[Freesurfer] WM segmentation question

Dear Freesurfer Experts, I am assessing the quality of the initial skull strip for some subject data after running autorecon1. I notice that in some cases non-brain matter near the eyes appears to remain, as well as some dura matter at the posterior of the brain. If these voxels are left untouc

Re: [Freesurfer] LGI in Qdec

Hi Marie, I have tried adding the .Qdecrc file into the home folder as well but that does not work. The lgi measure is not appearing in the dropdown menu in the design tab in Qdec. Further, when I ran recon-all -qcache -measure pial_lgi, there were error messages saying 'rm: No match', although th

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

Hi doug and others, It will be highly appreciated,if anyone can help me. Thanks. All the best. Rujing Zhas 2014-02-26 charujing123 发件人："charujing123" 发送时间：2014-02-25 12:01 主题：Re: [Freesurfer] time course in mri_info lh.gender_age.thickness.10.mgh 收件人："freesurfer@nmr.mgh.harvard.edu" 抄送： Hi

Re: [Freesurfer] questions about ROI analysis

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

Re: [Freesurfer] Fw: tessellate error in tksurfer

Hi doug and Zeke, Thanks doug. Zeke, would you please help me make it work so that I can check the construction of pial? Thanks. All the best. Rujing Zha 2014-02-26 charujing123 发件人：Douglas Greve 发送时间：2014-02-25 23:40 主题：Re: [Freesurfer] Fw: tessellate error in tksurfer 收件人："freesurfer" 抄送

Re: [Freesurfer] fsgdf and contrasts

Thanks doug. All the best. Rujing Zha 2014-02-26 charujing123 发件人：Douglas Greve 发送时间：2014-02-25 23:37 主题：Re: [Freesurfer] fsgdf and contrasts 收件人："freesurfer" 抄送： Yes doug On 2/24/14 8:32 PM, charujing123 wrote: Hi doug and others, Thanks doug. I can understand multiple regression. Howe

Re: [Freesurfer] contrast question

You need a new fsgd doug On 02/25/2014 04:04 PM, dgw wrote: > I'm trying to create a contrast that doesn't regress for age and mmse. > Is this possible or do i need to create a new fsgd? > > Thanks, > Dan > > On Tue, Feb 25, 2014 at 3:58 PM, Douglas N Greve > wrote: >> That contrast does not make

Re: [Freesurfer] contrast question

I'm trying to create a contrast that doesn't regress for age and mmse. Is this possible or do i need to create a new fsgd? Thanks, Dan On Tue, Feb 25, 2014 at 3:58 PM, Douglas N Greve wrote: > > That contrast does not make sense because it compares intercept, age > slope, and mmse slope. I'm not

Re: [Freesurfer] contrast question

That contrast does not make sense because it compares intercept, age slope, and mmse slope. I'm not sure what you are trying to do. Do you want an F-test to test whether the groups differ on intercept OR age OR mmse? On 02/25/2014 03:48 PM, dgw wrote: > Hi, > > I have a quick contrast question

[Freesurfer] contrast question

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

Re: [Freesurfer] Group Analysis Questions

That's great. Thanks a lot for your help, Doug! > > Those are the same things. The way you control for age is to compute a > value for both groups at the same age (eg, age=0). If you demean the > age, then the difference will be at age=meanage. With DOSS, the > difference is always the same regar

Re: [Freesurfer] Group Analysis Questions

Those are the same things. The way you control for age is to compute a value for both groups at the same age (eg, age=0). If you demean the age, then the difference will be at age=meanage. With DOSS, the difference is always the same regardless of age (which makes it more interpretable) doug

Re: [Freesurfer] Group Analysis Questions

Hi Doug, Thank you for your response. Concerning scenario 2, I believe I have some hard time understanding the term intercept. If I'm not mistaken the intercept represents the cortical thickness at "age 0." The resulting clusters by using a design matrix of [1 -1 0 0] will give me the areas where

Re: [Freesurfer] Group Analysis Questions

On 02/25/2014 02:07 PM, pfot...@nmr.mgh.harvard.edu wrote: > 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

