[Freesurfer] Showing graph of freesurfer atlas

t/mri/wm.mgz \ bert/mri/brainmask.mgz \ bert/mri/aseg.mgz:colormap=lut:opacity=0.2 \ -f \ bert/surf/lh.white:edgecolor=blue \ bert/surf/lh.pial:edgecolor=red \ bert/surf/rh.white:edgecolor=blue \ bert/surf/rh.pial:edgecolor=red " Thanks. Rujing 2019-01-23 ch

[Freesurfer] consistent brain regions of Frontal_Sup_Medial_L(AAL) in freesurfer template

. So which one is consistent with frontal_sup_medial in AAL. Thanks. rujing 2019-01-21 charujing123 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

[Freesurfer] 'lh_G_Ins_lg_cent_ins_volume' and 'lh_G_insular_short_volume'

External Email - Use Caution Hi, what is difference between 'lh_G_Ins_lg_cent_ins_volume' and 'lh_G_insular_short_volume'. Are these both insula? Thanks. Rujing 2018-11-21 charujing123 ___ Freesurfer mailing list Freesurfer

[Freesurfer] differences between 'lh_G_front_middle_thickness' and 'lh_S_front_middle_thickness'

External Email - Use Caution Hi FS experts and users I found two middle frontal cortex in thickness, with different prefix. So what is the difference? Another question: Can I get the thickness of hippocampus and amygdala? Thanks. Rujing 2018-11-21 charujing123

[Freesurfer] AAL template OFCant_L 2811 is lateral or medial in FS

External Email - Use Caution Hi FS experts, I want to know whether OFCant_L2811 is 'lh_S_orbital_lateral_meancurv'or 'lh_S_orbital_med-olfact_meancurv'? Thanks. Rujing 2018-09-14 charujing123 ___ Freesurfer mailing list Freesurfer

[Freesurfer] Are these regions orbitofrontal cortex

-H_Shaped_meancurv' and 'lh_G_orbital_meancurv' . Thanks. Rujing 2018-09-14 charujing123 ___ 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

[Freesurfer] recon-all cuda version 9.2 and 8.0

External Email - Use Caution Hi all How to download recon-all with GPU9.2 or 8.0? Thanks. Best 2018-07-24 charujing123 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo

Re: [Freesurfer] subcortical brain intensity

Hi Bruce Thanks Bruce. I know it is the mean intensity value in the aseg.stats file. However I cannot understand intensity itself. Intensity represents what. Other value, such as thickness, I know it represent brain gray matter thickness. Thanks again. rujing 2015-01-30 Zha Rujing University

Re: [Freesurfer] some questions about optseq

times, the other 40 times. Based on optseq2 --ntp 162 --tr 2 --psdwin 0 20 --ev ev1 2 40 --ev ev2 2 40 --nkeep 2 --o ex2 --nsearch 1000, how should I modify to get a efficient sequence, as I have no idea about NULL design. Thanks again All the best Rujing Zha 2014-06-20 charujing123 发件人

Re: [Freesurfer] some questions about optseq

Rujing Zha 2014-06-20 charujing123 发件人：Douglas Greve gr...@nmr.mgh.harvard.edu 发送时间：2014-06-20 21:18 主题：Re: [Freesurfer] some questions about optseq 收件人：freesurferfreesurfer@nmr.mgh.harvard.edu 抄送： I don't think there is anything wrong with what you have. Is there a problem? You could

[Freesurfer] some questions about optseq

40 --nkeep 2 --o ex2 --nsearch 1000 Although it echo a result, I know, it is not what I need, because of every condition having two trials. So how I complete that? Thanks. All the best. Rujing Zha 2014-06-20 charujing123 ___ Freesurfer mailing list

Re: [Freesurfer] change background color in tksurfer

Hi Bruce and Doug, Ok, I see. That's all right. All the best. Rujing Zha 2014-05-14 charujing123 发件人：Bruce Fischl fis...@nmr.mgh.harvard.edu 发送时间：2014-05-14 20:22 主题：Re: [Freesurfer] change background color in tksurfer 收件人：Freesurfer support listfreesurfer@nmr.mgh.harvard.edu 抄送： Sorry

