External Email - Use Caution
Hi Freesurfer developers
I’m trying to install the development package from github on my mac running osx
10.14.6. I ran CMake with the OSX package without any issue, although when I
ran make I got the following error:
[ 28%] Linking CXX executable s
Hi,
I was wondering if there was any existing freesurfer script to calculate
the roundness and/or the perimeter of a surface label? If anyone has ideas
on how to calculate this, I would appreciate it.
Thanks,
Jonathan
___
Freesurfer mailing list
Freesur
Hi Doug,
Thank you. I ran sampled the data and ran mri_glmfit as you suggested, although
the resulting bp file seems to only have binary clusters (in the attached image
the red cluster all have a value of 1 and everywhere else is 0). Is this the
normal output? I expected a more varying map.
Hi,
I’m trying to use the PETsurfer Pipeline to perform BP analysis, but I’m not
sure at which point in the pipeline to sample the data to the surface and what
registration to use?
I tried running the pipeline using dynamic kinetic modeling as described here:
http://surfer.nmr.mgh.harvard.ed
Hi Freesurfer developers,
I’m trying to perform BP analysis with mri_glmfit —mrtm1. I ran mri_gtmpvc
without PVC, which finished without error. However, the km.hb.tac.nii.gz
appears empty when I open it with fslview or tkmedit, although this may be due
to the nature of the file (I’m not sure w
v6.0
> To: freesurfer@nmr.mgh.harvard.edu
> Message-ID: <5609ba16.2090...@nmr.mgh.harvard.edu>
> Content-Type: text/plain; charset=windows-1252; format=flowed
> Can you upload the FS subject, pet data, and .lta?
> https://gate.nmr.mgh.harvard.edu/filedrop2
>
>
>
> On 09/28/2015
want to sample this to the
> surface using mri_vol2surf and the registration file aux/anat2pet.lta,
> then smooth on the surface.
>
>
> doug
>
>
>
> On 09/08/2015 02:11 PM, Jonathan DuBois wrote:
> > Hi FS experts,
> >
> > In FS development package I see th
.hb.tac.nii.gz --mrtm2 km.ref.tac.dat time.dat $k2p --o
> mrtm1 --no-est-fwhm --nii.gz
> If you want to run a voxel-wise analysis, then you can use the mgx
> volume as input (--y). Probably you'll want to sample this to the
> surface using mri_vol2surf and the registration file aux/a
Hi FS experts,
In FS development package I see that there have been tools added for
partial volume correction of PET data, but I was wondering if there were
also kinetic modeling tools similar to those described in Doug's 2014
paper? If you could let me know what PET processing tools have been
inc
Hi Bruce,
Thanks. It took some trial and error but I was able to fix the surface with
the reposition surface tool. However, it results in a fairly jagged surface
with some topology error. To correct this, should I use the smooth surface
tool in freeview or reprocess the surfaces with recon-all? Th
Hi Freesurfers,
I am having trouble manually correcting the surface of brain with an
abnorally thick cortex due to a malformation. It seems as though there is a
thickness threshold that constrains the pial surface reconstruction. I have
added control points to the white matter but the problem seem
Hi Freesurfers,
I am trying to use fscalc.fsl to do calculations on an fsaverage vertex map
of values (mgh files). In some of these files, but not all, I get the
following error:
** ERROR: nifti_convert_nhdr2nim: bad dim[1]
** ERROR (nifti_image_read): cannot create nifti image from header
'./tmp
Hi all,
I was wondering if there was a script like aparcstats2table that would
accept a functional overlay file that has been sampled to the surface as a
measure instead of the available options for structural measures?
In tksurfer there is a manual way to average over an ROI using the sig.mgh
an
Hi Doug,
Thanks for replying. We are currently working on this analysis, is there
anyway you could provide a beta version of the PVC code?
Thanks,
Jonathan
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailm
Hi Freesurfer experts,
I have been using freesurfer for surface-based PET analysis and was
wondering if the method for voxel-based partial volume correction, used
in the recent paper (Cortical surface-based analysis reduces bias and
variance in kinetic modeling of brain PET data), was implemente
Hi All,
I have run recon-all on a subject with a large cortical dysplasia, and
while the segmentation (aseg) seems to be relatively correct, there is a
large region of dysplasia not included by the pail surface. The normalized
intensity values for the cortex and the excluded region are very simila
Hi All,
In a previous post Doug suggested two methods for generating voxel-wise
z-score maps, one using glmfit with one subject in one group and the second
using fscalc.fsl. Link to post:
https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2010-June/014673.html
I have tried both methods using
Hi,
Is there a way to transpose a manual surface label in fsaverage space onto
the contralateral hemisphere? With tksurfer it opens in the opposite
hemisphere but it does not correspond to the contralateral region.
Thanks in advance.
Best,
Jonathan
___
Sorry, I wasn't adjusting the overlay values so I couldn't see it. Thanks
for your help!
Best,
Jonathan
On Mon, May 13, 2013 at 11:09 AM, Bruce Fischl
wrote:
> you should be able to load it into tksurfer as an overlay.
>
> cheers
> Bruce
>
> On Mon, 13 May 2013, Jo
at 4:55 PM, Bruce Fischl wrote:
> Hi Jonathan
>
> try -output_type mgh. It should create a "volume" that is nvertices long.
> Not sure if it can directly create a label file, maybe Doug knows?
>
>
> Bruce
>
>
> On Sun, 12 May 2013, Jonathan DuBois
file
/Users/label.mgh
tkmedit: Trying to open /Users/label.dat
surfer: Interpreting overlay volume /Users/label.mgh as encoded scalar
volume
Best,
Jonathan
On Sun, May 12, 2013 at 1:57 PM, Bruce Fischl wrote:
> try using --regheader
>
> cheers
>
> Bruce
> On Sun, 12 May 201
perly in tkmedit or
> freeview. Can you tell us more about what you are trying to do?
> Bruce
>
>
> On Sun, 12 May 2013, Jonathan DuBois wrote:
>
> Hi Bruce,
>> Thanks for the quick response. The label is a manually traced area of the
>> cortex. It is in subject scanner s
Hi Jonathan
>
> what is the label? What space is it in? If it has gray/white contrast you
> could try bbregister.
>
> cheers
> Bruce
>
> On Sat, 11 May 2013, Jonathan DuBois wrote:
>
> Hi Freesurfer Experts,
>> I have a binary volume label in subject space
Hi Freesurfer Experts,
I have a binary volume label in subject space that I converted from MINC to
MGZ. I would like to register it to the surface of that subject as a flat
label. I thought I would be able to do so with mri_vol2surf but I am not
sure how to generate the required registration file.
e the average and slope per time unit. But it depends on what you
> are trying to achieve, one could also compare rate of change in first
> year vs. rate of change in second year for a 3 tp study (each a year
> apart). Or more complex longitudinal models
>
> Best, Martin
>
> On
Hi Freesurfer users,
I have been working from the list posting below for vertex comparison of
longitudinal thickness data, although there are a couple issues I was hoping
someone could help with.
Using FS v5.0 with the fixed binaries, I have put together the following
steps for data comparison f
When correcting for multiple comparisons with Bonferroni for FS parcilation
statistics, is it necessary to adjust for all parcellations (35) or just the
variables (in our case mean thickness and surface area)? Assuming that no
prior hypothesis is used to constrain the number of parcellations.
Than
27 matches
Mail list logo
