from:"charujing123"

Hi FS experts and users,
May I ask some questions about clusterwise correction for multiple comparisons?
1,In mri_glmfit-sim command, there is a --sim(--sim nulltype nsim threshold 
csdbase) option. Choose the voxel/vertex-wise threshhold used to define 
clusters. This will be -log10(p), where p is the p-value. Eg, to use all 
voxels/vertices
   with p < .01, then set the threshhold = 2.I want to know what is meaning of 
"using all voxels with p < 0.01". Does it mean that considering all voxels 
whose p value below 0.01 in every iterations. Then it generates some clusters 
in every iteration. Is it right?
2,Also there is a --sim-sign option in this command. I want to know meaning of 
the sign: abs,pos,neg.Does it represent one- and two-tailed tests?
Thanks.
All the best.
Rujing Zha
2014-02-20



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[Freesurfer] viewing corrected result error

Hi all,
I try to see the cluster wised result by typing "freeview -f 
$SUBJECTS_DIR/fsaverage/surf/lh.inflated:overlay=./Diff-CON-IA-Intercept-thickness/mc-z.neg.sig.cluster.mgh:overlay_threshold=2,5:annot=./Diff-CON-IA-Intercept-thickness/mc-z.neg.sig.ocn.annot",but
 it feedback some error infomation as below:
Did not find any volume geometry information in the surface
ԥhreading colortable from annotation file...
colortable with 1 entries read (originally none)
colortable with 1 entries read (originally none)
Thanks.
All the best

2014-02-20



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Re: [Freesurfer] fsgdf and contrasts

Hidoug and others,
Thanks doug.
I see.If I want to implement multiple regression, i.e. two EVs(score1 and 
score2) explain pial thickness, what contrast I should design for this.
Thanks again.
All the best.
Rujing Zha

2014-02-21



charujing123



发件人：Douglas N Greve 
发送时间：2014-02-21 03:39
主题：Re: [Freesurfer] fsgdf and contrasts
收件人："freesurfer"
抄送：


yes, they are, though you don't need to do the positive and negative  
contrasts because the sign is preserved 
doug 

On 02/20/2014 12:47 AM, charujing123 wrote: 
> Hi FS experts and users, 
> I am trying to implement independent sample t-test and correlation  
> analysis. 
> Here is my fsgdf design: 
> - 
> GroupDescriptorFile 1 
> Title lh_ttest 
> Class CON_IA 
> Class PAT_IA 
> Variables score1 score2 
> Input CON_IA01 CON_IA 0 0 
> Input CON_IA03 CON_IA 0 0 
> Input CON_IA05 CON_IA 0 0 
> Input CON_IA06 CON_IA 0 0 
> Input CON_IA07 CON_IA 3 7 
> Input CON_IA09 CON_IA 0 0 
> Input CON_IA14 CON_IA 0 0 
> Input CON_IA15 CON_IA 0 0 
> Input CON_IA16 CON_IA 7 12 
> Input CON_IA19 CON_IA 6 15 
> Input CON_IA24 CON_IA 6 11 
> Input CON_IA27 CON_IA 3 3 
> Input CON_IA32 CON_IA 7 21 
> Input CON_IA33 CON_IA 7 21 
> Input CON_IA35 CON_IA 0 0 
> Input CON_IA38 CON_IA 7 15 
> Input CON_IA39 CON_IA 2 3 
> Input CON_IA40 CON_IA 6 8 
> Input CON_IA41 CON_IA 2 4 
> Input PAT_IA01 PAT_IA 8 13 
> Input PAT_IA02 PAT_IA 9 38 
> Input PAT_IA03 PAT_IA 9 33 
> Input PAT_IA04 PAT_IA 9 27 
> Input PAT_IA06 PAT_IA 9 26 
> Input PAT_IA08 PAT_IA 8 16 
> Input PAT_IA09 PAT_IA 9 33 
> Input PAT_IA16 PAT_IA 9 35 
> Input PAT_IA18 PAT_IA 9 39 
> Input PAT_IA21 PAT_IA 9 32 
> Input PAT_IA22 PAT_IA 9 31 
> Input PAT_IA23 PAT_IA 9 35 
> Input PAT_IA24 PAT_IA 9 40 
> Input PAT_IA25 PAT_IA 9 29 
> Input PAT_IA27 PAT_IA 9 30 
> Input PAT_IA29 PAT_IA 9 30 
> Input PAT_IA30 PAT_IA 8 32 
> Input PAT_IA33 PAT_IA 9 13 
> Input PAT_IA34 PAT_IA 9 21 
>  
> Contrasts for independent sample t-test: 
> 1,CON_IA>PAT_IA:1 -1 0 0 0 0 
> 2,PAT_IA>CON_IA:-1 1 0 0 0 0 
> Contrasts for correlation analysis: 
> 1,possitive correlation analysis between pial thickness and score1:0 0  
> 0.5 0.5 0 0 
> 2,negtive correlation analysis between pial thickness and score1:0 0  
> -0.5 -0.5 0 0 
> 3,positive correlation analysis between pial thickness and score2:0 0  
> 0 0 0.5 0.5 
> 4,negtive correlation analysis between pial thickness and score2:0 0 0  
> 0 -0.5 -0.5 
> Are my designs appropriate? 
> If I want to implement regression analysis(i.e. dependent variable is  
> thickness and independent variables are score1 and score2), how to  
> design my contrast? 
> Thanks. 
> All the best. 
> Rujing Zha 
> 2014-02-20 
>  
> charujing123 
> 
> 
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Re: [Freesurfer] questions of clusters defined and sign of the threshold in simulation

Hi doug,
Thanks doug.
I see.
All the best.
Rujing Zha

2014-02-21

charujing123

发件人：Douglas N Greve 
发送时间：2014-02-21 03:43
主题：Re: [Freesurfer] questions of clusters defined and sign of the threshold in 
simulation
收件人："freesurfer"
抄送：

On 02/20/2014 04:33 AM, charujing123 wrote: 
> Hi FS experts and users, 
> May I ask some questions about clusterwise correction for multiple  
> comparisons? 
> 1,In mri_glmfit-sim command, there is a --sim(--sim nulltype nsim  
> threshold csdbase) option. Choose the voxel/vertex-wise threshhold  
> used to define clusters. This will be -log10(p), where p is the  
> p-value. Eg, to use all voxels/vertices 
> with p < .01, then set the threshhold = 2.I want to know what is  
> meaning of "using all voxels with p < 0.01". Does it mean that  
> considering all voxels whose p value below 0.01 in every iterations.  
> Then it generates some clusters in every iteration. Is it right? 
At each iteration, it creates a random map, smooths it, then thresholds  
it to create clusters. It keeps track of how many clusters were created  
and the maximum cluster size at each iteration. It uses this info to  
compute a p-value for the clusters it finds in your real data. 

> 2,Also there is a --sim-sign option in this command. I want to know  
> meaning of the sign: abs,pos,neg.Does it represent one- and two-tailed  
> tests? 
Yes, abs is a two tailed, pos and neg are one-tailed either positive or  
negative tail 
doug 
> Thanks. 
> All the best. 
> Rujing Zha 
> 2014-02-20 
> ---- 
> charujing123 
> 
> 
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--  
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MGH-NMR Center 
gr...@nmr.mgh.harvard.edu 
Phone Number: 617-724-2358 
Fax: 617-726-7422 

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting 
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Re: [Freesurfer] viewing corrected result error

Hi doug,
It isnot.
Thanks.
All the best.
Rujing Zha

2014-02-21

charujing123

发件人：Douglas N Greve 
发送时间：2014-02-21 03:45
主题：Re: [Freesurfer] viewing corrected result error
收件人："freesurfer"
抄送：

Is the error preventing you from visualizing? Otherwise you can ignore  
it (it will be fixed in the next version) 
doug 

On 02/20/2014 06:50 AM, charujing123 wrote: 
> Hi all, 
> I try to see the cluster wised result by typing "freeview -f  
> $SUBJECTS_DIR/fsaverage/surf/lh.inflated:overlay=./Diff-CON-IA-Intercept-thickness/mc-z.neg.sig.cluster.mgh:overlay_threshold=2,5:annot=./Diff-CON-IA-Intercept-thickness/mc-z.neg.sig.ocn.annot",but
>   
> it feedback some error infomation as below: 
> Did not find any volume geometry information in the surface 
> ԥhreading colortable from annotation file... 
> colortable with 1 entries read (originally none) 
> colortable with 1 entries read (originally none) 
> Thanks. 
> All the best 
> 2014-02-20 
> ---- 
> charujing123 
> 
> 
> ___ 
> Freesurfer mailing list 
> Freesurfer@nmr.mgh.harvard.edu 
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 

--  
Douglas N. Greve, Ph.D. 
MGH-NMR Center 
gr...@nmr.mgh.harvard.edu 
Phone Number: 617-724-2358 
Fax: 617-726-7422 

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting 
FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 
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[Freesurfer] extracting mean thickness from specific cluster

Hi all,
I finished the mri_glmfit-sim, and got some clusters in the cluster summary. 
1,I want to know how to extract mean thickness for each subject in this 
cluster? 
2,If I want to extract mean thickness of each subject according to a 
uncorrected p value, i.e. 0.005, what should I do to perform it?
Thanks.
All the best.
Rujing Zha

2014-02-21



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Re: [Freesurfer] extracting mean thickness from specific cluster

Hi doug and others,
Thanks doug.
For 1st question:I find that file. However not all has that file.May I generate 
it manually?
Thanks doug.
All the best.
Rujing Zha

2014-02-22



charujing123



发件人：Douglas Greve 
发送时间：2014-02-21 23:46
主题：Re: [Freesurfer] extracting mean thickness from specific cluster
收件人："freesurfer"
抄送：



On 2/21/14 10:04 AM, charujing123 wrote:

Hi all,
I finished the mri_glmfit-sim, and got some clusters in the cluster summary. 
1,I want to know how to extract mean thickness for each subject in this 
cluster? 

There should already be a file there called something like something.y.ocn.dat. 
This will have a row for each subject and a column for each cluster. The value 
will be the mean for that subject inside that cluster.


2,If I want to extract mean thickness of each subject according to a 
uncorrected p value, i.e. 0.005, what should I do to perform it?

