[Freesurfer] a problem

[Ting Li]

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 badly. For instance, one is 
mapped onto the lateral surface on the left pial surface, the other may be 
mapped onto the medial surface on the opposite hemisphere, I can not see their 
symmetry.
Any comment?

How can I establish the correspondence between the rh and lh pial surfaces?

Ting


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[Freesurfer] TIV should be considered as a covariant for thickness, volume and area analyses

[Ting Li]

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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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Re: [Freesurfer] TIV should be considered as a covariant for thickness, volume and area analyses

[Ting Li]

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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 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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Re: [Freesurfer] convert nii to nii.gz

[Ting Li]

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. 
Setting up environment for FreeSurfer/FS-FAST (and FSL)
FREESURFER_HOME   /home/share/freesurfer
FSFAST_HOME   /home/share/freesurfer/fsfast
FSF_OUTPUT_FORMAT nii.gz
SUBJECTS_DIR  /home/share/freesurfer/subjects
MNI_DIR   /home/share/freesurfer/mni

And I defined my SUBJECTS_DIR is /home/ting/freesurfer_subjects_data.
When I do a ls,  I can’t see the share folder. Do you think I should install if 
under /home/ting instead of /home/share?

Thanks a lot!

Best,
Ting

On Jan 20, 2018, at 9:12 AM, Bruce Fischl <fis...@nmr.mgh.harvard.edu> wrote:
> 
> 
> Hi Ting
> 
> that means $FREESURFER_HOME/bin is not in your path and you need to add it 
> (and make sure that the environment variable FREESURFER_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 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!
>> 
>> Best,
>> Ting
>> 
>> 
>> 
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[Freesurfer] Anatomical ROI analysis

[Ting Li]

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 \
>   --segno 11 17 18 \
>   --tablefile aseg.vol.table
  File "/Applications/freesurfer/bin/asegstats2table", line 195
print 'ERROR: subjects are not specified (use --subjects SUBJECTS)'
  ^
SyntaxError: invalid syntax

Thanks for your help. 

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[Freesurfer] Curvature Index and Folding Index

[Ting Li]

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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[Freesurfer] Does this analysis work for new born baby

[Ting Li]

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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Re: [Freesurfer] Does this analysis work for new born baby

[Ting Li]

Thanks for your response.

Ting
> On Jan 3, 2018, at 9:48 AM, Lilla Zollei <lzol...@nmr.mgh.harvard.edu> 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 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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[Freesurfer] questions about the segamentation volume

[Ting Li]

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 wishes,
Ting

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Re: [Freesurfer] Using a cluster as an ROI for further analysis

[Ting Li]

External Email - Use Caution

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 information in every subjects. How should I do it? Thanks. 
> 
> Ting 
>> On Aug 14, 2018, at 10:51 AM, Douglas Greve > <mailto:dgr...@mgh.harvard.edu>> wrote:
>> 
>> First, run mris_preproc and mri_surf2surf commands as before to create a 
>> stack of P2 and P3. If you ran mri_glmfit-sim on P1,  then you will have an 
>> "ocn" output file. You can run
>> mri_segstats --i P2P3.stack.mgh --seg ocn.mgh --id N --avgwf 
>> P2P3.means-in-clusterN.dat
>> where N is the number of your cluster
>> P2P3.means-in-clusterN.dat will have a row for each subject in the stack, 
>> the value will be the mean in cluster N
>> 
>> 
>> On 8/13/18 11:48 PM, Martin Juneja wrote:
>>> External Email - Use Caution
>>> 
>>> For instance, if there is any way to extract spatial location of cluster X1 
>>> and use this location to extract thickness values of all the subjects from 
>>> P2 and P3, that way I can perform two-sample t-test. I am not sure if 
>>> that's feasible and if so, then how can we do that?
>>> 
>>> On Mon, Aug 13, 2018 at 7:04 PM, Martin Juneja >> <mailto:mj70...@gmail.com>> wrote:
>>> Hi experts,
>>> 
>>> I found a cluster X1, which showed significant difference in cortical 
>>> thickness between two groups C1 and P1, determined using mris_preproc, 
>>> mri_surf2surf and mri_glmfit commands.
>>> 
>>> I am interested in determining if the same cluster X1 has significantly 
>>> different cortical thickness group between two other groups P2 and P3.
>>> 
>>> I would really appreciate if you could please give me the step-by-step 
>>> guidance how this can be done.
>>> 
>>> Thanks.
>>> 
>>> 
>>> 
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Re: [Freesurfer] Using a cluster as an ROI for further analysis

[Ting Li]

External Email - Use Caution

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 create a 
> stack of P2 and P3. If you ran mri_glmfit-sim on P1,  then you will have an 
> "ocn" output file. You can run
> mri_segstats --i P2P3.stack.mgh --seg ocn.mgh --id N --avgwf 
> P2P3.means-in-clusterN.dat
> where N is the number of your cluster
> P2P3.means-in-clusterN.dat will have a row for each subject in the stack, the 
> value will be the mean in cluster N
> 
> 
> On 8/13/18 11:48 PM, Martin Juneja wrote:
>> External Email - Use Caution
>> 
>> For instance, if there is any way to extract spatial location of cluster X1 
>> and use this location to extract thickness values of all the subjects from 
>> P2 and P3, that way I can perform two-sample t-test. I am not sure if that's 
>> feasible and if so, then how can we do that?
>> 
>> On Mon, Aug 13, 2018 at 7:04 PM, Martin Juneja > > wrote:
>> Hi experts,
>> 
>> I found a cluster X1, which showed significant difference in cortical 
>> thickness between two groups C1 and P1, determined using mris_preproc, 
>> mri_surf2surf and mri_glmfit commands.
>> 
>> I am interested in determining if the same cluster X1 has significantly 
>> different cortical thickness group between two other groups P2 and P3.
>> 
>> I would really appreciate if you could please give me the step-by-step 
>> guidance how this can be done.
>> 
>> Thanks.
>> 
>> 
>> 
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Re: [Freesurfer] question about the GLM power

[Ting Li]

External Email - Use Caution

Thanks for your detail information. I will try it now. 

Ting
> On Jul 16, 2018, at 1:26 PM, Douglas N. Greve  wrote:
> 
> It is different than the MC simulations. When you run mri_glmfit, 
> specify the --save-yhat option. This will create a file called yhat.mgh 
> which will be used as the non-null basis of the simulation. You will 
> have to add noise to this file and analyze through mri_glmfit and 
> mri_glmfi-sim and see if you get your cluster. Do this many times 
> (~1000) with  different noise each time, then simply compute how often 
> you see your cluster (this is the true positive rate). You can add the 
> noise in matlab, something like
> 
> yhat = MRIread('yhat.mgh');
> rstd = MRIread('rstd.mgh'); % standard deviation
> for n = 1:1000
>   y = yhat;
>   y.vol = 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:
>> External Email - Use Caution
>> 
>> Hi Douglas,
>> 
>> Thanks for your response. I did the  monte carlo simulation. Could you give 
>> me any instructions about how to perform a simulation under non-null 
>> conditions? Thanks a lot!
>> 
>> Best,
>> Ting
>>> On Jul 16, 2018, at 12:15 PM, Douglas N. Greve  
>>> 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:
>>>> External Email - Use Caution
>>>> 
>>>> Hi Freesurfer Expert,
>>>> 
>>>> How can I know the power of my GLM test after I did the clusterwise 
>>>> correction? I got this question because I had a problem like this. I have 
>>>> 21 subjects for group A and B. Once I delete one subject from group A, one 
>>>> of the clusterwise correction results has disappeared. Can you help me on 
>>>> this? Thanks a lot!
>>>> 
>>>> Best wishes,
>>>> Ting Li
>>>> 
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>>> 
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>>> 
>> 
>> 
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Re: [Freesurfer] question about the GLM power

[Ting Li]

External Email - Use Caution

Hi Douglas,

Thanks for your response. I did the  monte carlo simulation. Could you give me 
any instructions about how to perform a simulation under non-null conditions? 
Thanks a lot!

