[Freesurfer] convert surface label on to functional image

hi, expert, By mapping a surface label to a functional template, I want to extract the corresponding cortical gray matter region in the functional space. I know I should use the mri_label2vol command.  In the help page of mri_label2vol, I see some examples of this command. 2. Convert a surface la

[Freesurfer] Monte carlo simulation and permutation test

Dear Mr or Ms, How can I do Monte carlo simulation for multiple comparison correction? I also want to know about permutation test. could you tell me how to use them? yczhang - 雅虎邮箱，您的终生邮箱！___ Freesurfer ma

[Freesurfer] Monte carlo simulation for multiple comparison on a surface

Dear Mr or Ms, How can I do Monte carlo simulation for multiple comparison correction on a surface. which command should I launch? I also want to know about permutation test. could you tell me how to use them? yczhang - 雅虎邮箱，您的终生邮箱！

[Freesurfer] A problem on groupanalysis

Dear Mr or Ms, I have read the FreeSurfer Tutorial: Group Analysis, but there are still something I do not quite understand. I want to make comparison of lgi between two groups, namely, normal control group and patient group. I want to regress out gender and age.For example,if I have 4 subjec

[Freesurfer] Hi, a problem!

Using lgi, I want to know whether I should mask out the corpus callosum and the structures which lies below the corpus callosum as I do it using thickness measure.    Thanks!   ___ 好玩贺卡等你发，邮箱贺卡全新上线！ http://card.mail.cn.yahoo.com/

[Freesurfer] Hi, a question on lgi

Dear Mr or Ms, If a subject was identified with severe polymicrogyria, which is a brain malformation marked by development of numerous microgyri, what will the lgi of the subject behave? I want to know whether the lgi of the subject would increase or decrease compared with that of the brain of

[Freesurfer] a question about symmetry between two hemisphere

Dear Mr or Ms,   I want to see the symmetry property of two hemispheres,for example, symmetry of cortical thickness or lgi,  I want to know whether the same ID of the two hemispheres after resampling using the average pial surface corespond to the same anatomical region.   Thanks a lot!   yczhan

[Freesurfer] A question about symmetry between two hemisphere

Dear Expert,   I want to exame the symmetry property of two hemispheres,for example, symmetry of cortical thickness or lgi,  I want to know whether the same ID of the two hemispheres after resampling using the average pial surface corespond to the same anatomical region.       For example,   ID

[Freesurfer] A question about cortical foldings

Dear Mr or Ms     Is there any way that we can obtain curvature value of the pial surface? I am not sure whether lh.curv is the curvature file that I want. How can I calculate the mean curvature, Gauss curvature of the pial surface and the GM/WM interface? Is there any built-in function in freesu

[Freesurfer] one more question about curvature

When I compare the thickness measure among subjects, I have to resample and smooth the thickness, so that each data have the same number of vertices and which are in correspondence with one another across subjects.   Now I have .curv files or .sulc files for each subject and would like to make

[Freesurfer] sulc and mid-surface

Dear Mr or Ms,   Thanks a lot for your previous help! In freesurfer wiki, I notice the description of 'sulc', that is how far removed a particular vertex point on a surface is from a hypothetical "mid-surface" that exists between the gyri and sulci."   I am still not quite clear about sulc and ho

[Freesurfer] A problem about average curvature value

Is there any build-in function that I can average a curvature file with Radius of 4mm on the surface, for example, lh.pial.H.crv file. in addition, lh.curv are smoothed in some way, is it smoothed simply by averaging the values?   Thanks!   Best Regards, yczhang __

[Freesurfer] Still not clear about average curvature

I am still not quite clear about the averaging of curvature. Sorry about that.   could you tell me exactly which function I should use, and How should I choose each parameter?     First, I get the curvature value of the pial surface, I think I should average the curvature value on the pial surfac

[Freesurfer] smooth sulc on only part of the surface

Hi,all   I am interested in only the positive sulc  and would like to make group analysis of the postive sulc values. Hence I would like to mask off the negative values (as the lh.sulc file has both positive and negative value). Before making group analysis, I have to resample and smooth the sul

[Freesurfer] "smooth sulc on only part of the surface" one more time

Hi, experts,   I am interested in only the positive sulc  and would like to make group analysis of the postive sulc values. Hence I would like to mask off the negative values (as the lh.sulc file has both positive and negative value). Before making group analysis, I have to resample and smooth t

[Freesurfer] cortical thickess of brains from a 7T scaner with resolution 0.6*0.6*0.6

Dear expert,   Our group have some data scaned from 7T scaner. I would like to calculate the cortical thickness of the data, however, when I processed them as I do for data from 3T scaner, I can not run recon-all command successfull to the end. Could you give me some suggestions on how to obtain

[Freesurfer] errors

Dear experts,   I have some data of format .dc3, I would like to calculate the cortical thickenss of the data. I launched the command "recon-all -i subjectname/***.dc3 -s subjectname", In addition, I also tried "recon-all -i ** -force", For some of the subjects, It runs without error, while

