Yes, the label is shifted off the brain when I run that command
On 04/11/2017 10:13 AM, Arnaud Boré wrote:
Hi Douglas,
Yes I would like to draw ROIs, I understand I can use tksurfer.2017-04-10 11:54 GMT-04:00 Douglas N Greve <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.
I would like to know if your fs version has the same behaviour as mine. I use: freesurfer-x86_64-unknown-linux-gnu-stable6-20170118
Can you replicate this command line and tell me if the label is well aligned to the surface ?
qdec --surface $SUBJECTS_DIR/bert/surf/rh.pial --label $SUBJECTS_DIR/bert/label/rh.V1 _exvivo.label
Thank you in advance
Arnaud
edu >>:<mailto:arnaud.bore@gmail.com> <mailto:arnaud.bore@gmail.com
Sorry, I don't know what is going on with qdec. Why do you need to
do this in qdec? If it is to draw labels, then you can also use
tksurfer.
On 04/10/2017 11:34 AM, Arnaud Boré wrote:
Hi Douglas,
What more can I do to help you figure out what's wrong ?
Thank you in advance
Arnaud
2017-04-07 16:50 GMT-04:00 Arnaud Boré <arnaud.bore@gmail.com<mailto:greve@nmr.mgh.harvard.
<mailto:arnaud.bore@gmail.com>>>:
There is no shift in freeview.
2017-04-07 16:35 GMT-04:00 Douglas N Greve
<greve@nmr.mgh.harvard.edu
<mailto:greve@nmr.mgh.harvard.edu >edu
<mailto:greve@nmr.mgh.harvard.edu >>>:
Not yet. Did you try to load it into freeview? If so,
do you
still see the shift?
On 04/07/2017 04:14 PM, Arnaud Boré wrote:
Do you want me to attach/upload a screenshot of
the shift ?
2017-04-07 13:10 GMT-04:00 Arnaud Boré
<arnaud.bore@gmail.com
<mailto:arnaud.bore@gmail.com> <mailto:arnaud.bore@gmail.com
<mailto:arnaud.bore@gmail.com>>
<mailto:arnaud.bore@gmail.com
<mailto:arnaud.bore@gmail.com>
<mailto:arnaud.bore@gmail.com
<mailto:arnaud.bore@gmail.com>>>>:
I try to view it on O_Nap_04MB.
I've tried these two command lines:
qdec --table qdec.all_subjs.table.dat --surface
O_Nap_04MB/surf/rh.pial --label
O_Nap_04MB/label/rh.M1_v4.label
qdec --table qdec.all_subjs.table.dat
--average O_Nap_04MB
--surface O_Nap_04MB/surf/rh.pial --label
O_Nap_04MB/label/rh.M1_v4.label
I get the same results.
2017-04-07 12:03 GMT-04:00 Douglas N Greve
<greve@nmr.mgh.harvard.edu
<mailto:greve@nmr.mgh.harvard.edu >
<mailto:greve@nmr.mgh.harvard.edu
<mailto:greve@nmr.mgh.harvard.edu >><mailto:greve@nmr.mgh.harvard.edu
<mailto:greve@nmr.mgh.harvard.edu >
<mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.<tel:617-726-7422 <tel:617-726-7422>>> <tel:617-726-7422edu >>>>:
when you view it in qdec, are you viewing
it on
fsaverage or
on O_Nap_04MB ?
On 04/07/2017 11:47 AM, Arnaud Boré wrote:
I used this command line: mri_label2label
--srclabel
rh.M1_v4.label --srcsubject fsaverage
--trgsubject
O_Nap_04MB --trglabel rh.M1_v4.label
--regmethod surface
--hemi rh
The output label overlaps the surface
using
freeview but
using qdec it is shifted.
Thank you for your help.