Best,
Ting
> On Jul 16, 2018, at 12:15 PM, Douglas N. Greve  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:
>> External Email - Use Caution
>> 
>> Hi Freesurfer Expert,
>> 
>> How can I know the power of my GLM test after I did the clusterwise 
>> correction? I got this question because I had a problem like this. I have 21 
>> subjects for group A and B. Once I delete one subject from group A, one of 
>> the clusterwise correction results has disappeared. Can you help me on this? 
>> Thanks a lot!
>> 
>> Best wishes,
>> Ting Li
>> 
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Re: [Freesurfer] Multiple comparison - permutation

[Ting Li]

External Email - Use Caution

Hi Douglas,

I just try your suggestion. It gives me information like the following. What 
does the design matrix stands for? Thanks. 

Ting

ERROR: design matrix is not orthogonal, cannot be used with permutation.
If this something you really want to do, run with --perm-force
> On Jul 16, 2018, at 1:09 PM, Douglas N. Greve  wrote:
> 
> 
> My guess is that something is going wrong with the backgrounding. Try 
> running it without the --bg option. You can run it with a few (eg, 100) 
> iterations just to see if it finishes.
> 
> 
> 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 has not finished yet. It 
>> gives me Poll jobs information without end. According to tutorial 
>> information, it will only take around 20 minutes. Do you know what 
>> should I do if I want to use this perm multiple comparison? I have 
>> attached my MAC system information and the Poll jobs information. 
>> Thanks a lot!
>> 
>> Best wishes,
>> Ting
>> 
>> mri_glmfit-sim \
>>>   --glmdir lh.volume_70_sTIV_perm.glmdir \
>>>   --perm 1000 4.0 neg \
>>>   --cwp  0.05\
>>>   --2spaces \
>>>   --bg 2
>> 
>> 
>> 
>> 
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Re: [Freesurfer] Using a cluster as an ROI for further analysis

[Ting Li]

External Email - Use Caution

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 group1_group2_volume_l.sum-clusters.dat

When I use a t-test for these two group summarized area value, the p value is 
0.1398. I did the same process for other significant clusters. However, it is 
the only one without significant p-value. The detail of the cluster information 
is listed below. 

# ClusterNo  Max   VtxMax   Size(mm^2)  MNIX   MNIY   MNIZCWPCWPLow
CWPHi   NVtxsWghtVtx   Annot

   1   -4.773   53922   1279.30-32.98.5   55.3  0.00300  0.00200  
0.00400   2126-5375.69  caudalmiddlefrontal

Could you give me some ideas where I should find the reason? Thanks a lot!

Regards,
Ting 
> On Aug 14, 2018, at 10:51 AM, Douglas Greve  wrote:
> 
> mri_segstats --i P2P3.stack.mgh --seg ocn.mgh --id N --avgwf 
> P2P3.means-in-clusterN.dat

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[Freesurfer] question about the GLM power

[Ting Li]

External Email - Use Caution

Hi Freesurfer Expert,

How can I know the power of my GLM test after I did the clusterwise correction? 
I got this question because I had a problem like this. I have 21 subjects for 
group A and B. Once I delete one subject from group A, one of the clusterwise 
correction results has disappeared. Can you help me on this? Thanks a lot!

Best wishes,
Ting Li

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Re: [Freesurfer] glmfit-sim FWHM 34?

[Ting Li]

External Email - Use Caution

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:
> 
> Also, I'm encouraging people to use permutation rather than 
> monte-carlo-based correction.

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[Freesurfer] convert nii to nii.gz

[Ting Li]

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!

Best,
Ting 



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Re: [Freesurfer] convert nii to nii.gz

[Ting Li]

Dear Bruce,

Thanks for your response. I will check it today.

Best,
Ting
> On Jan 21, 2018, at 10:41 AM, Bruce Fischl <fis...@nmr.mgh.harvard.edu> wrote:
> 
> Hi Ting
> 
> if you can't see the share folder then you can't access our binaries. Maybe 
> talk to your local sysadmins?
> 
> cheers
> 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. 
>> Setting up environment for FreeSurfer/FS-FAST (and FSL)
>> FREESURFER_HOME   /home/share/freesurfer
>> FSFAST_HOME   /home/share/freesurfer/fsfast
>> FSF_OUTPUT_FORMAT nii.gz
>> SUBJECTS_DIR  /home/share/freesurfer/subjects
>> MNI_DIR   /home/share/freesurfer/mni
>> And I defined my SUBJECTS_DIR is /home/ting/freesurfer_subjects_data.
>> When I do a ls,  I can’t see the share folder. Do you think I should install 
>> if
>> under /home/ting instead of /home/share?
>> Thanks a lot!
>> Best,
>> Ting
>> On Jan 20, 2018, at 9:12 AM, Bruce Fischl <fis...@nmr.mgh.harvard.edu> wrote:
>> 
>>  Hi Ting
>> 
>>  that means $FREESURFER_HOME/bin is not in your path and you need to add 
>> it
>>  (and make sure that the environment variable FREESURFER_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 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!
>> 
>>Best,
>>Ting
>> 
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[Freesurfer] Recon-all with custom atlas

[Ting Li]

External Email - Use Caution

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 
template or I use the custom template directly. I looked up your email database 
to search related topic and got lost. I have sent another email to your group 
and no response received. Please help me. 

Thanks for you time. I look forward to hearing from you. 

Best,
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Re: [Freesurfer] Recon-all with custom atlas

[Ting Li]

External Email - Use Caution

Douglas,

Thank you so much for your response. My atlas is nii.gz format. What should I 
do to get the cortical thickness, surface area and volume for various cortical 
regions? Thanks in advance. 

Best,
Ting


> On Apr 19, 2018, at 11:28 AM, Douglas N. Greve <dgr...@mgh.harvard.edu> 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 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 template or I use the custom template directly. I 
>> looked up your email database to search related topic and got lost. I 
>> have sent another email to your group and no response received. Please 
>> help me.
>> 
>> Thanks for you time. I look forward to hearing from you.
>> 
>> Best,
>> Ting
>> 
>> 
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Re: [Freesurfer] Recon-all with custom atlas

[Ting Li]

External Email - Use Caution

Douglas,

Sorry for bother you again. Our group want to study a cohort children’s brain 
using Freesurfer. We prefer to register our subjects to a custom children 
template. The template basically is an average of all the subjects we are going 
to study. It is constructed by ANTs. The format is nii.gz. My questions is 
where I should mention this registration template in the command Recon-all?  or 
how to get the cortical thickness, surface area and volume for various cortical 
regions for all subjects and perform the GLM analyses? 

