance between broadmann areas and freesurfer
labels
Hi Laouchedi
tha
Hi
i used freesurfer labels in a study and i want to identify the broadmann
areas corresponding to some labels, is there any correspondence between the two
?
Thanks
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Hi
i am using corticals parcels (destrieux) as nodes in a connectivity study
using the NBS (Network Based Statistics) tool; i want to assign MNI coordinates
for these nodes. is there any MNI coordinates in freesurfer for each component
of this parcellation (not for every vertex in those comp
, brain.finalsurfs.mgz,
wm.mgz, filled.mgz) are done at the autorecon2 step; Or should i run autorecon3
to fix the problem ?
Thanks
De : Bruce Fischl
À : LAOUCHEDI MAKHLOUF
Cc : "freesurfer@nmr.mgh.harvard.edu"
Envoyé le : Jeudi 18 juillet 2013 15h31
Hi
i run recon-all on a subject and when checking the surfaces, i noticed that
a big part of the temporal part is badly segmented; this concerned WM as well
as the grey matter. on the RecommendedReconstruction page, it is explained how
to remove parts of non-pial structures considered as s
Hi
i run recon-all on 13 subjects (severe TBI) using the condor cluster
environment, 10 of them were stopped with, mostly ending with this error (found
in SUBJECTS_DIR/subj/scripts/recon-all.log) :
ncvarput: ncid 4: Input/output error
miicv_put: MINC package entry point
nu_evaluat
De : Douglas N Greve
À : LAOUCHEDI MAKHLOUF
Cc : "freesurfer@nmr.mgh.harvard.edu"
Envoyé le : Vendredi 28 juin 2013 21h23
Objet : Re: [Freesurfer] mri_label2vol problem
Hi Laouchedi, I still cannot figure out why you are getting a volume of
all 0s. Are you sure it is all 0s an
z --proj frac 0 1 .1
but the result is a volume with zero values (i changed --fillthresh .5 to
--fillthresh 0 and i got the same probleme)
Thanks
De : Douglas N Greve
À : LAOUCHEDI MAKHLOUF
Envoyé le : Vendredi 28 juin 2
ve
À : freesurfer@nmr.mgh.harvard.edu
Envoyé le : Vendredi 28 juin 2013 16h49
Objet : Re: [Freesurfer] mri_label2vol problem
How does the annot look on the surface (ie, intksurfer)? What is the
full terminal output of mri_label2vol?
On 06/28/2013 10:19 AM, LAOUCHEDI MAKHLOUF wrote:
> Hi
>
after your run
the program.
doug
ps. Please remember to include all previous correspondence in your email.
On 06/28/2013 11:38 AM, LAOUCHEDI MAKHLOUF wrote:
> excuse me but i don't understand what you mean by "terminal of
> mri_label2volume"
&
excuse me but i don't understand what you mean by "terminal of mri_label2vol"
Thank you for help
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The information in this e-mail is i
excuse me but i don't understand what you mean by "terminal of mri_label2volume"
Thank you for help
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The information in this e-mail i
Hi
i run mri_label2annot to get individual annot files for all labels, then i
run mri_label2vol to get nifti volumes of my labels using the following command
:
mri_label2vol --annot lh.G_and_S_cingul-Ant.annot --temp
SUBJ_DIR/ctr2/mri/brain.mgz --subject ctr2 --hemi lh --identity --
Hi
I loaded an annotation file (that i generated using the command annot2label
then label2annot) on a pial surface using tksurfer :
tksurfer subj lh pial
then i loaded my annotation file (frontal association cortex). is it possible
to reload it with a unique color for all the g
Hi
i run recon-all -autorecon3 on a normal subject and after a while, it exited
with errors, looking in the SUBJECTS_DIR/subj/scripts/error.log and
recon-all.error and recon-all.log i found the following messages :
error.log :
mrisReadTriangleFile(../surf/rh.smoothwm): surface doesn't match
Hi
i used mri_annotation2label to extract the cortical labels. for this command
we must specify which hemisphere (--hemi ?h) and i want to extract the
brainstem which is not a lateralized structure, is there any command like
mri_annotation2label to extract the brainstem ?
