Hi Marcos, it is weird that the posterior*.mgz does not have that info.
Maybe Koen or Eugenio know why. In the mean time, you can use
mri_convert to change/set the parameters, eg
mri_convert in.mgz out.mgz -tr 0 -ti 0 -te 0 -flip_angle 0
doug
On 6/18/13 2:50 PM, Marcos Martins da Silva wr
try now
On 6/18/13 9:37 PM, amirhossein manzouri wrote:
I have version 5.1 so please recreate the links!
BR
On Tue, Jun 18, 2013 at 8:43 AM, Douglas Greve
mailto:gr...@nmr.mgh.harvard.edu>> wrote:
Hi Amir, if you are using 5.2 or 5.3, then you should already have
it. If not, I'll h
Hi Maria, can you elaborate on exactly what you have done? Is the data
the same and you are only changing the version of QDEC? What is the
nature of the difference? Can you send pics or stats?
doug
On 6/18/13 6:06 AM, Maria Kharitonova wrote:
> Hi,
>
> I'm learning how to use QDEC and was comp
Hi Gabriel, I don't have experience with the MR-PET yet. Why do you
think there is a problem? Try running wm-anat-snr on this subject. In
general, you don't want to be smoothing/denoising the anatomical
doug
On 6/18/13 1:13 PM, obre...@nmr.mgh.harvard.edu wrote:
Hi,
I've started segmentin
Hi,
I have a question about how to make surfaces in shape of inflated or white/pial
(fiducial) surface for the fsaverage atlas.
In my understanding, to make a population average surface from multiple
individual surfaces, the surfaces should be first in shape of sphere.
But, I'm not clear how ca
Dear freesurfer experts,
All of my other tutorial files are complete with the correct md5sum except
bert.recon.tgz. I re-downloaded bert.recon.tgz, and got the consistent
wrong answer again. I highly doubt that something is wrong with my
downloading. Would someone please take a look at the origin
Hi, Freesurfer experts
If you try to read one of the posterior*.mgz files generated by reco-all
-hippo-subfield into MatLab/Octave using MRIread.m it fails like this:
Ps=MRIread('posterior_left_subiculum.mgz')
WARNING: error reading MR params
Attempted to access mr_parms(1); index out of bound
Dear freesurfer support group,
I keep getting 9a5dcc7ebb7aa8564c4bba47ef0293e9 as the md5sum for the
bert.recon.tgz file which I downloaded from the following link
ftp://surfer.nmr.mgh.harvard.edu/pub/data/bert.recon.tgz
The correct md5sum is supposed to be 04d6fa1703787e546aaafbfade17cab2.
I d
Oh, I see what my error was: I need to use --sval-annot instead of
--srcsurfval.
Thanks!
Peter
On 06/18/2013 02:51 PM, Bruce Fischl wrote:
> this is what mri_surf2surf is for. What was your command line? Did you
> check the help?
>
> On Tue, 18 Jun 2013, Peter Savadjiev
> wrote:
>
>> Hi Louis,
Dear Bruce,
This is the command line I used:
mri_surf2surf --srcsubject fsaverage --srcsurfval
Yeo2011_7Networks_N1000.annot --trgsubject case01053 --trgsurfval
Yeo2011_7Networks_N1000.annot --hemi lh
and I get the error message:
ERROR: could not determine type of Yeo2011_7Networks_N1000.annot
this is what mri_surf2surf is for. What was your command line? Did you
check the help?
On Tue, 18 Jun 2013, Peter Savadjiev
wrote:
> Hi Louis,
>
> When I try mri_surf2surf, I get the error
> ERROR: could not determine type of Yeo2011_7Networks_N1000.annot
>
> Could it be because this is an anno
Hi Louis,
When I try mri_surf2surf, I get the error
ERROR: could not determine type of Yeo2011_7Networks_N1000.annot
Could it be because this is an annotation file, and not a surface such
as ?h.curv, ?h.thickness etc?
I guess I need something like "mri_annot2annot", does anything like this
exis
Hi Freesurfers,
I'm wondering if there is a way to figure out if a ct.anat.nii file is corrupt
or not. I'm using MRICro as a viewer, and the file doesn't look right.
Thanks,
Mia
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Hi Celine
the only existing way to correct this would be to create two volumes in
addition to brain.finalsurfs.mgz (say, lh.brain.finalsurfs.mgz and
rh.brain.finalsurfs.mgz) and edit each of them to remove voxels in the
contralateral hemisphere that are causing problems, then rerun
mris_make_su
Hi Bruce
The aseg is correctly labeled as regards right and left GM cortex, but
definitely some voxels are belonging to both hemisphere. The filled.mgz is
fine too. Should we delete from aseg the voxels that are at the border
between the lh and rh?