Re: [Freesurfer] problems about extracting specific vertex thickness value and getting a average thickness for a specific mask

rwxp 7ffe9000 00:00 0 [stack] e000-f000 r-xp e000 00:00 0 Aborted All the best Rujing Zha 2014-05-13 charujing123 发件人：Douglas N Greve gr...@nmr.mgh.harvard.edu 发送时间：2014-05-12 23:18 主题

Re: [Freesurfer] problems about extracting specific vertex thickness value and getting a average thickness for a specific mask

Hi doug, I read your last e-mail again. After changed my command, it worked. Thanks doug. Rujing Zha 2014-05-14 charujing123 发件人：Douglas N Greve gr...@nmr.mgh.harvard.edu 发送时间：2014-05-14 03:14 主题：Re: [Freesurfer] problems about extracting specific vertex thickness value and getting

[Freesurfer] change background color in tksurfer

Hi FS experts and users I want to change the background color of tksurfer from black to white. However I cannot find the drop-down list. Is there anyone who can tell me to desolve this? Thanks. All the best. Rujing Zha 2014-05-14 charujing123

[Freesurfer] get the max value

Hi all I want to get the maximum value in one surface-based file. How can I make it? Thanks. All the best. Rujing Zha 2014-05-11 charujing123 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo

Re: [Freesurfer] get the max value

charujing123 发件人：Bruce Fischl fis...@nmr.mgh.harvard.edu 发送时间：2014-05-12 00:42 主题：Re: [Freesurfer] get the max value 收件人：Freesurfer support listfreesurfer@nmr.mgh.harvard.edu 抄送： Hi Rujing the maximum value of what? Bruce On Mon, 12 May 2014, charujing123 wrote: Hi all I want to get

Re: [Freesurfer] get the max value

Hi doug Thanks doug. I will try. All the best Rujing Zha 2014-05-12 charujing123 发件人：Douglas Greve gr...@nmr.mgh.harvard.edu 发送时间：2014-05-12 09:55 主题：Re: [Freesurfer] get the max value 收件人：freesurferfreesurfer@nmr.mgh.harvard.edu 抄送： I think mris_calc will do it On 5/11/14 7:59 PM

[Freesurfer] problems about extracting specific vertex thickness value and getting a average thickness for a specific mask

charujing123 ___ 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

Re: [Freesurfer] problems about extracting specific vertex thickness value and getting a average thickness for a specific mask

Hi all, Looking forward someone can help me. Thanks. All the best. Rujing Zha 2014-05-02 charujing123 发件人：charujing123charujing...@163.com 发送时间：2014-05-01 11:38 主题：[Freesurfer] problems about extracting specific vertex thickness value and getting a average thickness for a specific mask 收件人

[Freesurfer] problems about extracting specific vertex thickness value and getting a average thickness for a specific mask

. How can I complete it? Any reply will be highly appreaciated. Thanks All the best. Rujing Zha 2014-05-01 charujing123 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

[Freesurfer] incongruent coordinates in freeview and *sig.cluster.summary

suspect the coordinate system is LPI. Is that right? Thanks. All the best. Rujing Zha 2014-04-26 charujing123 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information

[Freesurfer] converting volume-based mask into surface-based fsaverage

code = 0 Done loading volume regio_read_register(): No such file or directory Could not open register.dat Thanks All the best Rujing Zha 2014-04-26 charujing123 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https

[Freesurfer] convert volume-based mni152 space into fsaverage surface space(MNI305)

Hi FS experts and users, I created a mask volume, whose space is in MNI152 space. And I want to convert this volume into surface-based in fsaverage. How can I realize this? Thanks All the best. Rujing Zha 2014-04-22 charujing123___ Freesurfer

Re: [Freesurfer] convert tlrc mask into surface

Hi doug I am so sorry for i didnot describe my problem clearly. tlrc is a Talairach coordinates, whose format is *+tlrc.HEAD and *+tlrc.BRIK. This coordinate system is used in AFNI(Analysis of Functional MRI). Thanks doug. All the best. Rujing Zha 2014-04-18 charujing123 发件人：Douglas Greve

[Freesurfer] convert tlrc mask into surface

Hi FS experts, I have a ROI mask in tlrc coordinates in *.tlrc file format, which represents functional activation. Also I have a significant area in sig.mgh which represents cortical thickness difference between two groups, and I created a mask based on surface for it. Now I want to compare

Re: [Freesurfer] control numbers of cluster based on vertex numbers in each cluster