[Freesurfer] Group Analysis Questions

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 th

Re: [Freesurfer] FsAverage

the folders within $FREESURFER_HOME/subjects/fsaverage are: label, mri, mri.2mm, scripts, and surf. From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve [gr...@nmr.mgh.harvard.edu] Sent: Tuesd

Re: [Freesurfer] FsAverage

but fsaverage should already exist in $FREESURFER_HOME/subjects/fsaverage does it not? On 02/25/2014 11:15 AM, Boadu, Osei B wrote: > Sorry, I thought I replied all. I'm trying to do MNE analysis on some > subjects without MRIs. I was able to make the symlink but now I can't copy > the fsavera

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

Can you send the full terminal output? On 02/24/2014 09:52 PM, charujing123 wrote: > 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 i

Re: [Freesurfer] Temporal gray and white matter volume

Look in ?h.aparc.stats for temporal GM and wmparc.stats for WM doug On 02/25/2014 10:54 AM, Rashmi Singh wrote: > > Hi FreeSurfer experts, > > How do I get the volume measurements of just the temporal white > matter and gray matter. > > Thanks, > > Rashmi > > > > ___

Re: [Freesurfer] FsAverage

Sorry, I thought I replied all. I'm trying to do MNE analysis on some subjects without MRIs. I was able to make the symlink but now I can't copy the fsaverage file from $MNE_ROOT because of denied permissions. I thought I needed to this because it has the -trans file among others. __

Re: [Freesurfer] FW: Topological defect

Hi Siddharth it means you have a huge defect that we are unable to automatically correct. If you look at the ?h.inflated.nofix it should be obvious what it is cheers Bruce On Tue, 25 Feb 2014, Ray, Siddharth wrote: Hi all,   I am having an topological defect error while running few of

[Freesurfer] aseg stats left/right-vessel

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 Fax: (312) 563-4660 Email: douglas_merki...@rush.edu

[Freesurfer] FW: Topological defect

Hi all, I am having an topological defect error while running few of subjects. I have gone through the freesurfer correcting topological defects wikipage. But I was trying understand the log file. For an example, I got the following error for one subject: Correction of the Topology Finding tru

[Freesurfer] Temporal gray and white matter volume

Hi FreeSurfer experts, How do I get the volume measurements of just the temporal white matter and gray matter. Thanks, Rashmi ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer Th

Re: [Freesurfer] FsAverage

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

Re: [Freesurfer] questions about ROI analysis

On 2/25/14 10:09 AM, Rujing Zha wrote: Hi FS experts and others, I have done two group thickness difference analysis based on whole brain. Now I want to do correlation analysis between specific ROI thickness and behavior score. I searched roi in the FS website, but I cannot distinguish

Re: [Freesurfer] No labels file in label directory?

You did not run it all the way through (you stopped at autorecon2) doug On 2/25/14 9:00 AM, sabin khadka wrote: Thanks Doug. recon-all.log is attached herewith. On Monday, February 24, 2014 5:07 PM, Douglas N Greve wrote: are you sure it did not fail? Can you post the recon-all.log file

Re: [Freesurfer] Fw: tessellate error in tksurfer

Sorry, I don't know why tksurfer is failing to display the surface. I suspect that it is a video driver problem, but that is just a speculation, and I'm not qualified to debug video driver issues. Maybe Zeke can chime in. doug On 2/24/14 9:56 PM, charujing123 wrote: Sorry for this e-mail

Re: [Freesurfer] fsgdf and contrasts

Yes doug On 2/24/14 8:32 PM, charujing123 wrote: Hi doug and others, Thanks doug. I can understand multiple regression. However there is no obvious relationship between these two variables. So I try to test correlation between thickness and these two variables. If I try to consider all subjec

[Freesurfer] questions about ROI analysis

Hi FS experts and others, I have done two group thickness difference analysis based on whole brain. Now I want to do correlation analysis between specific ROI thickness and behavior score. I searched roi in the FS website, but I cannot distinguish the volume ROI and surface ROI very clear

Re: [Freesurfer] reg-feat2anat problem

Hello Doug, sorry for the delay. But thank you for going through the log and giving me helpful advice. The problems I was having with registration were down to the fact that the anatomical (brain mask) and functional were oriented differently and the flirt command line options (search angle in x