What do you mean? Over all vertices that survive? Or  for each  all cluster 
with a cluster-forming threshold of .005? If the latter, you can run 
mri_glmfit-sim with --cwp 1 --cache 2.3 abs



Thanks.
All the best.
Rujing Zha

2014-02-21



charujing123

 

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Re: [Freesurfer] error in mri_glmfit-sim when using --bg and doss

Hi doug and others,
Thanks doug.
According this information 
https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis#ViewCSDFile, 
I try to find the csd files in the csd folder(I am not sure this is what you 
just told me). But there are the csd files as I run simulation with --bg option.
 Also I try to find the csd files in the first contrast directory, but I think, 
maybe I am wrong, none of these is csd files that you suggest.
Doug, would you please describe it more detailly, as I am a new user for FS?
Thanks doug and others.
All the best.
Rujing Zha

2014-02-22



charujing123



发件人：Douglas Greve 
发送时间：2014-02-21 23:49
主题：Re: [Freesurfer] error in mri_glmfit-sim when using --bg and doss
收件人："freesurfer"
抄送：


When you actually run the simulation, it only runs it for the first contrast. 
The simulation is the same for all contrasts, so you can just copy the csd 
files from the first contrast to the others, then run mri_glmfit-sim with the 
--no-sim option
doug




On 2/21/14 5:47 AM, charujing123 wrote:

Hi FS experts,
I ran the mri_glmfit with DOSS, followed by the mri_glmfit-sim(running with 
--bg option). I have 4 contrasts, but only the first one has some files of 
corrected results(i.e. mc-z.neg.3.sig.cluster.summary). I donot know why. So I 
upload the log file in the attachment. However, previously I ran mri_glmfit by 
DODS, and mri_glmfit-sim with --bg option.All the contrasts have corrected 
results.
Thanks.
All the best.
Rujing Zha

2014-02-21



charujing123

 

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[Freesurfer] Fw: Re: error in mri_glmfit-sim when using --bg and doss

Hi doug and others,
I am sorry for pasting files in my first contrast directory, if it can help me 
desolve the question:
cache.th23.abs.pdf.dat  mc-z.abs.2.sig.cluster.summary  
mc-z.neg.3.sig.cluster.summary  mc-z.pos.3.sig.cluster.summary
cache.th23.abs.sig.cluster.mgh  mc-z.abs.2.sig.masked.mgh   
mc-z.neg.3.sig.masked.mgh   mc-z.pos.3.sig.masked.mgh
cache.th23.abs.sig.cluster.summary  mc-z.abs.2.sig.ocn.annot
mc-z.neg.3.sig.ocn.annotmc-z.pos.3.sig.ocn.annot
cache.th23.abs.sig.masked.mgh   mc-z.abs.2.sig.ocn.mgh  
mc-z.neg.3.sig.ocn.mgh  mc-z.pos.3.sig.ocn.mgh
cache.th23.abs.sig.ocn.annotmc-z.abs.2.sig.voxel.mgh
mc-z.neg.3.sig.voxel.mghmc-z.pos.3.sig.voxel.mgh
cache.th23.abs.sig.ocn.mgh  mc-z.abs.3.pdf.dat  
mc-z.neg.3.y.ocn.datmc-z.pos.3.y.ocn.dat
cache.th23.abs.sig.voxel.mghmc-z.abs.3.sig.cluster.mgh  
mc-z.neg.pdf.datmc-z.pos.pdf.dat
C.dat   mc-z.abs.3.sig.cluster.summary  
mc-z.neg.sig.cluster.mghmc-z.pos.sig.cluster.mgh
cnr.mgh mc-z.abs.3.sig.masked.mgh   
mc-z.neg.sig.cluster.summarymc-z.pos.sig.cluster.summary
F.mgh   mc-z.abs.3.sig.ocn.annot
mc-z.neg.sig.masked.mgh mc-z.pos.sig.masked.mgh
gamma.mgh   mc-z.abs.3.sig.ocn.mgh  
mc-z.neg.sig.ocn.annot  mc-z.pos.sig.ocn.annot
gammavar.mghmc-z.abs.3.sig.voxel.mgh
mc-z.neg.sig.ocn.mghmc-z.pos.sig.ocn.mgh
maxvox.dat  mc-z.abs.3.y.ocn.dat
mc-z.neg.sig.voxel.mgh  mc-z.pos.sig.voxel.mgh
mc-z.abs.2.pdf.dat  mc-z.neg.3.pdf.dat  
mc-z.pos.3.pdf.dat  mc-z.pos.y.ocn.dat
mc-z.abs.2.sig.cluster.mgh  mc-z.neg.3.sig.cluster.mgh  
mc-z.pos.3.sig.cluster.mgh  sig.mgh
Thanks.
All the best.
Rujing Zha

2014-02-22



charujing123



发件人："charujing123"
发送时间：2014-02-22 10:18
主题：Re: [Freesurfer] error in mri_glmfit-sim when using --bg and doss
收件人："freesurfer@nmr.mgh.harvard.edu"
抄送：

Hi doug and others,
Thanks doug.
According this information 
https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis#ViewCSDFile, 
I try to find the csd files in the csd folder(I am not sure this is what you 
just told me). But there are the csd files as I run simulation with --bg option.
 Also I try to find the csd files in the first contrast directory, but I think, 
maybe I am wrong, none of these is csd files that you suggest.
Doug, would you please describe it more detailly, as I am a new user for FS?
Thanks doug and others.
All the best.
Rujing Zha

2014-02-22



charujing123



发件人：Douglas Greve 
发送时间：2014-02-21 23:49
主题：Re: [Freesurfer] error in mri_glmfit-sim when using --bg and doss
收件人："freesurfer"
抄送：


When you actually run the simulation, it only runs it for the first contrast. 
The simulation is the same for all contrasts, so you can just copy the csd 
files from the first contrast to the others, then run mri_glmfit-sim with the 
--no-sim option
doug




On 2/21/14 5:47 AM, charujing123 wrote:

Hi FS experts,
I ran the mri_glmfit with DOSS, followed by the mri_glmfit-sim(running with 
--bg option). I have 4 contrasts, but only the first one has some files of 
corrected results(i.e. mc-z.neg.3.sig.cluster.summary). I donot know why. So I 
upload the log file in the attachment. However, previously I ran mri_glmfit by 
DODS, and mri_glmfit-sim with --bg option.All the contrasts have corrected 
results.
Thanks.
All the best.
Rujing Zha

2014-02-21



charujing123

 

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Re: [Freesurfer] fsgdf and contrasts

Hi doug and others,
I want to perform correlation analysis,just one dependent variable and one 
independent variable. Previously I think the contrast(i.e.0 0 0.5 0.5 0 0) I 
design is for correlation between score1 and thickness. But yestoday I found 
this information 
http://surfer.nmr.mgh.harvard.edu/fswiki/Fsgdf2G2V#Contrast6g1g2.age.mtx. It 
told me that "Null Hypothesis: does mean of group age slope differ from 0? Is 
there an average affect of age regressing out the effect of group and weight?". 
Regressing out the effect of group and weight represents this contrast is for 
multimple regression,not simple correlation between two varibles. I am confused.
Doug, would you please tell me where I am wrong?
Thanks.
All the best.
Rujing Zha.

2014-02-22



charujing123



发件人：Douglas Greve 
发送时间：2014-02-21 23:35
主题：Re: [Freesurfer] fsgdf and contrasts
收件人："freesurfer"
抄送：


I'm not sure I understand. Your contrasts below are fine. What are you unsure 
about?
doug





On 2/20/14 7:48 PM, charujing123 wrote:

Hidoug and others,
Thanks doug.
I see.If I want to implement multiple regression, i.e. two EVs(score1 and 
score2) explain pial thickness, what contrast I should design for this.
Thanks again.
All the best.
Rujing Zha

2014-02-21



charujing123



发件人：Douglas N Greve 
发送时间：2014-02-21 03:39
主题：Re: [Freesurfer] fsgdf and contrasts
收件人："freesurfer"
抄送：


yes, they are, though you don't need to do the positive and negative  
contrasts because the sign is preserved 
doug 

On 02/20/2014 12:47 AM, charujing123 wrote: 
> Hi FS experts and users, 
> I am trying to implement independent sample t-test and correlation  
> analysis. 
> Here is my fsgdf design: 
> - 
> GroupDescriptorFile 1 
> Title lh_ttest 
> Class CON_IA 
> Class PAT_IA 
> Variables score1 score2 
> Input CON_IA01 CON_IA 0 0 
> Input CON_IA03 CON_IA 0 0 
> Input CON_IA05 CON_IA 0 0 
> Input CON_IA06 CON_IA 0 0 
> Input CON_IA07 CON_IA 3 7 
> Input CON_IA09 CON_IA 0 0 
> Input CON_IA14 CON_IA 0 0 
> Input CON_IA15 CON_IA 0 0 
> Input CON_IA16 CON_IA 7 12 
> Input CON_IA19 CON_IA 6 15 
> Input CON_IA24 CON_IA 6 11 
> Input CON_IA27 CON_IA 3 3 
> Input CON_IA32 CON_IA 7 21 
> Input CON_IA33 CON_IA 7 21 
> Input CON_IA35 CON_IA 0 0 
> Input CON_IA38 CON_IA 7 15 
> Input CON_IA39 CON_IA 2 3 
> Input CON_IA40 CON_IA 6 8 
> Input CON_IA41 CON_IA 2 4 
> Input PAT_IA01 PAT_IA 8 13 
> Input PAT_IA02 PAT_IA 9 38 
> Input PAT_IA03 PAT_IA 9 33 
> Input PAT_IA04 PAT_IA 9 27 
> Input PAT_IA06 PAT_IA 9 26 
> Input PAT_IA08 PAT_IA 8 16 
> Input PAT_IA09 PAT_IA 9 33 
> Input PAT_IA16 PAT_IA 9 35 
> Input PAT_IA18 PAT_IA 9 39 
> Input PAT_IA21 PAT_IA 9 32 
> Input PAT_IA22 PAT_IA 9 31 
> Input PAT_IA23 PAT_IA 9 35 
> Input PAT_IA24 PAT_IA 9 40 
> Input PAT_IA25 PAT_IA 9 29 
> Input PAT_IA27 PAT_IA 9 30 
> Input PAT_IA29 PAT_IA 9 30 
> Input PAT_IA30 PAT_IA 8 32 
> Input PAT_IA33 PAT_IA 9 13 
> Input PAT_IA34 PAT_IA 9 21 
>  
> Contrasts for independent sample t-test: 
> 1,CON_IA>PAT_IA:1 -1 0 0 0 0 
> 2,PAT_IA>CON_IA:-1 1 0 0 0 0 
> Contrasts for correlation analysis: 
> 1,possitive correlation analysis between pial thickness and score1:0 0  
> 0.5 0.5 0 0 
> 2,negtive correlation analysis between pial thickness and score1:0 0  
> -0.5 -0.5 0 0 
> 3,positive correlation analysis between pial thickness and score2:0 0  
> 0 0 0.5 0.5 
> 4,negtive correlation analysis between pial thickness and score2:0 0 0  
> 0 -0.5 -0.5 
> Are my designs appropriate? 
> If I want to implement regression analysis(i.e. dependent variable is  
> thickness and independent variables are score1 and score2), how to  
> design my contrast? 
> Thanks. 
> All the best. 
> Rujing Zha 
> 2014-02-20 
>  
> charujing123 
> 
> 
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[Freesurfer] Fw: Re: extracting mean thickness from specific cluster

