Hi, experts,
I am trying to use the template fsaverage_sym and tried to map the same set of
vertices onto the left and right pial surface. Surprisingly, these vertices on
the two surfaces did not correspond to the same anatomical cortical regions.
Sometimes, they correspond to each other very ba
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Dear Freesurfer Expert,
Can I change the color of loading from the annot file in Freeview? Thanks a
lot!
Best regards,
Ting
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Dear Freesurfer Experts,
I have a very simple question.
The white surface area we extract from the ?h.aparc.stats is the same area
we used in the mri_surf2surf by parameter area? or the mri_surf2surf is the
pial surface area?
I am looking forward to
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Dear Freesurfer Expert,
Is there a way to get the aparc.pial.stats in one command like
aparcstats2table?
Thanks a lot!
Best regards,
Ting
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Thank you so much! It is really helpful.
Best regards,
Ting Li
> On May 9, 2019, at 3:15 PM, Greve, Douglas N.,Ph.D.
> wrote:
>
> You can use aparcstats2table, just specify -p aparc.pial
>
> On 5/8/19 11:17 PM, Ting Li wrote:
&
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Dear Freesurfer Expert:
I have used the simulation code as show below:
mri_glmfit-sim \
--glmdir lh.gender_age.glmdir \
--cache 4 neg \
--cwp 0.05\
--2spaces
My question is how many iterations are done during this simulation? I didn’t
speci
t; That will use the pre-computed ("cached") CSD files distributed with
> FreeSurfer. This used 10,000 iterations.
>
> On 12/1/2019 11:34 PM, Ting Li wrote:
>
> External Email - Use Caution
> Dear Freesurfer Expert:
>
> I have used the simulation code as
the analysis metrics that I have
used. Do I understand correctly?
Best regards,
Ting Li
On Mon, Dec 2, 2019 at 11:57 AM Greve, Douglas N.,Ph.D. <
dgr...@mgh.harvard.edu> wrote:
>
>
> On 12/2/2019 11:58 AM, Ting Li wrote:
>
> External Email - Use Caution
> Dear Dr
a t-test. Look in the back of a
> stats book from the 1950s and you will find a table of t-ratios and
> corresponding p-values. Obviously, they did not have access to any of the
> data being analyzed today:), but the tables are still valid.
>
> On 12/2/2019 2:03 PM, Ting Li wrote:
&g
his is no different than, eg, a t-test. Look in the back of a
> stats book from the 1950s and you will find a table of t-ratios and
> corresponding p-values. Obviously, they did not have access to any of the
> data being analyzed today:), but the tables are still valid.
>
> On 12/2/201
PM Greve, Douglas N.,Ph.D. <
dgr...@mgh.harvard.edu> wrote:
>
>
> On 12/3/2019 1:36 PM, Ting Li wrote:
>
> External Email - Use Caution
> Dear Dr. Douglas,
>
> Thank you so much for all the answers. I have two more questions.
>
> 1, When the Monte Car
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Dear Dr. Douglas,
Thank you so much!
Best regards,
Ting
On Thu, Dec 5, 2019 at 11:45 AM Greve, Douglas N.,Ph.D. <
dgr...@mgh.harvard.edu> wrote:
> I've attached a couple of papers
>
> On 12/3/19 9:24 PM, Ting Li wrote:
>
Dear Stuff,
Happy new year.
Does Freesurfer work for new born baby MRI or not? If I want to use it for baby
MRI, what should I pay attention to? Thanks a lot!
Best wishes,
Ting
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Thanks for your response.
Ting
> On Jan 3, 2018, at 9:48 AM, Lilla Zollei wrote:
>
>
> The currently available FS pipeline does not work for newborn infant brain
> MRI.
> Lilla
>
> On Tue, 2 Jan 2018, Ting Li wrote:
>
>> Dear Stuff,
>>
>> Happy
Hi Freesurfer Expert,
I am very new to Freesurfer and have a very basic question. How to convert .nii
files to nii.gz? I have tried the mri_convert subject_name.nii to
subject_name.nii.gz directly. It gives me an error information that
mri_convert: command not found. Thanks for your help!