Arnaud
2017-04-07 10:23 GMT-04:00 basile pinsard
<basile.pinsard@gmail.com
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<mailto:basile.pinsard@gmail.com >>>
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<mailto:basile.pinsard@gmail.com
<mailto:basile.pinsard@gmail.com >
<mailto:basile.pinsard@gmail.com
<mailto:basile.pinsard@gmail.com >>>>>:
---------- Forwarded message
----------
From: *Douglas N Greve*
<greve@nmr.mgh.harvard.edu
<mailto:greve@nmr.mgh.harvard.edu >
<mailto:greve@nmr.mgh.harvard.edu
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<mailto:greve@nmr.mgh.harvard.edu
<mailto:greve@nmr.mgh.harvard.edu >>>>>
Date: Thu, Apr 6, 2017 at 4:53 PM
Subject: Re: [Freesurfer] QDEC and
ROI drawing
To: freesurfer@nmr.mgh.harvard.edu
<mailto:freesurfer@nmr.mgh.harvard.edu >
<mailto:freesurfer@nmr.mgh.harvard.edu
<mailto:freesurfer@nmr.mgh.harvard.edu >>
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<mailto:freesurfer@nmr.mgh.harvard.edu >>>
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<mailto:freesurfer@nmr.mgh.harvard.edu >
<mailto:freesurfer@nmr.mgh.harvard.edu
<mailto:freesurfer@nmr.mgh.harvard.edu >>>>
what is your label2label command line?
On 04/06/2017 04:52 PM, Arnaud
Boré wrote:
> Dear Freesurfer's experts,
> I draw a specific region on
fsaverage
using QDEC,
then I mapped this
> label on each subject using
mri_label2label. I
looked at these
> registered labels using
freeview. Most
of them are
perfect but for
> some of them I would like to
correct the
segmentation. I would
like to
> modify it using QDEC but when I
overlay
this label
on the surface of
> my subject it has been shifted.
I think
this shift
is because
QDEC is
> using fsaverage as the standard
space. I
try opening
QDEC using the
> "average" option and use the
subject I
want but I
still get this
> shift. am I missing something ?
> Thank you in advance for your help.
> Arnaud Bore
>
>
>
>
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--
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MGH-NMR Center
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<https://gate.nmr.mgh.harvard.edu/filedrop2 >
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<https://gate.nmr.mgh.harvard.edu/filedrop2 >>>>
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<ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/gre >>ve/
<ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/gre ve/
<ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/gre >ve/
<ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/ flat/greve/
<ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/gre >>>ve/
<ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/ flat/greve/
<ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/gre >ve/
<ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/ flat/greve/
<ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/gre >>ve/
<ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/gre ve/
<ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/gre >ve/
<ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/ flat/greve/
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<https://gate.nmr.mgh.harvard.edu/filedrop2 >
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<http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html >>>
Outgoing:
ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/grev e/
<ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/gre >ve/
<ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/ flat/greve/
<ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/gre >>ve/
<ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/gre ve/
<ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/gre >ve/
<ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/ flat/greve/
<ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/gre >>>ve/
-- Arnaud BORE
Research assistant
Cellulaire : (001) 514-647-8649
<tel:514-647-8649> <tel:514-647-8649 <tel:514-647-8649>><tel:%28514%29%20647-8649>
-- Arnaud BORE
Research assistant
Cellulaire : (001) 514-647-8649 <tel:514-647-8649>
<tel:514-647-8649 <tel:514-647-8649>>
-- Douglas N. Greve, Ph.D.
MGH-NMR Center
greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu >
<mailto:greve@nmr.mgh.harvard.edu
<mailto:greve@nmr.mgh.harvard.edu >>
Phone Number: 617-724-2358 <tel:617-724-2358>
<tel:617-724-2358 <tel:617-724-2358>>
Fax: 617-726-7422 <tel:617-726-7422> <tel:617-726-7422
<tel:617-726-7422>>
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
<http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting >
<http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
<http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting >>
FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
<https://gate.nmr.mgh.harvard.edu/filedrop2 >
<https://gate.nmr.mgh.harvard.edu/filedrop2
<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 >
<http://www.nmr.mgh.harvard.edu/facility/filedrop/index.htm l
<http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html >>
Outgoing:
ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/grev e/
<ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/gre >ve/
<ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/ flat/greve/
<ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/gre >>ve/
-- Arnaud BORE
Research assistant
Cellulaire : (001) 514-647-8649 <tel:514-647-8649>
<tel:%28514%29%20647-8649>
-- Arnaud BORE
Research assistant
Cellulaire : (001) 514-647-8649 <tel:514-647-8649>
-- Douglas N. Greve, Ph.D.
MGH-NMR Center
greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu >
Phone Number: 617-724-2358 <tel:617-724-2358>
Fax: 617-726-7422 <tel: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
<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/grev e/
<ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/gre >ve/
--
Arnaud BORE
Research assistant
Cellulaire : (001) 514-647-8649
--
Douglas N. Greve, Ph.D.
MGH-NMR Center
greve@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/grev e/