Hi doug,
I tried to generate the mean thickness of the cluster in uncorrected p 
value<0.005 for each subject by this command "mri_glmfit-sim --glmdir 
lh.score.dir --cwp 1 --cache 2.3 neg". It generates some files named with 
suffix 
".pdf.dat,cluster.mgh,cluster.summary,masked.mgh,ocn.annot,ocn.mgh,voxel.mgh". 
I cannot find a file that can tell me the mean thickness for each subject. Did 
I miss something?
Thanks.
All the best.
Rujing Zha

2014-02-22



charujing123



发件人："charujing123"
发送时间：2014-02-22 10:08
主题：Re: [Freesurfer] extracting mean thickness from specific cluster
收件人："freesurfer@nmr.mgh.harvard.edu"
抄送：

Hi doug and others,
Thanks doug.
For 1st question:I find that file. However not all has that file.May I generate 
it manually?
Thanks doug.
All the best.
Rujing Zha

2014-02-22



charujing123



发件人：Douglas Greve 
发送时间：2014-02-21 23:46
主题：Re: [Freesurfer] extracting mean thickness from specific cluster
收件人："freesurfer"
抄送：



On 2/21/14 10:04 AM, charujing123 wrote:

Hi all,
I finished the mri_glmfit-sim, and got some clusters in the cluster summary. 
1,I want to know how to extract mean thickness for each subject in this 
cluster? 

There should already be a file there called something like something.y.ocn.dat. 
This will have a row for each subject and a column for each cluster. The value 
will be the mean for that subject inside that cluster.


2,If I want to extract mean thickness of each subject according to a 
uncorrected p value, i.e. 0.005, what should I do to perform it?

What do you mean? Over all vertices that survive? Or  for each  all cluster 
with a cluster-forming threshold of .005? If the latter, you can run 
mri_glmfit-sim with --cwp 1 --cache 2.3 abs



Thanks.
All the best.
Rujing Zha

2014-02-21



charujing123

 

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Re: [Freesurfer] Fw: Re: error in mri_glmfit-sim when using --bg and doss

2014-02-22 Thread charujing123

Hi doug and others,
I tried to perform it by this command "mri_glmfit-sim --glmdir my_dir --no-sim 
mc-z.neg.3 --cwpvalthresh 0.999". It worked at first.However it cannot work 
when I tried it again. It exited error after performing the first contrast. The 
export message is as below:
+++
Found   4 segmentations
Computing statistics for each segmentation
  1 1169 169.000
  2 2135 135.000
  3 3 90  90.000

Reporting on   3 segmentations
Computing spatial average of each frame
  0  1  2*** glibc detected *** mri_segstats: malloc(): memory corruption: 
0x2e61e810 ***
=== Backtrace: =
/lib/libc.so.6[0x9e11dd]
/lib/libc.so.6(__libc_malloc+0x67)[0x9e2d97]
/lib/libc.so.6[0x9cf4cf]
/lib/libc.so.6(fopen64+0x2c)[0x9d1a7c]
mri_segstats[0x80536cd]
/lib/libc.so.6(__libc_start_main+0xdc)[0x98ce9c]
mri_segstats(__gxx_personality_v0+0x1c9)[0x804f791]
=== Memory map: 
00958000-00973000 r-xp  fd:00 60785448   
/lib/ld-2.5.so
00973000-00974000 r-xp 0001a000 fd:00 60785448   
/lib/ld-2.5.so
00974000-00975000 rwxp 0001b000 fd:00 60785448   
/lib/ld-2.5.so
00977000-00acb000 r-xp  fd:00 60784655   
/lib/libc-2.5.so
00acb000-00acc000 ---p 00154000 fd:00 60784655   
/lib/libc-2.5.so
00acc000-00ace000 r-xp 00154000 fd:00 60784655   
/lib/libc-2.5.so
00ace000-00acf000 rwxp 00156000 fd:00 60784655   
/lib/libc-2.5.so
00acf000-00ad2000 rwxp 00acf000 00:00 0
00ad4000-00add000 r-xp  fd:00 60784725   
/lib/libcrypt-2.5.so
00add000-00ade000 r-xp 8000 fd:00 60784725   
/lib/libcrypt-2.5.so
00ade000-00adf000 rwxp 9000 fd:00 60784725   
/lib/libcrypt-2.5.so
00adf000-00b06000 rwxp 00adf000 00:00 0
00b22000-00b2d000 r-xp  fd:00 60784686   
/lib/libgcc_s-4.1.2-20080825.so.1
00b2d000-00b2e000 rwxp a000 fd:00 60784686   
/lib/libgcc_s-4.1.2-20080825.so.1
00c68000-00d48000 r-xp  fd:00 56176146   
/usr/lib/libstdc++.so.6.0.8
00d48000-00d4c000 r-xp 000df000 fd:00 56176146   
/usr/lib/libstdc++.so.6.0.8
00d4c000-00d4d000 rwxp 000e3000 fd:00 56176146   
/usr/lib/libstdc++.so.6.0.8
00d4d000-00d53000 rwxp 00d4d000 00:00 0
00d72000-00d84000 r-xp  fd:00 60784662   
/lib/libz.so.1.2.3
00d84000-00d85000 rwxp 00011000 fd:00 60784662   
/lib/libz.so.1.2.3
08048000-08817000 r-xp 08048000 00:00 0
08817000-2e63b000 rwxp 08817000 00:00 0  [heap]
f630-f6321000 rwxp f630 00:00 0
f6321000-f640 ---p f6321000 00:00 0
f6498000-f7e61000 rwxp f6498000 00:00 0
f7f02000-f7f04000 rwxp f7f02000 00:00 0
f7f04000-f7f2b000 r-xp  fd:00 60784705   
/lib/libm-2.5.so
f7f2b000-f7f2c000 r-xp 00026000 fd:00 60784705   
/lib/libm-2.5.so
f7f2c000-f7f2d000 rwxp 00027000 fd:00 60784705   
/lib/libm-2.5.so
f7f2d000-f7f42000 r-xp  fd:00 60784716   
/lib/libpthread-2.5.so
f7f42000-f7f43000 ---p 00015000 fd:00 60784716   
/lib/libpthread-2.5.so
f7f43000-f7f44000 r-xp 00015000 fd:00 60784716   
/lib/libpthread-2.5.so
f7f44000-f7f45000 rwxp 00016000 fd:00 60784716   
/lib/libpthread-2.5.so
f7f45000-f7f47000 rwxp f7f45000 00:00 0
f7f47000-f7f4a000 r-xp  fd:00 60784670   
/lib/libdl-2.5.so
f7f4a000-f7f4b000 r-xp 2000 fd:00 60784670   
/lib/libdl-2.5.so
f7f4b000-f7f4c000 rwxp 3000 fd:00 60784670   
/lib/libdl-2.5.so
f7f4c000-f7f4d000 rwxp f7f4c000 00:00 0
f7f6f000-f7f79000 r-xp  fd:00 60784678   
/lib/libnss_files-2.5.so
f7f79000-f7f7a000 r-xp 9000 fd:00 60784678   
/lib/libnss_files-2.5.so
f7f7a000-f7f7b000 rwxp a000 fd:00 60784678   
/lib/libnss_files-2.5.so
f7f7b000-f7f7c000 rwxp f7f7b000 00:00 0
ff8e2000-ff8f7000 rwxp 7ffe9000 00:00 0  [stack]
e000-f000 r-xp e000 00:00 0

Writing to ../rh.demo.glmdir/demo-doss-CON2IA/mc-z.neg.3.y.ocn.dat
Abort

Thanks.
All the best.
Rujing Zha
2014-02-22



charujing123



发件人："charujing123"
发送时间：2014-02-22 10:22
主题：[Freesurfer] Fw: Re: error in mri_glmfit-sim when

[Freesurfer] time course in mri_info lh.gender_age.thickness.10.mgh

2014-02-23 Thread charujing123

Hi all,
I have two questions.
1,If I want to get the value of specific voxel from the 
lh.gender_age.thickness.10.mgh, which code can I use to perform it?
2,How to graph the time course of specfic voxel from the 
lh.gender_age.thickness.10.mgh by freeview?
Thanks.
All the best.
Rujing Zha
2014-02-24



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[Freesurfer] tessellate error in tksurfer

2014-02-23 Thread charujing123

hi all,
I want to visually check the cortical reconstruction output with tksurfer, as 
being said in surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/FinalSurfEx. It 
represented nothing but black in the window when I type "tksurfer CON_EIU01 lh 
orig". The appearance can be got in the attachment.
Thanks.
All the best.
RujingZha
2014-02-24



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[Freesurfer] Fw: tessellate error in tksurfer

2014-02-23 Thread charujing123

sorry,this e-mail has the attachment.
Rujing Zha

2014-02-24



charujing123



发件人："charujing123"
发送时间：2014-02-24 11:23
主题：[Freesurfer] tessellate error in tksurfer
收件人："freesurfer@nmr.mgh.harvard.edu"
抄送：

hi all,
I want to visually check the cortical reconstruction output with tksurfer, as 
being said in surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/FinalSurfEx. It 
represented nothing but black in the window when I type "tksurfer CON_EIU01 lh 
orig". The appearance can be got in the attachment.
Thanks.
All the best.
RujingZha
2014-02-24



charujing123<>___
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https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


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Re: [Freesurfer] Fw: Re: extracting mean thickness from specific cluster

Hi doug and others,
Creating the something.y.ocn.dat,I find it can only creating an average
thickness for one cluster. When my numbers of clusters in *sig.cluster.summary
exceeding 1,then it cannot generate the something.y.ocn.dat,and error will be
exported in the window:memory corruption.
I know how to set the threshold, that is to say p0.1or some other value to get only one cluster average
thickness.
Thanks.
ALL the best.
Rujing Zha

2014-02-24

charujing123

发件人："charujing123"
发送时间：2014-02-22 12:39
主题：[Freesurfer] Fw: Re: extracting mean thickness from specific cluster
收件人："freesurfer@nmr.mgh.harvard.edu"
抄送：

Hi doug,
I tried to generate the mean thickness of the cluster in uncorrected p
value<0.005 for each subject by this command "mri_glmfit-sim --glmdir
lh.score.dir --cwp 1 --cache 2.3 neg". It generates some files named with
suffix
".pdf.dat,cluster.mgh,cluster.summary,masked.mgh,ocn.annot,ocn.mgh,voxel.mgh".
I cannot find a file that can tell me the mean thickness for each subject. Did
I miss something?
Thanks.
All the best.
Rujing Zha

2014-02-22

charujing123

发件人："charujing123"
发送时间：2014-02-22 10:08
主题：Re: [Freesurfer] extracting mean thickness from specific cluster
收件人："freesurfer@nmr.mgh.harvard.edu"
抄送：

Hi doug and others,
Thanks doug.
For 1st question:I find that file. However not all has that file.May I generate
it manually?
Thanks doug.
All the best.
Rujing Zha

2014-02-22

charujing123

发件人：Douglas Greve
发送时间：2014-02-21 23:46
主题：Re: [Freesurfer] extracting mean thickness from specific cluster
收件人："freesurfer"
抄送：

On 2/21/14 10:04 AM, charujing123 wrote:

Hi all,
I finished the mri_glmfit-sim, and got some clusters in the cluster summary.
1,I want to know how to extract mean thickness for each subject in this
cluster?

