ely,
Zheng
At 2021-01-28 23:27:27, "Douglas N. Greve" wrote:
No head motion correction because there is only one image
On 1/27/2021 6:59 PM, 郑凤莲 wrote:
External Email - Use Caution
Hi experts,
We have segmented hippocampus using Freesurfer 6.
External Email - Use Caution
Hi experts,
We have segmented hippocampus using Freesurfer 6.0. I have a question that is
there "head motion correct" in this step? If yes, how does it examined?
I am looking forward to your reply. Thanks very much.
Sincerely,
Zheng
| |
External Email - Use Caution
Hi experts,
I am using FS for some studies. Now, I have a question about format convertion.
How can I convert .mgz file to .nii file. Is there any way to complete?
Thanks for your contention in advance.
Sincerely,
Zheng
| |
郑凤莲
|
|
邮箱:zhengfenglian0
.
Sincerely,
Zhemg
| |
郑凤莲
|
|
邮箱:zhengfenglian0...@163.com
|
签名由 网易邮箱大师 定制___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
, "Iglesias Gonzalez, Juan E."
wrote:
Dear Zheng,
Can you please send us the log files?
Kind regards,
/Eugenio
--
Juan Eugenio Iglesias
Senior research fellow
CMIC (UCL), MGH (HMS) and CSAIL (MIT)
http://www.jeiglesias.com
From: on behalf of 郑凤莲
Reply-To: Freesurf
External Email - Use Caution
Hi exports,
I am using FS6.0 to segment hippocampus. I run "recon-all -s bert
-hippocampal-subfields-T1" and it said "recon all bert finished without error".
However, in mri directory, there is no l(r)h.hippoSfLabels-T1.v10.mgz file. And
in tmp
,
Zheng
| |
郑凤莲
|
|
邮箱:zhengfenglian0...@163.com
|
签名由 网易邮箱大师 定制___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
know the reason for this cese.
I am looking forward to your reply. Thanks very much in advance.
Sincerely,
Zheng
| |
郑凤莲
|
|
邮箱:zhengfenglian0...@163.com
|
签名由 网易邮箱大师 定制___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https
External Email - Use Caution
Hi Expert,
In the latest version of FS, I have segmented the thalamic successfully. But I
can't use Freeview to show the segmentation map. There is an error :"freeview:
/usr/lib/libpng15.so.15:version 'PNG15_0' not found (required by
External Email - Use Caution
Hi experts,
I have segmented the thalamic nuclei into 25 nuclei using the new FS version.
However, when I input "freeview -v nu.mgz -v
ThalamicNuclei.v10.T1.mgz:colormap=lut ", there is no 3D atlas in Freeview,
just nu.mgz. What's the matter? Please
External Email - Use Caution
Hi experts,
I am using qdec software for the statistic of LGI. I have created the .Qdecrc
file. However, when I set Monte Carlo Null-Z Simulation (fwhm=10), there is an
error: "Error running mri_surfcluster, Error: fwhm out-of-range(<1 or >30)".
. Is
there another new version for the thalamic? Could you share me the new version?
Thanks very much in advance. Look forward to your reply.
Sincerely,
Zheng
| |
郑凤莲
|
|
邮箱:zhengfenglian0...@163.com
|
签名由 网易邮箱大师 定制___
Freesurfer mailing list
Freesurfer
,
Zheng
| |
郑凤莲
|
|
邮箱:zhengfenglian0...@163.com
|
签名由 网易邮箱大师 定制___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
External Email - Use Caution
Hi experts,
I am using FS 6.0 for analyzing the cortical thickness difference between 3
groups: patient1, patient2 and control. In DODS model, I need to creat 2 files,
FSDG and mtx file. And we have 3 variables: age, gender and cortical
External Email - Use Caution
Dear experts,
I am using FS 6.0 for some studies. I want to calculate the thickness
difference between males and females in two group, Young group and Old group.
In DODS model:
The first step: creat a FSDG file:
GroupDescriptorFile 2
Title
On 8/12/18 5:17 AM, 郑凤莲 wrote:
External Email - Use Caution
Dear experts,
I an using FS 6.0 for cortical reconstructions. I can show whole brain
regions (tksurfer...), as shown in the picture. However, I just want to show
insular region. Is there any way to complet
External Email - Use Caution
Dear experts,
I an using FS 6.0 for cortical reconstructions. I can show whole brain
regions (tksurfer...), as shown in the picture. However, I just want to show
insular region. Is there any way to complete it? I am looking forward to your
External Email - Use Caution
Hi experts,
I am using FS dev version for hippocampal and amygdala subfields. It's an
automatic progress. Reviewers suggested that "Was the hippocampal and amygdala
segmentation visually inspected?" We have visually inspected the segmentation
and
.
