[Freesurfer] Sub cortical volumes and CVS

[Jennifer Eastman]

Hello, I am interested in comparing sub-cortical volumes across subjects in my 
data set. I am wondering if using the CVS registration step is useful in 
improving the accuracy of the sub-cortical volume measurements independently. I 
will not be examining the cortical thickness  just sub-cortical. I have combed 
the literature that is available and watched the training video, but I am not 
clear if there is benefit to using CVS registration if I am just looking at the 
sub cortical structures. Thank you.

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

[charujing123]

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 pthreshod value. So I want to 
know how to set 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：charujing123charujing...@163.com
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.edufreesurfer@nmr.mgh.harvard.edu
抄送：

Hi doug,
I tried to generate the mean thickness of the cluster in uncorrected p 
value0.005 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：charujing123charujing...@163.com
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.edufreesurfer@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 gr...@nmr.mgh.harvard.edu
发送时间：2014-02-21 23:46
主题：Re: [Freesurfer] extracting mean thickness from specific cluster
收件人：freesurferfreesurfer@nmr.mgh.harvard.edu
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] testing a quadratic effect of age

[Douglas N Greve]

Yes, though you might want to demean age before computing the quadratic.
doug


On 02/24/2014 10:13 AM, Yang, Daniel wrote:
 Hi FreeSurfer Experts,

 With age as a continuous variable, qdec can test the linear effect of 
 age. To test the quadratic effect of age, do I just create a 
 curvilinear term like age*age and add into the existing equation?

 For example:

 original equation:  Y = intercept + age + Factor + age*Factor

 new equation: Y = intercept + age + Factor + age*Factor + age*age + 
 age*age*Factor

 Best,
 Daniel

 -- 
 Daniel (Yung-Jui) Yang, Ph.D.
 Postdoctoral Researcher
 Yale Child Study Center
 New Haven, CT
 Tel: (203) 737-5454
 E-mail: _yung-jui.yang@yale.edu_


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Re: [Freesurfer] fsgdf and contrasts

[Douglas N Greve]

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 gr...@nmr.mgh.harvard.edu
 *发送时间：*2014-02-21 23:35
 *主题：*Re: [Freesurfer] fsgdf and contrasts
 *收件人：*freesurferfreesurfer@nmr.mgh.harvard.edu
 *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 gr...@nmr.mgh.harvard.edu
 *发送时间：*2014-02-21 03:39
 *主题：*Re: [Freesurfer] fsgdf and contrasts
 *收件人：*freesurferfreesurfer@nmr.mgh.harvard.edu
 *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_IAPAT_IA:1 -1 0 0 0 0
  2,PAT_IACON_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] testing a quadratic effect of age

[Douglas N Greve]

yes, that works too

On 02/24/2014 11:20 AM, Yang, Daniel wrote:
 Thanks, Doug. I will standardize the age first.

 I can also think of another way of doing this: divide the sample into 
 4 age bins and treat age as a Discrete Factor with 4 levels.

 Best,
 Daniel

 -- 
 Daniel (Yung-Jui) Yang, Ph.D.
 Postdoctoral Researcher
 Yale Child Study Center
 New Haven, CT
 Tel: (203) 737-5454
 E-mail: _yung-jui.yang@yale.edu_

 On 2/24/14 11:10 AM, Douglas N Greve gr...@nmr.mgh.harvard.edu 
 mailto:gr...@nmr.mgh.harvard.edu wrote:

 Yes, though you might want to demean age before computing the
 quadratic.
 doug


 On 02/24/2014 10:13 AM, Yang, Daniel wrote:

 Hi FreeSurfer Experts,

 With age as a continuous variable, qdec can test the linear
 effect of
 age. To test the quadratic effect of age, do I just create a
 curvilinear term like age*age and add into the existing equation?