[Freesurfer] LGI:default value of the radius when calculating LGI

Hi, expert,   I would to know what is the exact value of the radius when calculating lGI; How could I check that value?   Thanks a lot!     yuanchao ___ 好玩贺卡等你发，邮箱贺卡全新上线！ http://card.mail.cn.yahoo.com/_

[Freesurfer] A questions on the calculation of LGI

Hi,Marie   In the paper "A surface based approach to quantify local gyrification" on TMI. There is a discussion the relation between lGI and curvature-based method. I noticed the following discussion:  "In the current study, all the GI measurements were computed on cortical surfaces based on ima

[Freesurfer] effect of the radius on lGI

Hi, expert,   Could anyone tell me the effect of the radius on lGI. After reading the paper on lGI carefully, I still can not get a clear view of the effect of the radius on lGI. I still wonder why the default radius are chosen to be 25mm since there is very little discussion of the standard in

[Freesurfer] in what space each subject has been processed following freesurfer pipeline

Hi, there,   Following the freesurfer pipeline, we can perform volume-based analysis and surface-based analysis. I would like to know in what space each subject has been processed. Is the processing of each subject in native space or standard space?  When I say standard space, I mean stereotaxic

[Freesurfer] Are the average subjects generated by different version of Freesurfer differ greatly?

Are the average subjects generated by different version of Freesurfer differ greatly? I obtained the cortical thickness,lGI using Freesurfer 4.0.3, However, average subject can not be generated using Freesurfer 4.0.3 because of error.Can I use the average subject generated using Freesurfer of

[Freesurfer] segmentation fault (core dumped)

Dear Mr or Ms, My computer was installed with Freesurfer v4.0.3,centos4, To make an average surface,I launch "make_average_subject" command, I come across an error : Processing subject 25/52 sh45 ... Reading /media/sda5/yczhang/sh45/surf/lh.sphere.reg Segmentation fault (core dumped)

[Freesurfer] segmentation fault (core dumped), when making average subject

Dear Mr or Ms, My computer was installed with Freesurfer v4.0.3,centos4, To make an average surface,I launch "make_average_subject" command, I come across an error : Processing subject 25/52 sh45 ... Reading /media/sda5/yczhang/sh45/surf/lh.sphere.reg Segmentation fault (core dumped)

[Freesurfer] Processing need more time using freesurfer

Hi, expert,   I used freesurfer on a 32bit ubuntu operation system some days ago. For one subject, the "recon-all -s $filename -all" command need 30 hours or less. I changed it to 64bit Centos operation system, however, the precessing time needed for one subject seems longer than on 32bit system

[Freesurfer] hippocampus volume

Hi, expert,   I would like to measure the volume of hippocampus, is there any way i can obtain the raw volume of hippocampus for each subject? How can I obtain it?   In fact, in the folder stats, there is a file named aseg.stat, where I can find a line which contains "ColHeaders  Index SegId NVox

Re: [Freesurfer] hippocampus volume

写道： 发件人: Pedro Paulo de Magalhães Oliveira Junior 主题: Re: [Freesurfer] hippocampus volume 收件人: "Zhangyuanchao" 抄送: freesurfer@nmr.mgh.harvard.edu 日期: 2010年8月6日,周五,下午10:22 look at the aseg.stats sum left with right -

{Disarmed} [Freesurfer] {Disarmed} Re: hippocampus volume

!       --- 10年8月6日，周五, Bruce Fischl 写道： 发件人: Bruce Fischl 主题: Re: [Freesurfer] hippocampus volume 收件人: "Zhangyuanchao" 抄送: freesurfer@nmr.mgh.harvard.edu 日期: 2010年8月6日,周五,下午10:59 the volume of each is given separately. I think what PPJ was saying is that you can sum them to get the to

[Freesurfer] hippocampus volume

hi, expert,   In a paper named "MRI of hippocampal volume loss in early Alzheimer's disease", I can see the average volume of hippocampus is 2133mm^3 for 279 normal controls with std=25 as well as 1631mm^3 for 330 AD subjects with std=34. However, in the aseg.stats, the volume of a normal subject

[Freesurfer] surface-based aal template

hi, expert   I need a surface-based aal template which is compatible with freesurfer surface files.   Is there any way I can obtain such a surface-based aal template?   Thanks! ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://ma

[Freesurfer] recon-all exited with ERRORS

Dear expert，        We compute the MRI data with FREESURFER using   instruction recon-all -s < > -all,but some data will  show  recon -all exited with ERRORS  in the recon-all-status.log. The flowing display error information :status file for recon-allThu Nov 11 19:22:13 HKT 2010recon-all finishe

[Freesurfer] calculating the surface area of each region on Desikan template

hi, expert,   How could I obtain the surface area of each region on the Desikan template? How can I obtain this area in both native space and the average template space? In the surf folder of each subjects, I noticed there is lh.area file, what is meaning of this file? Do I need ?h.area for calcul