In Freesurfer, there is a command of making own template for registration. If I 
generate my template from there, how can I run recon-all for the next to make 
sure my subjects all register to this template? and how to get the cortical 
thickness, surface area and volume for various cortical regions for all 
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 <tx...@ualr.edu> wrote:
> 
> Douglas,
> 
> Thank you so much for your response. My atlas is nii.gz format. What should I 
> do to get the cortical thickness, surface area and volume for various 
> cortical regions? Thanks in advance. 
> 
> Best,
> Ting
> 
> 
>> On Apr 19, 2018, at 11:28 AM, Douglas N. Greve <dgr...@mgh.harvard.edu> 
>> 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 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 template or I use the custom template directly. I 
>>> looked up your email database to search related topic and got lost. I 
>>> have sent another email to your group and no response received. Please 
>>> help me.
>>> 
>>> Thanks for you time. I look forward to hearing from you.
>>> 
>>> Best,
>>> Ting
>>> 
>>> 
>>> ___
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>>> Freesurfer@nmr.mgh.harvard.edu
>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>> 
>> ___
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>> 
>> 
>> The information in this e-mail is intended only for the person to whom it is
>> addressed. If you believe this e-mail was sent to you in error and the e-mail
>> contains patient information, please contact the Partners Compliance 
>> HelpLine at
>> http://www.partners.org/complianceline . If the e-mail was sent to you in 
>> error
>> but does not contain patient information, please contact the sender and 
>> properly
>> dispose of the e-mail.
>> 
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Re: [Freesurfer] Recon-all with custom atlas

[Ting Li]

External Email - Use Caution

Douglas,

Thanks for your quick response. If I only want the information of cortical 
thickness, surface area, volume for various cortical regions and LGI, then the 
Freesurfer template is good enough and I don’t need to apply my own template. 
This is really helpful. Is there any documents that you will recommend to get a 
better understanding about Freesurfer? 

Thanks a lot.

Ting 
> On Apr 19, 2018, at 12:39 PM, Douglas N. Greve <dgr...@mgh.harvard.edu> wrote:
> 
> If you want to do a surface-based analysis, then you don't need to have 
> an accurate 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 for bother you again. Our group want to study a cohort children’s 
>> brain using Freesurfer. We prefer to register our subjects to a custom 
>> children template. The template basically is an average of all the subjects 
>> we are going to study. It is constructed by ANTs. The format is nii.gz. My 
>> questions is where I should mention this registration template in the 
>> command Recon-all?  or how to get the cortical thickness, surface area and 
>> volume for various cortical regions for all subjects and perform the GLM 
>> analyses?
>> 
>> In Freesurfer, there is a command of making own template for registration. 
>> If I generate my template from there, how can I run recon-all for the next 
>> to make sure my subjects all register to this template? and how to get the 
>> cortical thickness, surface area and volume for various cortical regions for 
>> all 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 <tx...@ualr.edu> wrote:
>>> 
>>> Douglas,
>>> 
>>> Thank you so much for your response. My atlas is nii.gz format. What should 
>>> I do to get the cortical thickness, surface area and volume for various 
>>> cortical regions? Thanks in advance.
>>> 
>>> Best,
>>> Ting
>>> 
>>> 
>>>> On Apr 19, 2018, at 11:28 AM, Douglas N. Greve <dgr...@mgh.harvard.edu> 
>>>> 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 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 template or I use the custom template directly. I
>>>>> looked up your email database to search related topic and got lost. I
>>>>> have sent another email to your group and no response received. Please
>>>>> help me.
>>>>> 
>>>>> Thanks for you time. I look forward to hearing from you.
>>>>> 
>>>>> Best,
>>>>> Ting
>>>>> 
>>>>> 
>>>>> ___
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>>>>> Freesurfer@nmr.mgh.harvard.edu
>>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>>> ___
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>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>>> 
>>>> 
>>>> The information in this e-mail is intended only for the person to whom it 
>>>> is
>>>> addressed. If you believe this e-mail was sent to you in error and the 
>>>> e-mail
>>>> contains patient information, please contact the Partners Compliance 
>>>> HelpLine at
>>>> http://www.partners.org/complianceline . If the e-mail was sent to you in 
>>>> error
>>>> but does not contain patient information, please contact the sender and 
>>>> properly
>>>> dispose of the e-mail.
>>>> 
>> 
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Re: [Freesurfer] Recon-all with custom atlas

[Ting Li]

External Email - Use Caution

Douglas,

I have one more question. Do I need an accurate surface template for my 
surface-based analysis? Does this ( 
https://surfer.nmr.mgh.harvard.edu/fswiki/SurfaceRegAndTemplates 
<https://surfer.nmr.mgh.harvard.edu/fswiki/SurfaceRegAndTemplates> ) is the 
right way to go? Thanks for your time.

Best,
Ting
> On Apr 19, 2018, at 2:22 PM, Ting Li <tx...@ualr.edu> 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, then 
> the Freesurfer template is good enough and I don’t need to apply my own 
> template. This is really helpful. Is there any documents that you will 
> recommend to get a better understanding about Freesurfer? 
> 
> Thanks a lot.
> 
> Ting 
>> On Apr 19, 2018, at 12:39 PM, Douglas N. Greve <dgr...@mgh.harvard.edu> 
>> wrote:
>> 
>> If you want to do a surface-based analysis, then you don't need to have 
>> an accurate 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 for bother you again. Our group want to study a cohort children’s 
>>> brain using Freesurfer. We prefer to register our subjects to a custom 
>>> children template. The template basically is an average of all the subjects 
>>> we are going to study. It is constructed by ANTs. The format is nii.gz. My 
>>> questions is where I should mention this registration template in the 
>>> command Recon-all?  or how to get the cortical thickness, surface area and 
>>> volume for various cortical regions for all subjects and perform the GLM 
>>> analyses?
>>> 
>>> In Freesurfer, there is a command of making own template for registration. 
>>> If I generate my template from there, how can I run recon-all for the next 
>>> to make sure my subjects all register to this template? and how to get the 
>>> cortical thickness, surface area and volume for various cortical regions 
>>> for all 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 <tx...@ualr.edu> wrote:
>>>> 
>>>> Douglas,
>>>> 
>>>> Thank you so much for your response. My atlas is nii.gz format. What 
>>>> should I do to get the cortical thickness, surface area and volume for 
>>>> various cortical regions? Thanks in advance.
>>>> 
>>>> Best,
>>>> Ting
>>>> 
>>>> 
>>>>> On Apr 19, 2018, at 11:28 AM, Douglas N. Greve <dgr...@mgh.harvard.edu> 
>>>>> 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 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 template or I use the custom template directly. I
>>>>>> looked up your email database to search related topic and got lost. I
>>>>>> have sent another email to your group and no response received. Please
>>>>>> help me.
>>>>>> 
>>>>>> Thanks for you time. I look forward to hearing from you.
>>>>>> 
>>>>>> Best,
>>>>>> Ting
>>>>>> 
>>>>>> 
>>>>>> ___
>>>>>> Freesurfer mailing list
>>>>>> Freesurfer@nmr.mgh.harvard.edu
>>>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>>>> ___
>>>>> 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 to whom it 
&g

Re: [Freesurfer] Recon-all with custom atlas

[Ting Li]

External Email - Use Caution

Thanks for your patience with me. I am really appreciate. : )