Bes
SURFER_HOME is set
> properly). If it is, you can do:
>
> source $FREESURFER_HOME/SetUpFreeSurfer.csh
>
> Are you new to Linux also? If so, you might want to go through some basic
> tutorials.
>
> cheers
> Bruce
>
> On Fri, 19 Jan 2018, Ting Li wrote:
>
>&
Hi, all experts,
I am studying the AnatomicalROIV6.0 tutorials. In the Anatomical ROI analysis
tutorial, the first four part work well. While in the Group stats files, I got
an error information like this.
group_analysis_tutorial ting$ asegstats2table --subjects 004 021 040 067 080
092 \
>
eers
> Bruce
> On Sat, 20 Jan 2018, Ting Li wrote:
>
>> Hi Bruce,
>> Thanks for your quickly response. Sorry for my late.
>> I try to run FreeSurfer in a server. It was installed in my home share
>> folder. Here is the setting
>> environment information.
>
Dear FreeSurfer Expert,
Could you explain me what does the curvature index and folding index mean in
the Parcellation Stats File? In which way they are calculated? or you can give
me some related documents. Thanks a lot.
Ting
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Hi FreeSurfer Expert,
I followed the Anatomical ROI analysis tutorial and make a aseg.vol.table for
the 40 subjects. However, the segment volume can various a lot in different
subjects, such as Left-Lateral-Ventricle, Left-Inf-Lat-Vent. I attached a
screenshot. Thanks for your response.
Best
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Hi Freesurfer Experts,
We want to run recon-all with a custom atlas which is generated from ANTs
multivariate template construction. What is the right procedure to run
recon-all? Run recon-all to my atlas itself first and them use this output as a
t
las N. Greve wrote:
>
> Is the atlas in GCA format? If so, then you can use gca-apply
>
>
> On 04/19/2018 10:09 AM, Ting Li wrote:
>> Hi Freesurfer Experts,
>>
>> We want to run recon-all with a custom atlas which is generated from
>> ANTs multivariat
subjects and perform the GLM analyses?
I really need your help for this. Thanks for your time.
Best,
Ting
> On Apr 19, 2018, at 11:42 AM, Ting Li wrote:
>
> Douglas,
>
> Thank you so much for your response. My atlas is nii.gz format. What should I
> do to get the cortical
e volume template. If you want to use a custom volume-based
> segmentation atlas, then you'll need to run gcatrain and gca-apply
>
>
> On 04/19/2018 01:28 PM, Ting Li wrote:
>> External Email - Use Caution
>>
>> Douglas,
>>
>> Sorry f
tes> ) is the
right way to go? Thanks for your time.
Best,
Ting
> On Apr 19, 2018, at 2:22 PM, Ting Li wrote:
>
> Douglas,
>
> Thanks for your quick response. If I only want the information of cortical
> thickness, surface area, volume for various cortical regions and LGI
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Thanks for your patience with me. I am really appreciate. : )
Ting
> On Apr 19, 2018, at 3:14 PM, Douglas N. Greve wrote:
>
> The wiki and the papers :)
>
>
> On 04/19/2018 03:22 PM, Ting Li wrote:
>> Exte
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Hi FreeSurfer Experts,
I would like to do the surface analysis among two groups, like the thickness,
volume and area. When I run the GLM, do I have to consider the eTIV as a
covariant or not? Thanks a lot!
Best wishes,
Ting
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Thank you so much!
Ting
> On Jun 29, 2018, at 2:10 PM, Douglas Greve wrote:
>
> Yes, for area and volume, no for thickness
>
> On 6/29/18 3:06 PM, Ting Li wrote:
>> External Email - Use Caution
>>
>> Hi F
clusterwise
correction results has disappeared. Can you help me on this? Thanks a lot!