There should already be a file there called something like something.y.ocn.dat.
This will have a row for each subject and a column for each cluster. The value
will be the mean for that subject inside that cluster.

2,If I want to extract mean thickness of each subject according to a
uncorrected p value, i.e. 0.005, what should I do to perform it?

What do you mean? Over all vertices that survive? Or for each all cluster
with a cluster-forming threshold of .005? If the latter, you can run
mri_glmfit-sim with --cwp 1 --cache 2.3 abs

Thanks.
All the best.
Rujing Zha

2014-02-21

charujing123

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Re: [Freesurfer] fsgdf and contrasts

Hi doug and others,
Thanks doug.
I can understand multiple regression. However there is no obvious relationship 
between these two variables. So I try to test correlation between thickness and 
these two variables. If I try to consider all subjects as one group, and test 
correlation between this one group thickness and one variable, can I design 
matrix like this 
:http://surfer.nmr.mgh.harvard.edu/fswiki/Fsgdf1G1V#Contrast2.28slope.mtx.29 ?
Thanks.
All the best.
Rujing Zha

2014-02-25



charujing123



发件人：Douglas N Greve 
发送时间：2014-02-25 00:25
主题：Re: [Freesurfer] fsgdf and contrasts
收件人："charujing123"
抄送："freesurfer@nmr.mgh.harvard.edu"

if you have multiple variables then you have to do multiple regression  
before testing the correlation 
doug 

On 02/21/2014 09:35 PM, charujing123 wrote: 
> Hi doug and others, 
> I want to perform correlation analysis,just one dependent variable and  
> one independent variable. Previously I think the contrast(i.e.0 0 0.5  
> 0.5 0 0) I design is for correlation between score1 and thickness. But  
> yestoday I found this information  
> http://surfer.nmr.mgh.harvard.edu/fswiki/Fsgdf2G2V#Contrast6g1g2.age.mtx.  
> It told me that "Null Hypothesis: does mean of group age slope differ  
> from 0? Is there anaverage affect of age regressing out the effect of  
> group and weight?". Regressing out the effect of group and weight  
> represents this contrast is for multimple regression,not simple  
> correlation between two varibles. I am confused. 
> Doug, would you please tell me where I am wrong? 
> Thanks. 
> All the best. 
> Rujing Zha. 
> 2014-02-22 
> ---- 
> charujing123 
>  
> *发件人：*Douglas Greve  
> *发送时间：*2014-02-21 23:35 
> *主题：*Re: [Freesurfer] fsgdf and contrasts 
> *收件人：*"freesurfer" 
> *抄送：* 
> 
> I'm not sure I understand. Your contrasts below are fine. What are you  
> unsure about? 
> doug 
> 
> 
> 
> 
> On 2/20/14 7:48 PM, charujing123 wrote: 
>> Hidoug and others, 
>> Thanks doug. 
>> I see.If I want to implement multiple regression, i.e. two EVs(score1  
>> and score2) explain pial thickness, what contrast I should design for  
>> this. 
>> Thanks again. 
>> All the best. 
>> Rujing Zha 
>> 2014-02-21 
>>  
>> charujing123 
>>  
>> *发件人：*Douglas N Greve  
>> *发送时间：*2014-02-21 03:39 
>> *主题：*Re: [Freesurfer] fsgdf and contrasts 
>> *收件人：*"freesurfer" 
>> *抄送：* 
>> yes, they are, though you don't need to do the positive and negative 
>> contrasts because the sign is preserved 
>> doug 
>> On 02/20/2014 12:47 AM, charujing123 wrote: 
>> > Hi FS experts and users, 
>> > I am trying to implement independent sample t-test and correlation 
>> > analysis. 
>> > Here is my fsgdf design: 
>> > - 
>> > GroupDescriptorFile 1 
>> > Title lh_ttest 
>> > Class CON_IA 
>> > Class PAT_IA 
>> > Variables score1 score2 
>> > Input CON_IA01 CON_IA 0 0 
>> > Input CON_IA03 CON_IA 0 0 
>> > Input CON_IA05 CON_IA 0 0 
>> > Input CON_IA06 CON_IA 0 0 
>> > Input CON_IA07 CON_IA 3 7 
>> > Input CON_IA09 CON_IA 0 0 
>> > Input CON_IA14 CON_IA 0 0 
>> > Input CON_IA15 CON_IA 0 0 
>> > Input CON_IA16 CON_IA 7 12 
>> > Input CON_IA19 CON_IA 6 15 
>> > Input CON_IA24 CON_IA 6 11 
>> > Input CON_IA27 CON_IA 3 3 
>> > Input CON_IA32 CON_IA 7 21 
>> > Input CON_IA33 CON_IA 7 21 
>> > Input CON_IA35 CON_IA 0 0 
>> > Input CON_IA38 CON_IA 7 15 
>> > Input CON_IA39 CON_IA 2 3 
>> > Input CON_IA40 CON_IA 6 8 
>> > Input CON_IA41 CON_IA 2 4 
>> > Input PAT_IA01 PAT_IA 8 13 
>> > Input PAT_IA02 PAT_IA 9 38 
>> > Input PAT_IA03 PAT_IA 9 33 
>> > Input PAT_IA04 PAT_IA 9 27 
>> > Input PAT_IA06 PAT_IA 9 26 
>> > Input PAT_IA08 PAT_IA 8 16 
>> > Input PAT_IA09 PAT_IA 9 33 
>> > Input PAT_IA16 PAT_IA 9 35 
>> > Input PAT_IA18 PAT_IA 9 39 
>> > Input PAT_IA21 PAT_IA 9 32 
>> > Input PAT_IA22 PAT_IA 9 31 
>> > Input PAT_IA23 PAT_IA 9 35 
>> > Input PAT_IA24 PAT_IA 9 40 
>> > Input PAT_IA25 PAT_IA 9 29 
>> > Input PAT_IA27 PAT_IA 9 30 
>> > Input PAT_IA29 PAT_IA 9 30 
>> > Input PAT_IA30 PAT_IA 8 32 
>

Re: [Freesurfer] time course in mri_info lh.gender_age.thickness.10.mgh

Thanks doug
All the best.
Rujing Zha

2014-02-25

charujing123

发件人：Douglas N Greve 
发送时间：2014-02-25 00:31
主题：Re: [Freesurfer] time course in mri_info lh.gender_age.thickness.10.mgh
收件人："freesurfer"
抄送：

On 02/23/2014 08:32 PM, charujing123 wrote: 
> Hi all, 
> I have two questions. 
> 1,If I want to get the value of specific voxel from the  
> lh.gender_age.thickness.10.mgh, which code can I use to perform it? 
You can go to that vertex when you have it loaded into FreeView,  
otherwise you can load it into matlab (MRIread.m). Make sure to account  
for the fact that matlab uses 1-based indices whereas FS uses 0-based. 
> 2,How to graph the time course of specfic voxel from the  
> lh.gender_age.thickness.10.mgh by freeview? 
Add "-v lh.gender_age.thickness.10.mgh" to your freeview command line 
> Thanks. 
> All the best. 
> Rujing Zha 
> 2014-02-24 
> ---- 
> charujing123 
> 
> 
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gr...@nmr.mgh.harvard.edu 
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Fax: 617-726-7422 

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Re: [Freesurfer] Fw: tessellate error in tksurfer

Hi doug,
I try "freeview -f $SUBJECTS_DIR/CON_EIU01/surf/rh.orig", and it works. The 
appearance can be got in the attachment. Is that appropriate?
Thanks.
All the best.
Rujing Zha

2014-02-25

charujing123

发件人：Douglas N Greve 
发送时间：2014-02-25 00:32
主题：Re: [Freesurfer] Fw: tessellate error in tksurfer
收件人："freesurfer"
抄送：

Looks like it could be a video driver problem. Can you see it in freeview? 
doug 

On 02/23/2014 11:38 PM, charujing123 wrote: 
> sorry,this e-mail has the attachment. 
> Rujing Zha 
> 2014-02-24 
>  
> charujing123 
> ---- 
> *发件人：*"charujing123" 
> *发送时间：*2014-02-24 11:23 
> *主题：*[Freesurfer] tessellate error in tksurfer 
> *收件人：*"freesurfer@nmr.mgh.harvard.edu" 
> *抄送：* 
> hi all, 
> I want to visually check the cortical reconstruction output with  
> tksurfer, as being said in  
> surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/FinalSurfEx. It  
> represented nothing but black in the window when I type "tksurfer  
> CON_EIU01 lh orig". The appearance can be got in the attachment. 
> Thanks. 
> All the best. 
> RujingZha 
> 2014-02-24 
>  
> charujing123 
> 
> 
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Re: [Freesurfer] Fw: Re: error in mri_glmfit-sim when using --bg and doss

 Hi doug and others,
Thanks doug.
Creating the something.y.ocn.dat,I find it can only creating an average 
thickness for one cluster. When my numbers of clusters in *sig.cluster.summary 
exceeding 1,then it cannot generate the something.y.ocn.dat,and error will be 
exported in the window:memory corruption.
I know how to set the threshold, that is to say p0.1or some other value to get only one cluster average 
thickness.
Thanks.
ALL the best.
Rujing Zha

2014-02-25



charujing123



发件人：Douglas N Greve 
发送时间：2014-02-25 00:28
主题：Re: [Freesurfer] Fw: Re: error in mri_glmfit-sim when using --bg and doss
收件人："freesurfer"
抄送：


