Hi Michael, Thanks for your help and suggestions! > I'd have to try to recreate
the error, but I have an idea of what it
> could be (assuming
> /home/control/marhoo/Projects/BIG/Freesurfer_CorticalThickness/BIG1026_1
> is a directory).
Actually not yet,
/home/control/marhoo/Projects/BIG/Freesurfe
Hi Rey,
We are working on a 64 bit Mac version, but don't quite have one yet
Cheers
Bruce
On Mar 5, 2012, at 6:36 PM, Rey Ramirez wrote:
> Dear colleagues, especially Lilla Zollei,
>
> I am trying to run mri_cvs_register on a 64-bit Mac but it crashes at the
> same place where other people h
Dear Freesurfer experts,
I installed the QAtools and tried a subject with this commond:
$QA_TOOLS/recon_checker -s sub13 -snaps-detailed -gen-asegLUT aseglut.txt
but I encountered the following Error message, can someone help me figure it
out? Any help is appreciated, thanks!
Error message 1:
Re
Dear all
I just want to ask a sample question.What's the best number of the
parameter of 'recon-all' , -i invol1 -i invol2.That is, how many slices should
we use?If the invol1 is the fist slice of the fMRI series or any one of the
data?
Yours
_
Hi,
recon-all takes an anatomical volume as input, not a functional one. You
can give it any slice that is in the correct series (just specify one) and
it will find the others.
cheers
Bruce
On Tue, 6 Mar 2012, bowan...@mail.ustc.edu.cn wrote:
> Dear all
>I just want to ask a sample quest
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Hi Chunhui,
I believe this is a dependency issue, since the convert command is part of
the ImageMagick Studio. You'll need to download and install the binaries
(http://www.imagemagick.org/). I'll make of note of this on the wiki
page.
-Louis
On Tue, 6 Mar 2012, chenchunhuichina wrote:
> Dear
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audition, University of Geneva
-
Applications are invited at the PhD or at the Post-Doctoral level at the
Departm
Hi Catherine,
Does the individual have good surfaces? If so, then it would be better
to map the sig.mgh into the individual using the surface transform,
something like (run with --help for more info):
mri_surf2surf --srcval sig.mgh --srcsubject fsaverage --hemi lh
--trgsubject yoursubject --trgv
#x27;QA_check.html'
By the way, I do not have solid anatomical background, is it acceptable that I
only use QAtools for quality control, without manual editing? I am thinking
manual editing by non-experts will induce incorrect data. Any suggestion?
Thanks a lot!
2012-03-05
Chunhui Che
at Sat Feb 25 02:34:14 EST 2012
>>
>> To report a problem, see
>> http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
>>
>>
>>
>> ?? -Ryan
>>
>>
>>
>
> --
>
> Message: 7
> Date: Tue, 6 Mar
Allie, to be more precise, you have selected control Hi All,
>
> I'm having trouble reconciling the cluster colours with the graph that
> can be made when you load the group descriptor file and click on a
> point. I've attached an example.
>
> In this study, I'm comparing thickness in a patient
Hi Allie, yes, it means that each group is affected differently by age.
The controls are increasing their thickness with age in this area (which
seems strange, usually you expect general decreases with age). You might
check the quality of the surfaces in this area.
doug
Allie Rosen wrote:
> Hi
If this makes sense, there aren't any topological defects in the regions of
other similar results.
On Tue, Mar 6, 2012 at 4:05 PM, Allie Rosen wrote:
> Hi Doug,
>
> Yes, I think there actually may be a topologic defect in this area,
> although not directly where the cluster is (attached). Could
Yes, you can do this in a few steps. Use mri_binarize to convert the
ribbon.mgz into a binary mask of just the cortex (use the --match
option). Then use mri_binarize with aseg.mgz to get the hippocampus (17
for left, see $FREESURFER_HOME/FreeSurferColorLUT.txt). Then add them
together with fsc
It might, don't know
Allie Rosen wrote:
> Hi Doug,
>
> Yes, I think there actually may be a topologic defect in this area,
> although not directly where the cluster is (attached). Could this be
> the cause of the thickness result? If I go back and try to repair the
> defect, will that make the
So if my findings show that each group ages differently, does that mean I
can't compare them at all because I can't regress out age? Or is there some
way of comparing the groups despite this difference in aging patterns?
Thanks again,
Allie
On Tue, Mar 6, 2012 at 4:44 PM, Douglas N Greve
wrote:
It means that any comparison depends on age. Eg, if you compare them at
an age where the lines cross, you will see no effect. If you compare
them at age=0 (what you were doing before), then you see a big effect.
Some statisticians will say that you cannot do the comparison in the
presence of an
do you have a big outlier in the thickness measures? I didn't see one. It
seems unlikely that all your subject have a defect in that spot
On Tue, 6
Mar 2012, Douglas N Greve wrote:
> It means that any comparison depends on age. Eg, if you compare them at
> an age where the lines cross, you will
my comments inserted below...
On Sat, 2012-03-03 at 20:08 -0500, R Edgar wrote:
> On Sat, Mar 3, 2012 at 6:57 PM, Abdulkadir Ahmed
> wrote:
>
> > Freesurfer supports GPU acceleration since version 5.0. To assess the
> > utility of this functionality, particularly the gain in performance, I
> >
Hi Freesurfers,
I am using preproc-sess in Freesurfer/Fsfast 5 with per-run motion
correction (these subjects have a lot of between-run motion), and I want to
analyze the volumes in each subject's individual space (I'd prefer native
functional space, but I am happy to do it in each subject's anato
Hi Alex, analyzing in the anatomical space is going to be very, very
costly in terms of space and memory (and I don't really have a way to do
it). It is probably better to do it in mni305 space and turn off the
masking out of cortex (-no-subcort-mask). You can then run
reg-mni305.2mm to create
Dear all,
I have just ran the command 'recon-all'.
recon-all -i 3098704 -s BianYP -sd /home/wb/test/ -all
In the parameters,3098704 is a function slice,but this parameter need a
anatomical volume.Could it can find the correct ones itself? Whether the
anatomical volume is just 3D slice or 2D
you need to give it one slice from the anatomical series. It will find
the rest.
cheers
Bruce
On Wed, 7 Mar 2012, bowan...@mail.ustc.edu.cn wrote:
> Dear all,
>I have just ran the command 'recon-all'.
> recon-all -i 3098704 -s BianYP -sd /home/wb/test/ -all
> In the parameters,3098704 is a f
Hello,
I have a couple of subjects with poor quality scans. The grey/white
contrast is not so good. I wonder if the newest version of freesurfer
might help with the pial and white surfaces.
Do I need to make some minor edits to key images/files in order to
force freesurfer to take a second shot a
Hi Christine
it really depends on the details of what went wrong. Can you send
snapshots or upload some subjects?
cheers
Bruce
On Tue, 6 Mar 2012, Christine Smith wrote:
> Hello,
>
> I have a couple of subjects with poor quality scans. The grey/white
> contrast is not so good. I wonder if the n
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