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Yes, it solved my problem. Thank you Greve.
Hope next FS version will fix this bug.
Best,
Chenfei
-- 原始邮件 --
发件人: "Greve, Douglas N.,Ph.D.";
发送时间: 2019年3月7日(星期四) 凌晨2:30
收件人: "freesurfer@nmr.mgh.harvard.edu";
主题: Re:
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Dear FS List,
(apologies for reposting under different title)
I wanted to check if my GLM design for a surface based analysis is sound. I
am new to FS so please don’t skip over details.
I have 3 groups of monozygotic twins: low-risk, high-risk, ill.
Hello,
I am wondering how to generate a label in FreeSurfer from peak activation in a
cluster - is there a specific command?
Thank you.
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This does appear to be a bug. Are you using FS version 6? If so, I put a
test in that distriubtion called preproc-sess.test. Can you try running
that on a subject and see if you get the desired behavior?
On 3/6/19 1:31 PM, Nasiriavanaki, Zahra wrote:
>
> Hi Doug
>
>
> I re-analyzed one of my
Procedurally, you would create stacks (eg, mris_preproc) of the
thickness and the PET data, then you would use one as the --y input to
mri_glmfit and the other as --pvr input (in addition to your fsgd file
or design matrix). The PVR is per-voxel regresssor, so it will create a
design matrix
Your FSGD file is incorrect in several ways. Under "variables" you have
"Sex" and list "Male" and "Female". The variables must be numbers, not
strings. The variables should also represent continuous quantities, not
categories. To handle sex, you should have a total of 6 categories, the
3 that
Only one mask and one threshold is used. If you need to combine masks in
some way, you can use fscalc (or mri_binarize).
On 3/5/19 12:47 PM, Zhi Li wrote:
>
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>
> Hello Freesurfer experts,
>
> I would like to use mri_segstats with two different masks and
>
you can use mri_segstats with the --slabel option
On 3/5/19 10:35 AM, Bruce Fischl wrote:
> Hi Kan
>
> you can give the surface-based label to mris_anatomical_stats and it
> will constrain it's calculations to the label (where it makes sense):
>
> mris_anatomical_stats -l ...
>
> you can
Can you tar up and upload the subjects to
ftp://surfer.nmr.mgh.harvard.edu/transfer/incoming
Let me know when they are there
On 3/4/19 4:59 PM, Maxime Perron wrote:
>
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>
> Hi Freesurfer Experts,
>
>
> I was wondering if you have had time to look at my
What is actually in the gii file? It is expecting only to read in
overlay information (eg, a binary mask with values of 0 or 1 at each
vertex). I have not used gifti all that much
On 3/4/19 10:55 AM, CAGNA Bastien wrote:
>
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>
> Hi everyone,
> I need to
that mri_tessellate command should have worked. It might be a gifti
problem. Can you run it with our standard surface as an output and view
it in freeview?
On 3/3/19 11:47 AM, Max Crayen wrote:
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>
> Hi Bruce,
>
> we are 3D printing brains in our lab, at
Sorry Riya, you have to run it all.
doug
On 3/3/19 11:36 AM, Riya Chatterjee wrote:
>
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>
> Hi,
>
> I am new to FreeSurfer - I am a high school sophomore trying to learn
> more about processing brain MRI's. I have read through most of the
> documentation,
Dear Freesurfer community,
We acquired images in Bay3 and would like to know where the gradient
inhomogeneity correction files would be on cluster, if any.
We are familiar with the Bay4 procedure for correcting for inhomogeneity and
were also wondering if similar steps would be followed for
I don't think so. The surfaces are at about 1mm resolution, which should
be fine for this. The reason that RBV had to be upsampled is that there
is no way to represent the different tissue types at a single (big) voxel
On 3/6/19 4:46 PM, Matthieu Vanhoutte wrote:
>
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Dear Douglas,
RBV PVC use the advantage of upsampled gtmseg space at 0.5 mm3 to compute
PVCorrected images. Would it be beneficial to project this PVCorrected
images onto gtmseg space surfaces to keep this upsampled resolution ?
Or would it be
Hi Daniel
left and right hippocampus have different indices (17 and 53)
cheers
Bruce
On Wed, 6 Mar
2019, Daniel Callow wrote:
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Never mind. I see that I can use those to id #'s to call from
FreeSurferColorLUT.txt.
I assume that those Id's are
Hi Atena
the vertex indices are stored in the first column. You should be able to
use them to look up into any overlay you want
cheers
Bruce
On Wed, 6 Mar 2019, Atena Rezaei wrote:
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Hi Bruce,
I am going to extract the cortical parcellation
Hello - I'm wondering how to generate a label in FreeSurfer from peak
activation in a cluster? Is there a specific command?
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Hi Doug
I re-analyzed one of my subjects from the very beginning with -projfrac 0.2.
But still, in mri_vol2surf, the projfrac is 0.5 (copied below). Could you
please let me know what I'm doing wrong?