Ting
> On Apr 19, 2018, at 3:14 PM, Douglas N. Greve <dgr...@mgh.harvard.edu> wrote:
> 
> The wiki and the papers :)
> 
> 
> On 04/19/2018 03:22 PM, Ting Li wrote:
>> External Email - Use Caution
>> 
>> Douglas,
>> 
>> Thanks for your quick response. If I only want the information of cortical 
>> thickness, surface area, volume for various cortical regions and LGI, then 
>> the Freesurfer template is good enough and I don’t need to apply my own 
>> template. This is really helpful. Is there any documents that you will 
>> recommend to get a better understanding about Freesurfer?
>> 
>> Thanks a lot.
>> 
>> Ting
>>> On Apr 19, 2018, at 12:39 PM, Douglas N. Greve <dgr...@mgh.harvard.edu> 
>>> wrote:
>>> 
>>> If you want to do a surface-based analysis, then you don't need to have
>>> an accurate 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 for bother you again. Our group want to study a cohort children’s 
>>>> brain using Freesurfer. We prefer to register our subjects to a custom 
>>>> children template. The template basically is an average of all the 
>>>> subjects we are going to study. It is constructed by ANTs. The format is 
>>>> nii.gz. My questions is where I should mention this registration template 
>>>> in the command Recon-all?  or how to get the cortical thickness, surface 
>>>> area and volume for various cortical regions for all subjects and perform 
>>>> the GLM analyses?
>>>> 
>>>> In Freesurfer, there is a command of making own template for registration. 
>>>> If I generate my template from there, how can I run recon-all for the next 
>>>> to make sure my subjects all register to this template? and how to get the 
>>>> cortical thickness, surface area and volume for various cortical regions 
>>>> for all 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 <tx...@ualr.edu> wrote:
>>>>> 
>>>>> Douglas,
>>>>> 
>>>>> Thank you so much for your response. My atlas is nii.gz format. What 
>>>>> should I do to get the cortical thickness, surface area and volume for 
>>>>> various cortical regions? Thanks in advance.
>>>>> 
>>>>> Best,
>>>>> Ting
>>>>> 
>>>>> 
>>>>>> On Apr 19, 2018, at 11:28 AM, Douglas N. Greve <dgr...@mgh.harvard.edu> 
>>>>>> 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 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 template or I use the custom template directly. I
>>>>>>> looked up your email database to search related topic and got lost. I
>>>>>>> have sent another email to your group and no response received. Please
>>>>>>> help me.
>>>>>>> 
>>>>>>> Thanks for you time. I look forward to hearing from you.
>>>>>>> 
>>>>>>> Best,
>>>>>>> Ting
>>>>>>> 
>>>>>>> 
>>>>>>> ___
>>>>>>> Freesurfer mailing list
>>>>>>> Freesurfer@nmr.mgh.harvard.edu
>>>>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>>>>> ___
>>>>>> Freesurfer mailing list
>>>>>> Fre

Re: [Freesurfer] create label from cluster obtained with mri_glm-fit-sim

[Ting Li]

External Email - Use Caution

Dear Dr. Douglas,

Thank you so much for your response. With your instruction, it works. This is 
how I did. 

First, copy the significant cluster annot file from the simulation fold to one 
of subject label folder.
Secondly, use the mir_annotation2label command to make this cluster into a 
label file
Thirdly, copy this label file to fsaverage label folder
Finally, I can load the label to the fsaverage surf. 

Is this the right procedure? Thanks a lot!

Regards,
Ting
> On Oct 10, 2018, at 1:30 PM, Greve, Douglas N.,Ph.D.  
> wrote:
> 
> 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 figured out the problem is that I didn’t specify lh before the 
>> annot file. However, in this method, I didn’t get the right label for 
>> I have loaded the label into the subject file. It is the scatter points.
>> 
>> I want to 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 >> <mailto:tx...@ualr.edu <mailto:tx...@ualr.edu>>> wrote:
>>> 
>>> 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 >>> <mailto:tx...@ualr.edu> 
>>>> <mailto:tx...@ualr.edu <mailto:tx...@ualr.edu>>> wrote:
>>>> 
>>>> 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. If you think it is not the right 
>>>> way, could you give me an example to do it right. I really 
>>>> appreciate your great help. Thanks a lot.
>>>> 
>>>> Here is my code:
>>>> 
>>>> mri_annotation2label --subject F999  --hemi lh --annotation 
>>>> cache.th20.neg.sig.ocn.annot --labelbase lh.test_label
>>>> 
>>>> Here is my error information:
>>>> subject = F999
>>>> annotation = cache.th20.neg.sig.ocn.annot
>>>> hemi = lh
>>>> labelbase = lh.test_label
>>>> surface   = white
>>>> 
>>>> Reading surface
>>>>  /media/set2iscsi/ting/origin_gz_data/F999/surf/lh.white
>>>> Loading annotations from 
>>>> /media/set2iscsi/ting/origin_gz_data/F999/label/lh.cache.th20.neg.sig.ocn.annot.annot
>>>> could not read annot file 
>>>> /media/set2iscsi/ting/origin_gz_data/F999/label/lh.cache.th20.neg.sig.ocn.annot.annot
>>>> No such file or directory
>>>> INFO: could not load from 
>>>> /media/set2iscsi/ting/origin_gz_data/F999/label/lh.cache.th20.neg.sig.ocn.annot.annot,
>>>>  
>>>> trying 
>>>> /media/set2iscsi/ting/origin_gz_data/F999/label/lh_cache.th20.neg.sig.ocn.annot.annot
>>>> could not read annot file 
>>>> /media/set2iscsi/ting/origin_gz_data/F999/label/lh_cache.th20.neg.sig.ocn.annot.annot
>>>> No such file or directory
>>>> ERROR: MRISreadAnnotation() failed
>>>> 
>>>> This is the annot files in my directory F999:
>>>> ls F999/label/*.annot
>>>> F999/label/cache.th20.neg.sig.ocn.annot 
>>>> F999/label/lh.BA_exvivo.annot F999/label/rh.aparc.DKTatlas.annot
>>>> F999/label/lh.aparc.a2009s.annot 
>>>> F999/label/lh.BA_exvivo.thresh.annot F999/label/rh.BA_exvivo.annot
>>>> F999/label/lh.aparc.annot F999/label/rh.aparc.a2009s.annot 
>>>> F999/label/rh.BA_exvivo.thresh.annot
>>>> F999/label/lh.aparc.DKTatlas.annot   F999/label/rh.aparc.annot
>>> 
>> 
>> 
>> 
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>> <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>
> 
> 
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Re: [Freesurfer] create label from cluster obtained with mri_glm-fit-sim

[Ting Li]

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, Douglas N.,Ph.D.  
> wrote:
> 
> Click on the surface file name in the upper left corner of FreeView, 
> then load 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 the annot file. I just use the annot file to create the 
>> label. if I check the clusters in a inflated brain, they are looks 
>> fine. If I need to load annot file for checking, how can I do it? 
>> Thanks a lot.
>> 
>> Ting
>> 
>> On Mon, Oct 15, 2018 at 9:25 AM Greve, Douglas N.,Ph.D. 
>> mailto:dgr...@mgh.harvard.edu>> wrote:
>> 
>>does the same thing happen when you load the annot file?
>> 
>>On 10/13/18 10:03 PM, Ting Li wrote:
>>> 
>>>External Email - Use Caution
>>> 
>>>Dear Dr. Douglas,
>>> 
>>>I can load the label, but some clusters have branches. Some of
>>>them are just looks fine. Do you know the reason? Thanks a lot.
>>> 
>>>Regards,
>>>Ting
>>> 
>>> 
>>> 
>>> 
>>>>On Oct 12, 2018, at 10:35 AM, Greve, Douglas N.,Ph.D.
>>>>mailto:dgr...@mgh.harvard.edu>> wrote:
>>>> 
>>>>yes, that is fine
>>>> 
>>>>On 10/11/18 11:21 PM, Ting Li wrote:
>>>>> 
>>>>>External Email - Use Caution
>>>>> 
>>>>>Dear Dr. Douglas,
>>>>> 
>>>>>Thank you so much for your response. With your instruction, it
>>>>>works. This is how I did.
>>>>> 
>>>>>First, copy the significant cluster annot file from the
>>>>>simulation fold to one of subject label folder.
>>>>>Secondly, use the mir_annotation2label command to make this
>>>>>cluster into a label file
>>>>>Thirdly, copy this label file to fsaverage label folder
>>>>>Finally, I can load the label to the fsaverage surf.
>>>>> 
>>>>>Is this the right procedure? Thanks a lot!
>>>>> 
>>>>>Regards,
>>>>>Ting
>>>>>>On Oct 10, 2018, at 1:30 PM, Greve, Douglas N.,Ph.D.
>>>>>>mailto:dgr...@mgh.harvard.edu>> wrote:
>>>>>> 
>>>>>>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 figured out the problem is that I didn’t specify lh
>>>>>>>before the
>>>>>>>annot file. However, in this method, I didn’t get the right
>>>>>>>label for
>>>>>>>I have loaded the label into the subject file. It is the
>>>>>>>scatter points.
>>>>>>> 
>>>>>>>I want to 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 >>>>>>><mailto:tx...@ualr.edu>
>>>>>>>><mailto:tx...@ualr.edu>> wrote:
>>>>>>>> 
>>>>>>>>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 >>>>>>>><mailto:tx...@ualr.edu>
>>>&