Sincerely,
Zheng
| |
郑凤莲
|
|
邮箱:zhengfenglian0...@163.com
|
签名由 网易邮箱大师 定制___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person
Hi FS list,
When I sent an e-mail to you, I always recieved a disarmed e-mail, as follows:
What' wrong? Is there any way to resolve it?
Sincerely,
Zheng
| |
13181786167
邮箱:13181786...@163.com
|
签名由 网易邮箱大师 定制___
Freesurfer mailing list
Hi experts,
I am using FS 6.0 for LGI. My data is fetal images. I ran "recon-all" pipeline
for cotical thickness and LGI. Is it suitable? Or are the results reliable,
such as the LGI value of precental?
I am looking forward to your reply. Thank you very much.
Sincerely,
Zheng
Hi experts,
I am using FS 6.0 to calculate LGI. But when l ran recon-all, there is an
error: couldn't find DWI parameters. I don't know how to resolve this problem.
Looking forward to your reply. Thanks very much.
Sincerely,
Zheng
| |
13181786167
邮箱:13181786...@163.com
|
签名由 网易邮箱大师
Hi Experts,
I ran the segmentation of hippocampus in Freesurfer dev version. The left or
right whole volume isn't equal to the sum of 12 subfields. But it is equal to
the sum of the volume of tail, whole head and body. Why?
I am looking forward to your reply. Thank you very much.
Sincerely,
Hi professors,
I ran the segmentation of hippocampus in Freesurfer dev version. The left or
right whole volume isn't equal to the sum of 12 subfields. But it is equal to
the sum of the volume of tail, whole head and body. Why?
I am looking forward to your reply. Thank you very much.
Hi all experts,
I am using freesurfer dev version for segmentation of hippocampus and
amydala. I have a doubt about it.
1. In FS 6.0, I can type '203-226' in freeview for viewing subfields of
hippocampus. In dev version, When I type 'freeview -v nu.mgz -v
Hi FS experts,
I ran "segmentHA_T1.sh 0010006 $SUBJECTS_DIR" for amydala segmentations. But
there is only hippocampal subfields, no amydala segmentation .txt file in mri
file.
I ran ''recon-all'' in FS 6.0, and copy segmentHA_T1.sh and checkMCR to
FREESURFER_HOME.
Why there is no files
Hi professor,
I am using FS 6.0 for hippocampal subfield. I have a doubt what is the full
name of GC-DG? I didn't find it in the wiki.
Sincerely,
Zheng
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
ed from the data itself. The final
FWHM is a mixture of the applied FWHM and smoothness inherent in the data. LGI
has a lot of inherent smoothness, so the final FWHM is very large. The MC sim
table only goes up to 30mm, after that it generates an error
On 12/13/17 2:19 AM, 郑凤莲 wrote:
Hi profes
Hi professors,
I am using Freesurfer 6.0 for calculating LGI. I have done 'recon-all' for
it. When I ran Monte Carlo in qdec (FWHM=10), it has errors:
However, when FWHM=5, It was ok. What led to this result? I don't know why.
Thanks in advance !
Zheng
Hi FS professors,
I am using FS 6.0 for subcortical structures. I have a doubt about
thalamus and thalamus-Proper. I added thalamus to brainmask.mgz in Freeview,
it shows nothing. However, choose thalamus-Proper, it's ok. I just want to
ensure whether the thalamus-Proper in Freesurfer
h.harvard.edu> wrote:
>Hi Zheng
>
>For volume, usually including eTIV reduces the variance and increases power
>more than you lose for having one additional regressor. Not sure about
>gender - how unbalanced is your sample? You might be ok with just eTIV
>Bruce
>
>
&
sure what you mean by
>"which stat analysis".
>
>
>On 12/01/2017 07:50 PM, 郑凤莲 wrote:
>> Hi professor,
>>
>>I am using Freesurfer 6.0 and get the volume of subcortical
>> structures. I want to get the relationship between age and volume. I
t whatever you find to
>only reflect differences in head size
>
>cheers
>Bruce
>On Sat, 2 Dec 2017, 郑凤莲 wrote:
>
>> Hi Bruce,
>>
>> I think I get it. I have 27 males and 28 females and 26 males. It isn't
>> necessary to corrected by eTIV. Is it right?