 For example:

 original equation:  Y = intercept + age + Factor + age*Factor

 new equation: Y = intercept + age + Factor + age*Factor +
 age*age +
 age*age*Factor

 Best,
 Daniel

 -- 
 Daniel (Yung-Jui) Yang, Ph.D.
 Postdoctoral Researcher
 Yale Child Study Center
 New Haven, CT
 Tel: (203) 737-5454
 E-mail: _yung-jui.yang@yale.edu_ mailto:_yung-jui.yang@yale.edu_


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

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 the e-mail
 contains patient information, please contact the Partners
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Phone Number: 617-724-2358
Fax: 617-726-7422

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

[Douglas N Greve]

what version of FS are you using? there should be a file with summary 
in the name. Also, try looking at the help with mri_glmfit-sim --help
doug


On 02/21/2014 11:39 PM, charujing123 wrote:
 Hi doug,
 I tried to generate the mean thickness of the cluster in uncorrected p 
 value0.005 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：*charujing123charujing...@163.com
 *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.edufreesurfer@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 gr...@nmr.mgh.harvard.edu
 *发送时间：*2014-02-21 23:46
 *主题：*Re: [Freesurfer] extracting mean thickness from specific cluster
 *收件人：*freesurferfreesurfer@nmr.mgh.harvard.edu
 *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 
 clusterwith 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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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] time course in mri_info lh.gender_age.thickness.10.mgh

[Douglas N Greve]

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

[Douglas N Greve]

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
 
 Thanks.
 All the best.
 Rujing Zha
 2014-02-22
 
 charujing123
 
 *发件人：*charujing123charujing...@163.com
 *发送时间：*2014-02-22 10:22
 *主题：*[Freesurfer] Fw: Re: error in mri_glmfit-sim when using --bg 
 and doss
 *收件人：*freesurfer@nmr.mgh.harvard.edufreesurfer@nmr.mgh.harvard.edu
 *抄送：*
 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.annot mc-z.pos.3.sig.ocn.annot
 cache.th23.abs.sig.masked.mgh mc-z.abs.2.sig.ocn.mgh 
 

Re: [Freesurfer] Fw: tessellate error in tksurfer

[Douglas N Greve]

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：*charujing123charujing...@163.com
 *发送时间：*2014-02-24 11:23
 *主题：*[Freesurfer] tessellate error in tksurfer
 *收件人：*freesurfer@nmr.mgh.harvard.edufreesurfer@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: extracting mean thickness from specific cluster

[Douglas N Greve]

Sorry, the summary file is not what you want. Can you send a list of the 
files in the folder?
doug


On 02/24/2014 11:26 AM, Douglas N Greve wrote:

 what version of FS are you using? there should be a file with 
 summary in the name. Also, try looking at the help with 
 mri_glmfit-sim --help
 doug


 On 02/21/2014 11:39 PM, charujing123 wrote:
 Hi doug,
 I tried to generate the mean thickness of the cluster in uncorrected 
 p value0.005 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：*charujing123charujing...@163.com
 *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 
 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 gr...@nmr.mgh.harvard.edu
 *发送时间：*2014-02-21 23:46
 *主题：*Re: [Freesurfer] extracting mean thickness from specific cluster
 *收件人：*freesurferfreesurfer@nmr.mgh.harvard.edu
 *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 
 clusterwith 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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Fax: 617-726-7422

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

[Douglas N Greve]

sorry, you are right, the csd files are in the csd folder. The csf file 
will have a name with the contrast name in it. Copy it to a file with a 
name where you substitute the old contrast name for another contrast name.
doug


On 02/21/2014 09:18 PM, charujing123 wrote:
 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 gr...@nmr.mgh.harvard.edu
 *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：*freesurferfreesurfer@nmr.mgh.harvard.edu
 *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] fwhm31+ ?

[Douglas N Greve]

The files in the mult-comp-cor folder are generated from a simulation, 
so the simulation has to be run with larger FWHMs. In the end, I think 
that 25 is probably too much smoothing. You can start to see low spatial 
frequency artifacts when you smooth too much. I usually use 10-15

doug




On 02/24/2014 11:38 AM, Yan


g, Daniel wrote:
 Dear FreeSurfer Experts,

 In the folder, 
 $FREESURFER_HOME/average/mult-comp-cor/fsaverage/rh/cortex, there are 
 fwhm01-fwhm30. I am wondering why there is no fwhm31+ and how to 
 generate one if needed? (Sorry for two questions)

 I used a fwhm=25 in qdec and see the error message when doing cluster 
 analysis:

 ERROR: cannot find 
 $FREESURFER_HOME/average/mult-comp-cor/fsaverage/lh/cortex/fwhm36/...

