[Freesurfer] Confused with Coordinate System in FS

Hi all: I am confused with coordinate systems in FS. I have several questions bellow. 1. when we run recon-all -s subjid -all, Is the individual native space transformed to talairach coordinate system?. when run recon-all -s subjid -qcache, does the talairach system go into MNI syst

Re: [Freesurfer] How to get surface-based AAL template

is_ca_train. >> Now I can segment surfaces just by calling mris_ca_label which works >> flawlessly and consistent throughout subjects. >> >> >> >> Best, >> >> Martijn >> >> >> >> Van: freesurfer-boun...@nmr.mgh.harvard.edu >

Re: [Freesurfer] How to get surface-based AAL template

some minimal translation. If you see both T1-s with tkregister you will see that they are almost the same (the spm version a little bit blurred, because of the resolution). You use this register.dat when doing vol2surf of the AAL.nii to your AAL.mgh surface ROI. Hope this helps! Gari On 27/0

[Freesurfer] FS version of Colin27

Hi FS experts: I am trying to map AAL template onto FS surface to create surface-based AAL template. Several days ago, i asked this question, and Garikoitz Lerma gave me some suggestions. Possibly, i think the process is like as folllows: 1. downloa the Colin27 subject in Surfrend page, a

Re: [Freesurfer] How to get surface-based AAL template

e. - now you can use surf2surf or label2label to go to your subjects and obtain stats. Br! On 27/03/2013, at 05:35, ZhiLiangLong wrote: Hi all; I need a suface-based aal template which is compatible with FS surface file. Is there a way i can get the surface-based aal template? I have

[Freesurfer] How to get surface-based AAL template

Hi all; I need a suface-based aal template which is compatible with FS surface file. Is there a way i can get the surface-based aal template? I have an idea, that is to just transform the AAL template (.nii file) in MNI space onto the surface template (e.g. fsaverage template) in FS. Is it

[Freesurfer] How to get transform matrix from Vertex Index to Vertex RAS

Hi all: I am studying the coordinate system transforms within subject across imaging modalities on web page: http://surfer.nmr.mgh.harvard.edu/fswiki/CoordinateSystems. I met a problem. First, i run tksurfer : tksurfer subjectname lh inflated -reg register.dat -ov mov.nii , then i chose a p

[Freesurfer] cortical thickness of ROIs derived from VBM results

Hi all: I got some regions of interest showing significant diffencese in VBM between two groups. Now, i attemp to compare cortical thickness of these ROIs. However, i don't know how to map the ROIs to cortical surface and extract cortical thickness values? I need help._

[Freesurfer] recon-all process on brain regions of interest

Hi everyone: I met problem about the recon-all process. I got some brain regions showing group-differences of activation in task. Now, i want to compare the difference of cortical thickness on these brain regions. I prefer to limit the compution of cortical thickness on my regions of int

[Freesurfer] question about MNI coordinates or talariach coordinate in Qdec

Hi all: In qdec, when i left-clicked on a point of pial surface, there would be a coordinate displayed at the bottom of qdec. my qestion is that does the coordinate belong to the MNI space or talariach space?___ Freesurfer mailing list Freesurfer@nm

[Freesurfer] Does the fsaverage template belong to MNI space or Talairach space

Hi all: In FS, does the fsaverage template belong to MNI space or Talairach space? Thanks!___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is int

[Freesurfer] Question about DODS model and DOSS model

Hi all: I'm a little confused about the DODS model and DOSS model. I have two groups (patient and control) and one covariate (age), and I want to compare the diffirence of thickness between the groups with age as the covariate. In DODS model, is the process the analysis of variance substant

[Freesurfer] How to obtain cortical thickness in fsaverage space

Hi all: After finishing group analysis, how can i obtain the thickness value of each ROIs showing significant group-difference in fsaverage space? That is to say, how i get the value of each ROIs which have been normalized to the fsaverage template. The method suggested in tutorials page(ht

[Freesurfer] question about Correction for Multiple Comparison

Hi all: A few days ago, i have asked about some questions about Correction for Multiple Comparison. But i'm still confused about it. The version of FS is 5.1.0. when i performed Correction for Multiple Comparison using command line with 'mris_glmfit-sim', it usually took many hours to complet

