Hi,
i am trying to add new measures (pial_lgi) to qdec. I created the .Qdecrc file
in my SUBJECTS_DIR/qdec, with the described text (MEASURE1 = pial_lgi), but it
does not work, i cannot select in the qdec menu pial_lgi as a dependent
variable. A qdec.fsgd file is also in the same place.
I
Hi FreeSurfer experts,
I have a doubt regarding the atlas coordinates that uses QDEC. In the power
point titulated "fscoordinates" found in the FreeSurferWiki seems that the
coordinates used are aligned with Talairach Atlas, but when you enter de
coordinates provided by QDEC in a particular area
Hi,
Thank you for your help! I think there might be something wrong just with
the display, as in fact more brains looked strange. I have re-run the
concatenation with the same commands after killing many processes on my
computer and now all brains look correct and in the expected order.
Cheers,
Hi Silvia,
qdec does not support any longitudinal analysis (only cross sectional).
So I assume you either compare groups cross sectionally (e.g. at
baseline) or you constructed your own longitudinal measure (e.g. percent
change, within each subject) and then do a cross sectional analysis of
that s
Hi Natalia,
the images in 5.0 are not in the same voxel space across time. Probably
that is what's causing your problems. In 5.1 they are all resampled and
processed in the subjects' template space. So you cannot simply open
stuff on top of each other with 5.0 data.
However, surfaces are in verte
Hi freesurfers
After checking recon-all -autorecon-all processing, I realized that a part
of the duramadre has been not fully removed (please see attached file).
Can anyone help me how to solve this please.
Best regards.
--
Leo Kay.
<>___
Freesurfer m
Hi Derin,
there is a know and fixed bug in mris_calc in the 5.1 release. It has
difficulties with very long file names and returns a non zero exit code,
which stops my script in some situations.
I'll ask Nick if he can put up a fixed version of mris_calc for
download.
Best, Martin
On Thu, 2011-
Hi Natalia,
check your qdec/.QDECRC file, it needs to contain:
MEASURE1 = long.thickness-avg
MEASURE2 = long.thickness-rate
MEASURE3 = long.thickness-pc1
MEASURE4 = long.thickness-spc
probably you put a .spc instead of -spc
Best, Martin
On Fri, 2011-07-22 at 18:51 +0200, Natalia h wrote:
> Dea
Hi Leo
if the pial surface is in the right place in those regions you don't have
to worry about it.
cheers
Bruce
On Mon, 25 Jul 2011, leonardo kay wrote:
> Hi freesurfers
>
> After checking recon-all -autorecon-all processing, I realized that a part of
> the duramadre has been not fully remov
Hi
I have a problem when using qdec. When I check the option reverse values
there color on the brain switch color, but the color bar stays the same.
Is there anything that might be wrongs in my files? Is there anything
that I might edit in Qdec configuration file? I do not know what kind
of log t
Hi,
yes, rerunning with force in this case is correct.
If you made edits to cross and want to rerun base, I would recommend to
delete the base first and recreate it from scratch. Any edits in the
base will not be meaningful anyway as the images (and maybe even the
space) will change underneath.
Hello, I have tried troubleshooting this problem in various ways, but I am
still not able to figure out the problem.
I probably gave more output than necessary.
Does anyone have any idea?
Thank you!
> I am getting an error when using a script that combines these 3 actions:
>
> preproc.sh
> st
Hi Chindhuri, I don't know anything about those scripts (I don't think
that they are distributed with FS). Why are you using version 4?
doug
Chindhuri Selvadurai wrote:
> Hello, I have tried troubleshooting this problem in various ways, but I am
> still not able to figure out the problem.
>
> I p
Hi Chindhuri,
I don't think we have access to that path where the scripts are.
Double-check the path names in your script, it looks like some of the path
names are relative. Also, make sure you are running the script from the
right directory to begin with.
-Louis
On Mon, 25 Jul 2011, Chindhuri
That almost works; tkmedit is giving talairach coordinates of, for a few
examples:
14.7 23.9 -22.3
24.8 21.9 -18.8
35.6 20.8 -20.9
54.2 14.1 -17.1
61.1 10.9 -9.6
62.3 6.0 -1.8
Running mri_label2label with fsaverage as the target subject yields a label in
which those same points have the coordin
I'm still looking for an answer on this. If the answer is you can't do it,
I'm ok with that, I just would like to know! Thanks!
Hi all,
>
> I was wondering if anyone had any idea if it was possible to combine
> together ROIs from the separate hemispheres into one ROI (for example LH V1
> and RH
Hi Katie,
you could do it in the volume, but I doubt there's any way to do it on
the surface.
cheers
Bruce
On Mon, 25 Jul 2011, Katie Bettencourt wrote:
I'm still looking for an answer on this. If the answer is you can't do it, I'm
ok with that, I just would like to know! Thanks!
H
Hi freesurfers,
I performed ROI cortical thickness measurements earlier on an older version
of FS as described on
http://surfer.nmr.mgh.harvard.edu/fswiki/VolumeRoiCorticalThickness and I
was able to get the required values.
Now I have the latest version of FS. I draw an ROI mask using FSL softwa
HI
I have reproduce the error by using the group data from
buckner_tutorials. The files may be download
from this link with the error
http://vedlegg.uib.no/?id=0c18c8445e29c173fcf02a208ca1c255 and with none
reversal of values
http://vedlegg.uib.no/?id=20e06d09dcc450ff4abcd85e1e5ab1c5. Is there a
e
Are there instructions for how to do volume functional analysis and how to
do it that way? I've only ever done surface based analysis.
Katie
On Mon, Jul 25, 2011 at 3:58 PM, Bruce Fischl wrote:
> Hi Katie,
>
> you could do it in the volume, but I doubt there's any way to do it on the
> surface.
to sidestep
> this dimensions problem will be greatly appreciated.
>
> Is there any other workflow to define a volume ROI and then get the
> cortical
> thickness in the area.
>
> Thanks!
> Jaichander
> ------ next part --
>
Hello everyone,
I have several patients with large cortical lesions (haemorrhage). I want
to have subcortical structure volumes reflect the lesion, i.e. show up as
hypointensities in aseg.mgz (which they're not right now). However I also
want to calculate cortical thickness, and the WM & GM surfa
Hi
I editted the wm.mgz and aseg.mgz files... Which recon-all command
must I use to continue the processing ?...
Sincerely,
Gonzalo Rojas Costa
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/lis
-make all should work.
cheers
Bruce
On Mon, 25 Jul 2011, Gonzalo Rojas Costa wrote:
> Hi
>
> I editted the wm.mgz and aseg.mgz files... Which recon-all command
> must I use to continue the processing ?...
>
> Sincerely,
>
>
> Gonzalo Rojas Costa
> ___
Dear Freesurfers,
I know that Qdec outputs coordinates in a "Freesurfer specific space", rather
than in Talairach space, per this old thread
https://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/2008-November/008878.html
However, I found that mri_surfcluster (Freesurfer v5.0) in its summary out
Hi Bruce:
Maybe I didn't explain clearly my question... I did a complete
processing of a patient, then I must edit wm.mgz and aseg.mgz because I
found some segmentation errors... Which recon-all command must I run to
reprocess the study to use the edited files (wm.mgz and aseg.mgz) ?...
I sent a wrong link. The correct link is here.
I have gone through the tutorials using qdec and when I reverse the values the
color bar is not reversed.
With reversed color values age verse thickens
http://tjinfo.uib.no/Vedlegg?id=9720b934c5a5a437924453ddb23497b2
Without reversed color values
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