thanks
hi
i send you the rawavg.mgz of the subject with the massive artefact. i inform
you that i proceeded differently by splitting the recon-all -all into three
steps (as in freesurfer wiki) : (1) recon-all -autorecon1, (2) recon-all
-autorecon2 (3) recon-all -autorecon3. i just finished with the
hi
i send you further information of the -nuintensitycor and skullstrip
problem,about three control subjects. after running "recon_all -i", i decided
to process my data step by step, i run "recon_all -autorecon1" for all of them
and it ended with errors. i picked up three cases of the recon-al
hi all
i run recon_all on some subjects having 512x512x154 , i noticed (using
tkmedit) that there are no problems with orig.mgz, and rawavg.mgz but most of
them were cropped (more than half of the brain disappeared) after the
"-nuintensity" step (nu.mgz); for one of these patients, the
hi
I am working on severe TBI and most of
them suffer from large hematoma and according to litterarture, the
apearance on T1 changes accordind to the stage of the trauma, from
3days (early suba acute) to 14 days (late subacute) the T1 signal
from hematoma is Hyperintense and after that it becom
hi all
i use mri_anot2label to extract sulci, is there a tool allowing to keep
just the deepest line of the sulcus and if possible get the list of talairach
coordinates of that line's points.
thanks a lot for your help
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hi all
i have still a problem to load an activation map on a pial surface (colin27).
here are the steps followed to this end :
first i run bbregister :
bbregister --s colin27 --mov /home/mlaouche/bashr/V8.nii.gz --init-fsl --reg
/home/mlaouche/bashr/regester1.dat --bold --surf pial
then i u
gistration file exists.
If you were trying to load a volume-encoded value file,
make sure it has the same number of values as this surface
does vertices (166454).
thanks a lot for your help
De: Bruce Fischl
Objet: Re: [Freesurfer] overlay question
À: "LAOUCHEDI MAKHLOUF"
Cc: freesurfer
hi all
excuse me for this "simple question" but i am quiet new to freesurfer (i
use it just for the parcellations). i've some functionnal maps (i've used spm
for that) that i want to use as an overlay on the pial surface of the subject.
is there an easy way to do it
thanks
_
hi i have run freesurfer using -notalairach flag and i had the following
message :
mri_nu_correct.mni --i orig.mgz --o nu.mgz --uchar
transforms/talairach.xfm --n 2
ERROR: cannot find transforms/talairach.xfm
can anyone know why is it searching the transforms/talairach.xfm when
: get_4dfp_dimoe problem
À: "LAOUCHEDI MAKHLOUF"
Cc: Freesurfer@nmr.mgh.harvard.edu
Date: Samedi 7 janvier
2012, 21h28
laouchedi,
the file 'endianio.c' is not a module that can be installed by the
end-user. it is source code. did you install the files that i referred
to in my pri
hi everyone
thank you very much for your help; i've sent the link to the
Administrator of the grid and wil have the answer tomorow
thank you again
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hi everyone
we run recon-all on a cloud and we obtained this error:
mpr2mni305 failed, see transforms/talairach_avi.log
The log says the file name is too long perhaps because of the tmp dir file
names:
get_4dfp_dimoe:
/var/spool/pbs/tmpdir/169536.gridgate.scg.nuigalway.ie/https_3a_2f_2fwms01.ihep
--- En date de : Lun 2.1.12, LAOUCHEDI MAKHLOUF a écrit :
De: LAOUCHEDI MAKHLOUF
Objet: recon all problem
À: freesurfer@nmr.mgh.harvard.edu
Date: Lundi 2 janvier 2012, 11h15
hi everyone
i run recon-all on 200 subjects on a cloud system and i had
the following message
hi everyone
i run recon-all on 200 subjects on a cloud system and i had
the following message :
mpr2mni305 failed, see transforms/talairach_avi.log
so i attached the corresponding log to this message. does anyone have an idea
of the error
thanks
i looked in the .bashrc file and it is written :
FREESURFER_HOME=/home/amesse/software/freesurfer5.1 ;
but freesurfer is installed in another account to which i have no
access for the moment. i'll see it on monday
thank you michael
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hi everyone
i run recon-all on 27 subjects using the 5.1 version, and i
don't find aparc.a2009s+aseg.mgz neither lh.aparc.a2009s.annot so i can't use
the command mri_aparc2aseg ( mri_aparc2aseg --s subject --a2009s). what must i
do to have aparc.a2009s+aseg.mgz.
