[Freesurfer] can I run Monte Carlo simulation without calling mri_glmfit

Hello, I repeated same mri_glmfit at multiple depth of cortical thickness and merged the maximal values of the sig.mghs for all depths to a merged_sig.mgh (as in Wang X, et al. Neuroimage. 49(4):3075-85; 2010). I need to run Monte Carlo simulation

[Freesurfer] Fwd: can I run Monte Carlo simulation without calling mri_glmfit

Subject: can I run Monte Carlo simulation without calling mri_glmfit Hello, I repeated same mri_glmfit at multiple depth of cortical thickness and merged the maximal values of the sig.mghs for all depths to a merged_sig.mgh (as in Wang X, et al. Neuroimage. 49(4):3075-85; 2010). I need to run Mo

[Freesurfer] the program for analysis of SI cortex

Hello, group I need to compare thickness of left v.s. the right SI and MI cortices. I saw some matlab tools for comparsion of left and right hippocampus in Lundervold.pdf. I could not find similar tools in the matlab folder of Freesurfer stable release 3.0.5 that I just installed. Could anybody

[Freesurfer] ROI of SI cortex

Hello, group I need to compare thickness of left v.s. the right SI and MI cortices. I saw some matlab tools for comparsion of left and right hippocampus in Lundervold.pdf. I could not find similar tools in the matlab folder of Freesurfer stable release 3.0.5 that I just installed. Could anybody

[Freesurfer] problem of group analysis

Hello, Group I have a question about mri_glmfit. I can not run this commend on my data. An error "MatrixReadTxT: could not scan value [1] [2] file exists ERROR: loading C age.mat" appeared. I do not know what is wrong. The only warning I saw is "ERROR: cound not find volume $SUBJECTS_DIR/ave

答复: [Freesurfer] ROI of SI cortex

Doug XIn From: Rahul Desikan [mailto:[EMAIL PROTECTED] Sent: 2007-4-30 (星期一) 16:06 To: Wang, Xin Cc: freesurfer@nmr.mgh.harvard.edu Subject: RE: [Freesurfer] ROI of SI cortex Hi Xin, Within the *h.aparc.annot files for each subject, there should be indivi

RE: [Freesurfer] problem of group analysis

Thank you, Doug. My problem is solved after I removed the commas. Xin From: Doug Greve [mailto:[EMAIL PROTECTED] Sent: Thu 5/3/2007 8:38 PM To: Wang, Xin Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] problem of group analysis It's h

[Freesurfer] problem to save images

Hello, group I have problems to save the display in TKsurfer. I tried 'Save RGB as', but I could not open the file with photoshop in windows, and it was total black when I opened it with adobe illustrator in windows or GIMP in Linux. Please tell me how to save the images so that I can open them

[Freesurfer] mean thickness of whole cortex

Hello, Group Could anybody please tell me how to get the mean thickness of whole cortex? I got only the average thickness of each hemisphere with mris_anatomical_stats -a subject/lable/lh.aparc.annot -b subject lh Thank you in advance, Xin Wang ___

[Freesurfer] add the gray matter

Hello, Group I need to edit the pial surface. I learned to remove points with tkmedit from the tutorial. But how to add gray matter in the pial surface? Thank you in advance. Xin ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://m

RE: [Freesurfer] add the gray matter

[mailto:[EMAIL PROTECTED] Sent: Mon 7/9/2007 5:53 PM To: Wang, Xin Cc: freesurfer Subject: Re: [Freesurfer] add the gray matter it depends why it's not getting out far enough. Usually you need to add control points in the nearby white matter that are <110 on the brainmask.mgz volume. On Mo

[Freesurfer] statistical designs

Hello, group I want to learn more about designs of the general linear models for different statistical tests, such as paired T, ANOVA, and correlation tests. Could anybody suggest some examples of the designs for each model? I am facing a few problems of correlation analysis. If I want to do the

RE: [Freesurfer] statistical designs

Thank you, Doug. Do you have more examples of different designs? Could anyone answer the rest of my questions? Thank you again, Xin From: Doug Greve [mailto:[EMAIL PROTECTED] Sent: Fri 7/20/2007 2:45 PM To: Wang, Xin Cc: freesurfer Subject: Re

[Freesurfer] left-right comparsion

Hello, Group Could anyone kindly share the method to compare the thickness between left and right hemispheres (vertex-by-vertex)? Did David C. Van Essen use Freesurfer in his article (NeuroImage 28 (2005) 635 - 662) to do the left-right comparison? Thank you in advance, Xin Wang

[Freesurfer] images use different protocols

Hello, Group I have two set of images acquired with different imaging protocols (e.g., TRs and bandwidth are different). Can I poll them together for the analysis? I saw in the email list that some groups reported problems in generating the average of images with different TR for the group a

RE: [Freesurfer] images use different protocols

:32 AM To: Wang, Xin Cc: freesurfer Subject: Re: [Freesurfer] images use different protocols can you give us the details of the protocols? And are you talking about 2 different acquisitions on the same subject, or two groups of subjects with different acquisitions? If the latter then your groups

Re: [Freesurfer] Re: Freesurfer Digest, Vol 41, Issue 13-add gray matter

TED] wrote: Message: 9 Date: Mon, 9 Jul 2007 17:01:42 -0400 From: "Wang, Xin" <[EMAIL PROTECTED]> Subject: [Freesurfer] add the gray matter To: "freesurfer" Message-ID: <[EMAIL PROTECTED]> Content-Type: text/plain; charset="iso-8859-1" Hello, Group

[Freesurfer] parcellation problem

Hello, Group, After I manually removed the skull around cerebellum in the brainmask.mgz, the parcellation of the final inflated brain is totally messed up. Manual corrections of talairach transform and white matter surface did not mess up the parcellation. Could anyone tell me what is wrong?