Thanks
Celine
> Hi Celine
>
> is the aseg correct
There was a bug with mris_make_face_parcellation that merged some of the
rois together when you tried to run the command twice to subdivide the
parcellations further. So if you want to use it
for this purpose make sure you use the newest version as it has been fixed
now.
Best,
Maritza
On Tu
Hi Jeff
there are two utilities we provide for this (and yes, David is always
correct!):
1. mris_make_face_parcellation - create approximately unifom-sized parcels
using icosahedral subdivisions. These can be uniform in the native space
using the ?h.sphere, or in register and uniform in the gr
I just attended the pre-OHBM FSL/FS course, and spoke to David Salat there
about possibilities to create more detailed sub-parcellationsfrom the two
major structural atlases. Could someone please let me know if David was
right that such tools exist, and/or point me to them?
My goal is essentially
wow, why is your FOV so big?
On Tue, 18 Jun 2013, Ray, Siddharth wrote:
Hi all,
I am coming across this error for couple of my subjects:
WARNING
=====
The physical sizes are (240.00 mm, 240.00 mm, 347.20 mm),
Hi Lior
it looks like you have significant darkening in the MTL complicated by
pretty noisy scans. Can you tell us more about what you are doing? What
sequences and scanner are you using? What is your subject population?
Control points would probably be your best bet, but this might be able to
Hello Siddharth,
The error message says "Include the flag -cw256 with recon-all!" So I
would recommend giving that a try.
-Zeke
On 06/18/2013 12:33 PM, Ray, Siddharth wrote:
> Hi all,
>
> I am coming across this error for couple of my subjects:
>
> WARNING
> ==++
Hi all,
I am coming across this error for couple of my subjects:
WARNING
=====
The physical sizes are (240.00 mm, 240.00 mm, 347.20 mm), which cannot fit in
256^3 mm^3 volume.
The resulting volume will have 348 slices.
Hi Celine
is the aseg correctly labeled in these regions? Is the filled.mgz? That's a
tough case as it's not clear from looking at it which hemi those voxels
belong to (probably some of each)
Bruce
On Tue,
18 Jun 2013, cel...@nmr.mgh.harvard.edu wrote:
> Sorry here is a snapshot for an exam
Hi Jane
that means it is trying to correct the topology of a very large defect.
46K vertices is about 1/3 of a normal human hemisphere. Check the
?h.orig.nofix and see if something big has gone wrong - the skull being
attached or the cerebellum or something like that. I don't have much
experi
> Hi Freesurfer team
> I am wondering if there would be a way to improve surfaces on the medial
> wall, not for the measurement of cortical thickness, but also for laminar
> analysis in the cortex. We would need them to be accurate even for the
> medial wall. What would you suggest?
> Thanks
> Celi
Hi Freesurfer team
I am wondering if there would be a way to improve surfaces on the medial
wall, not for the measurement of cortical thickness, but also for laminar
analysis in the cortex. We would need them to be accurate even for the
medial wall. What would you suggest?
Thanks
Celine
--
Celine
Dear Freesurfer group
I am interested to do group analysis on my data. If I want to do
inter-individual group analysis, what is the minimum number of subjects I
need to have?
Also if I want to do intra-individual analysis, what is the best way in FS?
I appreciate your time and your help.
Thanks a
.H is mean and .K is Gaussian curvature. It should also write a .max and
.min, doesn't it? Those are the principal curvatures that you want.
Bruce
On Tue, 18 Jun 2013, Jürgen Hänggi
wrote:
Dear Bruce
Thanks a lot for the info. It worked fine, but how can I open the resulting
.H and .K file
Hi,
I'm learning how to use QDEC and was comparing results that it produces under
FresSurfer 5.0 vs 5.3. I know the 5.0 has an option for either DODS or DOSS
method of producing a design matrix, while the 5.3 only has DODS. This suggests
that results should be identical (or at least similar) a
Hi all,
Any news on the libboost_program_options.so.5 issue, as relates to
mri_cvs_register? I've encountered it using mris_resample (as part of
mri_cvs_register) using.
When I run:
qsub -S /bin/tcsh -pe make 2 -b y -v PATH=${FREESURFER_HOME}/bin:$PATH -V
${FREESURFER_HOME}/bin/mri_cvs_register
Dear Freesurfer group.
I am having some concerns about Freesurfer and the different steps. I have
used version 5.0 for the cross-sectional timepoints, and I am now using
version 5.3 for the longitudinal processing. I am doing therefore the
several different steps involved in longitudinal processin
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