Here is my command:
preproc-sess -s $subj -per-run -nostc -fwhm 0 -projfrac 0.2 -surface
This is a bug in mris_preproc. I have created a new version here
https://gate.nmr.mgh.harvard.edu/safelinks/greve/mris_preproc
Copy this to $FREESURFER_HOME/bin (after making a backup of the one that
is there)
let us know if this works
On 3/2/19 8:57 AM, Chenfei YE wrote:
>
> External
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Never mind. I see that I can use those to id #'s to call
from FreeSurferColorLUT.txt.
I assume that those Id's are consistent for both left and right hippocampus.
Thanks for the help!
*Daniel Callow*
*PhD Student, Neuroscience and Cognitive Science*
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Hi Bruce,
I am going to extract the cortical parcellation file with its color table
from freesurfer then import that in the other interface to detect and
visualize the somatosensory (3b broadmann ) area. Therefore, I need the
fifth column with some
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Hi Doug,
Thank you for your reply!
Unfortunately when I run the same code as before but by calling to
/Applications/freesurfer/average/HippoSF/atlas/compressionLookupTable.txt
instead of /Applications/freesurfer/FreeSurferColorLUT.txt and using the
look in $FREESURFER_HOME/average/HippoSF/atlas/compressionLookupTable.txt
The first number should be the one you are looking for.
On 3/6/19 12:26 PM, Daniel Callow wrote:
>
> External Email - Use Caution
>
> Hello,
>
> I am trying to extract stats from the hippocampal subfield volumes
>
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Thank you very much. I would like to whiten the data. May I know the
details of the whitening process used in FSFAST? If I could get the
whitening matrix (maybe from the source codes)?
Best regards,
Lizhi
On Wed, 6 Mar 2019 at 11:54, Greve, Douglas
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Hello,
I am trying to extract stats from the hippocampal subfield volumes that I
have warped to diffusion space.
mri_vol2vol --mov
/Volumes/DANIEL/dti_freesurf/dtrecon/${subj}.${cond}./lowb.nii.gz --targ
On 3/4/19 10:11 AM, Hengameh Marzbani wrote:
>
> External Email - Use Caution
>
> Hi Freesurfers,
>
> I want to do group analysis on four groups and use the volume values
> in aseg,stats.
> 1- Is it correct that each subcortical segmentation is based on a
> "volumetric segmentation
Whitening is done by default (you can turn it off with -nowhiten to
mkanalysis-sess). It uses an AR1 model.
On 3/4/19 12:46 PM, Zhi Li wrote:
>
> External Email - Use Caution
>
> Hello Freesurfer Experts,
>
> May I ask if there is a whitening/weighting matrix used to give
> weighted
There was not freesurfer specific publication from dt_recon. It is
really basic, so any publication that talks about fitting tensors to the
diffusion data will do.
On 3/4/19 12:30 PM, Daniel Callow wrote:
>
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>
> Hello,
>
> How should I go about properly
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Hi Ben -
Although I have not worked on this myself, it is my belief that FS
quantifies the CP fairly accurately. The volumes of the CP are being used
in understanding etiology and pathogenesis of psychiatric disorders such as
Schizophrenia. The lab I
Hi Atena
what were you hoping would be in the fifth column? What are you hoping to
create your own annotation files from? Can you give us a bigger picture of
what you are trying to achieve?
cheers
Bruce
On Wed, 6 Mar 2019, Atena Rezaei
wrote:
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Hi:
How can I get in an automatic way curved reformat images (for
example, see paper
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5009174/)
Sincerely,
Gonzalo Rojas Costa
Laboratory for Advanced Medical Image Processing
Department of Radiology
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Hi Bruce,
Thanks for your comment!
I used mri_annotation2label to existed lh.aparc.annot file in label folder
and got the labels. but the labels' text file contain 0 in fifth column.
I need to create atlas from my own data including surface
are they currently labeled 0? Where did you get your color LUT from?
On Wed,
6 Mar 2019, Jörg Stadler wrote:
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Hi Bruce,
this did not change anything. But I tried the process of mris_ca_train,
mris_ca_label with lh.oasis.chubs.annot and this worked fine.
A
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Dear Colleagues,
We are pleased to announce the release of DPABISurf! DPABISurf is a
surface-based resting-state fMRI data analysis toolbox evolved from
DPABI/DPARSF, as easy-to-use as DPABI/DPARSF. DPABISurf is based on
fMRIPprep 1.3.0.post3 (Esteban
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Dear FS List,
I wanted to check if my GLM design for a surface based analysis is sound. I
am new to FS so please don’t skip over details.
I have 3 groups of monozygotic twins: low-risk, high-risk, ill. Twin pairs
may be present in the same group (e.g
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Got it :)
filling the unassigned vertices with 'unknown' using tksurfer solved my
problem.
cheers,
Joerg
> Hi Bruce,
> this did not change anything. But I tried the process of mris_ca_train,
> mris_ca_label with lh.oasis.chubs.annot and this
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