hi, expert,
By mapping a surface label to a functional template, I want to extract the
corresponding cortical gray matter region in the functional space. I know I
should use the mri_label2vol command.
In the help page of mri_label2vol, I see some examples of this command.
2. Convert a surface
hi, expert,
How could I obtain the surface area of each region on the Desikan template?
How can I obtain this area in both native space and the average template space?
In the surf folder of each subjects, I noticed there is lh.area file, what is
meaning of this file? Do I need ?h.area for
Dear expert, We compute the MRI data with FREESURFER using
instruction recon-all -s -all,but some data will show recon -all exited
with ERRORS in the recon-all-status.log. The flowing display error information
:status file for recon-allThu Nov 11 19:22:13 HKT 2010recon-all finished
hi, expert,
In a paper named MRI of hippocampal volume loss in early Alzheimer's disease,
I can see the average volume of hippocampus is 2133mm^3 for 279 normal controls
with std=25 as well as 1631mm^3 for 330 AD subjects with std=34.
However, in the aseg.stats, the volume of a normal subject
Hi, expert,
I would like to measure the volume of hippocampus, is there any way i can
obtain the raw volume of hippocampus for each subject? How can I obtain it?
In fact, in the folder stats, there is a file named aseg.stat, where I can find
a line which contains ColHeaders Index SegId
p...@netfilter.com.br 写道:
发件人: Pedro Paulo de Magalhães Oliveira Junior p...@netfilter.com.br
主题: Re: [Freesurfer] hippocampus volume
收件人: Zhangyuanchao woshizhan...@yahoo.cn
抄送: freesurfer@nmr.mgh.harvard.edu
日期: 2010年8月6日,周五,下午10:22
look at the aseg.stats
sum left with right
!
--- 10年8月6日,周五, Bruce Fischl fis...@nmr.mgh.harvard.edu 写道:
发件人: Bruce Fischl fis...@nmr.mgh.harvard.edu
主题: Re: [Freesurfer] hippocampus volume
收件人: Zhangyuanchao woshizhan...@yahoo.cn
抄送: freesurfer@nmr.mgh.harvard.edu
日期: 2010年8月6日,周五,下午10:59
the volume of each is given separately. I think
Hi, expert,
I used freesurfer on a 32bit ubuntu operation system some days ago. For one
subject, the recon-all -s $filename -all command need 30 hours or less. I
changed it to 64bit Centos operation system, however, the precessing time
needed for one subject seems longer than on 32bit system,
Hi, expert,
Could anyone tell me the effect of the radius on lGI. After reading the paper
on lGI carefully, I still can not get a clear view of the effect of the radius
on lGI.
I still wonder why the default radius are chosen to be 25mm since there is very
little discussion of the standard
Hi,Marie
In the paper A surface based approach to quantify local gyrification on TMI.
There is a discussion the relation between lGI and curvature-based method. I
noticed the following discussion:
In the current study, all the GI measurements were computed on cortical
surfaces based on
Hi, expert,
I would to know what is the exact value of the radius when calculating lGI;
How could I check that value?
Thanks a lot!
yuanchao
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Dear experts,
I have some data of format .dc3, I would like to calculate the cortical
thickenss of the data.
I launched the command recon-all -i subjectname/***.dc3 -s subjectname, In
addition, I also tried recon-all -i ** -force, For some of the subjects,
It runs without error, while for
Dear expert,
Our group have some data scaned from 7T scaner. I would like to calculate the
cortical thickness of the data, however, when I processed them as I do for data
from 3T scaner, I can not run recon-all command successfull to the end. Could
you give me some suggestions on how to
Hi, experts,
I am interested in only the positive sulc and would like to make group
analysis of the postive sulc values. Hence I would like to mask off the
negative values (as the lh.sulc file has both positive and negative value).
Before making group analysis, I have to resample and smooth
Hi,all
I am interested in only the positive sulc and would like to make group
analysis of the postive sulc values. Hence I would like to mask off the
negative values (as the lh.sulc file has both positive and negative value).
Before making group analysis, I have to resample and smooth the
Is there any build-in function that I can average a curvature file with Radius
of 4mm on the surface, for example, lh.pial.H.crv file. in addition, lh.curv
are smoothed in some way, is it smoothed simply by averaging the values?
Thanks!
Best Regards,
yczhang
Dear Mr or Ms
Is there any way that we can obtain curvature value of the pial surface? I am
not sure whether lh.curv is the curvature file that I want. How can I calculate
the mean curvature, Gauss curvature of the pial surface and the GM/WM interface?
Is there any built-in function in
When I compare the thickness measure among subjects, I have to resample and
smooth the thickness, so that each data have the same number of vertices and
which are in correspondence with one another across subjects.
Now I have .curv files or .sulc files for each subject and would like to make
Dear Expert,
I want to exame the symmetry property of two hemispheres,for example, symmetry
of cortical thickness or lgi, I want to know whether the same ID of the two
hemispheres after resampling using the average pial surface corespond to the
same anatomical region.
For example,
Dear Mr or Ms,
I want to see the symmetry property of two hemispheres,for example, symmetry of
cortical thickness or lgi, I want to know whether the same ID of the two
hemispheres after resampling using the average pial surface corespond to the
same anatomical region.
Thanks a lot!
Using lgi, I want to know whether I should mask out the corpus callosum and the
structures which lies below the corpus callosum as I do it using thickness
measure.
Thanks!
___
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Dear Mr or Ms,
My computer was installed with Freesurfer v4.0.3,centos4,
To make an average surface,I launch make_average_subject command,
I come across an error :
Processing subject 25/52 sh45 ...
Reading /media/sda5/yczhang/sh45/surf/lh.sphere.reg
Segmentation fault (core dumped).
Are the average subjects generated by different version of Freesurfer differ
greatly?
I obtained the cortical thickness,lGI using Freesurfer 4.0.3,
However, average subject can not be generated using Freesurfer 4.0.3 because
of error.Can I use the average subject generated using Freesurfer
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