Thanks doug; All the best. Rujing Zha 2014-04-15 charujing123 发件人：Douglas N Greve gr...@nmr.mgh.harvard.edu 发送时间：2014-04-15 02:16 主题：Re: [Freesurfer] control numbers of cluster based on vertex numbers in each cluster 收件人：freesurferfreesurfer@nmr.mgh.harvard.edu 抄送： Look in the summary

[Freesurfer] control numbers of cluster based on vertex numbers in each cluster

Hi FS experts and users After completing the mri_glmfit-sim, I get some cluster in the *.cluster.summary. I want to threshold some clusters whose vertex number are smaller than specific number such as 150. How can I do that? Thanks All the best Rujing Zha 2014-04-14

Re: [Freesurfer] control numbers of cluster based on vertex numbers in each cluster

By the way, I just want to see clusters whose numbers of vertex is over thresholded norm in the sig.mgh while using freeview. Thanks All the best Rujing Zha 2014-04-14 charujing123 发件人：charujing123charujing...@163.com 发送时间：2014-04-14 10:41 主题：[Freesurfer] control numbers of cluster based

[Freesurfer] see result by tksurfer

Hi FS experts I completed group analysis by this method:http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis#ClusterwiseCorrectionforMultipleComparisons . Now I want to represent the result just the way as non-surface(please see attachment). I want to know how to load sig.mgh by

[Freesurfer] transform common space into original space

Hi FS experts I have done the group thickness analysis(two group t-test), and get the result(i.e. sig.mgh). I got one cluster in the sig.mgh file. I want to convert this cluster into each subject specific original space(i.e brainmask.mgz). Thanks. All the best. Rujing Zha 2014-03-30

[Freesurfer] space conversion in the mri_surf2vol

Dear FS experts, I completed mri_surf2vol converting lh.gender_age.thickness.10.mgh into test.nii based on the fsaverage template. I want to know what space for the two files(*.mgh and *.nii) respectively? Thanks. All the best. Rujing Zha 2014-03-27

Re: [Freesurfer] space conversion in the mri_surf2vol

Hi Bruce It's mri_surf2vol --surfval ./lh.gender_age.thickness.10.mgh --hemi rh --fillribbon --subject fsaverage --identity fsaverage --template $SUBJECTS_DIR/fsaverage/mri/orig.mgz --o test.nii Thanks All the best. Rujing Zha 2014-03-27 charujing123 发件人：Bruce Fischl fis

Re: [Freesurfer] Fw: Re: view time course in freeview

Hi doug It worked. Thanks. All the best. Rujing Zha 2014-03-18 charujing123 发件人：Douglas N Greve gr...@nmr.mgh.harvard.edu 发送时间：2014-03-17 23:26 主题：Re: [Freesurfer] Fw: Re: view time course in freeview 收件人：freesurferfreesurfer@nmr.mgh.harvard.edu 抄送： Try tksurfer subjectname rh inflated

Re: [Freesurfer] Fw: Re: convert sig.mgh into *.nii

Hi Bruce and other FS experts, Thanks Bruce. 1,How can I adding them? 2,--identity option need to applied one subject's name. Which subject should I supply? or can it be anyone? Thanks again. All the best. Rujing Zha 2014-03-15 charujing123 发件人：Bruce Fischl fis...@nmr.mgh.harvard.edu 发送时间

Re: [Freesurfer] Fw: Re: convert sig.mgh into *.nii

you please help me? All the best. Rujing Zha 2014-03-15 charujing123 发件人：Bruce Fischl fis...@nmr.mgh.harvard.edu 发送时间：2014-03-15 21:41 主题：Re: [Freesurfer] Fw: Re: convert sig.mgh into *.nii 收件人：charujing123charujing...@163.com 抄送：freesurfer@nmr.mgh.harvard.edufreesurfer@nmr.mgh.harvard.edu Hi

[Freesurfer] Fw: Re: view time course in freeview

told me freeview has a new version to see time course for this file. I wonder where I can download it. Thanks doug, All the best. Rujing Zha 2014-03-13 charujing123 发件人：Douglas Greve gr...@nmr.mgh.harvard.edu 发送时间：2014-03-12 22:57 主题：Re: [Freesurfer] view time course in freeview 收件人

