Freesurfer

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30134 discussions

Fw: tessellate error in tksurfer
by charujing123 25 Feb '14

25 Feb '14

sorry,this e-mail has the attachment. Rujing Zha 2014-02-24 charujing123 发件人："charujing123"<charujing123(a)163.com> 发送时间：2014-02-24 11:23 主题：[Freesurfer] tessellate error in tksurfer 收件人："freesurfer(a)nmr.mgh.harvard.edu"<freesurfer(a)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

3 5

fsgdf and contrasts
by charujing123 25 Feb '14

25 Feb '14

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

3 8

contrast question
by dgw 25 Feb '14

25 Feb '14

Hi, I have a quick contrast question. If I don't want to regress out one of my variables for a contrast how do i set that up in a contrast file? For example fsgd: Class a Class b Class c Class d Class e Variables age mmse Input s1 a 23 30 Input s1 b 25 21 Input s1 c 29 25 Input s1 d 26 23 Input s1 e 27 22 Would I have an mtx that looked like this to contrast e from c and d ? 0 0 -.167 -.167 .333 0 0 -.167 -.167 .333 0 0 -.167 -.167 .333 Does this make sense? Would i need to setup different fsgd files? Thank You, Dan

2 3

Group Analysis Questions
by pfotiad＠nmr.mgh.harvard.edu 25 Feb '14

25 Feb '14

Hi FS community, I had a few questions regarding my understanding of the group analysis in FS: 1) If I use an fsgd file with Two Groups (One Factor/Two Levels), No Covariates, and my contrast matrix is [1 -1], do the resulting clusters (if any) show the regional significant differences between the two groups by comparing just the means of the values that I am comparing? For instance, if I'm comparing cortical thickness between a diseased and a control group, is this going to give me the clusters where the Diseased subjects' (no age included in the fsgd file, just the two groups) mean/regional cortical thickness differs significantly from the controls'? In other words, is a 50 yo subject's mean/regional cortical thickness going to be treated the same as a 80 yo subject's? 2) Now suppose that I would like to control for age. Then I'm assuming that I need to create an fsgd file with two Groups (One Factor/Two Levels) and One Covariate (age). Similarly, if I would want to visualize the differences in the regional values of cortical thickness between the two groups but after they have been controlled/adjusted for age, what contrast matrix should I use? Normally I would use [0 0 1 -1] but this will give me the significant differences in the age slopes not the mean values, unless I am missing something here. Thanks in advance for your help and sorry for the lengthy message. Best, Panos

2 4

Re: [Freesurfer] FsAverage
by Douglas Greve 25 Feb '14

25 Feb '14

Please post questions to the list. Thanks! You need fsaverage. What are you trying to do? Usually people point SUBJECTS_DIR to a folder in space where they have write permission, then create a symlink from fsaverage to that space. Can you not do this? doug On 2/25/14 10:04 AM, Boadu, Osei B wrote: > Apparently I don't. Is there another way to get fsaverage? > ________________________________________ > From: freesurfer-bounces(a)nmr.mgh.harvard.edu [freesurfer-bounces(a)nmr.mgh.harvard.edu] on behalf of Douglas N Greve [greve(a)nmr.mgh.harvard.edu] > Sent: Monday, February 24, 2014 6:39 PM > To: freesurfer(a)nmr.mgh.harvard.edu > Subject: Re: [Freesurfer] FsAverage > > 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 >> >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer(a)nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > greve(a)nmr.mgh.harvard.edu > Phone Number: 617-724-2358 > Fax: 617-726-7422 > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 > www.nmr.mgh.harvard.edu/facility/filedrop/index.html > Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > >

3 3

Temporal gray and white matter volume
by Rashmi Singh 25 Feb '14

25 Feb '14

Hi FreeSurfer experts, How do I get the volume measurements of just the temporal white matter and gray matter. Thanks, Rashmi

2 1

aseg stats left/right-vessel
by Douglas Merkitch 25 Feb '14

25 Feb '14

Hello all, What exactly is included in the Left/Right Vessel labels? I've found hints as to what they are, but no exact definition. Thanks in advance! Doug Merkitch Neurological Sciences Rush University Medical Center Phone: (312) 563-3853<tel:%28312%29%20563-3853> Fax: (312) 563-4660<tel:%28312%29%20563-4660> Email: Douglas_Merkitch(a)rush.edu<mailto:Douglas_Merkitch@rush.edu>

1 0

reg-feat2anat problem
by Mariam Sood 25 Feb '14

25 Feb '14

Hello, I am running reg-feat2anat and facing some problems. First I ran the command in its default mode using FSL initialisation reg-feat2anat --feat featdir.feat --subject s. That gave me a bad registration. There is a warning coming up WARNING: initial G-W contrast is negative, but expecting positive. If the mov data has a T1 contrast, re-run with --T1 Next I tried the command using -spm option. The within-subject registration (anat2exf) looks good, but the registration to the standard does not look that good, although not as bad as with -fsl option. The structural and the functional are using different conventions (structural is in radiological convention, whereas functional is neurological). I presume the determinants are associated with this and they have opposite signs. The orientations are also different. Additionally in both the log files (one with -fsl option and -spm option), I get another warning WARNING:: Flipping Left/Right orientation (as det < 0). Not sure whether this warning is something I should worry about. Much appreciate your help. Many thanks, Mariam.

2 4

FsAverage
by Boadu, Osei B 24 Feb '14

24 Feb '14

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

2 1

Resolution information
by 赵越 24 Feb '14

24 Feb '14

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

2 1

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