Dear Douglas,
If I understand well no PVC corrected pet images from any method (MG,RBV or
GTM) have corrected white matter values ?
Where do you get the pons intensity,that has been PVC'ed, used to normalize
?
Best regards,
Matthieu
2016-01-11 21:04 GMT+01:00 Douglas N Greve :
> Yes with MGPVC
Dear Bruce,
thanks for answering. What we did to transform the original dicom files in
nii.gz files is the following freesurfer command:
mri_convert
the nii.gz files to standard oriented and cut files are the following commands
in FSL:
fsl swapdim -z -x -y
robustfov -i input -r output -i
Hi Susanne
I don't know enough about FSL to tell you. If you change the orientation
of the image so that our process of putting it in coronal slices
("conforming") changes, or you interpolate the image before giving it to
recon-all it will certainly change the results a bit. ALso, when you send
Hi Freesurfer users,
I am recently testing the QA Tools in order to identify errors, especially
aseg outliers.
I don''t know if this is the right place to make this question, but I
followed the instructions for download, install and usage, explained on:
https://surfer.nmr.mgh.harvard.edu/fswiki/Q
Hi All,
Currently running freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0
We replaced our mri_convert function in freesurfer/bin/ with the new
mri_convert function that was patched to appropriately handle 16bit
SMS/Multiband sequences (the patch intended to fix errors related to the
SMS-BOLD vo
GTM corrects for all ROIs, including WM and pons. The GTM is always run
and so pons is always available for normalization. RBV is derived from
the GTM so is also corrects in WM. MG does not correct in WM.
On 01/15/2016 04:22 AM, Matthieu Vanhoutte wrote:
> Dear Douglas,
>
> If I understand well
Hi Doug,
After reading your most recent reply, I just found that many of previous
freesurfer emails had gone to my junk box automatically, so I missed some of
your replies. Sorry!
Looking at the strace output I generated last time, here are the lines where
the program tries to stat and mkdir s
That all looks like hippocampal subfield stuff, which is Eugenio's realm.
On 01/15/2016 11:41 AM, Fengji Geng wrote:
> Hi Doug,
>
> After reading your most recent reply, I just found that many of
> previous freesurfer emails had gone to my junk box automatically, so I
> missed some of your repli
it is hard to tell from that view. Can you click on a point that appears
to be outside the brain so we can see what it looks like around that
point in all three views?
On 01/15/2016 10:56 AM, Xiaomin Yue wrote:
> Hi All,
>
> In fs5.3, I tried to generate a volume mask from the pial surface
> us
Did you only replace mri_convert? If so, that should not have affected
mri_parse_sdcmdir. Can you restore the original mri_convert and see if
the mri_parse_sdcmdir problem goes away?
On 01/15/2016 10:54 AM, Hunter Johndro wrote:
> Hi All,
>
> Currently running freesurfer-Linux-centos6_x86_64-sta
What happens if you try to run mri_convert ?
On 01/14/2016 05:10 PM, Jasmin Alves wrote:
>
> Jasmins-MacBook-Pro:freesurfer jasminalves$ ls -l
> $FREESURFER_HOME/bin/tksurfer
>
> -rwxr-xr-x 1 root wheel 103 May 14 2013
> /Applications/freesurfer/bin/tksurfer
>
>
> Jasmins-MacBook-Pro:freesur
That point is fairly close to the pial surface. What is your voxel size?
It will include any voxel even if only a corner of it has some surface
in it.
On 01/15/2016 12:16 PM, Xiaomin Yue wrote:
> here it is. thanks,
>
>
>
> > To: freesurfer@nmr.mgh.harvard.edu
> > From: gr...@nmr.mgh.harvard.ed
There are no rules for choosing the number. Usually the first couple
have most of the variance but it looks like yours are spread out a bit.
It looks like you reach a point of diminishing returns after 4 or so.
On 01/14/2016 03:43 PM, Afzal, Afsana wrote:
> Hi Doug,
>
> These are the first few
The voxel size is 1.5mm. Some of voxels in the gray matter are not included in
the mask as well. Why?
Xiaomin
On Fri, Jan 15, 2016 at 9:21 AM -0800, "Douglas N Greve"
wrote:
That point is fairly close to the pial surface. What is your voxel size?
It will include any voxel even if only
The xhemi analysis was set up to perform interhemispheric analysis (eg,
looking at asymmetries). You can use it to do the analysis you describe
though. Alternatively, you can also run
cd $SUBJECTS_DIR/yoursubject/surf
mris_left_right_register lh.sphere rh.sphere lh.sphere.left_right
rh.sphere.l
I think you could easily hit all those voxels with a 1.5mm voxel size.