[Freesurfer] Fw: Re: convert sig.mgh into *.nii

/psylab16/BACKUP/freesurfer/freesurfer/subjects/fsaverage/mri/orig --o test.nii. the command window echo this error message: gdiagno = -1 A volume registration file must be supplied Thanks. All the best. Rujing Zha 2014-03-13 charujing123 发件人：Douglas Greve gr...@nmr.mgh.harvard.edu 发送时间：2014

Re: [Freesurfer] convert sig.mgh into *.nii

/freesurfer/freesurfer/subjects/fsaverage/mri/orig --o test.nii. the command window echo this error message: gdiagno = -1 A volume registration file must be supplied Thanks. All the best. Rujing Zha 2014-03-13 charujing123 发件人：Douglas Greve gr...@nmr.mgh.harvard.edu 发送时间：2014-03-12 23:00 主题：Re

[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 charujing123___

[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___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The

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 gr...@nmr.mgh.harvard.edu 发送时间：2014

Re: [Freesurfer] convert sig.mgh into *.nii

$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 fis...@nmr.mgh.harvard.edu 发送时间：2014

Re: [Freesurfer] convert sig.mgh into *.nii

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 gr...@nmr.mgh.harvard.edu 发送时间：2014-03-12

Re: [Freesurfer] fix this error in segmentation

Hi Bruce, Thanks Bruce. I fixed it. All the best. Rujing Zha 2014-03-09 charujing123 发件人：Bruce Fischl fis...@nmr.mgh.harvard.edu 发送时间：2014-03-08 22:07 主题：Re: [Freesurfer] fix this error in segmentation 收件人：charujing123charujing...@163.com 抄送：freesurfer@nmr.mgh.harvard.edufreesurfer

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

Hi Louis, Thanks. I will try that. Best wishes. Rujing Zha 2014-03-08 charujing123 发件人：Louis Nicholas Vinke vi...@nmr.mgh.harvard.edu 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：charujing123charujing...@163.com 抄送

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

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 rpw...@nmr.mgh.harvard.edu 发送时间：2014-02-28 05:10 主题：Re: [Freesurfer] time course in mri_info lh.gender_age.thickness.10.mgh

Re: [Freesurfer] questions about ROI analysis

Thanks doug, All the best. Rujing Zha 2014-02-27 charujing123 发件人：Douglas N Greve gr...@nmr.mgh.harvard.edu 发送时间：2014-02-27 01:49 主题：Re: [Freesurfer] questions about ROI analysis 收件人：freesurferfreesurfer@nmr.mgh.harvard.edu 抄送： On 02/25/2014 08:34 PM, charujing123 wrote: Hidoug

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

charujing123 发件人：Douglas N Greve gr...@nmr.mgh.harvard.edu 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：freesurferfreesurfer@nmr.mgh.harvard.edu 抄送： Try this freeview -f $SUBJECTS_DIR/fsaverage/surf/lh.inflated:overlay=$SUBJECTS_DIR/glm

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

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 gr...@nmr.mgh.harvard.edu 发送时间：2014-02-27 11:13 主题：Re

Re: [Freesurfer] fsgdf and contrasts

Thanks doug. All the best. Rujing Zha 2014-02-26 charujing123 发件人：Douglas Greve gr...@nmr.mgh.harvard.edu 发送时间：2014-02-25 23:37 主题：Re: [Freesurfer] fsgdf and contrasts 收件人：freesurferfreesurfer@nmr.mgh.harvard.edu 抄送： Yes doug On 2/24/14 8:32 PM, charujing123 wrote: Hi doug and others

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 gr...@nmr.mgh.harvard.edu 发送时间：2014-02-25 23:40 主题：Re: [Freesurfer] Fw: tessellate error

Re: [Freesurfer] questions about ROI analysis

. All the best. Rujing Zha 2014-02-26 charujing123 发件人：Douglas Greve gr...@nmr.mgh.harvard.edu 发送时间：2014-02-25 23:46 主题：Re: [Freesurfer] questions about ROI analysis 收件人：freesurferfreesurfer@nmr.mgh.harvard.edu 抄送： On 2/25/14 10:09 AM, Rujing Zha wrote: Hi FS experts and others, I

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：charujing123charujing...@163.com 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

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

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: [Freesurfer] fsgdf and contrasts

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

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 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

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 gr...@nmr.mgh.harvard.edu 发送时间：2014-02-25 00:32 主题：Re: [Freesurfer

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

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

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

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

[Freesurfer] tessellate error in tksurfer

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.