Try setting the cwpvalthresh to .9 or so. I think this is a numerical  
error that occurs when the cwpthreshold is close to 1 
doug 

On 02/22/2014 04:53 AM, charujing123 wrote: 
> Hi doug and others, 
> I tried to perform it by this command "mri_glmfit-sim --glmdir my_dir  
> --no-sim mc-z.neg.3 --cwpvalthresh 0.999". It worked at first.However  
> it cannot work when I tried it again. It exited error after performing  
> the first contrast. The export message is as below: 
> +++
>  
> Found 4 segmentations 
> Computing statistics for each segmentation 
> 1 1 169 169.000 
> 2 2 135 135.000 
> 3 3 90 90.000 
> Reporting on 3 segmentations 
> Computing spatial average of each frame 
> 0 1 2*** glibc detected *** mri_segstats: malloc(): memory corruption:  
> 0x2e61e810 *** 
> === Backtrace: = 
> /lib/libc.so.6[0x9e11dd] 
> /lib/libc.so.6(__libc_malloc+0x67)[0x9e2d97] 
> /lib/libc.so.6[0x9cf4cf] 
> /lib/libc.so.6(fopen64+0x2c)[0x9d1a7c] 
> mri_segstats[0x80536cd] 
> /lib/libc.so.6(__libc_start_main+0xdc)[0x98ce9c] 
> mri_segstats(__gxx_personality_v0+0x1c9)[0x804f791] 
> === Memory map:  
> 00958000-00973000 r-xp  fd:00 60785448 /lib/ld-2.5.so 
> 00973000-00974000 r-xp 0001a000 fd:00 60785448 /lib/ld-2.5.so 
> 00974000-00975000 rwxp 0001b000 fd:00 60785448 /lib/ld-2.5.so 
> 00977000-00acb000 r-xp  fd:00 60784655 /lib/libc-2.5.so 
> 00acb000-00acc000 ---p 00154000 fd:00 60784655 /lib/libc-2.5.so 
> 00acc000-00ace000 r-xp 00154000 fd:00 60784655 /lib/libc-2.5.so 
> 00ace000-00acf000 rwxp 00156000 fd:00 60784655 /lib/libc-2.5.so 
> 00acf000-00ad2000 rwxp 00acf000 00:00 0 
> 00ad4000-00add000 r-xp  fd:00 60784725 /lib/libcrypt-2.5.so 
> 00add000-00ade000 r-xp 8000 fd:00 60784725 /lib/libcrypt-2.5.so 
> 00ade000-00adf000 rwxp 9000 fd:00 60784725 /lib/libcrypt-2.5.so 
> 00adf000-00b06000 rwxp 00adf000 00:00 0 
> 00b22000-00b2d000 r-xp  fd:00 60784686  
> /lib/libgcc_s-4.1.2-20080825.so.1 
> 00b2d000-00b2e000 rwxp a000 fd:00 60784686  
> /lib/libgcc_s-4.1.2-20080825.so.1 
> 00c68000-00d48000 r-xp  fd:00 56176146 /usr/lib/libstdc++.so.6.0.8 
> 00d48000-00d4c000 r-xp 000df000 fd:00 56176146 /usr/lib/libstdc++.so.6.0.8 
> 00d4c000-00d4d000 rwxp 000e3000 fd:00 56176146 /usr/lib/libstdc++.so.6.0.8 
> 00d4d000-00d53000 rwxp 00d4d000 00:00 0 
> 00d72000-00d84000 r-xp  fd:00 60784662 /lib/libz.so.1.2.3 
> 00d84000-00d85000 rwxp 00011000 fd:00 60784662 /lib/libz.so.1.2.3 
> 08048000-08817000 r-xp 08048000 00:00 0 
> 08817000-2e63b000 rwxp 08817000 00:00 0 [heap] 
> f630-f6321000 rwxp f630 00:00 0 
> f6321000-f640 ---p f6321000 00:00 0 
> f6498000-f7e61000 rwxp f6498000 00:00 0 
> f7f02000-f7f04000 rwxp f7f02000 00:00 0 
> f7f04000-f7f2b000 r-xp  fd:00 60784705 /lib/libm-2.5.so 
> f7f2b000-f7f2c000 r-xp 00026000 fd:00 60784705 /lib/libm-2.5.so 
> f7f2c000-f7f2d000 rwxp 00027000 fd:00 60784705 /lib/libm-2.5.so 
> f7f2d000-f7f42000 r-xp  fd:00 60784716 /lib/libpthread-2.5.so 
> f7f42000-f7f43000 ---p 00015000 fd:00 60784716 /lib/libpthread-2.5.so 
> f7f43000-f7f44000 r-xp 00015000 fd:00 60784716 /lib/libpthread-2.5.so 
> f7f44000-f7f45000 rwxp 00016000 fd:00 60784716 /lib/libpthread-2.5.so 
> f7f45000-f7f47000 rwxp f7f45000 00:00 0 
> f7f47000-f7f4a000 r-xp  fd:00 60784670 /lib/libdl-2.5.so 
> f7f4a000-f7f4b000 r-xp 2000 fd:00 60784670 /lib/libdl-2.5.so 
> f7f4b000-f7f4c000 rwxp 3000 fd:00 60784670 /lib/libdl-2.5.so 
> f7f4c000-f7f4d000 rwxp f7f4c000 00:00 0 
> f7f6f000-f7f79000 r-xp  fd:00 60784678 /lib/libnss_files-2.5.so 
> f7f79000-f7f7a000 r-xp 9000 fd:00 60784678 /lib/libnss_files-2.5.so 
> f7f7a000-f7f7b000 rwxp a000 fd:00 60784678 /lib/libnss_files-2.5.so 
> f7f7b000-f7f7c000 rwxp f7f7b000 00:00 0 
> ff8e2000-ff8f7000 rwxp 7ffe9000 00:00 0 [stack] 
> e000-f000 r-xp e000 00:00 0 
> Writing to ../rh.demo.glmdir/demo-doss-CON2IA/mc-z.neg.3.y.ocn.dat 
> Abort 
> +

Re: [Freesurfer] fsgdf and contrasts

Thanks doug.
All the best.
Rujing Zha

2014-02-26



charujing123



发件人：Douglas Greve 
发送时间：2014-02-25 23:37
主题：Re: [Freesurfer] fsgdf and contrasts
收件人："freesurfer"
抄送：

Yes
doug


On 2/24/14 8:32 PM, charujing123 wrote:

Hi doug and others,
Thanks doug.
I can understand multiple regression. However there is no obvious relationship 
between these two variables. So I try to test correlation between thickness and 
these two variables. If I try to consider all subjects as one group, and test 
correlation between this one group thickness and one variable, can I design 
matrix like this 
:http://surfer.nmr.mgh.harvard.edu/fswiki/Fsgdf1G1V#Contrast2.28slope.mtx.29 ?
Thanks.
All the best.
Rujing Zha

2014-02-25



charujing123



发件人：Douglas N Greve 
发送时间：2014-02-25 00:25
主题：Re: [Freesurfer] fsgdf and contrasts
收件人："charujing123"
抄送："freesurfer@nmr.mgh.harvard.edu"

if you have multiple variables then you have to do multiple regression  
before testing the correlation 
doug 

On 02/21/2014 09:35 PM, charujing123 wrote: 
> Hi doug and others, 
> I want to perform correlation analysis,just one dependent variable and  
> one independent variable. Previously I think the contrast(i.e.0 0 0.5  
> 0.5 0 0) I design is for correlation between score1 and thickness. But  
> yestoday I found this information  
> http://surfer.nmr.mgh.harvard.edu/fswiki/Fsgdf2G2V#Contrast6g1g2.age.mtx.  
> It told me that "Null Hypothesis: does mean of group age slope differ  
> from 0? Is there anaverage affect of age regressing out the effect of  
> group and weight?". Regressing out the effect of group and weight  
> represents this contrast is for multimple regression,not simple  
> correlation between two varibles. I am confused. 
> Doug, would you please tell me where I am wrong? 
> Thanks. 
> All the best. 
> Rujing Zha. 
> 2014-02-22 
>  
> charujing123 
>  
> *发件 人：*Douglas Greve  
> *发送时间：*2014-02-21 23:35 
> *主题：*Re: [Freesurfer] fsgdf and contrasts 
> *收件 人：*"freesurfer" 
> *抄送：* 
> 
> I'm not sure I understand. Your contrasts below are fine. What are you  
> unsure about? 
> doug 
> 
> 
> 
> 
> On 2/20/14 7:48 PM, charujing123 wrote: 
>> Hidoug and others, 
>> Thanks doug. 
>> I see.If I want to implement multiple regression, i.e. two EVs(score1  
>> and score2) explain pial thickness, what contrast I should design for  
>> this. 
>> Thanks again. 
>> All the best. 
>> Rujing Zha 
>> 2014-02-21 
>>  
>> charujing123 
>>  
>> *发件 人：*Douglas N Greve  
>> *发送时间：*2014-02-21 03:39 
>> *主题：*Re: [Freesurfer] fsgdf and contrasts 
>> *收件 人：*"freesurfer" 
>> *抄送：* 
>> yes, they are, though you don't need to do the positive and negative 
>> contrasts because the sign is preserved 
>> doug 
>> On 02/20/2014 12:47 AM, charujing123 wrote: 
>> > Hi FS experts and users, 
>> > I am trying to implement independent sample t-test and correlation 
>> > analysis. 
>> > Here is my fsgdf design: 
>> > - 
>> > GroupDescriptorFile 1 
>> > Title lh_ttest 
>> > Class CON_IA 
>> > Class PAT_IA 
>> > Variables score1 score2 
>> > Input CON_IA01 CON_IA 0 0 
>> > Input CON_IA03 CON_IA 0 0 
>> > Input CON_IA05 CON_IA 0 0 
>> > Input CON_IA06 CON_IA 0 0 
>> > Input CON_IA07 CON_IA 3 7 
>> > Input CON_IA09 CON_IA 0 0 
>> > Input CON_IA14 CON_IA 0 0 
>> > Input CON_IA15 CON_IA 0 0 
>> > Input CON_IA16 CON_IA 7 12 
>> > Input CON_IA19 CON_IA 6 15 
>> > Input CON_IA24 CON_IA 6 11 
>> > Input CON_IA27 CON_IA 3 3 
>> > Input CON_IA32 CON_IA 7 21 
>> > Input CON_IA33 CON_IA 7 21 
>> > Input CON_IA35 CON_IA 0 0 
>> > Input CON_IA38 CON_IA 7 15 
>> > Input CON_IA39 CON_IA 2 3 
>> > Input CON_IA40 CON_IA 6 8 
>> > Input CON_IA41 CON_IA 2 4 
>> > Input PAT_IA01 PAT_IA 8 13 
>> > Input PAT_IA02 PAT_IA 9 38 
>> > Input PAT_IA03 PAT_IA 9 33 
>> > Input PAT_IA04 PAT_IA 9 27 
>> > Input PAT_IA06 PAT_IA 9 26 
>> > Input PAT_IA08 PAT_IA 8 16 
>> > Input PAT_IA09 PAT_IA 9 33 
>> > Input PAT_IA16 PAT_IA 9 35 
>> > Input PAT_IA18 PAT_IA 9 39 
>> > Input PAT_IA21 PAT_IA 9 32 
>> > Input PAT_IA22 PAT_IA 9 31 
>> > Input