Not sure what you are asking about in terms of gray matter.
On 01/15/2016 12:27 PM, Xiaomin Yue wrote:
> The voxel size is 1.5mm. Some of voxels in the gray matter are not
> included in the mask as well. Why?
>
> Xiaomin
>
Maybe, I misunderstand it. Is the pial surface same as gray matter? If not,
how could I create a gray matter mask?
Thanks,
Xiaomin
On Fri, Jan 15, 2016 at 9:31 AM -0800, "Douglas N Greve"
wrote:
I think you could easily hit all those voxels with a 1.5mm voxel size.
Not sure what you
That command seems to work; Here is the output. However in order to prevent
the message "access denied" though, should I re-download freesurfer and
make a new license text file?
EXAMPLE 1
APPLYING TRANSFORMS (INCLUDING TALAIRACH)
The volume can be resampled into another space by supplying a
tr
The pial surface is the boundary between the gray matter and the tissue
on the outside of the brain. It is not gray matter itself. If you want a
mask of cortical gray matter, then use mri_label2vol --seg ribbon.mgz
..., then binarize the output of that to give you cortical GM.
On 01/15/2016 1
or you can add --fillribbon to your surf2vol command (but the label2vol
method is probably better)
On 01/15/2016 12:32 PM, Xiaomin Yue wrote:
> Maybe, I misunderstand it. Is the pial surface same as gray matter?
> If not, how could I create a gray matter mask?
>
> Thanks,
>
> Xiaomin
>
>
>
>
Dear FreeSurfer colleagues,
We’re working with MS data and wanted your input on how we could best handle
patients with extensive cortical pathology causing inaccurate reconstructions
of the surfaces. In short the pial surfaces “dips” in too deep towards the WM
surface due to the T1-hypointensit
I do not think it is easy to solve the problem, because often it is unknown
were the exact GM/WM border is in the lesion. Manual editing may introduce a
bias to the CT, so probably it is better to leave it as a limitation of the
method.
Best, Martijn
Van: freesurfer-boun...@nmr.mgh.h
Hi Martijn,
Thank you for the response! I believe you are right that it is a complex
problem. It is true that the GM/WM border can sometimes by hard to identify in
type I (leukocortical) lesions, but in in purely intracortical lesions, it is
still readily identifiable. We also have correspondin
In that case it may be better to apply some form of GM lesion filling. Studies
have shown that (at least in FAST and SPM) WM lesions affect the GM
segmentation throughout the brain (i.e. Chard et al, Gelinau-Morel et al,
Battaglini et al) – and I have the feeling that the same is true for
FreeS
Hello Tobias,
The lesion segmentation toolbox, which has been validated in MS patients
(http://www.applied-statistics.de/lst.html) has a useful tool to fill in T1
hypointensities (based on Chard et al., 2010;
http://onlinelibrary.wiley.com/doi/10.1002/jmri.22214/abstract ).
The toolbox gener
Thanks.
Xiaomin
On Fri, Jan 15, 2016 at 11:41 AM -0800, "Douglas N Greve"
wrote:
or you can add --fillribbon to your surf2vol command (but the label2vol
method is probably better)
On 01/15/2016 12:32 PM, Xiaomin Yue wrote:
> Maybe, I misunderstand it. Is the pial surface same as gray
Hi again,
Thank you again for the response. We have been discussing such an approach as a
backup plan if it is not possible to adjust the pial surface with manual
interventions. It does not feel straightforward though as the lesion filling
techniques have only been used in WM before (AFAIK). As
Hi Prad,
Thank you for your response! Unfortunately the problematic issue here is
cortical MS lesions, which is not as easily fixed as WM lesions. If you plan on
using LST (which is a nice tool indeed) be sure to be attentive to
juxtacortical lesions as these, from my experience, are not always
Hello,
I have already downloaded freesurfer but kept getting a permission denied
response to trying any of the freesurfer commands. So I have re-downloaded
freesurfer and am on the "testing freesurfer" phase when I still receive
the same error
-bash: freeview: Permission denied
Thanks,
Jasmin
Hi John,
the lowess plot can be misleading sometimes (as it is just the smoothed scatter
data per group and not controlled for anything). It is not a regression
analysis. Also note that the columns in your M matrix are not the same as in
the table (because you usually drop the first 2 columns a
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