Thank you very much for your help Douglas!
I had a few problems running these commands.
1) recon-all -autorecon1 -autorecon2 -> no problems
2) The matlab script
The aseg.auto.mgz (256x256x256) didn't have the same size as the FLAIR
(resliced to 1mm, co-registered in MNI-space and with manual
Dear FS,
I figured out how to list my ctabe-file (attached). Again, the file myaparc was
created but this time I got the following error:
Colortable:aparc.annot.ctab
Annotname: myaparc
Nhitsfile nhits.mgh
Nlabels 6
Labeltresh 0 0.0
Loading freesurfer/fsaverage/surf/lh.orig
1 9345678 fusi
Dear all,
If you have some suggestions I'd greatly appreciate them.
Thank you very much,
Best wishes,
Barbara
Forwarded Message
Subject:TRACULA tract endpoints on cortical surface
Date: Fri, 5 Aug 2016 12:03:02 +0200
From: Barbara Kreilkamp
To: Freesurfer
Dear FS experts,
I need to crate a mask for whole white matter in the brain including the cerebellum. Also I need a mask for the whoe gray matter.
Can I binzarize ( i.e. use mri_binarize) and input the files:
wm.seg.mgz from the output of recon-all to create a a mask for global white matter
Hello,
I am trying to have the atlases aparc.a2009+aseg.mgz, hippocampal subfield
etc ...
in a matrix with the same size as the input of recon-all (and not the cubic
matrix 256x256x256) and with the same orientation.
what is the best way to do it ?
Cheers,
Pierre
--
DEMAN Pierre
Mobile : +33 7
You can always run mri_convert with the -rl (“reslice like”) flag to achieve
this. Something like: mri_convert input.mgz output.mgz -rl reference.mgz -odt
float
If it’s a segmentation volume, you should add -rt nearest, in order to use
nearest neighbor interpolation.
Cheers,
Eugenio
Juan Eugeni
Try
mri_binarize --i aparc+aseg.mgz --wm --o wm.mask.mgz
On 08/10/2016 07:21 AM, John Anderson wrote:
> Dear FS experts,
> I need to crate a mask for whole white matter in the brain including
> the cerebellum. Also I need a mask for the whoe gray matter.
> Can I binzarize ( i.e. use mri_binarize
Dear FS experts:
I noticed that there is a "normal Range" results in the aseg.stats table.
I am wondering how can I consider of this normal range? is that based on
population or what.
thanks
Lawrence
Emory University
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Freesurf
Dear FS experts:
How can I only out put the volume value in the aseg.stats file?
I applied following command: but it will produce a table with lots of
values such as brainsegvol, brainsegvolnotvent, which I donot want to use.
thanks
asegstats2table --subjects 004 021 040 067 080 092 \
--segno
Hello FreeSurfer experts,
I am running surfaced based analysis using ROI approach. My mris_preproc,
mri_surf2surf and mri_glmfit worked as expected. Since i restricted the
region i built my own monte carlo "mri_mcsim --o
roianalysis/average/mult-comp-cor/fsaverage/rh/rightmaskforcomp --base mc-z
--
Hello,
Never mind. I was able to figure it out. I only needed to add
"Users/Paul/Desktop" to the command line
On Wed, Aug 10, 2016 at 12:50 PM, miracle ozzoude
wrote:
> Hello FreeSurfer experts,
> I am running surfaced based analysis using ROI approach. My mris_preproc,
> mri_surf2surf and mri_g
first, you'll need to get two new things:
ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/cvs152.mri2.mm.tar.gz
ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_vol2vol
cd $FREESURFER_HOME/subjects/cvs_avg35_inMNI152
tar xvfz cvs152.mri2.mm.tar.gz
# Make a backup o
Use mri_label2vol
On 08/08/2016 02:33 PM, Kami Koldewyn wrote:
> Hi All,
>
> I have a set of ROIs that were created in structural space, currently
> saved as volume masks. I would like to transform these into functional
> space, re-sampled to the functional resolution. Can anyone suggest a
> g
It says "normRange" not "normalRange" "norm" refers to the fact that the
norm.mgz was used to generate the values. It has nothing to do with
normal range of human values
On 08/10/2016 11:41 AM, shi yao wang wrote:
> Dear FS experts:
> I noticed that there is a "normal Range" results in the aseg.
With the version 5.3 asegstats2table, you will always get these. In
version 6, you'll have the opportunity to get only the segs you specify.