Re: [Freesurfer] Fw: tessellate error in tksurfer

Hi doug and Zeke,
Thanks doug.
Zeke, would you please help me make it work so that I can check the 
construction of pial?
Thanks.
All the best.
Rujing Zha

2014-02-26

charujing123

发件人：Douglas Greve 
发送时间：2014-02-25 23:40
主题：Re: [Freesurfer] Fw: tessellate error in tksurfer
收件人："freesurfer"
抄送：

Sorry, I don't know why tksurfer is failing to display the surface. I suspect 
that it is a video driver problem, but that is just a speculation, and I'm not 
qualified to debug video driver issues. Maybe Zeke can chime in.

doug

On 2/24/14 9:56 PM, charujing123 wrote:

Sorry for this e-mail has the attachment.
Rujing Zha

2014-02-25

charujing123

发件人："charujing123"
发送时间：2014-02-25 10:40
主题：Re: [Freesurfer] Fw: tessellate error in tksurfer
收件人："freesurfer@nmr.mgh.harvard.edu"
抄送：

Hi doug,
I try "freeview -f $SUBJECTS_DIR/CON_EIU01/surf/rh.orig", and it works. The 
appearance can be got in the attachment. Is that appropriate?
Thanks.
All the best.
Rujing Zha

2014-02-25

charujing123

发件人：Douglas N Greve 
发送时间：2014-02-25 00:32
主题：Re: [Freesurfer] Fw: tessellate error in tksurfer
收件人："freesurfer"
抄送：

Looks like it could be a video driver problem. Can you see it in freeview? 
doug 

On 02/23/2014 11:38 PM, charujing123 wrote: 
> sorry,this e-mail has the attachment. 
> Rujing Zha 
> 2014-02-24 
>  
> charujing123 
> ---- 
> *发件 人：*"charujing123" 
> *发送时间：*2014-02-24 11:23 
> *主题：*[Freesurfer] tessellate error in tksurfer 
> *收件人：*"freesurfer@nmr.mgh.harvard.edu" 
> *抄送：* 
> hi all, 
> I want to visually check the cortical reconstruction output with  
> tksurfer, as being said in  
> surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/FinalSurfEx. It  
> represented nothing but black in the window when I type "tksurfer  
> CON_EIU01 lh orig". The appearance can be got in the attachment. 
> Thanks. 
> All the best. 
> RujingZha 
> 2014-02-24 
>  
> charujing123 
> 
> 
> ___ 
> Freesurfer mailing list 
> Freesurfer@nmr.mgh.harvard.edu 
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 

--  
Douglas N. Greve, Ph.D. 
MGH-NMR Center 
gr...@nmr.mgh.harvard.edu 
Phone Number: 617-724-2358 
Fax: 617-726-7422 

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting 
FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 
www.nmr.mgh.harvard.edu/facility/filedrop/index.html 
Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ 

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The information in this e-mail is intended only for the person to whom it is
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Re: [Freesurfer] questions about ROI analysis

Hidoug,
Thanks doug.
For 1st question,I want to reduce the search space of vertex-wise analysis to a 
cluster.
For 2nd question, i try freeview as tksurfer cannot work. However this website 
cannot be logged 
in:http://surfer.nmr.mgh.harvard.edu/fswiki/FreeviewGuide/FreeviewTools/RoiEdit.
Thanks.
All the best.
Rujing Zha 

2014-02-26



charujing123



发件人：Douglas Greve 
发送时间：2014-02-25 23:46
主题：Re: [Freesurfer] questions about ROI analysis
收件人："freesurfer"
抄送：



On 2/25/14 10:09 AM, Rujing Zha wrote:

Hi FS experts and others, 
   I have done two group thickness difference analysis based on whole 
brain. Now I want to do correlation analysis between specific ROI thickness and 
behavior score. I searched roi in the FS website, but I cannot distinguish the 
volume ROI and surface ROI very clearly. So I have some questions as below:
   1,As I get some clusters in the two group t-test,I want to use one of 
these clusters to correlate thickness with behavior score. How to generate this 
mask and how to use this mask in the mri_glmfit and mri_glmfit-sim?
Do you mean you want to reduce the search space of a vertex-wise analysis to a 
cluster or that you want to compute the mean thickness within the cluster and 
correlate with your behavioral score?

   2,If I want to draw ROI manually or set ROI according previous studies, 
how to create this ROI mask.
tksurfer can draw a label (as can freeview I think)


Any detailed information will be highly appreaciated.
   Thanks.
   All the best.
Rujing Zha



 

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Re: [Freesurfer] time course in mri_info lh.gender_age.thickness.10.mgh

Hi doug and others,
It will be highly appreciated,if anyone can help me.
Thanks.
All the best.
Rujing Zhas

2014-02-26

charujing123

发件人："charujing123"
发送时间：2014-02-25 12:01
主题：Re: [Freesurfer] time course in mri_info lh.gender_age.thickness.10.mgh
收件人："freesurfer@nmr.mgh.harvard.edu"
抄送：

Hi doug,
When I try to do this by "freeview -f 
$SUBJECTS_DIR/fsaverage/surf/lh.inflated:overlay=$SUBJECTS_DIR/glm/lh.score.thickness.00.mgh
 -v lh.score.thickness.00.mgh" or "freeview -v lh.score.thickness.00.mgh", it 
did create a window of time course. However there is nothing in the freeview 
window except darkness((i.e.fig1 in the attachment)). By the way, I can see 
something by "freeview -f 
$SUBJECTS_DIR/fsaverage/surf/lh.inflated:overlay=$SUBJECTS_DIR/glm/lh.score.thickness.00.mgh"(i.e.fig2
 in the attachment). All of these can be got in the attachment.
Thanks.
All the best.
Rujing Zha

2014-02-25

charujing123

发件人："charujing123"
发送时间：2014-02-25 10:28
主题：Re: [Freesurfer] time course in mri_info lh.gender_age.thickness.10.mgh
收件人："freesurfer@nmr.mgh.harvard.edu"
抄送：

Thanks doug
All the best.
Rujing Zha

2014-02-25

charujing123

发件人：Douglas N Greve 
发送时间：2014-02-25 00:31
主题：Re: [Freesurfer] time course in mri_info lh.gender_age.thickness.10.mgh
收件人："freesurfer"
抄送：

On 02/23/2014 08:32 PM, charujing123 wrote: 
> Hi all, 
> I have two questions. 
> 1,If I want to get the value of specific voxel from the  
> lh.gender_age.thickness.10.mgh, which code can I use to perform it? 
You can go to that vertex when you have it loaded into FreeView,  
otherwise you can load it into matlab (MRIread.m). Make sure to account  
for the fact that matlab uses 1-based indices whereas FS uses 0-based. 
> 2,How to graph the time course of specfic voxel from the  
> lh.gender_age.thickness.10.mgh by freeview? 
Add "-v lh.gender_age.thickness.10.mgh" to your freeview command line 
> Thanks. 
> All the best. 
> Rujing Zha 
> 2014-02-24 
>  
> charujing123 
> 
> 
> ___ 
> Freesurfer mailing list 
> Freesurfer@nmr.mgh.harvard.edu 
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 

--  
Douglas N. Greve, Ph.D. 
MGH-NMR Center 
gr...@nmr.mgh.harvard.edu 
Phone Number: 617-724-2358 
Fax: 617-726-7422 

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting 
FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 
www.nmr.mgh.harvard.edu/facility/filedrop/index.html 
Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ 

___ 
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 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. ___
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 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.

Re: [Freesurfer] questions about ROI analysis

2014-02-26 Thread charujing123

Thanks doug,
All the best.
Rujing Zha

2014-02-27



charujing123



发件人：Douglas N Greve 
发送时间：2014-02-27 01:49
主题：Re: [Freesurfer] questions about ROI analysis
收件人："freesurfer"
抄送：


On 02/25/2014 08:34 PM, charujing123 wrote: 
> Hidoug, 
> Thanks doug. 
> For 1st question,I want to reduce the search space of vertex-wise  
> analysis to a cluster. 
Extract the cluster that you want from the ocn to create a mask, eg, to  
get cluster2 
mri_binarize --i ocn.mgh --match 2 --o cluster2.mgh 
The run mri_glmfit with --mask cluster2.mgh 
Then run mri_glmfit-sim with simulation 

> For 2nd question, i try freeview as tksurfer cannot work. However this  
> website cannot be logged  
> in:http://surfer.nmr.mgh.harvard.edu/fswiki/FreeviewGuide/FreeviewTools/RoiEdit.
>  
try 
http://surfer.nmr.mgh.harvard.edu/fswiki/FreeviewGuide 
> Thanks. 
> All the best. 
> Rujing Zha 
> 2014-02-26 
> ---- 
> charujing123 
>  
> *发件人：*Douglas Greve  
> *发送时间：*2014-02-25 23:46 
> *主题：*Re: [Freesurfer] questions about ROI analysis 
> *收件人：*"freesurfer" 
> *抄送：* 
> 
> On 2/25/14 10:09 AM, Rujing Zha wrote: 
>> Hi FS experts and others, 
>> I have done two group thickness difference analysis based on whole  
>> brain. Now I want to do correlation analysis between specific ROI  
>> thickness and behavior score. I searched roi in the FS website, but I  
>> cannot distinguish the volume ROI and surface ROI very clearly. So I  
>> have some questions as below: 
>> 1,As I get some clusters in the two group t-test,I want to use one of  
>> these clusters to correlate thickness with behavior score. How to  
>> generate this mask and how to use this mask in the mri_glmfit and  
>> mri_glmfit-sim? 
> Do you mean you want to reduce the search space of a vertex-wise  
> analysis to a cluster or that you want to compute the mean thickness  
> within the cluster and correlate with your behavioral score? 
>> 2,If I want to draw ROI manually or set ROI according previous  
>> studies, how to create this ROI mask. 
> tksurfer can draw a label (as can freeview I think) 
> 
>> Any detailed information will be highly appreaciated. 
>> Thanks. 
>> All the best. 
>> Rujing Zha 
>> 
>> 
>> 
>> 
>> ___ 
>> 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 

--  
Douglas N. Greve, Ph.D. 
MGH-NMR Center 
gr...@nmr.mgh.harvard.edu 
Phone Number: 617-724-2358 
Fax: 617-726-7422 

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting 
FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 
www.nmr.mgh.harvard.edu/facility/filedrop/index.html 
Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ 

___ 
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 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. ___
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 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.