 I also don't understand why mri_glmfit-sim looks for fwhm36 when I 
 specify fwhm25?

 Sorry for the multiple questions!

 Best,
 Daniel

 -- 
 Daniel (Yung-Jui) Yang, Ph.D.
 Postdoctoral Researcher
 Yale Child Study Center
 New Haven, CT
 Tel: (203) 737-5454
 E-mail: _yung-jui.yang@yale.edu_


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Re: [Freesurfer] Brodmann atlas

[Douglas N Greve]

We don't have coverage for all BAs yet. Note that the BAs we do supply 
are based on actual histology, as opposed to other atlases which just 
give a best guess. Getting histology-based BAs is very difficult. 
Best guesses are free :-)
doug



On 02/24/2014 08:35 AM, Brahim Belaoucha wrote:
 Dear Freesurfer's,
 I am new in using this software, but from what i know is that the 
 Brodmann cortex segmentation should cover the entire cortex, but I 
 obtained the result attached to this message (26 regions). Knowing 
 that I have used recon-all to generate it.
 Is this a bug?
 Until I recieve your answer accept all my salutations.

 -- 

 Sincerely,
 Brahim.

 PhD Student at University of Nice Sophia Antipolis.
 Athena Team-project
 Phone:(+33) 4-9238-7557


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Re: [Freesurfer] Contrast Vectors

[Douglas N Greve]

When you design an analysis, you postulate certain effects (eg, 
diagnosis, age). Each of these effects gets a column in the design 
matrix (eg, normal, AD, age or young/old). Each column has a regression 
coefficient that gets fit in the analysis that indicates the size of 
each of the effects. To test a hypothesis, you need to state the 
hypothesis in terms of the regression coefficients of the effects, eg, 
AD != normal, which can be translated into AD-normal ?= 0. The values in 
the contrast represent weights in the above equation (eg, weight for AD 
= 1, weight for normal= -1).

doug


On 02/24/2014 10:16 AM, Jonathan Holt wrote:
 Hi all,

 I humbly ask for an explanation of contrast vectors, specifically what do 0, 
 1, -1 indicate, exactly?

 best,
 Jon
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[Freesurfer] stats from a volume ROI (in diffusion space)

[Garikoitz Lerma-Usabiaga]

Hi,
I have some volume ROIs in diffusion space (1-s and 0-s). I would like to
obtain, for example, the average FA values in that ROI.

I tried using mri_segstats, but it gives me an error, it needs a
segmentation volume.
mri_segstats --i dmri/dtifit_FA.nii.gz --mask
FSL_waypoint2Hipplh.unc_AS_avg33_mni_bbrlh_headHPC/thres_mask5.nii.gz --sum
fa.stats

If I substitute --i for --seg I obtain a different error.

Which command should I use? I tried dmri_pathstats but it is asking  for
the file length.samples.txt, which I don't have and don't know how to
generate.

thanks!
Gari
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[Freesurfer] recon-all subject folder size

[Durai Arasan]

Hi Freesurfer experts,

I am successfully running recon-all on my cluster. However I find that the
subject folders have sizes ranging from 300mb to 900mb.

I grepped all recon-all.log files for finished without error and that
seemed fine for all subjects.

But I would like to know what is the expected subject folder size when you
run recon-all (with -all option) starting from a standard MPRAGE T1 image.
This might be useful since I have limited control over the cluster nodes
where the processing takes place.

Thank you
Durai


On Mon, Feb 17, 2014 at 2:55 AM, Durai Arasan dura...@gmail.com wrote:

 Hi Freesurfer experts,

 so I got this error when I ran recon-all on my cluster. I am really hoping
 this is just a case of missing GCC libraries and nothing is wrong with the
 Freesurfer installation on the nodes. Kindly confirm this.