On 08/10/2016 12:38 PM, shi yao wang wrote:
> Dear FS experts:
> How can I only out put the volume value in the aseg.stats file?
>
> I applied following com
On 08/05/2016 12:33 PM, Vikas Bandalli wrote:
> Thank you Doug,
>
> I am very sorry I hadn't explained our subject considered for analysis.
> The subjects group consists of Patients who are classified into
> a.Those with Psychosis - Psychotic-pt
> b. Those without Psychosis - Non-Psychotic-pt
>
On 08/05/2016 02:35 PM, miracoo...@gmail.com wrote:
> Hello doug,
> Should I add --label-src in addition to --label-trg or should I replace the
> latter with the former?
It does not matter as both the source and target are fsaveage
> Thanks. Also, Just to conform, I should run mri_glmfit-sim aft
I don't know what you mean. Can you elaborate?
On 08/05/2016 04:10 PM, Mahtab Farahbakhsh wrote:
> Dear FreeSurfer,
>
> I am comparing two groups of my subjects together in qdec and when I
> want to visualize each subject, I can see two different regions for
> inferior parietal lobe and supramar
which "native" space? the pet native? the anatomical native?
On 08/09/2016 05:46 PM, Pradeep wrote:
> Hello Doug,
>
> The aux/seg.nii image which has all the ROI's defined does not seem to
> be in the subject's native space or the CVS template space.
>
> How do I bring it to the subjects native s
did you look at the aseg.mgz to see if the lesions were in the right place?
On 08/10/2016 03:28 AM, Silas wrote:
>
> Thank you very much for your help Douglas!
>
>
> I had a few problems running these commands.
>
> 1) recon-all -autorecon1 -autorecon2 -> no problems
>
>
> 2) The matlab script
>
>
what is the error?
On 08/10/2016 04:45 AM, Caroline Beelen wrote:
>
> Dear FS,
>
> I figured out how to list my ctabe-file (attached). Again, the file
> myaparc was created but this time I got the following error:
>
> Colortable:aparc.annot.ctab
>
> Annotname: myaparc
>
> Nhitsfile nhits.mgh
>
>
did you look at the file it points to as the source of the error?
/local/limachiagv/freesurfer/subjects/CON_201/stats/aseg.stats
On 07/27/2016 05:00 PM, Limachia, Gaurang (NIH/NINDS) [F] wrote:
> Hello All,
>
> My table.dat file loaded fine. However, I came across the following
> error when I wa
I have no idea. You can try copying the 5.3 version of mri_segreg to 5.1
On 07/28/2016 04:10 AM, Fred Sampedro wrote:
> Hi Douglas,
>
>
> Thanks a lot for your help, I understand. I tried replacing the
> mri_convert in 5.1 from the 5.3 and the bbregister command went a
> little bit further. Unfo
Try normalizing your continuous variables (ie, subtract the mean and
divide by the stddev)
On 07/28/2016 06:06 AM, Mahtab Farahbakhsh wrote:
> Dear FreeSurfer,
>
> I am trying to compare my subjects to the healthy group, but when I
> put the matrix into qdec, I get the following error:
>
> Norma
You can use the "per vertex regressor" functionality in mri_glmfit. You
create a stack of on of the modalities that you pass with the --pvr
flag. This adds the value for each subject as a column in the design
matrix. You'll need to create contrast matrices with this extra
regressor in mind
On
Its in PET native space.
On Wed, Aug 10, 2016 at 2:55 PM Douglas N Greve
wrote:
> which "native" space? the pet native? the anatomical native?
>
> On 08/09/2016 05:46 PM, Pradeep wrote:
> > Hello Doug,
> >
> > The aux/seg.nii image which has all the ROI's defined does not seem to
> > be in the s
Use the pet2bbpet.lta in the aux folder. If you add --no-reduce-fov, it
will not change the FoV of the output image
On 08/10/2016 06:06 PM, Pradeep wrote:
> Its in PET native space.
>
> On Wed, Aug 10, 2016 at 2:55 PM Douglas N Greve
> mailto:gr...@nmr.mgh.harvard.edu>> wrote:
>
> which "nat
Neither of these are easily fixable in FSFAST. You can remove the extra
time points for the first problem. For the 2nd one, I guess you can do
two analyses, one at each frequency, then ignore the one with the wrong
frequency
On 08/02/2016 05:55 PM, Xiaomin Yue wrote:
> Hi,
>
> I am running a re
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