Re: [Freesurfer] time course in mri_info lh.gender_age.thickness.10.mgh

2014-02-26 Thread charujing123

Hi doug,
Thanks doug. 
I am sorry to describe my question no very clearly.It did work,but I want to 
view time course of lh.score.thickness.00.mgh vertex by vertex. So I need to 
try -v option to view time course manually as you just told me. However I 
cannot view anything but darkness when I try ""freeview -v 
lh.score.thickness.00.mgh"". Is there any tool or method to present a time 
course window(or a colume of numbers) when I click one voxel or vertex. And 
numbers in time course window will change when I click other voxel or vertex.
Thanks,
All the best.
Rujing Zha

2014-02-27



charujing123



发件人：Douglas N Greve 
发送时间：2014-02-27 01:51
主题：Re: [Freesurfer] time course in mri_info lh.gender_age.thickness.10.mgh
收件人："freesurfer"
抄送：

Try this 
freeview -f  
$SUBJECTS_DIR/fsaverage/surf/lh.inflated:overlay=$SUBJECTS_DIR/glm/lh.score.thickness.00.mgh
 
Don't use -v in this case because -v is for a volumes and volume  
overlays and all your data are surface overlays 


On 02/25/2014 08:38 PM, charujing123 wrote: 
> Hi doug and others, 
> It will be highly appreciated,if anyone can help me. 
> Thanks. 
> All the best. 
> Rujing Zhas 
> 2014-02-26 
>  
> charujing123 
> ---- 
> *发件人：*"charujing123" 
> *发送时间：*2014-02-25 12:01 
> *主题：*Re: [Freesurfer] time course in mri_info  
> lh.gender_age.thickness.10.mgh 
> *收件人：*"freesurfer@nmr.mgh.harvard.edu" 
> *抄送：* 
> Hi doug, 
> When I try to do this by "freeview -f  
> $SUBJECTS_DIR/fsaverage/surf/lh.inflated:overlay=$SUBJECTS_DIR/glm/lh.score.thickness.00.mgh
>   
> -v lh.score.thickness.00.mgh" or "freeview -v  
> lh.score.thickness.00.mgh", it did create a window of time course.  
> However there is nothing in the freeview window except  
> darkness((i.e.fig1 in the attachment)). By the way, I can see  
> something by "freeview -f  
> $SUBJECTS_DIR/fsaverage/surf/lh.inflated:overlay=$SUBJECTS_DIR/glm/lh.score.thickness.00.mgh"(i.e.fig2
>   
> in the attachment). All of these can be got in the attachment. 
> Thanks. 
> All the best. 
> Rujing Zha 
> 2014-02-25 
> ---- 
> charujing123 
>  
> *发件人：*"charujing123" 
> *发送时间：*2014-02-25 10:28 
> *主题：*Re: [Freesurfer] time course in mri_info  
> lh.gender_age.thickness.10.mgh 
> *收件人：*"freesurfer@nmr.mgh.harvard.edu" 
> *抄送：* 
> Thanks doug 
> All the best. 
> Rujing Zha 
> 2014-02-25 
>  
> charujing123 
> ---- 
> *发件人：*Douglas N Greve  
> *发送时间：*2014-02-25 00:31 
> *主题：*Re: [Freesurfer] time course in mri_info  
> lh.gender_age.thickness.10.mgh 
> *收件人：*"freesurfer" 
> *抄送：* 
> On 02/23/2014 08:32 PM, charujing123 wrote: 
> > Hi all, 
> > I have two questions. 
> > 1,If I want to get the value of specific voxel from the 
> > lh.gender_age.thickness.10.mgh, which code can I use to perform it? 
> You can go to that vertex when you have it loaded into FreeView, 
> otherwise you can load it into matlab (MRIread.m). Make sure to account 
> for the fact that matlab uses 1-based indices whereas FS uses 0-based. 
> > 2,How to graph the time course of specfic voxel from the 
> > lh.gender_age.thickness.10.mgh by freeview? 
> Add "-v lh.gender_age.thickness.10.mgh" to your freeview command line 
> > Thanks. 
> > All the best. 
> > Rujing Zha 
> > 2014-02-24 
> >  
>  
> > charujing123 
> > 
> > 
> > ___ 
> > Freesurfer mailing list 
> > Freesurfer@nmr.mgh.harvard.edu 
> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 
> --  
> Douglas N. Greve, Ph.D. 
> MGH-NMR Center 
> gr...@nmr.mgh.harvard.edu 
> Phone Number: 617-724-2358 
> Fax: 617-726-7422 
> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting 
> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 
> www.nmr.mgh.harvard.edu/facility/filedrop/index.html 
> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ 
> ___ 
> 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

Re: [Freesurfer] time course in mri_info lh.gender_age.thickness.10.mgh

2014-02-26 Thread charujing123

Hi doug and Ruopeng,
Thanks doug.
The command you sent did show something on the surface, but the button of "show 
time course" can not be clicked.
Thanks doug and ruopeng.
All the best.
Rujing Zha

2014-02-27



charujing123



发件人：Douglas Greve 
发送时间：2014-02-27 11:13
主题：Re: [Freesurfer] time course in mri_info lh.gender_age.thickness.10.mgh
收件人："freesurfer","Ruopeng 
Wang"
抄送：


That command definitely will not work. When you ran the command I sent, did it 
at least show you something on the surface? 

Ruopeng, is there a way to load a surface-based timecourse in freeview?

doug





On 2/26/14 9:11 PM, charujing123 wrote:

Hi doug,
Thanks doug. 
I am sorry to describe my question no very clearly.It did work,but I want to 
view time course of lh.score.thickness.00.mgh vertex by vertex. So I need to 
try -v option to view time course manually as you just told me. However I 
cannot view anything but darkness when I try ""freeview -v 
lh.score.thickness.00.mgh"". Is there any tool or method to present a time 
course window(or a colume of numbers) when I click one voxel or vertex. And 
numbers in time course window will change when I click other voxel or vertex.
Thanks,
All the best.
Rujing Zha

2014-02-27



charujing123



发件人：Douglas N Greve 
发送时间：2014-02-27 01:51
主题：Re: [Freesurfer] time course in mri_info lh.gender_age.thickness.10.mgh
收件人："freesurfer"
抄送：

Try this 
freeview -f  
$SUBJECTS_DIR/fsaverage/surf/lh.inflated:overlay=$SUBJECTS_DIR/glm/lh.score.thickness.00.mgh
 
Don't use -v in this case because -v is for a volumes and volume  
overlays and all your data are surface overlays 


On 02/25/2014 08:38 PM, charujing123 wrote: 
> Hi doug and others, 
> It will be highly appreciated,if anyone can help me. 
> Thanks. 
> All the best. 
> Rujing Zhas 
> 2014-02-26 
> ---- 
> charujing123 
> ---- 
> *发件人：*"charujing123" 
> *发送时间：*2014-02-25 12:01 
> *主题：*Re: [Freesurfer] time course in mri_info  
> lh.gender_age.thickness.10.mgh 
> *收件人：*"freesurfer@nmr.mgh.harvard.edu" 
> *抄送：* 
> Hi doug, 
> When I try to do this by "freeview -f  
> $SUBJECTS_DIR/fsaverage/surf/lh.inflated:overlay=$SUBJECTS_DIR/glm/lh.score.thickness.00.mgh
>   
> -v lh.score.thickness.00.mgh" or "freeview -v  
> lh.score.thickness.00.mgh", it did create a window of time course.  
> However there is nothing in the freeview window except  
> darkness((i.e.fig1 in the attachment)). By the way, I can see  
> something by "freeview -f  
> $SUBJECTS_DIR/fsaverage/surf/lh.inflated:overlay=$SUBJECTS_DIR/glm/lh.score.thickness.00.mgh"(i.e.fig2
>   
> in the attachment). All of these can be got in the attachment. 
> Thanks. 
> All the best. 
> Rujing Zha 
> 2014-02-25 
>  
> charujing123 
>  
> *发件人：*"charujing123" 
> *发送时间：*2014-02-25 10:28 
> *主题：*Re: [Freesurfer] time course in mri_info  
> lh.gender_age.thickness.10.mgh 
> *收件人：*"freesurfer@nmr.mgh.harvard.edu" 
> *抄送：* 
> Thanks doug 
> All the best. 
> Rujing Zha 
> 2014-02-25 
>  
> charujing123 
> ---- 
> *发件 人：*Douglas N Greve  
> *发送时间：*2014-02-25 00:31 
> *主题：*Re: [Freesurfer] time course in mri_info  
> lh.gender_age.thickness.10.mgh 
> *收件 人：*"freesurfer" 
> *抄送：* 
> On 02/23/2014 08:32 PM, charujing123 wrote: 
> > Hi all, 
> > I have two questions. 
> > 1,If I want to get the value of specific voxel from the 
> > lh.gender_age.thickness.10.mgh, which code can I use to perform it? 
> You can go to that vertex when you have it loaded into FreeView, 
> otherwise you can load it into matlab (MRIread.m). Make sure to account 
> for the fact that matlab uses 1-based indices whereas FS uses 0-based. 
> > 2,How to graph the time course of specfic voxel from the 
> > lh.gender_age.thickness.10.mgh by freeview? 
> Add "-v lh.gender_age.thickness.10.mgh" to your freeview command line 
> > Thanks. 
> > All the best. 
> > Rujing Zha 
> > 2014-02-24 
> >  
>  
> > charujing123 
> > 
> > 
> > ___ 
> > Freesurfer mailing list 
> > Freesurfer@nmr.mgh.harvard.edu 
> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 
> --

Re: [Freesurfer] time course in mri_info lh.gender_age.thickness.10.mgh

2014-02-27 Thread charujing123

Hi Ruopeng,
Thanks Ruopeng.
If you complete it, please tell me how to get it on the website.
Thanks.
All the best.
Rujing Zha

2014-02-28



charujing123



发件人：Ruopeng Wang 
发送时间：2014-02-28 05:10
主题：Re: [Freesurfer] time course in mri_info lh.gender_age.thickness.10.mgh
收件人："charujing123"
抄送："freesurfer@nmr.mgh.harvard.edu"

I have added support to display surface-based timecourse data in Time Course 
window. It should be available in the dev build tomorrow.