 Thank you


 **

 Subject Stamp: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0
 Current Stamp: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0
 INFO: SUBJECTS_DIR is /**
 Actual FREESURFER_HOME /**
 Linux *  SMP Fri Mar 22 05:41:51 EDT 2013
 x86_64 x86_64 x86_64 GNU/Linux
 mri_convert: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.11' not found
 (required by mri_convert)
 mri_convert: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.9' not found
 (required by mri_convert)
 mri_convert: /lib64/libc.so.6: version `GLIBC_2.7' not found (required by
 mri_convert)
 mri_convert: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.11' not found
 (required by mri_convert)
 mri_convert: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.9' not found
 (required by mri_convert)
 mri_convert: /lib64/libc.so.6: version `GLIBC_2.7' not found (required by
 mri_convert)
 tkregister2_cmdl: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.11' not
 found (required by tkregister2_cmdl)
 tkregister2_cmdl: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.9' not
 found (required by tkregister2_cmdl)
 tkregister2_cmdl: /lib64/libc.so.6: version `GLIBC_2.7' not found
 (required by tkregister2_cmdl)
 mri_make_uchar: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.11' not
 found (required by mri_make_uchar)
 mri_make_uchar: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.9' not
 found (required by mri_make_uchar)
 mri_make_uchar: /lib64/libc.so.6: version `GLIBC_2.7' not found (required
 by mri_make_uchar)
 mri_normalize: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.11' not
 found (required by mri_normalize)
 mri_normalize: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.9' not
 found (required by mri_normalize)
 mri_normalize: /lib64/libc.so.6: version `GLIBC_2.7' not found (required
 by mri_normalize)
 mri_watershed: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.11' not
 found (required by mri_watershed)
 mri_watershed: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.9' not
 found (required by mri_watershed)
 mri_watershed: /lib64/libc.so.6: version `GLIBC_2.7' not found (required
 by mri_watershed)
 mri_gcut: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.11' not found
 (required by mri_gcut)
 mri_gcut: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.9' not found
 (required by mri_gcut)
 mri_gcut: /lib64/libc.so.6: version `GLIBC_2.7' not found (required by
 mri_gcut)
 mri_segment: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.11' not found
 (required by mri_segment)
 mri_segment: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.9' not found
 (required by mri_segment)
 mri_segment: /lib64/libc.so.6: version `GLIBC_2.7' not found (required by
 mri_segment)
 mri_label2label: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.11' not
 found (required by mri_label2label)
 mri_label2label: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.9' not
 found (required by mri_label2label)
 mri_label2label: /lib64/libc.so.6: version `GLIBC_2.7' not found (required
 by mri_label2label)
 mri_em_register: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.11' not
 found (required by mri_em_register)
 mri_em_register: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.9' not
 found (required by mri_em_register)
 mri_em_register: /lib64/libc.so.6: version `GLIBC_2.7' not found (required
 by mri_em_register)
 mri_ca_normalize: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.11' not
 found (required by mri_ca_normalize)
 mri_ca_normalize: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.9' not
 found (required by mri_ca_normalize)
 mri_ca_normalize: /lib64/libc.so.6: version `GLIBC_2.7' not found
 (required by mri_ca_normalize)
 mri_ca_register: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.11' not
 found (required by mri_ca_register)
 mri_ca_register: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.9' not
 found (required by mri_ca_register)
 mri_ca_register: /lib64/libc.so.6: version `GLIBC_2.7' not found (required
 by 

Re: [Freesurfer] stats from a volume ROI (in diffusion space)

[Douglas N Greve]

Use --seg instead of --mask. Also, use --id 1 to get only the ROI in the 
mask (otherwise it will give you the mask as one ROI and everything 
outside of the mask as a 2nd ROI)

doug


On 02/24/2014 12:51 PM, Garikoitz Lerma-Usabiaga wrote:
 Hi,
 I have some volume ROIs in diffusion space (1-s and 0-s). I would like 
 to obtain, for example, the average FA values in that ROI.

 I tried using mri_segstats, but it gives me an error, it needs a 
 segmentation volume.
 mri_segstats --i dmri/dtifit_FA.nii.gz --mask 
 FSL_waypoint2Hipplh.unc_AS_avg33_mni_bbrlh_headHPC/thres_mask5.nii.gz 
 --sum fa.stats

 If I substitute --i for --seg I obtain a different error.

 Which command should I use? I tried dmri_pathstats but it is asking  
 for the file length.samples.txt, which I don't have and don't know how 
 to generate.

 thanks!
 Gari


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gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

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Re: [Freesurfer] stats from a volume ROI (in diffusion space)

[Garikoitz Lerma-Usabiaga]

Thanks Doug!