Re: [Freesurfer] create label from cluster obtained with mri_glm-fit-sim

[Ting Li]

External Email - Use Caution

If I loaded the label to the inflated surface, it also gives me the cluster 
with branches. As you can see in the below. 

If I loaded the annot file to the inflated surface, it works well. Thanks for 
your help. 

Ting 



> On Oct 16, 2018, at 1:51 PM, Greve, Douglas N.,Ph.D.  
> wrote:
> 
> Hmm, not sure what to tell you. The label is derived directly from the 
> annot. If you click on a vertex in the branch, does it appear to be in 
> the label based on what displays in the control panel? If you load it on 
> the inflated 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, Douglas N.,Ph.D. 
>>>  wrote:
>>> 
>>> Click on the surface file name in the upper left corner of FreeView,
>>> then load 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 the annot file. I just use the annot file to create the
>>>> label. if I check the clusters in a inflated brain, they are looks
>>>> fine. If I need to load annot file for checking, how can I do it?
>>>> Thanks a lot.
>>>> 
>>>> Ting
>>>> 
>>>> On Mon, Oct 15, 2018 at 9:25 AM Greve, Douglas N.,Ph.D.
>>>> mailto:dgr...@mgh.harvard.edu>> wrote:
>>>> 
>>>>does the same thing happen when you load the annot file?
>>>> 
>>>>On 10/13/18 10:03 PM, Ting Li wrote:
>>>>>External Email - Use Caution
>>>>> 
>>>>>Dear Dr. Douglas,
>>>>> 
>>>>>    I can load the label, but some clusters have branches. Some of
>>>>>them are just looks fine. Do you know the reason? Thanks a lot.
>>>>> 
>>>>>Regards,
>>>>>Ting
>>>>> 
>>>>> 
>>>>> 
>>>>> 
>>>>>>On Oct 12, 2018, at 10:35 AM, Greve, Douglas N.,Ph.D.
>>>>>>mailto:dgr...@mgh.harvard.edu>> wrote:
>>>>>> 
>>>>>>yes, that is fine
>>>>>> 
>>>>>>On 10/11/18 11:21 PM, Ting Li wrote:
>>>>>>>External Email - Use Caution
>>>>>>> 
>>>>>>>Dear Dr. Douglas,
>>>>>>> 
>>>>>>>Thank you so much for your response. With your instruction, it
>>>>>>>works. This is how I did.
>>>>>>> 
>>>>>>>First, copy the significant cluster annot file from the
>>>>>>>simulation fold to one of subject label folder.
>>>>>>>Secondly, use the mir_annotation2label command to make this
>>>>>>>cluster into a label file
>>>>>>>Thirdly, copy this label file to fsaverage label folder
>>>>>>>Finally, I can load the label to the fsaverage surf.
>>>>>>> 
>>>>>>>Is this the right procedure? Thanks a lot!
>>>>>>> 
>>>>>>>Regards,
>>>>>>>Ting
>>>>>>>>    On Oct 10, 2018, at 1:30 PM, Greve, Douglas N.,Ph.D.
>>>>>>>>mailto:dgr...@mgh.harvard.edu>> wrote:
>>>>>>>> 
>>>>>>>>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 figured out the problem is that I didn’t specify lh
>>>>>>>>>before the
>>>>>>>>>annot file. However, in this method, I didn’t get the right
>>>>>>>>>label for
>>>>>>>>>I h

[Freesurfer] create label from cluster obtained with mri_glm-fit-sim

[Ting Li]

External Email - Use Caution

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. If you think it is not the right way, could you give 
me an example to do it right. I really appreciate your great help. Thanks a lot.

Here is my code:

mri_annotation2label --subject F999  --hemi lh --annotation 
cache.th20.neg.sig.ocn.annot --labelbase lh.test_label

Here is my error information:
subject = F999
annotation = cache.th20.neg.sig.ocn.annot
hemi = lh
labelbase = lh.test_label
surface   = white

Reading surface 
 /media/set2iscsi/ting/origin_gz_data/F999/surf/lh.white
Loading annotations from 
/media/set2iscsi/ting/origin_gz_data/F999/label/lh.cache.th20.neg.sig.ocn.annot.annot
could not read annot file 
/media/set2iscsi/ting/origin_gz_data/F999/label/lh.cache.th20.neg.sig.ocn.annot.annot
No such file or directory
INFO: could not load from 
/media/set2iscsi/ting/origin_gz_data/F999/label/lh.cache.th20.neg.sig.ocn.annot.annot,
 trying 
/media/set2iscsi/ting/origin_gz_data/F999/label/lh_cache.th20.neg.sig.ocn.annot.annot
could not read annot file 
/media/set2iscsi/ting/origin_gz_data/F999/label/lh_cache.th20.neg.sig.ocn.annot.annot
No such file or directory
ERROR: MRISreadAnnotation() failed

This is the annot files in my directory F999:
ls F999/label/*.annot
F999/label/cache.th20.neg.sig.ocn.annot  F999/label/lh.BA_exvivo.annot 
F999/label/rh.aparc.DKTatlas.annot
F999/label/lh.aparc.a2009s.annot F999/label/lh.BA_exvivo.thresh.annot  
F999/label/rh.BA_exvivo.annot
F999/label/lh.aparc.annotF999/label/rh.aparc.a2009s.annot  
F999/label/rh.BA_exvivo.thresh.annot
F999/label/lh.aparc.DKTatlas.annot   F999/label/rh.aparc.annot___
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Re: [Freesurfer] create label from cluster obtained with mri_glm-fit-sim

[Ting Li]