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

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

[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

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 gr...@nmr.mgh.harvard.edu 发送时间：2014-02-21 23:46 主题：Re: [Freesurfer] extracting mean

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

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

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

.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：charujing123charujing...@163.com 发送时间：2014-02-22 10

Re: [Freesurfer] fsgdf and contrasts

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

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

,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

[Freesurfer] questions of clusters defined and sign of the threshold in simulation

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

[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

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 gr...@nmr.mgh.harvard.edu 发送时

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 gr...@nmr.mgh.harvard.edu 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：freesurferfreesurfer@nmr.mgh.harvard.edu 抄送

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 gr...@nmr.mgh.harvard.edu 发送时间：2014-02-21 03:45 主题：Re: [Freesurfer] viewing corrected result error 收件人：freesurferfreesurfer@nmr.mgh.harvard.edu 抄送： Is the error preventing you from visualizing

[Freesurfer] fsgdf and contrasts

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

[Freesurfer] running error in mris_preproc

Hi FS experts, When I ran the mris_preproc, the left hemisphere completely done well, but the right hemisphere exit error.How to fix the error? Thanks. All the best. Here is error back information: --- #@# 35/38 PAT_IA29 Thu Feb 20 14:53:26 CST 2014

Re: [Freesurfer] recon-all pial reconstruction error

Hi Bruce, Thanks Bruce. I see. I will try. All the best. Rujing Zha 2014-02-15 charujing123 发件人：Bruce Fischl fis...@nmr.mgh.harvard.edu 发送时间：2014-02-15 12:26 主题：Re: [Freesurfer] recon-all pial reconstruction error 收件人：charujing123charujing...@163.com 抄送：freesurfer

Re: [Freesurfer] recon-all CTABreadASCII error

access. But it was still report similar error. And I ran this command as root, then it terminated as a similar situation. Thanks Bruce. All the best. Rujing Zha 2014-02-13 charujing123 发件人：Bruce Fischl fis...@nmr.mgh.harvard.edu 发送时间：2014-02-13 21:33 主题：Re: [Freesurfer] recon-all

Re: [Freesurfer] {Filename?} Re: Re: recon-all CTABreadASCII error

Hi Bruce, I did try, but I am so sorry that size of the attachment is too big to send in the mail list. All the best. Rujing Zha 2014-02-13 charujing123 发件人：Bruce Fischl fis...@nmr.mgh.harvard.edu 发送时间：2014-02-13 22:00 主题：Re: {Filename?} Re: Re: [Freesurfer] recon-all CTABreadASCII error 收

[Freesurfer] recon-all CTABreadASCII error

Dear FS experts, It represents this message in the command window after ran recon-all -autorecon-pial -s CON_EIU01 -no-isrunning: Reading annotation reading colortable from annotation file... colortable with 36 entries read originally

Re: [Freesurfer] data uploaded

Hi Louis, I'm sorry to reply so late. I resolved my question. Thanks. All the best. Rujing Zha 2014-01-13 charujing123 发件人：Louis Nicholas Vinke vi...@nmr.mgh.harvard.edu 发送时间：2014-01-09 23:38 主题：Re: Re: Re: [Freesurfer] data uploaded 收件人：Rujing Zhacharujing...@163.com 抄送：Bruce Fischlfis

Re: [Freesurfer] problems about freeview

发件人：charujing charuj...@gmail.com 发送时间：2014-01-05 10:26 主题：Fw: Re: Re: [Freesurfer] problems about freeview 收件人：charujing123charujing...@163.com 抄送：freesurferfreesurfer@nmr.mgh.harvard.edu 发件人：charujingcharuj...@gmail.com 发送时间：2014-01-05 09:55 主题：Re: Re: [Freesurfer] problems about freeview

[Freesurfer] appropriate graphic card in freeview and tksurfer

Hi Gari and others, When I ran freeview -f $SUBJECTS_DIR/fsaverage/surf/lh.inflated:overlay=lh.gender_age.glmdir/lh-Avg-thickness-age-Cor/mc-z.negative.sig.cluster.mgh:overlay_threshold=2,5:annot=lh.gender_age.glmdir/lh-Avg-thickness-age-Cor/mc-z.negative.sig.ocn.annot in Windows server VM