On Mon, Feb 24, 2014 at 7:12 PM, Douglas N Greve
gr...@nmr.mgh.harvard.eduwrote:


 Use --seg instead of --mask. Also, use --id 1 to get only the ROI in the
 mask (otherwise it will give you the mask as one ROI and everything
 outside of the mask as a 2nd ROI)

 doug


 On 02/24/2014 12:51 PM, Garikoitz Lerma-Usabiaga wrote:
  Hi,
  I have some volume ROIs in diffusion space (1-s and 0-s). I would like
  to obtain, for example, the average FA values in that ROI.
 
  I tried using mri_segstats, but it gives me an error, it needs a
  segmentation volume.
  mri_segstats --i dmri/dtifit_FA.nii.gz --mask
  FSL_waypoint2Hipplh.unc_AS_avg33_mni_bbrlh_headHPC/thres_mask5.nii.gz
  --sum fa.stats
 
  If I substitute --i for --seg I obtain a different error.
 
  Which command should I use? I tried dmri_pathstats but it is asking
  for the file length.samples.txt, which I don't have and don't know how
  to generate.
 
  thanks!
  Gari
 
 
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 --
 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
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 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
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Re: [Freesurfer] recon-all subject folder size

[Pedro Paulo de Magalhães Oliveira Junior]

300mb is fine.

-
Pedro Paulo de Magalhães Oliveira Junior
Netfilter  SpeedComm Telecom
-- www.netfilter.com.br
-- For mobile: http://itunes.apple.com/br/artist/netfilter/id365306441



On Mon, Feb 24, 2014 at 3:01 PM, Durai Arasan dura...@gmail.com wrote:

 Hi Freesurfer experts,

 I am successfully running recon-all on my cluster. However I find that the
 subject folders have sizes ranging from 300mb to 900mb.

 I grepped all recon-all.log files for finished without error and that
 seemed fine for all subjects.

 But I would like to know what is the expected subject folder size when you
 run recon-all (with -all option) starting from a standard MPRAGE T1 image.
 This might be useful since I have limited control over the cluster nodes
 where the processing takes place.

 Thank you
 Durai


 On Mon, Feb 17, 2014 at 2:55 AM, Durai Arasan dura...@gmail.com wrote:

 Hi Freesurfer experts,

 so I got this error when I ran recon-all on my cluster. I am really
 hoping this is just a case of missing GCC libraries and nothing is wrong
 with the Freesurfer installation on the nodes. Kindly confirm this.

 Thank you


 **

 Subject Stamp: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0
 Current Stamp: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0
 INFO: SUBJECTS_DIR is /**
 Actual FREESURFER_HOME /**
 Linux *  SMP Fri Mar 22 05:41:51 EDT 2013
 x86_64 x86_64 x86_64 GNU/Linux
 mri_convert: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.11' not
 found (required by mri_convert)
 mri_convert: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.9' not found
 (required by mri_convert)
 mri_convert: /lib64/libc.so.6: version `GLIBC_2.7' not found (required by
 mri_convert)
 mri_convert: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.11' not
 found (required by mri_convert)
 mri_convert: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.9' not found
 (required by mri_convert)
 mri_convert: /lib64/libc.so.6: version `GLIBC_2.7' not found (required by
 mri_convert)
 tkregister2_cmdl: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.11' not
 found (required by tkregister2_cmdl)
 tkregister2_cmdl: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.9' not
 found (required by tkregister2_cmdl)
 tkregister2_cmdl: /lib64/libc.so.6: version `GLIBC_2.7' not found
 (required by tkregister2_cmdl)
 mri_make_uchar: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.11' not
 found (required by mri_make_uchar)
 mri_make_uchar: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.9' not
 found (required by mri_make_uchar)
 mri_make_uchar: /lib64/libc.so.6: version `GLIBC_2.7' not found (required
 by mri_make_uchar)
 mri_normalize: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.11' not
 found (required by mri_normalize)
 mri_normalize: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.9' not
 found (required by mri_normalize)
 mri_normalize: /lib64/libc.so.6: version `GLIBC_2.7' not found (required
 by mri_normalize)
 mri_watershed: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.11' not
 found (required by mri_watershed)
 mri_watershed: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.9' not
 found (required by mri_watershed)
 mri_watershed: /lib64/libc.so.6: version `GLIBC_2.7' not found (required
 by mri_watershed)
 mri_gcut: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.11' not found
 (required by mri_gcut)
 mri_gcut: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.9' not found
 (required by mri_gcut)
 mri_gcut: /lib64/libc.so.6: version `GLIBC_2.7' not found (required by
 mri_gcut)
 mri_segment: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.11' not
 found (required by mri_segment)
 mri_segment: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.9' not found
 (required by mri_segment)
 mri_segment: /lib64/libc.so.6: version `GLIBC_2.7' not found (required by
 mri_segment)
 mri_label2label: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.11' not
 found (required by mri_label2label)
 mri_label2label: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.9' not
 found (required by mri_label2label)
 mri_label2label: /lib64/libc.so.6: version `GLIBC_2.7' not found
 (required by mri_label2label)
 mri_em_register: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.11' not
 found (required by mri_em_register)
 mri_em_register: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.9' not
 found (required by mri_em_register)
 mri_em_register: /lib64/libc.so.6: version `GLIBC_2.7' not found
 (required by mri_em_register)
 mri_ca_normalize: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.11' not
 found (required by mri_ca_normalize)
 mri_ca_normalize: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.9' not
 found (required by mri_ca_normalize)
 mri_ca_normalize: /lib64/libc.so.6: version `GLIBC_2.7' not 