External Email - Use Caution

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 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. If you think it is not the right way, could you 
> give me an example to do it right. I really appreciate your great help. 
> Thanks a lot.
> 
> Here is my code:
> 
> mri_annotation2label --subject F999  --hemi lh --annotation 
> cache.th20.neg.sig.ocn.annot --labelbase lh.test_label
> 
> Here is my error information:
> subject = F999
> annotation = cache.th20.neg.sig.ocn.annot
> hemi = lh
> labelbase = lh.test_label
> surface   = white
> 
> Reading surface 
>  /media/set2iscsi/ting/origin_gz_data/F999/surf/lh.white
> Loading annotations from 
> /media/set2iscsi/ting/origin_gz_data/F999/label/lh.cache.th20.neg.sig.ocn.annot.annot
> could not read annot file 
> /media/set2iscsi/ting/origin_gz_data/F999/label/lh.cache.th20.neg.sig.ocn.annot.annot
> No such file or directory
> INFO: could not load from 
> /media/set2iscsi/ting/origin_gz_data/F999/label/lh.cache.th20.neg.sig.ocn.annot.annot,
>  trying 
> /media/set2iscsi/ting/origin_gz_data/F999/label/lh_cache.th20.neg.sig.ocn.annot.annot
> could not read annot file 
> /media/set2iscsi/ting/origin_gz_data/F999/label/lh_cache.th20.neg.sig.ocn.annot.annot
> No such file or directory
> ERROR: MRISreadAnnotation() failed
> 
> This is the annot files in my directory F999:
> ls F999/label/*.annot
> F999/label/cache.th20.neg.sig.ocn.annot  F999/label/lh.BA_exvivo.annot
>  F999/label/rh.aparc.DKTatlas.annot
> F999/label/lh.aparc.a2009s.annot F999/label/lh.BA_exvivo.thresh.annot 
>  F999/label/rh.BA_exvivo.annot
> F999/label/lh.aparc.annotF999/label/rh.aparc.a2009s.annot 
>  F999/label/rh.BA_exvivo.thresh.annot
> F999/label/lh.aparc.DKTatlas.annot   F999/label/rh.aparc.annot

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Re: [Freesurfer] create label from cluster obtained with mri_glm-fit-sim

[Ting Li]

External Email - Use Caution

Dear Freesurfer Expert,

I have figured out the problem is that I didn’t specify lh before the annot 
file. However, in this method, I didn’t get the right label for I have loaded 
the label into the subject file. It is the scatter points. 

I want to 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 
> file. Thanks a lot.
> 
> Regards,
> 
> Ting
>> On Oct 3, 2018, at 9:36 PM, Ting Li mailto:tx...@ualr.edu>> 
>> wrote:
>> 
>> 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. If you think it is not the right way, could you 
>> give me an example to do it right. I really appreciate your great help. 
>> Thanks a lot.
>> 
>> Here is my code:
>> 
>> mri_annotation2label --subject F999  --hemi lh --annotation 
>> cache.th20.neg.sig.ocn.annot --labelbase lh.test_label
>> 
>> Here is my error information:
>> subject = F999
>> annotation = cache.th20.neg.sig.ocn.annot
>> hemi = lh
>> labelbase = lh.test_label
>> surface   = white
>> 
>> Reading surface 
>>  /media/set2iscsi/ting/origin_gz_data/F999/surf/lh.white
>> Loading annotations from 
>> /media/set2iscsi/ting/origin_gz_data/F999/label/lh.cache.th20.neg.sig.ocn.annot.annot
>> could not read annot file 
>> /media/set2iscsi/ting/origin_gz_data/F999/label/lh.cache.th20.neg.sig.ocn.annot.annot
>> No such file or directory
>> INFO: could not load from 
>> /media/set2iscsi/ting/origin_gz_data/F999/label/lh.cache.th20.neg.sig.ocn.annot.annot,
>>  trying 
>> /media/set2iscsi/ting/origin_gz_data/F999/label/lh_cache.th20.neg.sig.ocn.annot.annot
>> could not read annot file 
>> /media/set2iscsi/ting/origin_gz_data/F999/label/lh_cache.th20.neg.sig.ocn.annot.annot
>> No such file or directory
>> ERROR: MRISreadAnnotation() failed
>> 
>> This is the annot files in my directory F999:
>> ls F999/label/*.annot
>> F999/label/cache.th20.neg.sig.ocn.annot  F999/label/lh.BA_exvivo.annot   
>>   F999/label/rh.aparc.DKTatlas.annot
>> F999/label/lh.aparc.a2009s.annot 
>> F999/label/lh.BA_exvivo.thresh.annot  F999/label/rh.BA_exvivo.annot
>> F999/label/lh.aparc.annotF999/label/rh.aparc.a2009s.annot
>>   F999/label/rh.BA_exvivo.thresh.annot
>> F999/label/lh.aparc.DKTatlas.annot   F999/label/rh.aparc.annot
> 

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[Freesurfer] Set annotation cluster color

[Ting Li]

External Email - Use Caution

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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Re: [Freesurfer] aparc.pial.stats

[Ting Li]

External Email - Use Caution

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:
>> External Email - Use Caution
>> 
>> 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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> 
> 
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[Freesurfer] aparc.pial.stats

[Ting Li]

External Email - Use Caution

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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[Freesurfer] White surface area and cortical surface area

[Ting Li]

External Email - Use Caution

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 your response. Thanks a lot!

Best regards,
Ting
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Re: [Freesurfer] Multiple comparison using Monte Carlo

[Ting Li]

External Email - Use Caution

Dear Dr. Douglas,

Thank  you so much for all the answers. I have two more questions.

1, When the Monte Carlo simulation is doing, how does one simulation is
done?

   - synthesize z map (synthesize z map for how many subjects?)
   - smooth z map (You have mentioned the FWHM comes from an estimate from
   the residuals of the analysis, which analysis? or the way we process the
   real data with the command mris_preproc with FWHM value? )
   - threshold z map (Does it mean a GLM analysis so we can have threshold
   z map?)

2, When we reference to the CSD files in freesurfer, will it correct the
cluster size p-value based on DOF (degree of freedom), like the t-ratios
table including a DOF? Thanks a lot!

Best regards,
Ting

On Mon, Dec 2, 2019 at 1:59 PM Greve, Douglas N.,Ph.D. <
dgr...@mgh.harvard.edu> wrote:

> Correct. This 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 12/2/2019 2:03 PM, Ting Li wrote:
>
> External Email - Use Caution
> Dear Dr. Douglas,
>
> Thank you so much for your detailed response.
>
> The simulation here is to get the probability of a maximum cluster that
> size or larger in the cached CSD files. It checks the probability of  the
> cluster size but have nothing to do with 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. Douglas,
>>
>> Thank you so much for your quick response! You saved my half life.
>>
>> From the introduction of clusterwise correction for multiple comparisons,
>> I have a few questions.
>>
>> 1, What is the null hypothesis here ?
>>
>> In the tutorial, the null hypothesis is that there is no effect of age
>> (age slope = 0)
>>
>> 2, What is a z map? Do you mean synthesize cortical datasets?
>>
>> A z-map is just a map where all the values are from a gaussian
>> distribution with mean=0 and stddev=1. This just assigns a random z-value
>> to each vertex on fsaverage
>>
>> 3. Smooth z map, what FWHM do you use, if it is not consistent with my
>> FWHM, how will it affect the results?
>>
>> The FWHM comes from an estimate from the residuals of the analysis. The
>> residuals are everything that does not fit the linear model and represent
>> noise. We use the residuals to estimate the underlying smoothness (FWHM),
>>
>> 4, Threshold z map, what does level mean? Does it mean the vertex p-value?
>>
>> Basically, it is the vertex p-value, but we use  the "sig" = -log10(p).
>> You also have to specify the sign. If you have an a priori hypothesis about
>> the direction, then you can specify pos (positive) or neg (negative). If
>> you do not have an a priori hypothesis, then use abs (for absolute, for an
>> unsigned test).
>>
>>
>> Clusterwise Correction for Multiple Comparisons
>> To perform a cluster-wise correction for multiple comparisons, we will run
>> a simulation. The simulation is a way to get a measure of the distribution
>> of the maximum cluster size under the *null **hypothesis*. This is done
>> by iterating over the following steps:
>> 1. Synthesize a z map
>> 2. Smooth z map (using residual FWHM)
>> 3. Threshold z map (level and sign)
>> 4. Find clusters in thresholded map
>> 5. Record area of maximum cluster
>> 6. Repeat over desired number of iterations (usually > 5000)
>>
>> Thank you so much!
>>
>> Best regards,
>> Ting
>>
>> On Mon, Dec 2, 2019 at 10:20 AM Greve, Douglas N.,Ph.D. <
>> dgr...@mgh.harvard.edu> wrote:
>>
>>> 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 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 spec