thanks
Hi everyone
I run freesurfer recon-all command with the flag -all and I have this error
ERROR:mpr2mni305 failed, see transforms/talairach_avi.log
Some one have any idea?
Thanks
this is the whole process:
Checking for (invalid) multi-frame inputs...
WARNING: only one run found. This is OK
hi eveyone
i am quite new in freesurfer, is it possible to generate
aparc.a2009s+aseg.mgz from aparc.a2005s+aseg.mgz without re running recon-all
thanks
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hi everyone
i run recon-all -all on some subjects using the 5.1 version
of freesurfer and instead of getting aparc.a2009s+aseg.mgz i got
aparc.a2005s+aseg.mgz. the components of the cingulate cortex are quite
different in both files a2005s and a2009s :
in a2009s i used in my w
hi everyone
i run recon-all on some datasets using freesurfer version
5.1. Instead of having aparc.a2009s+aseg.mgz at the end of recon-all, i had
aparc.a2005s+aseg.mgz. what to do to have the good dataset (2009 instead of
2005)
thanks
_
hi eveyone
i ru the command recon-all of the 5.1 version of freesurfer
on some subjects using the following arguments : recon-all -i database/ctr/ctr1
-subjid ctr1. it created a directory ctr1 in my SUBJECTS_DIR directory with all
the sub-directories inside, but with no orig.mg
hi everyone
i have made an annotation file from somme labels and i want
to make a mask from the result (from the annotation file). i mean i want keep
just the part of the brain covered by the annotation file in order to transform
it by mri_convert to nifti format and make my ma
hi everyone
i have run recon-all on somme subjects and i want to make
build a masque containing somme geri (pre and post central for example) and
with some color, to load on a pial surface (as overlay). i tried to understand
the commands like mri_annotation2label and mris_label
hi everyone
i am new in freesurfer and i want to create a masque of some
color made of somme régions labels (say for ex. the post central gyrus and
precentral gyrus or any combination of geri and sulcus) to put it as a layer on
an a pial or inflated surface. how can i proceed?
hi everyone
i am working on traumatic brain injury and noticed that some
exams i received recently (T1datasets) were conducted using à contrast medium:
sometimes the whole memisphere presents hypersignal. can i run recon-all (if
there is a way) on such subjects?
thanks
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hi everyone
i am trying to use the mri_aparc2aseg command with the --a2009s
flag to have the aparc.a2009s labels and i have the following message " Option
--a2009s unknown"
thanks
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hi
i am new in freesurfer (even if i used it many times doing reonstructions
using the script reconn-all in the past and on another machine), i launched a
reconstruction of one patient using the reconn-all script and i gave before
this the path to the SUBJECTS_dir. and one or two minutes la
hi
i am new to freesurfer, i want to load somme specific (individuel) labels on a
brain.mgz
thanks
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The information in thi
hi everyone
after running recon-all i noticed (on somme normal
patients) overlaping in some labels: part of image with 11165 and 3 wich
correspond to
p { margin-bottom: 0.21cm; }
- ctx_lh_G_front_inf-Orbital
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