Ruopeng

On 02/27/2014 12:17 AM, charujing123 wrote:

Hi doug and Ruopeng,
Thanks doug.
The command you sent did show something on the surface, but the button of "show 
time course" can not be clicked.
Thanks doug and ruopeng.
All the best.
Rujing Zha

2014-02-27



charujing123



发件人：Douglas Greve 
发送时间：2014-02-27 11:13
主题：Re: [Freesurfer] time course in mri_info lh.gender_age.thickness.10.mgh
收件人："freesurfer","Ruopeng 
Wang"
抄送：


That command definitely will not work. When you ran the command I sent, did it 
at least show you something on the surface? 

Ruopeng, is there a way to load a surface-based timecourse in freeview?

doug





On 2/26/14 9:11 PM, charujing123 wrote:

Hi doug,
Thanks doug. 
I am sorry to describe my question no very clearly.It did work,but I want to 
view time course of lh.score.thickness.00.mgh vertex by vertex. So I need to 
try -v option to view time course manually as you just told me. However I 
cannot view anything but darkness when I try ""freeview -v 
lh.score.thickness.00.mgh"". Is there any tool or method to present a time 
course window(or a colume of numbers) when I click one voxel or vertex. And 
numbers in time course window will change when I click other voxel or vertex.
Thanks,
All the best.
Rujing Zha

2014-02-27



charujing123



发件人：Douglas N Greve 
发送时间：2014-02-27 01:51
主题：Re: [Freesurfer] time course in mri_info lh.gender_age.thickness.10.mgh
收件人："freesurfer"
抄送：

Try this 
freeview -f  
$SUBJECTS_DIR/fsaverage/surf/lh.inflated:overlay=$SUBJECTS_DIR/glm/lh.score.thickness.00.mgh
 
Don't use -v in this case because -v is for a volumes and volume  
overlays and all your data are surface overlays 


On 02/25/2014 08:38 PM, charujing123 wrote: 
> Hi doug and others, 
> It will be highly appreciated,if anyone can help me. 
> Thanks. 
> All the best. 
> Rujing Zhas 
> 2014-02-26 
> ---- 
> charujing123 
>  
> *发件人：*"charujing123" 
> *发送时间：*2014-02-25 12:01 
> *主 题：*Re: [Freesurfer] time course in mri_info  
> lh.gender_age.thickness.10.mgh 
> *收件人：*"freesurfer@nmr.mgh.harvard.edu" 
> *抄送：* 
> Hi doug, 
> When I try to do this by "freeview -f  
> $SUBJECTS_DIR/fsaverage/surf/lh.inflated:overlay=$SUBJECTS_DIR/glm/lh.score.thickness.00.mgh
>   
> -v lh.score.thickness.00.mgh" or "freeview -v  
> lh.score.thickness.00.mgh", it did create a window of time course.  
> However there is nothing in the freeview window except  
> darkness((i.e.fig1 in the attachment)). By the way, I can see  
> something by "freeview -f  
> $SUBJECTS_DIR/fsaverage/surf/lh.inflated:overlay=$SUBJECTS_DIR/glm/lh.score.thickness.00.mgh"(i.e.fig2
>   
> in the attachment). All of these can be got in the attachment. 
> Thanks. 
> All the best. 
> Rujing Zha 
> 2014-02-25 
>  
> charujing123 
>  
> *发件人：*"charujing123" 
> *发送时间：*2014-02-25 10:28 
> *主 题：*Re: [Freesurfer] time course in mri_info  
> lh.gender_age.thickness.10.mgh 
> *收件人：*"freesurfer@nmr.mgh.harvard.edu" 
> *抄送：* 
> Thanks doug 
> All the best. 
> Rujing Zha 
> 2014-02-25 
>  
> charujing123 
>  
> *发件 人：*Douglas N Greve  
> *发送时间：*2014-02-25 00:31 
> *主 题：*Re: [Freesurfer] time course in mri_info  
> lh.gender_age.thickness.10.mgh 
> *收件 人：*"freesurfer" 
> *抄送：* 
> On 02/23/2014 08:32 PM, charujing123 wrote: 
> > Hi all, 
> > I have two questions. 
> > 1,If I want to get the value of specific voxel from the 
> > lh.gender_age.thickness.10.mgh, which code can I use to perform it? 
> You can go to that vertex when you have it loaded into FreeView, 
> otherwise you can load it into matlab (MRIread.m). Make sure to account 
> for the fact that matlab uses 1-based indices whereas FS uses 0-based. 
> > 2,How to graph the time course of specfic voxel from the 
> > lh.gender_age.th

Re: [Freesurfer] cannot sign white matter area by control point and white matter edit

2014-03-08 Thread charujing123

Hi Louis,
Thanks.
I will try that.
Best wishes.
Rujing Zha

2014-03-08

charujing123

发件人：Louis Nicholas Vinke 
发送时间：2014-03-08 05:44
主题：Re: [Freesurfer] cannot sign white matter area by control point and white 
matter edit
收件人："charujing123"
抄送："freesurfer@nmr.mgh.harvard.edu"

Hi Rujing, 
You might try drawing in the wm thicker than it is already.  Also, check  
there are no disconnects between the wm voxels in the wm.mgz. 
-Louis 

On Tue, 4 Mar 2014, charujing123 wrote: 

> Hi all. 
> In troubleshooting, I want to sign some area as white matter by control point 
> and wm edit. However neither of them can 
> work. 
> Thanks. the picture can be got in the attachment. 
> All the best. 
> Rujing Zha 
>   
> 2014-03-04 
>  
> ___
>  
> charujing123 
>  
> 

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Re: [Freesurfer] fix this error in segmentation

2014-03-09 Thread charujing123

Hi Bruce,
Thanks Bruce.
I fixed it.
All the best.
Rujing Zha

2014-03-09

charujing123

发件人：Bruce Fischl 
发送时间：2014-03-08 22:07
主题：Re: [Freesurfer] fix this error in segmentation
收件人："charujing123"
抄送："freesurfer@nmr.mgh.harvard.edu"

Hi Rujing 

that is probably the result of a topology correction. You'll need to  
track down the source of it which is probably most easily seen in the  
?h.inflated.nofix and ?h.orig.nofix. 

cheers 
Bruce 
On Sat, 8 Mar 2014, charujing123 wrote: 

> Hi all, 
> How to fix this problem in segmentation, which can be got in the attachment? 
> Thanks.All the best. 
> Rujing Zha 
>   
> 2014-03-08 
>  
> ____ 
> charujing123 
>  
> 

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[Freesurfer] convert sig.mgh into *.nii

Hi FS experts,
I want to extract time course from sig.mgh. But the *.y.ocn.mgh cannot be 
created. So I want to view it in other formats, such as nii. So how to convert 
it into nii format.
Thanks.
All the best.
Rujing Zha

2014-03-11



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[Freesurfer] view time course in freeview

Hi FS experts,
For the sig.mgh, can I see the time course vertex by vertex in freeview?
Thanks.
All the best.
Rujing Zha___
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Re: [Freesurfer] view time course in freeview

Hi doug,
sig.mgh is my result for two group t-test on pial thickness of whole brain. So 
I want to see the time course of thickness of rh.ttest.thickness.10.mgh vertex 
by vertex.
Thanks.
All the best.
Rujing Zha
2014-03-12

charujing123

发件人：Douglas N Greve 
发送时间：2014-03-12 00:16
主题：Re: [Freesurfer] view time course in freeview
收件人："freesurfer"
抄送：

the time course of what? 
On 03/11/2014 07:18 AM, charujing123 wrote: 
> Hi FS experts, 
> For the sig.mgh, can I see the time course vertex by vertex in freeview? 
> Thanks. 
> All the best. 
> Rujing Zha 
> 
> 
> ___ 
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> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 

--  
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gr...@nmr.mgh.harvard.edu 
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Re: [Freesurfer] convert sig.mgh into *.nii

Hi Bruce,
Thanks Bruce.
I knew that code, but I have no idea to deal with my problem after reading the 
help. Would you please tell me how to use mri_surf2vol after I describe my 
problem details?
I have a file named rh.36sb.score.thickness.10.mgh which is created from the 
"mris_preproc --fsgd $FSGDFILE --target fsaverage --hemi $style --meas 
thickness --out ${style}.${FSGDFILE%_*}.00.mgh". I want to convert this file 
into nii format volume-based, so I can read it by AFNI.
Thanks.
All the best.
Rujing Zha

2014-03-12



charujing123



发件人：Bruce Fischl 
发送时间：2014-03-12 09:44
主题：Re: [Freesurfer] convert sig.mgh into *.nii
收件人："charujing123"
抄送："freesurfer@nmr.mgh.harvard.edu"

try mri_surf2vol with the output volume named .nii 

cheers 
Bruce 
On Wed, 12 Mar 2014,  
charujing123 wrote: 

> Hi doug, 
> Thanks doug. 
> I try this code, but it represent two dimension for each subject data when 
> loaded in the AFNI. Is there any code to volume-based conversion from mgh to 
> nii? 
> All the best. 
> Rujing Zha 
>   
> 2014-03-12 
>  
> ____ 
> charujing123 
>  
>  
> 发件人：Douglas N Greve  
> 发送时间：2014-03-12 00:16 
> 主题：Re: [Freesurfer] convert sig.mgh into *.nii 
> 收件人："freesurfer" 
> 抄送： 
>   
>   
> mri_convert file.mgh file.nii  
>   
> doug  
>   
> On 03/11/2014 05:55 AM, charujing123 wrote:  
> > Hi FS experts,  
> > I want to extract time course from sig.mgh. But the *.y.ocn.mgh cannot   
> > be created. So I want to view it in other formats, such as nii. So how   
> > to convert it into nii format.  
> > Thanks.  
> > All the best.  
> > Rujing Zha  
> > 2014-03-11  
> >  
?? ?> charujing123  
> >  
> >  
> > ___  
> > Freesurfer mailing list  
> > Freesurfer@nmr.mgh.harvard.edu  
> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer  
>   
> --   
> Douglas N. Greve, Ph.D.  
> MGH-NMR Center  
> gr...@nmr.mgh.harvard.edu  
> Phone Number: 617-724-2358  
> Fax: 617-726-7422  
>   
> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting  
> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2  
> www.nmr.mgh.harvard.edu/facility/filedrop/index.html  
> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/  
>   
> ___  
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>   
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> s  
> addressed. If you believe this e-mail was sent to you in error and the e-ma 
> il  
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> ne at  
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> rror  
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> perly  
> dispose of the e-mail.  
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Re: [Freesurfer] convert sig.mgh into *.nii