Re: [Freesurfer] Tracula: from anatomical to diffusion space and FSL probtracx

[Anastasia Yendiki]

Hi Gari - The authors of probtrackx would be able to give you more 
information on how to normalize probtrackx outputs, but I'd suggest taking 
a look at the methods section of this paper as an example:


	S. B. Eickhoff, S. Jbabdi, S. Caspers, A. R. Laird, P. T. Fox, K. 
Zilles, and T. E. J. Behrens, “Anatomical and Functional Connectivity of 
Cytoarchitectonic Areas within the Human Parietal Operculum,” J Neurosci, 
vol. 30, no. 18, pp. 6409–6421, May 2010.


Hope this helps,
a.y

On Mon, 24 Feb 2014, Garikoitz Lerma-Usabiaga wrote:


Thanks Anastasia!


On Thu, Feb 6, 2014 at 1:11 AM, Anastasia Yendiki 
ayend...@nmr.mgh.harvard.edu wrote:

  Hi Gari - You're talking about thresholding the probtrackx maps, right?


Yes
 
  If so the 20% at which the tracula maps are thresholded by default is 
probably too high for
  probtrackx, I'd try something like 2%. (Tracula is global and probtrackx 
is local tractography, so
  their outputs are different beasts.)


OK, thanks! The problem is that at 2% I think the tracts I obtain are too big. 
I attached a subject example
(S_02) with thresholds at 2%, 5%, 20% and 30% in order to have an idea of what 
do you think it would be normal.
The file is called tracts.png.


Inline image 2
 

  Are the waytotal values very different among subjects?


I think there is quite high variability, but I don't know what's normal. In the 
next figure, values.png, you can
find the values:
- Waytotal values for the two new tracts
- Max values in the tracts after normalizing
- Seed mask size

Inline image 1


 
  Are the anatomical seed mask sizes very different?

I don't think so. They are in values.png as well if you want to take a look. 

 
  Did you take that into account? Probtrackx will generate X sample paths 
for each voxel in the seed
  mask.

I didn't take either the waytotal or seed mask or waypoint mask sizes into 
account when thresholding. How would
you recommend doing that?


 
  Did you threshold the tracula tracts before using them as waymasks?

Yes, using fslmath I used -thrp 20 first to threshold them and after that I 
binarize it to create the waypoint.



Thank you very much for your help again,
Gari


 
  a.y

  On Tue, 14 Jan 2014, Garikoitz Lerma-Usabiaga wrote:

Hi Anastasia, it worked perfectly and I could run probtrack between 
my anatomical seed
and using waypoints from Tracula tracts.

