you can apply the brainmask to any volume using mri_mask, including the
orig if you want. The skull stripping shouldn't amplify noise though. What
amplified noise regions do you mean? Maybe you can send a picture?
cheers
Bruce
On Thu, 4 Jul
2019, Admin wrote:
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Dear Freesurfer：
I am a graduate student of Northeastern University in China, and I do brain
image analysis . Now,I want generated a brain mask including the brain but
excluding the amplified noise regions after skull strip, but I can't find the
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Dear Antonin,
It is difficult to see what’s going on in the images you sent. Would you mind
uploading the subject, or at least sending us the image without the
segmentation overlaid (and ideally, a sagittal view as well)?
Cheers,
/Eugenio
--
Juan
Why do you want to convert it to ascii? We have tools that will smooth it. In
any event, you need something like
mris_convert -c lh.thickness lh.white lh.thickness.asc
On 7/3/2019 6:47 PM, Jee Su Suh wrote:
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Hello,
I am trying to convert ascii files
Hi JeeSu
if you look at the help for mris_convert, you'll see this example:
Convert a scalar overlay file in "curv" format to ascii:
mris_convert -c lh.thickness lh.white lh.thickness.asc
which you should follow
cheers
Bruce
On Wed, 3 Jul 2019,
Jee Su Suh wrote:
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thanks doug
paul
On Wed, Jul 3, 2019 at 4:10 PM Greve, Douglas N.,Ph.D. <
dgr...@mgh.harvard.edu> wrote:
> yes
>
> On 7/3/2019 4:03 PM, miracle ozzoude wrote:
>
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> E.g. if there are 68 ROIs, single SUVr for each
yes
On 7/3/2019 4:03 PM, miracle ozzoude wrote:
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E.g. if there are 68 ROIs, single SUVr for each subject will be:
(# of voxels in ROI 1*(suvr of ROI1 ) + + # of voxels in ROI 68*(suvr
of ROI 68))
_
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E.g. if there are 68 ROIs, single SUVr for each subject will be:
(# of voxels in ROI 1*(suvr of ROI1 ) + + # of voxels in ROI
68*(suvr of ROI 68))
_ __
(# of voxels in ROI 1 +
You can look in the gtm.stats file for all the cortical ROIs. Multiply the
uptake value by the number of voxels in the ROI and then divide by the sum of
the number of voxels across all ROIs. See
https://surfer.nmr.mgh.harvard.edu/fswiki/PetSurfer here for the identity of
the columns in the
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Over the cortex.
On Wed, Jul 3, 2019 at 2:59 PM Greve, Douglas N.,Ph.D. <
dgr...@mgh.harvard.edu> wrote:
> The mean over what area? Whole brain or just cortex?
>
> On 7/3/2019 2:15 PM, miracle ozzoude wrote:
>
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Actually, I was able to figure it out. Class h_r_m only has one subject, so you
are asking it to compute the slope using a single data point. This is not
possible.
On 7/3/2019 2:44 PM, Marie Hill wrote:
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Command line: mri_glmfit --y lh.g4v1.10.mgh --fsgd
The mean over what area? Whole brain or just cortex?
On 7/3/2019 2:15 PM, miracle ozzoude wrote:
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Hello Expert,
How do i get a single SUVr value for PETsurfer? Similar to Mean_Thickness from
Freesurfer, I want to extract a global/Mean SUVr value for each of
Can you send the Xg.dat file?
On 7/3/2019 2:44 PM, Marie Hill wrote:
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Command line: mri_glmfit --y lh.g4v1.10.mgh --fsgd g4v1.fsgd dods --C
healthy-vs-bipolar-and-schizophrenia.mtx --C healthy-vs-bipolar.mtx --C
healthy-vs-schizophrenia.mtx --C
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Command line: mri_glmfit --y lh.g4v1.10.mgh --fsgd g4v1.fsgd dods --C
healthy-vs-bipolar-and-schizophrenia.mtx --C healthy-vs-bipolar.mtx --C
healthy-vs-schizophrenia.mtx --C bipolar-vs-schizophrenia.mtx --C
none-vs-risk-allele.mtx --surf fsaverage
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Hello Expert,
How do i get a single SUVr value for PETsurfer? Similar to Mean_Thickness
from Freesurfer, I want to extract a global/Mean SUVr value for each of my
subjects.
Thank you.
Paul
___
Freesurfer
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Hello,
I am running trac-all preproc with the following code
setenv FREESURFER_HOME /Applications/freesurfer_dev
source $FREESURFER_HOME/SetUpFreeSurfer.csh
*#Must set SUBJECTS_DIR to where data is or else uses what was set up when
installing
can you send the command line, full terminal output, your fsgd file, and the
Xg.dat created in the output?
On 7/3/2019 11:05 AM, Marie Hill wrote:
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Thanks. When I run mri-glmfit I get Error: matrix is ill-conditioned or badly
scaled.
I have normalised
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Thanks. When I run mri-glmfit I get Error: matrix is ill-conditioned or badly
scaled.
I have normalised the continuous variable Age.
Kind regards,
Marie
From: freesurfer-boun...@nmr.mgh.harvard.edu
on behalf
yes, qdec can only have 2 factors with 2 levels. both qdec and mri_glmfit are
linear methods (in fact, qdec just calls mri_glmfit).
On 7/3/2019 9:39 AM, Marie Hill wrote:
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Dear Sir/Madam,
Could I post the following message to the mailing list:
I am running
Hi Kayti
it's hard to say a priori. Run them all through and see how bad the
scanner effect is. Depending on which scans have which parameters some of
your differences may cancel or they may add.
cheers
Bruce
On Wed, 3 Jul 2019, Keith, Kathryn wrote:
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You're probably ok if design is balanced across scanner. So if you had
two groups that you want to compare, you should make sure that they are
represented equally across scanner.
On 7/3/2019 9:56 AM, Keith, Kathryn wrote:
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>
> Hi Bruce,
>
> Thanks so much
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Hi Bruce,
Thanks so much for the quick reply.
We have images from two studies that have two different T1 acquisitions. Both
have 1 mm3 voxels but have different TR's (2300 vs. 2500 ms), TE's (2.26 vs.
2.9 ms), TI's (900 vs 1070 ms), etc. They were
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Dear Sir/Madam,
Could I post the following message to the mailing list:
I am running a regression testing for significant difference in cortical
volume, thickness etc with 3 factors: diagnosis, genotype and gender, with age
as a nuisance factor.
I
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