>
ly including eTIV reduces the variance and increases power
>more than you lose for having one additional regressor. Not sure about
>gender - how unbalanced is your sample? You might be ok with just eTIV
>Bruce
>
>
>On Sat, 2 Dec 2017, 郑凤莲
>wrote:
>
>> Hi professor,
Hi professor,
I am using Freesurfer 6.0 and get the volume of subcortical structures. I
want to get the relationship between age and volume. I only have one group, is
it necessary to take gender and eTIV as a covariate? If it is necessary, Which
statistical analysis should be used?
I
should I do?
The picture is my result, but it doesn't corrected by eTIV. I appreciate your
help, please.
Thanks a lot!
Zheng
At 2017-11-22 10:29:43, "Bruce Fischl" <fis...@nmr.mgh.harvard.edu> wrote:
>you would include it as a nuisance variable in the glm
>On W
,
Zheng
At 2017-11-27 11:54:33, "Douglas Greve" <gr...@nmr.mgh.harvard.edu> wrote:
yes, that should work too
On 11/26/17 8:38 PM, 郑凤莲 wrote:
Hi Greve,
Tnahks for your reply. I used "mri_segstats --annot my_subject_id lh aparc
--i $SUBJECTS_DIR/my_subject_id/s
I get it. Thank you very much.
Best,
Zheng
At 2017-11-27 11:46:46, "Bruce Fischl" <fis...@nmr.mgh.harvard.edu> wrote:
It’s because people have found empirically that surface area and volume are
correlated with TIV, but thickness is not
cheers
Bruce
On Nov 26, 2017,
Hi Bruce,
Thanks for your help. But I have a doubt in why we should do in this way?
Are there any principles or mechanisms in Qdec?
Sincerely,
Zheng
At 2017-11-27 10:47:49, "Bruce Fischl" <fis...@nmr.mgh.harvard.edu> wrote:
Yes
On Nov 26, 2017, at 9:40 PM, 郑凤莲
)
>On Mon, 27
>Nov 2017, 郑凤莲 wrote:
>
>> Hi Greve,
>> Only for age and surface area, no thickness or volume, is it right?
>>
>> Thanks!
>> Zheng
>>
>>
>>
>>
>> At 2017-11-26 03:04:26, "Douglas Greve" <gr...@nmr.m
Hi Greve,
Only for age and surface area, no thickness or volume, is it right?
Thanks!
Zheng
At 2017-11-26 03:04:26, "Douglas Greve" <gr...@nmr.mgh.harvard.edu> wrote:
Yes, for age and surface area.
On 11/23/17 2:05 AM, 郑凤莲 wrote:
Hi professors,
.annot -c
../label/aparc.annot.ctab subject lh white
In the output, the mean LGI will be under the "ThickAvg" column
On 11/23/17 1:58 AM, 郑凤莲 wrote:
Hi experts,
I am using Freesurfer 6.0 for LGI. I ran recon-all and got the map of LGI.
My question is that can I get
Hi professors,
I am using Qdec in Freesurfer. I want to study the relationships between
age and cortical thickness, age and cortical volume, age and surface area. Is
it necessary to corrected by eTIV for volume and surface area in Qdec?
I am looking forward to your reply.
Thanks,
Hi experts,
I am using Freesurfer 6.0 for LGI. I ran recon-all and got the map of LGI.
My question is that can I get the specific value of every gyrus as the value of
thickness in the file of lh.aparc.stats? I can't find it from stats direction.
Thanks a lot !
On Nov 22, 2017, at 8:30 PM, 郑凤莲 <13181786...@163.com> wrote:
Hi Bruce,
Could tell me which is the whole brain volume,please? I'm not sure which is
right. I need your help.
Thanks very much.
Zheng
At 2017-11-22 11:07:36, "Bruce Fischl" <fis...@nm
racranial vault, so it
>included sulcal CSF. I think we include a whole brain volume in the
>aseg.stats file that you can use, although I don't remember what it's
>called
>
>cheers
>Bruce
>On Wed, 22 Nov 2017, 郑凤莲 wrote:
>
>> Hi Bruce,
>> Thank you very m
although I don't remember what it's
>called
>
>cheers
>Bruce
>On Wed, 22 Nov 2017, 郑凤莲 wrote:
>
>> Hi Bruce,
>> Thank you very much. I will try it. And I have another question. I also
>> want to study the
>> relation between age and the whole brain v
:43, "Bruce Fischl" <fis...@nmr.mgh.harvard.edu> wrote:
>you would include it as a nuisance variable in the glm
>On Wed, 22 Nov 2017,
>郑凤莲 wrote:
>
>> Hi Bruce,
>>
>> Thanks for your quick reply. These results are not correted by eTIV, If
>&g
10:14:16,"Bruce Fischl" <fis...@nmr.mgh.harvard.edu> 写道:
>is this eTIV corrected? I would look at some of the outliers and make
>sure that the segmentations are accurate. Certainly the trend is in the
>correct (and depressing) direction.