[Freesurfer] question about Cluster-wise Correction for Multiple Comparisions

Hi all: I'm performing the group analysis on my own data using command line on FS5.1.0 and i'm a little confused about the Clusterwise Correction for Multiple Comparisions. the command is as follows: mri_glmfit-sim \ --glmdir lh.gender_age.glmdir \ --sim mc-

[Freesurfer] question about FSGD file

Hi, FS experts: I'm scanning freesurfer pages about FSGD files here: http://surfer.nmr.mgh.harvard.edu/fswiki/Fsgdf4G1V and i'm interested in one contrast file(the example of Contrast 5 right-left.intercept.mtx). The original FSGD file is list as follows: GroupDescriptorFile 1 Title OSGM

[Freesurfer] In Qdec, what does the 'area' mean within 'Measure' menu in 'Design' tab

Hi freesurfer experts: i'm using qdec to perform statistical analysis in Freesurfer 5.0.0, within 'Measure' menu in 'Design' tab, the default is 'thickness', however, there are other measurements such as 'area' and 'area.pial'. the latter seems meaning area in pial surface. what does t

[Freesurfer] Does the SurfArea in the lh.aparc.a2009s.stats calculated based on white matter surface or pial surface

Hi, all Does the SurfArea in the lh.aparc.a2009s.stats, as presented below(red color), calculated based on white matter surface or pial surface? any suggestions appreciated. # TableCol 10 Units unitless # ColHeaders StructName NumVert SurfArea GrayVol ThickAvg ThickStd MeanCurv

[Freesurfer] question about thickness file

Hi all: After finishing recon-all steps, there are some thickness files generated such as lh.thickness and lh.thickness.fwhm10.fsaverage.mgh which contain cortical thickness values at each vertex. Are the thickness values in lh.thickness file calculated in individual space ,that is , they

[Freesurfer] question about contrast file during group analysis with command line

Hi all : I'm performing general linear model (GLM) analysis in the surface,the attachments above are FSGD file and contrast files(the last three attachments).i wonder if my contrast files are correct. the attachment named diff-C-H-thickness.txt is about difference between C and H and t

[Freesurfer] questions about mapping volume data to brain surface and extracting cortical thickness

Hi FS experts: I have two questions about FS. (1) Is there a way that can map volume data(.hdr and .img file) to brain surface in FS? (2) I find a way that can extract cortical thickness automatically,first,the statistical significant areas derived from group analysis on qdec

[Freesurfer] ANOVA(analysis of variance)

Hi all: Is there a way that can perform a test to compare the difference of cortical thickness between groups (at least three) using ANOVA (analysis of variance) in FS? If it is how can i do that? Any suggestions will be appreciative___ Free

[Freesurfer] convert .annot file to lable

Hi all: Are there some FS commands that can convert .annot file to lable file? Thanks!_

[Freesurfer] question about qdec

Hi all: I have three groups of subjects (major depression disorder,slight depression disorder and contrast),i want to use qdec to obtain the statistical significant areas containing difference of cortical thickness measurment among them. But there are some errors appearing when i run the gr

[Freesurfer] correct mris_anatomical_stats syntax for lgi

Hi FS experts: I have run a group analysis with Local Gyrification Index (LGI) and obtained some statistical significant areas.Now I want to extract the information (lgi) of each area.Based on the QDec Group Analysis page, the following command is ran to examine cortical thickness: mris_an

[Freesurfer] How to obtain volume of specific structure

Hi all: After all "recon-all -all" processing has been completed for all subjects ,I want to obtain volume of specific structure of each subject(e.g., the volume of Caudate Nucleus). But i have no idea about it,Are there some tools or commands that can help? I hope you can give me some sug

[Freesurfer] qustions about contents of label file

Hello: I use qdec to generate statistical significant areas and draw ROI and map the ROI to each subject ,finally i get a label file of each subject called lh.supriorfrontal.label which can be seen in attachment below.But i'm a little confused with content of the label file, Is it correct