Re: [Freesurfer] Multiple comparison using Monte Carlo

[Ting Li]

External Email - Use Caution

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:
> >
> > External Email - Use Caution
> >
> > Dear Dr. Douglas,
> >
> > Thank you so much.
> >
> > I have difficulty to understand z map is essentially an infinite # of
> > subjects.
> > Before smooth, there is no GLM analysis. Does the smooth include in
> > the GLM process?
> >
> > Best regards,
> > Ting
> >
> > On Tue, Dec 3, 2019 at 2:14 PM Greve, Douglas N.,Ph.D.
> > mailto: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 Carlo simulation is doing, how does one
> >> simulation is done?
> >>
> >>   * synthesize z map (synthesize z map for how many subjects?)
> >>
> > The Z is essentailly an infinite # of subjects (it is just a
> > single map).
> >>
> >>   * smooth z map (You have mentioned the FWHM comes from an
> >> estimate from the residuals of the analysis, which analysis?
> >> or the way we process the real data with the command
> >> mris_preproc with FWHM value? )
> >>
> > The GLM analysis, from the residual.
> >>
> >>   * threshold z map (Does it mean a GLM analysis so we can have
> >> threshold z map?)
> >>
> > No, the z-map is synthesized directly
> >
> > The simulation is done in mri_glmfit-sim and in mri_mcsim.
> >
> >> 2, When we reference to the CSD files in freesurfer, will it
> >> correct the cluster size p-value based on DOF (degree of
> >> freedom), like the t-ratios table including a DOF? Thanks a lot!
> > I don't know what you mean.
> >>
> >> Best regards,
> >> Ting
> >>
> >> On Mon, Dec 2, 2019 at 1:59 PM Greve, Douglas N.,Ph.D.
> >> mailto:dgr...@mgh.harvard.edu>> wrote:
> >>
> >> Correct. This 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 12/2/2019 2:03 PM, Ting Li wrote:
> >>>
> >>> External Email - Use Caution
> >>>
> >>> Dear Dr. Douglas,
> >>>
> >>>     Thank you so much for your detailed response.
> >>>
> >>> The simulation here is to get the probability of a maximum
> >>> cluster that size or larger in the cached CSD files. It
> >>> checks the probability of  the cluster size but have nothing
> >>> to do with 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.
> >>> mailto:dgr...@mgh.harvard.edu>>
> wrote:
> >>>
> >>>
> >>>
> >>> On 12/2/2019 11:58 AM, Ting Li wrote:
> >>>>
> >>>> External Email - Use Caution
> >>>>
> >>>> Dear Dr. Douglas,
> >>>>
> >>>> Thank you so much for your quick response! You saved my
> >>>> half life.
> >>>>
> >>>> From the introduction of clusterwise correction for
> >>>> multiple comparisons, I have a few questions.
> >>>>
> >>>> 1, What is the null hypothesis here ?
> >>> In the tutorial, the null hypothesis is that there is no
> >>> effect of age (age slope = 0)
> >>>> 2, What is a z map? Do you mean synthesize cortical
> >>>> datasets?

Re: [Freesurfer] Multiple comparison using Monte Carlo

[Ting Li]

External Email - Use Caution

Dear Dr. Douglas,

Thank you so much.

I have difficulty to understand z map is essentially an infinite # of
subjects.
Before smooth, there is no GLM analysis. Does the smooth include in the GLM
process?

Best regards,
Ting

On Tue, Dec 3, 2019 at 2:14 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 Carlo simulation is doing, how does one simulation is
> done?
>
>- synthesize z map (synthesize z map for how many subjects?)
>
> The Z is essentailly an infinite # of subjects (it is just a single map).
>
>
>- smooth z map (You have mentioned the FWHM comes from an estimate
>from the residuals of the analysis, which analysis? or the way we process
>the real data with the command mris_preproc with FWHM value? )
>
> The GLM analysis, from the residual.
>
>
>- threshold z map (Does it mean a GLM analysis so we can have
>threshold z map?)
>
> No, the z-map is synthesized directly
>
> The simulation is done in mri_glmfit-sim and in mri_mcsim.
>
> 2, When we reference to the CSD files in freesurfer, will it correct the
> cluster size p-value based on DOF (degree of freedom), like the t-ratios
> table including a DOF? Thanks a lot!
>
> I don't know what you mean.
>
>
> Best regards,
> Ting
>
> On Mon, Dec 2, 2019 at 1:59 PM Greve, Douglas N.,Ph.D. <
> dgr...@mgh.harvard.edu> wrote:
>
>> Correct. This 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 12/2/2019 2:03 PM, Ting Li wrote:
>>
>> External Email - Use Caution
>> Dear Dr. Douglas,
>>
>> Thank you so much for your detailed response.
>>
>> The simulation here is to get the probability of a maximum cluster that
>> size or larger in the cached CSD files. It checks the probability of  the
>> cluster size but have nothing to do with 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. Douglas,
>>>
>>> Thank you so much for your quick response! You saved my half life.
>>>
>>> From the introduction of clusterwise correction for multiple
>>> comparisons, I have a few questions.
>>>
>>> 1, What is the null hypothesis here ?
>>>
>>> In the tutorial, the null hypothesis is that there is no effect of age
>>> (age slope = 0)
>>>
>>> 2, What is a z map? Do you mean synthesize cortical datasets?
>>>
>>> A z-map is just a map where all the values are from a gaussian
>>> distribution with mean=0 and stddev=1. This just assigns a random z-value
>>> to each vertex on fsaverage
>>>
>>> 3. Smooth z map, what FWHM do you use, if it is not consistent with my
>>> FWHM, how will it affect the results?
>>>
>>> The FWHM comes from an estimate from the residuals of the analysis. The
>>> residuals are everything that does not fit the linear model and represent
>>> noise. We use the residuals to estimate the underlying smoothness (FWHM),
>>>
>>> 4, Threshold z map, what does level mean? Does it mean the vertex
>>> p-value?
>>>
>>> Basically, it is the vertex p-value, but we use  the "sig" = -log10(p).
>>> You also have to specify the sign. If you have an a priori hypothesis about
>>> the direction, then you can specify pos (positive) or neg (negative). If
>>> you do not have an a priori hypothesis, then use abs (for absolute, for an
>>> unsigned test).
>>>
>>>
>>> Clusterwise Correction for Multiple Comparisons
>>> To perform a cluster-wise correction for multiple comparisons, we will run
>>> a simulation. The simulation is a way to get a measure of the distribution
>>> of the maximum cluster size under the *null **hypothesis*. This is done
>>> by iterating over the following steps:
>>> 1. Synthesize a z map
>>> 2. Smo

Re: [Freesurfer] Multiple comparison using Monte Carlo

[Ting Li]

External Email - Use Caution

Dear Dr. Douglas,

Thank you so much for your quick response! You saved my half life.