I have another doubt right now. The probabilities in each new tract 
are very different.
I divided every value with waytotal using fslmaths -div in order to 
normalize them, and
obtained something like this: 
subject: S_20, Max Value after normalizing with waytotal: 0.75533
subject: S_23, Max Value after normalizing with waytotal: 0.27883
subject: S_25, Max Value after normalizing with waytotal: 0.60251
subject: S_27, Max Value after normalizing with waytotal: 0.32355 


Should I consider the same absolute value for all tracts in order 
to threshold them or
should I threshold all tracts independently with the 20%?

I want to check visually the existence of the tract between the 
anatomical and the
tract, with the same probability across subjects, and afterwards 
obtain the FA values
in order to correlate with behavior.

Thanks again!
Gari







On Mon, Jan 13, 2014 at 7:55 PM, Anastasia Yendiki 
ayend...@nmr.mgh.harvard.edu
wrote:

      Hi Gari - Yes, fslmaths should be able to do it, with -thrp 
20.

      a.y

      On Mon, 13 Jan 2014, Garikoitz Lerma-Usabiaga wrote:

            Thanks Anastasia, I finally got it, I had to do 
mri_vol2vol
            twice to have it
            in the diffusion space. 
            I have an additional question: 
            I want to create waypoint masks for probtracx from 
Tracula
            tracts (for
            example, uncinate). 

            Should I use mri_binarize on path.pd.nii to create the 
mask?
            Should I use 20% of the maximum value as the threshold 
in order
            to do so? (a
            little help with the command line will be greatly 
appreciated)

            thanks again!
            Gari


            On Sun, Jan 12, 2014 at 3:08 AM, Anastasia Yendiki
            ayend...@nmr.mgh.harvard.edu wrote:

                  Has mri/hippo_subfield_in_diffusion_space.nii been
            actually
                  transformed to diffusion space by applying the
            anatorig2diff
                  transformation? I'm assuming that your diffusion 
data is
   

[Freesurfer] (no subject)

[Joshua Lee]

Hello,

I noticed that Freesurfer's latest release offers an expert option added
-first_wm_peak flag to mris_make_surfaces, which may aid accurate more
white matter surfaces especially in heavily myelinated areas like visual
cortex on data that is higher res than 1mm. enable the flag via an
expert.opts file.

Are these expert options doing something similar to what was done in
Lüsebrink, Wollrab, Speck, 2013 in *NeuroImage*, in which they  conforms
the data to the minimum voxel size, which is equal in all directions if
data with an isotropic resolution is used

Thanks

Joshua
-
Joshua Lee
Doctoral Candidate
Department of Psychology 
Center for Mind and Brain
University of California, Davis
530.747.3805
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[Freesurfer] LGI in Qdec

[krista kelly]

Hello,

I followed instructions on how to incorporate the lgi_pial measure into
QDec, however, it's not coming up when I go to choose this as a measure. I
ran recon-all -s my_subject_id -qcache -measure pial_lgi and created a
Qdecrc file in my $SUBJECTS_DIR directory. Does anyone have any insight as
to why this may be occurring?

Thanks,
Krista
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[Freesurfer] No labels file in label directory?

[sabin khadka]

Hi all,
I ran recon-all -all and all the subjects finished without any error. However 
in few subjects directory, labels sub-directory only have lh.cortex.label and 
rh.cortex.label and not other label files like *.label and *.annot. Could 
anyone help me on how to fix this.

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Re: [Freesurfer] LGI in Qdec

[Marie Schaer]

Hi Krista,

Can you be more specific about what is not coming up? If lGI not listed in the 
menu of qdec, look at the following post: 
http://www.mail-archive.com/freesurfer%40nmr.mgh.harvard.edu/msg33427.html 

Otherwise can you describe more precisely the issue?

Best,

Marie

On Feb 24, 2014, at 1:21 PM, krista kelly krista.kell...@gmail.com
 wrote:

 Hello,
 
 I followed instructions on how to incorporate the lgi_pial measure into QDec, 
 however, it's not coming up when I go to choose this as a measure. I ran 
 recon-all -s my_subject_id -qcache -measure pial_lgi and created a Qdecrc 
 file in my $SUBJECTS_DIR directory. Does anyone have any insight as to why 
 this may be occurring?
 