Best wishes,
Ting Li
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The information in this e
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Hi Douglas,
I try to use permutation but it takes forever. I never see the end. Do I have
to update the freesurfer to use the permutation? As it was recommended in this
year?
Best,
Ting
> On Jul 3, 2018, at 11:07 AM, Douglas N. Greve wrote:
>
> A
eve wrote:
>
> I'm not sure what you mean by this. power with clusterwise corrections
> is quite tricky. You'd have to do a simulation under non-null conditions
> to see what the true positive rate is
>
>
>
> On 07/10/2018 11:53 AM, Ting Li wrote:
>>
;
>
> On 07/05/2018 12:34 PM, Ting Li wrote:
>>
>> External Email - Use Caution
>>
>> Dear Freesurfer Experts,
>>
>> I am running the multiple comparison (permutation) on a MAC with the
>> following code. It has taken 8 hours and ha
= yhat.vol + randn(size(rstd.vol)).*rstd.vol; % add noise
> fname = sprintf('synth%04d.mgh',n);
> MRIwrite(y,fname);
> end
>
> On 07/16/2018 01:43 PM, Ting Li wrote:
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>>
>> Hi Douglas,
>>
>> Thanks for
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Hi experts,
How to create the stack of P2P3.stack.mgh after mris_preproc and mir_surf2surf?
Great thanks.
Regards,
Ting
> On Aug 14, 2018, at 10:51 AM, Douglas Greve wrote:
>
> First, run mris_preproc and mri_surf2surf commands as before to creat
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Hi Douglas,
You instruction works perfect. Thanks a lot.
Regards,
Ting
> On Aug 14, 2018, at 11:01 AM, Ting Li wrote:
>
> Hi experts,
>
> I have a significant cortical thickness cluster and want the cluster
> thickness in
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Hi experts,
I have extracted the area of the significant cluster with the command like the
following:
mri_segstats --i mgh/lh.volume.all.mgh --seg
glmdir_az_vz/lh.volume.all.glmdir/av-group2-vs-group2/cache.th20.neg.sig.ocn.mgh
--id 1 --sumwf gro
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Dear Freesurfer Experts,
I really need your attention and help. Thanks a lot.
We want to create label through the mri_glm-fit-sim cluster results.
We have found the same topic in 2013 and tried the method you have provided.
However, it doesn’t work
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I have also tried the command without annot in specifying the annotation file.
Thanks a lot.
Regards,
Ting
> On Oct 3, 2018, at 9:36 PM, Ting Li wrote:
>
> Dear Freesurfer Experts,
>
> I really need your attention and help. Thanks
create label through mri_glm-fit-sim clusters. What command I should
use? Please specify it for me. Thanks a lot!
Your help means a lot.
Regards,
Ting
> On Oct 3, 2018, at 9:38 PM, Ting Li wrote:
>
> I have also tried the command without annot in specifying the annotation
> fi
> Which subject did you load it on? It must be fsaverage. Can you send the
> terminal output and command line?
>
> On 10/03/2018 11:31 PM, Ting Li wrote:
>>
>> External Email - Use Caution
>>
>> Dear Freesurfer Expert,
>>
>> I have figur
the Annotation from the panel just below it. It does not make
> sense that you would see the branches on the folded surface but not on
> the inflated.
>
> On 10/15/2018 03:06 PM, Ting Li wrote:
>>
>> External Email - Use Caution
>>
>> I didn't load
lated surface, do you still see the branch?
>
> On 10/15/2018 08:42 PM, Ting Li wrote:
>> External Email - Use Caution
>>
>> The annot file loaded successfully and without any branches. Thanks a lot.
>>
>> Ting
>>> On Oct 15, 2018, at 2:22 PM, Greve
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Dear Freesurfer Experts,
Where I can find any document that explaining how the cortical area and volume
were calculated? or Could you give me an introduction about it.
Thank you so much!
Best regards,
Ting
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