From the introduction of clusterwise correction for multiple comparisons, I
have a few questions.

1, What is the null hypothesis here ?
2, What is a z map? Do you mean synthesize cortical datasets?
3. Smooth z map, what FWHM do you use, if it is not consistent with my
FWHM, how will it affect the results?
4, Threshold z map, what does level mean? Does it mean the vertex p-value?

Clusterwise Correction for Multiple Comparisons
To perform a cluster-wise correction for multiple comparisons, we will run
a simulation. The simulation is a way to get a measure of the distribution
of the maximum cluster size under the *null **hypothesis*. This is done by
iterating over the following steps:
1. Synthesize a z map
2. Smooth z map (using residual FWHM)
3. Threshold z map (level and sign)
4. Find clusters in thresholded map
5. Record area of maximum cluster
6. Repeat over desired number of iterations (usually > 5000)

Thank you so much!

Best regards,
Ting

On Mon, Dec 2, 2019 at 10:20 AM Greve, Douglas N.,Ph.D. <
dgr...@mgh.harvard.edu> wrote:

> 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 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 specify the iteration number.
>
> Why I didn’t have the csd file?
>
> Thanks a lot for your response!
>
> Best regards,
> Ting
>
> ___
> Freesurfer mailing 
> listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
___
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Re: [Freesurfer] Multiple comparison using Monte Carlo

[Ting Li]

External Email - Use Caution

Dear Dr. Douglas,

Thank you so much for your detailed response.

The simulation here is to get the probability of a maximum cluster that
size or larger in the cached CSD files. It checks the probability of  the
cluster size but have nothing to do with 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. Douglas,
>
> Thank you so much for your quick response! You saved my half life.
>
> From the introduction of clusterwise correction for multiple comparisons,
> I have a few questions.
>
> 1, What is the null hypothesis here ?
>
> In the tutorial, the null hypothesis is that there is no effect of age
> (age slope = 0)
>
> 2, What is a z map? Do you mean synthesize cortical datasets?
>
> A z-map is just a map where all the values are from a gaussian
> distribution with mean=0 and stddev=1. This just assigns a random z-value
> to each vertex on fsaverage
>
> 3. Smooth z map, what FWHM do you use, if it is not consistent with my
> FWHM, how will it affect the results?
>
> The FWHM comes from an estimate from the residuals of the analysis. The
> residuals are everything that does not fit the linear model and represent
> noise. We use the residuals to estimate the underlying smoothness (FWHM),
>
> 4, Threshold z map, what does level mean? Does it mean the vertex p-value?
>
> Basically, it is the vertex p-value, but we use  the "sig" = -log10(p).
> You also have to specify the sign. If you have an a priori hypothesis about
> the direction, then you can specify pos (positive) or neg (negative). If
> you do not have an a priori hypothesis, then use abs (for absolute, for an
> unsigned test).
>
>
> Clusterwise Correction for Multiple Comparisons
> To perform a cluster-wise correction for multiple comparisons, we will run
> a simulation. The simulation is a way to get a measure of the distribution
> of the maximum cluster size under the *null **hypothesis*. This is done
> by iterating over the following steps:
> 1. Synthesize a z map
> 2. Smooth z map (using residual FWHM)
> 3. Threshold z map (level and sign)
> 4. Find clusters in thresholded map
> 5. Record area of maximum cluster
> 6. Repeat over desired number of iterations (usually > 5000)
>
> Thank you so much!
>
> Best regards,
> Ting
>
> On Mon, Dec 2, 2019 at 10:20 AM Greve, Douglas N.,Ph.D. <
> dgr...@mgh.harvard.edu> wrote:
>
>> 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 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 specify the iteration number.
>>
>> Why I didn’t have the csd file?
>>
>> Thanks a lot for your response!
>>
>> Best regards,
>> Ting
>>
>> ___
>> Freesurfer mailing 
>> listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>
>>
>> ___
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
> ___
> Freesurfer mailing 
> listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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[Freesurfer] Multiple comparison using Monte Carlo

[Ting Li]

External Email - Use Caution

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 
specify the iteration number.

Why I didn’t have the csd file? 

Thanks a lot for your response!

Best regards,
Ting___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
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Re: [Freesurfer] Multiple comparison using Monte Carlo

[Ting Li]

External Email - Use Caution

Dear Dr. Douglas,

Thank you so much for your explanation. You really helped me a lot!

Best regards,
Ting

On Mon, Dec 2, 2019 at 1:59 PM Greve, Douglas N.,Ph.D. <
dgr...@mgh.harvard.edu> wrote:

> Correct. This 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 12/2/2019 2:03 PM, Ting Li wrote:
>
> External Email - Use Caution
> Dear Dr. Douglas,
>
> Thank you so much for your detailed response.
>
> The simulation here is to get the probability of a maximum cluster that
> size or larger in the cached CSD files. It checks the probability of  the
> cluster size but have nothing to do with 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. Douglas,
>>
>> Thank you so much for your quick response! You saved my half life.
>>
>> From the introduction of clusterwise correction for multiple comparisons,
>> I have a few questions.
>>
>> 1, What is the null hypothesis here ?
>>
>> In the tutorial, the null hypothesis is that there is no effect of age
>> (age slope = 0)
>>
>> 2, What is a z map? Do you mean synthesize cortical datasets?
>>
>> A z-map is just a map where all the values are from a gaussian
>> distribution with mean=0 and stddev=1. This just assigns a random z-value
>> to each vertex on fsaverage
>>
>> 3. Smooth z map, what FWHM do you use, if it is not consistent with my
>> FWHM, how will it affect the results?
>>
>> The FWHM comes from an estimate from the residuals of the analysis. The
>> residuals are everything that does not fit the linear model and represent
>> noise. We use the residuals to estimate the underlying smoothness (FWHM),
>>
>> 4, Threshold z map, what does level mean? Does it mean the vertex p-value?
>>
>> Basically, it is the vertex p-value, but we use  the "sig" = -log10(p).
>> You also have to specify the sign. If you have an a priori hypothesis about
>> the direction, then you can specify pos (positive) or neg (negative). If
>> you do not have an a priori hypothesis, then use abs (for absolute, for an
>> unsigned test).
>>
>>
>> Clusterwise Correction for Multiple Comparisons
>> To perform a cluster-wise correction for multiple comparisons, we will run
>> a simulation. The simulation is a way to get a measure of the distribution
>> of the maximum cluster size under the *null **hypothesis*. This is done
>> by iterating over the following steps:
>> 1. Synthesize a z map
>> 2. Smooth z map (using residual FWHM)
>> 3. Threshold z map (level and sign)
>> 4. Find clusters in thresholded map
>> 5. Record area of maximum cluster
>> 6. Repeat over desired number of iterations (usually > 5000)
>>
>> Thank you so much!
>>
>> Best regards,
>> Ting
>>
>> On Mon, Dec 2, 2019 at 10:20 AM Greve, Douglas N.,Ph.D. <
>> dgr...@mgh.harvard.edu> wrote:
>>
>>> 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 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 specify the iteration number.
>>>
>>> Why I didn’t have the csd file?
>>>
>>> Thanks a lot for your response!
>>>
>>> Best regards,
>>> Ting
>>>
>>> ___
>>> Freesurfer mailing 
>>> listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>>
>>>
>>> ___
>>> Freesurfer mailing list
>>> Freesurfer@nmr.mgh.harvard.edu
>

[Freesurfer] cortical area and volume calculation method

[Ting Li]

External Email - Use Caution

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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