>
>cheers
>Bruce
>On
quot; <fis...@nmr.mgh.harvard.edu> wrote:
>Hi Zheng
>
>I would scatter plot age vs. volume, coloring men and women differently
>(or different symbols) with and without eTIV correction to get an idea of
>what is going on
>
>cheers
>Bruce
>
>
>On Mon, 20 Nov
>2017,
.
Sincerely,
Zheng
At 2017-11-01 21:59:11, "Yendiki, Anastasia" <ayend...@mgh.harvard.edu> wrote:
Hi Zheng - I'll need the trac-all.log file, the gradient table, and the b-value
table. Please do not send other data at the moment.
Thanks,
Anastasia.
From: 郑凤莲 <13181786...@163
Bruce Fischl" <fis...@nmr.mgh.harvard.edu> wrote:
>Hi Zheng
>
>how uniform is your distribution? I'm hardly an expert on this, but I
>wouldn't expect very large effects until you get into the older end of
>that range. Have you scatter plotted your data?
>Bruce
>On Mon,
ls for us to help.
>Are you correcting for eTIV? What measure are you comparing?
>
>cheers
>Bruce
> On Sun, 19 Nov 2017, 郑凤莲 wrote:
>
>> Hi Bruce,
>>
>> I am sorry for this situation.
>> In the first way, there was an statistical differe
this result.
Can you understand me this time?
Thanks,
Zheng
At 2017-11-18 22:58:56, "Bruce Fischl" <fis...@nmr.mgh.harvard.edu> wrote:
>Hi Zheng
>
>no difference between what and what?
>
>cheers
>Bruce
>On Fri, 17 Nov 2017, 郑凤莲 wrote:
>
>> Hi profe
Hi Professor,
I ran three steps of "recon-all" and get the cortical thickness, surfarea,
GrayVol in lh.aparc.stats and subcotical volume in aseg.stats. If I want to use
SPSS software for statistics, should I use eTIV as a covariate for everyone?
Thank you very much.
Sincerely,
Zheng
Hi Professor,
I ran three steps of "recon-all" and get the cortical thickness, surfarea,
GrayVol in lh.aparc.stats and subcotical volume in aseg.stats. If I want to use
SPSS software for statistics.
___
Freesurfer mailing list
ial volume? What is
the age range?
--
Juan Eugenio Iglesias
ERC Senior Research Fellow
Translational Imaging Group
University College London
http://www.jeiglesias.com
http://cmictig.cs.ucl.ac.uk/
From: <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of 郑凤莲
<1
-
Juan Eugenio Iglesias
ERC Senior Research Fellow
Translational Imaging Group
University College London
http://www.jeiglesias.com
http://cmictig.cs.ucl.ac.uk/
From: <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of 郑凤莲
<13181786...@163.com>
Reply-To: Freesur
Hi professor,
I am using Freesurfer for DTI data. When I run 'mri_segstats', I got the
result that there was anobvious difference in left hippocampus, but no
difference in right hippocampus. Then, I run segmentation of hippocampus
subfields.The result showed there is no difference in
Hi professor,
I am using Freesurfer for DTI data. When I run 'mri_segstats', I got the
result that there was an obvious difference in left hippocampus, but no
difference in right hippocampus. Then, I run segmentation of hippocampus
subfields. The result showed there is no difference in
Hi Melanie,
I don't understand what you mean. Could you tell me what I am going to do
to solve my problem?
Thanks,
Zheng
At 2017-10-30 16:33:02, "Melanie Ganz" wrote:
Hi,
So here’s the Wiki page for the human Allen brain data recons:
Hi Professor,
Thank you for publishing Freesurfer software. Now I am studying DTI using
Freesurfer. And I am interested in the technology of TRACULA. But when I run
it, I encountered an error about valid frame numbers, as shown in the picture.
And there is my dmrirc file. Do you know which
Hi Professor,
Thank you for publishing Freesurfer software. Now I am studying DTI using
Freesurfer. And I am interested in the technology of TRACULA. But when I run
it, I encountered an error about valid frame numbers, as shown in the picture.
And there is my dmrirc file. Do you know which
63 matches
Mail list logo