 Thanks,
 Krista
 ___
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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 
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 properly
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Re: [Freesurfer] No labels file in label directory?

[Douglas N Greve]

are you sure it did not fail? Can you post the recon-all.log file to the 
list?


On 02/24/2014 04:22 PM, sabin khadka wrote:
 Hi all,
 I ran recon-all -all and all the subjects finished without any error. 
 However in few subjects directory, labels sub-directory only have 
 lh.cortex.label and rh.cortex.label and not other label files like 
 *.label and *.annot. Could anyone help me on how to fix this.

 -Sabin



 ___
 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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[Freesurfer] FsAverage

[Boadu, Osei B]

Hello,

When trying to either create a symbolic link or copy the fsaverage folder, I am 
told that permission has been denied. E.g.:
ln -s $FREESURFER_HOME/subjects/fsaverage fsaverage
ln: creating symbolic link `fsaverage/fsaverage': Permission denied

I'm not sure what I should do.

Thanks,
Osei
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[Freesurfer] Resolution information

[赵越]

Hi all,
I got a few copies of freesurfer data from some data base. Is it possible to 
know the resolution of the MRI images, for example, the brainmask.mgz file, in 
freesurfer?
Thanks,Yue___
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Re: [Freesurfer] Resolution information

[Douglas N Greve]

1mm3
doug
On 02/24/2014 06:24 PM, 赵越 wrote:
 Hi all,

 I got a few copies of freesurfer data from some data base. Is it 
 possible to know the resolution of the MRI images, for example, the 
 brainmask.mgz file, in freesurfer?

 Thanks,
 Yue


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Re: [Freesurfer] FsAverage

[Douglas N Greve]

Do you have write permission into that folder?


On 02/24/2014 05:28 PM, Boadu, Osei B wrote:
 Hello,

 When trying to either create a symbolic link or copy the fsaverage 
 folder, I am told that permission has been denied. E.g.:
 ln -s $FREESURFER_HOME/subjects/fsaverage fsaverage
 ln: creating symbolic link `fsaverage/fsaverage': Permission denied

 I'm not sure what I should do.

 Thanks,
 Osei


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Re: [Freesurfer] fsgdf and contrasts

[charujing123]

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 gr...@nmr.mgh.harvard.edu
发送时间：2014-02-25 00:25
主题：Re: [Freesurfer] fsgdf and contrasts
收件人：charujing123charujing...@163.com
抄送：freesurfer@nmr.mgh.harvard.edufreesurfer@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 gr...@nmr.mgh.harvard.edu 
 *发送时间：*2014-02-21 23:35 
 *主题：*Re: [Freesurfer] fsgdf and contrasts 
 *收件人：*freesurferfreesurfer@nmr.mgh.harvard.edu 
 *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 gr...@nmr.mgh.harvard.edu 
 *发送时间：*2014-02-21 03:39 
 *主题：*Re: [Freesurfer] fsgdf and contrasts 
 *收件人：*freesurferfreesurfer@nmr.mgh.harvard.edu 
 *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_IAPAT_IA:1 -1 0 0 0 0 
  2,PAT_IACON_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 

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

[charujing123]

Thanks doug
All the best.
Rujing Zha

2014-02-25



charujing123



发件人：Douglas N Greve gr...@nmr.mgh.harvard.edu
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：freesurferfreesurfer@nmr.mgh.harvard.edu
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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Re: [Freesurfer] Fw: tessellate error in tksurfer

[charujing123]

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 gr...@nmr.mgh.harvard.edu
发送时间：2014-02-25 00:32
主题：Re: [Freesurfer] Fw: tessellate error in tksurfer
收件人：freesurferfreesurfer@nmr.mgh.harvard.edu
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：*charujing123charujing...@163.com 
 *发送时间：*2014-02-24 11:23 
 *主题：*[Freesurfer] tessellate error in tksurfer 
 *收件人：*freesurfer@nmr.mgh.harvard.edufreesurfer@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

[charujing123]

 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 pthreshod value. So I want to 
know how to set 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 gr...@nmr.mgh.harvard.edu
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：freesurferfreesurfer@nmr.mgh.harvard.edu
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 
 
  
 Thanks. 
 All the best. 
 Rujing Zha 
 2014-02-22 
  
 charujing123