[Freesurfer] Fwd: trouble in manual editing of pial surface

External Email - Use Caution -- Forwarded message - From: 박경일 Date: 2018년 12월 1일 (토) 오전 11:27 Subject: Re: [Freesurfer] trouble in manual editing of pial surface To: Freesurfer support list Thanks for you quick reply. I am uploading a compressed file to

Re: [Freesurfer] trouble in manual editing of pial surface

gt; think are incorrect we will take a look > > cheers > Bruce > On Thu, 29 Nov 2018, 박경일 wrote: > > > > > External Email - Use Caution > > > > Dear experts > > I met a problem during manual editing. My version is 5.3. > > Following F

Re: [Freesurfer] [freesurfer] Extracting values of cortical thickness in each vertex.

cii: > > > Convert a scalar overlay file to ascii: > mris_convert -c lh.thickness lh.white lh.thickness.asc > > > it needs the surface as an input to do the conversion properly. > > cheers > Bruce > > > On Fri, 2 Feb 2018, 박경일 wrote: > > Hi Bruce >>

Re: [Freesurfer] [freesurfer] Extracting values of cortical thickness in each vertex.

ts location that way > > cheers > Bruce > > On Tue, 30 Jan 2018, 박경일 wrote: > > Hi Bruce, I am very new for FS, so did not understand you comments >> completely. sorry.. >> >> For cortical thickness from each vertex in one subject, which scripts >> shoul

Re: [Freesurfer] [freesurfer] Extracting values of cortical thickness in each vertex.

d > across subjects) > > On Mon, 13 Nov 2017, 박경일 wrote: > > Hi Bruce,What I want is the values of cortical thickness in each vertex in >> each subject. Is that >> >> possible? >> Thanks so much. >> >> Kyung >> >> >> >> 2017-11-1

Re: [Freesurfer] Question about an error during recon-all process

you can re-run with -no-talcheck. If it does, not look > good, then fix it and rerun. > > On 12/28/17 6:15 PM, 박경일 wrote: > > Dear experts, I am sorry for asking again. > > I have some problems in running recon-all. > Recon-all process was shut down with this error message

[Freesurfer] Question about an error during recon-all process

Dear experts, I am sorry for asking again. I have some problems in running recon-all. Recon-all process was shut down with this error message ERROR: talairach_afd: Talairach Transform: transforms/talairach.xfm ***FAILED*** (p=0., pval=0. < threshold=0.0050) Manual Talairach alignment ma

[Freesurfer] Question about an error during recon-all process

Dear experts, I am sorry for asking again. I have some problems in running recon-all. Recon-all process was shut down with this error message ERROR: talairach_afd: Talairach Transform: transforms/talairach.xfm ***FAILED*** (p=0., pval=0. < threshold=0.0050) Manual Talairach alignment ma

[Freesurfer] error in Talairach transformation

Dear experts, I have some problems in running recon-all. Recon-all process was stopped with this error message ERROR: talairach_afd: Talairach Transform: transforms/talairach.xfm ***FAILED*** (p=0., pval=0. < threshold=0.0050) Manual Talairach alignment may be necessary, or include the

[Freesurfer] covariates in Qdec

Dear experts, I am trying to compare 2 groups with 2 covariates (age, sex) using qdec. After loading data, design tab displays "diagnosis" in discrete, "age" and "sex" in both continuous (covariates) and nuisance factor boxes. I just selected "diagnosis" and click "analyze". Is this a right way

[Freesurfer] contrasts mat file

Dear experts, I am trying to perform mri_glmfit to generate images indicating cortical thickness differences between groups. My data has 6 or 7 covariates such age, sex, smoking, hypertension, diabetes etc. I wonder how to make contrasts.mat files.Those are supposed to be a lot of files.

[Freesurfer] contrasts mat file

Dear experts, I am trying to perform mri_glmfit to generate images indicating cortical thickness differences between groups. My data has 6 or 7 covariates such age, sex, smoking, hypertension, diabetes etc. I wonder how to make contrasts.mat files.Those are supposed to be a lot of files. FSTut

Re: [Freesurfer] changing qdec path?

> > > On 11/15/2017 04:06 AM, 박경일 wrote: > > Dear experts, > > Based on my knowledge, all image folders should be within subject_dir > > for qdec process. > > But, my data are so huge to be included in this directory in my > > default setting. > > Do yo

[Freesurfer] changing qdec path?

Dear experts, Based on my knowledge, all image folders should be within subject_dir for qdec process. But, my data are so huge to be included in this directory in my default setting. Do you have any idea to change qdec path by which qdec can import image files in external hard drive or other bigger

Re: [Freesurfer] [freesurfer] Extracting values of cortical thickness in each vertex.

Hi Bruce, What I want is the values of cortical thickness in each vertex in each subject. Is that possible? Thanks so much. Kyung 2017-11-13 0:43 GMT+09:00 Bruce Fischl : > Hi Kyung > > you can load them into matlab or convert them to ascii if you want > Bruce > > On Sun

[Freesurfer] [freesurfer] Extracting values of cortical thickness in each vertex.

Dear FS experts, I could get QDEC image comparing two groups. However, is there a way to get numerical values of cortical thickness in each vertex? Thank you Best, Kyung ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.har

Re: [Freesurfer] Qdec image considering multiple variables

So, I'm wondering if there is another way to draw statistical map considering multiple factors including missing variables. Thanks a lot. Kyung 2017-10-10 6:09 GMT+09:00 Douglas Greve : > You can't run it with missing variables > > On 10/9/17 12:40 AM, 박경일 wrote: > >

[Freesurfer] [freesurfer] Qdec image considering multiple variables

. Kyung Il Park, MD 전달된 메시지 시작: > 보낸 사람: 박경일 > 날짜: 2017년 10월 9일 오후 1시 40분 36초 GMT+9 > 받는 사람: freesurfer@nmr.mgh.harvard.edu > 제목: Qdec image considering multiple variables > > Dear FS developer, > I am a FS beginner and trying to make QDEC images of cortical thickness >

[Freesurfer] Qdec image considering multiple variables

Dear FS developer, I am a FS beginner and trying to make QDEC images of cortical thickness difference (color-coded inflated brain) between groups. No problem when fsid, diagnosis, age, and sex were only included in qdec.table.dat file. However, adding any other factors such as hypertension, diabet