Hi, Dear Experts:
*I am trying to use FsFast to do retinotopy analysis and have been
following the
**instructions at: **
https://surfer.nmr.mgh.harvard.edu/fswiki/FsFastIndividualRetinotopyAnalysis
*
* It sees that I can get some visulization results through these scripts*
* However if I ne
Hi Rudolph,
and thanks for the offer. I think I have to appologize to the author of the
thread for jumping into his discussion. I just felt that the topic of my
question was so close to his that I didn't resist.
In fact in my analysis, label dilation as implemented in tksurfer and
suggested by
Hi Shriks,
as far as I can see -cortparc, -cortparc2, -parcstats, and -parcstats2 flags
(and possibly beyond) of the autorecon3 stage do the parcallation. But I am
not sure whether there have been any significant changes between your version
and the current version of the FS, which could impact
no, sorry
On Mon, 9 Nov 2009, Rajagopalan, Venkateswaran wrote:
> Hello,
>
> I am new to the field of cortical thickness analysis and freesurfer software.
> I looked at the tutorials (mainly Powerpoint slides and research articles)on
> freesurfer documentation pages. Being new to the field and w
True, I am using version 4.3.1.
Can I update only mri_glmfit-sim script??
Thanks
2009/11/9 Douglas N Greve
> What version are you using? I think this was a problem with 4.3.
>
> doug
>
> Roser Sala wrote:
>
>> Dear all,
>>
>> I am running a surface-based group analysis. When I try to run
>> mr
Hello,
I am new to the field of cortical thickness analysis and freesurfer software. I
looked at the tutorials (mainly Powerpoint slides and research articles)on
freesurfer documentation pages. Being new to the field and with very little
image processing background i find it difficult to grasp
What version are you using? I think this was a problem with 4.3.
doug
Roser Sala wrote:
> Dear all,
>
> I am running a surface-based group analysis. When I try to run
> mri_glmfit-sim, I always get the following error:
>
> ERROR: you must supply --fwhm with --sim, even if it is 0
>
> I get this
Use mri_label2label to map from one subject to another. See the help for
how to do this. then
cd subject/surf
mris_anatomical_stats -l yourlabel.label -t lh.thickness -f table.dat
subject lh
doug
Dankner, Nathan (NIH/NIMH) [F] wrote:
> Doug,
>
> I'm mostly looking to pull out cortical thicknes
Dear all,
I am running a surface-based group analysis. When I try to run
mri_glmfit-sim, I always get the following error:
ERROR: you must supply --fwhm with --sim, even if it is 0
I get this error (which does not make any sense, since there is not fwhm
info in the simulation) using both qdec-ge
Doug,
I'm mostly looking to pull out cortical thickness. Could you give me an
example of the command line which I would use to map the labels back to the
individual subjects and pull the stats? Thanks,
Nathan
On 11/9/09 12:03 PM, "Douglas N Greve" wrote:
what kind of stats? It will create
what kind of stats? It will create labels of the clusters, and you can
map those labels back to the individual subjects, then run
mris_anatomical_stats to pull out, eg, thickness for each subject.
doug
Dankner, Nathan (NIH/NIMH) [F] wrote:
> Hello all,
>
> I sent this last week but I think it m
The color wheel in tksurfer is not well supported. It's pretty old code,
and it is surprisingly not very useful. It is not really appropriate for
retinotopy, despite all the pubs that use it! It is good for
applications where there is a spatial discontinuity in phase.
doug
Andreas Schindler wr
Hi Matt,
looked at the log. Everything before seems fine. Not sure what's going
on. Can you send the following files:
>From the two cross sectional runs (tp1 and tp2):
The two norms:
/space/md8/6/data/TEST/FSContainers/FREESURFERRECON_TEST_005_S_0221_45_20070321.105506_1/mri/norm.mgz
/space/md8/6
yes, or you can use aparc+aseg.mgz. They should give the same result.
Mehul Sampat wrote:
> I just realized that a simpler way to create this mask would be to use
> "ribbon.mgz" and find all the voxels with the labels 2 and 41 which
> correspond to "Left_White" and "Right_White".
> https://surfe
Hi !!
I am currently using FreeSurfer version Stable 4. I want to update my
annotation files from aparc.a2005s to the latest aparc.a2009s atlas.
How can I re-create just the annotation files from the existing files, without
having to redo the entire recon-all process ? Re-creating using Stable
Hi Bruce:
And, How can I send you ?...
Sincerely
Gonzalo Rojas Costa
Department of Radiology
Las Condes Clinic
Lo Fontecilla 441, Las Condes, Santiago, Chile.
Tel: 56-2-2105170
Cel: 56-9-97771785
www.clc.cl
Bruce Fischl escribió:
> Hi Gonzalo,
>
> we'll need to see the data and the ana
Hi Gonzalo,
we'll need to see the data and the analysis results to have any advice.
Bruce
On
Mon, 9 Nov 2009, Gonzalo Rojas wrote:
> Hi:
>
> I tried to segment a T1 volume of a 3 years old patient... It fails
> to segment the cortex in some specific regions, and the corpus callosum
> appears s
What version do you have? I've put a copy of it here:
ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/stem2fname
but the fact that it does not exist in your distribution could be an
indication that something else is wrong.
doug
Sharmili 57 wrote:
> Dear all,
>
> i want to run clus
Hi:
I tried to segment a T1 volume of a 3 years old patient... It fails
to segment the cortex in some specific regions, and the corpus callosum
appears such as white matter... Why ?... Could I correct it ?...
Sincerely
--
Gonzalo Rojas Costa
Department of Radiology
Las Condes Clinic
Lo
Hello all,
I sent this last week but I think it may have slipped through the cracks.
I have recently run a cluster correction on some data, and was hoping to use
these clusters as ROIs and pull stats from them. What is the best way to do
so? Thank you in advance for your help,
Nathan
__
Hi Matt,
no that is not a fix. The command is supposed to invert the map from the
current time point to the base (so that we have the map from base to
this tp). Therefore the second transform in mri_concatenate is the
identity.
Your code is inverting the identity.
Again, the error happens somewhe
Hi Wouter,
don't they just want you to show your aseg results? That's how I read it.
cheers,
Bruce
On Mon, 9 Nov 2009, Wouter Groen wrote:
>
> Hi,
>
>
>
> a recently investigated hippocampal and amygdala volumes in a patient and
control group using Freesurfer. The reviewers appreciate the met
Hi,
a recently investigated hippocampal and amygdala volumes in a patient and
control group using Freesurfer. The reviewers appreciate the method
(Freesurfer's automated segmentation), but like to see an example of the
anatomic definitions:
"Please include examples of amygdala and hi
Dear all
I realised that freesurfer can handle overlays of complex numbers (e.g.
as given by a fourier analyis) when they are split up in two separate
volumes: one containing the real and the other containing the imaginary
part of each voxel ("complex numbers" flag in the overlay configuration
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