RE: [Freesurfer] parcellation problem

I did not run the autorecon3 before I checked the parcellation. Thank you, Xin From: Bruce Fischl [mailto:[EMAIL PROTECTED] Sent: Tue 9/11/2007 11:33 AM To: Wang, Xin Cc: freesurfer Subject: RE: [Freesurfer] parcellation problem that type of pattern

[Freesurfer] model for pair-T test

Hello, group, Could anybody tell me how to do the pair T test and the repeat measurement F test? I will really appreciate if you can share the steps and GLM of the tests. I am using the old freesurfer group analysis. Thank you, very much, Xin Wang _

RE: [Freesurfer] model for pair-T test

:[EMAIL PROTECTED] Sent: Fri 10/5/2007 5:20 PM To: Wang, Xin Cc: freesurfer Subject: Re: [Freesurfer] model for pair-T test Can you use the --paired-diff to mris_preproc? Wang, Xin wrote: Hello, group, Could anybody tell me how to do the pair T test and the repeat measurement F

RE: [Freesurfer] model for pair-T test

PROTECTED] Sent: Fri 10/12/2007 4:21 PM To: Wang, Xin Cc: freesurfer Subject: Re: [Freesurfer] model for pair-T test The --paired-diff options just take the difference between adjacently specfied inputs. You then set up your design matrix or FSGD file and then run mri_glmfit. The --help for

[Freesurfer] thickness difference map

Hello, Group, We want to make a figure as Fig2 in Han X et al. 2006 reliability paper. Does anyone kindly share his/her way to make a map of difference in average thickness between two groups? Thank you in advance, Xin Wang ___ Freesurfer mailing

RE: [Freesurfer] thickness difference map

EMAIL PROTECTED] Sent: Sat 10/20/2007 5:34 PM To: Wang, Xin Cc: Freesurfer Mailing List Subject: Re: [Freesurfer] thickness difference map Xin, Have a look at this wiki page written by Xiao (the author of the paper): http://surfer.nmr.mgh.harvard.edu/fswiki/ThicknessRepeatibility It describe

[Freesurfer] the unknown zone in the average

Hello, Group, We calculate the globe mean of thickness by using mris_convert -c lh.thickness lh.white lh.thickness.asc mris_convert -c rh.thickness rh.white rh.thickness.asc and then merge two .asc files to calculate the average Does this procedure include the neo

RE: [Freesurfer] the unknown zone in the average

From: Bruce Fischl [mailto:[EMAIL PROTECTED] Sent: Wed 12/19/2007 10:26 AM To: Wang, Xin Cc: freesurfer Subject: Re: [Freesurfer] the unknown zone in the average Hi Xin, you can use mris_anatomical_stats with -l ?h.cortex.label, which should be generated automatically

[Freesurfer] where is the patient information in the mgz files

Hello, Group, I have a problem to read patient information in the .mgz files. this information was stored in the header files of dicom files. Could sb. tell me how to read this information from the .mgz files? Thank you in advance, Xin Wang ___ Fre

[Freesurfer] zero cortical thickness in the lingual and precuneus

Hello, Dr. Fischl, I asked this quesion about zero thickness in the sulcus next to the lateral vertricle before, and corrected the wrong label of lateral vertricle in the aseg.mgz file and added white matter between lateral vertricle and this sulcus in the wm.mgz. But the problem is still ex

Re: [Freesurfer] zero cortical thickness in the lingual and precuneus

one more question: I replace the mislabeled lateral ventricle with CSF because I can not find the "none" in the FreesurfercolorLUT.txt. How to change the mislabeled lateral ventricle to none? Thank you, Xin ____ From: Wang, Xin Sent: Thu 10/7/2010 1

Re: [Freesurfer] zero cortical thickness in the lingual and precuneus

Thank you, Allison. Is Unknown for the empty space between gyri? I did label the gray matter vertices as cortex. Xin From: Allison Stevens [mailto:astev...@nmr.mgh.harvard.edu] Sent: Thu 10/7/2010 12:16 PM To: Wang, Xin Cc: freesurfer@nmr.mgh.harvard.edu

Re: [Freesurfer] zero cortical thickness in the lingual and precuneus

/2010 12:17 PM To: Wang, Xin Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] zero cortical thickness in the lingual and precuneus Hi Xin, can you upload this dataset so we can take a look? Bruce On Thu, 7 Oct 2010, Wang, Xin wrote: > > Hello, Dr. Fischl, > > I asked

[Freesurfer] fsl ROIs become smaller after registered to freesurfer

Hello, Group, I tried to registered the fsl average of one subject .gfeat to his freesurfer surface. After manual correction of register files, the ROIs of ,gfeat become much smaller on the freesufer surface (including less cortical areas). please help me with this problem. Thank in advance,

[Freesurfer] (no subject)

Hello, Group, I have a hard time to register the functional ROIs to the exact location (x,y,z) on thickness map. I can't find articles that register the fsl result onto freesurfer thickness map and then do the ROI analysis. Could someone kindly list some references for me? I appreciate if anyo

[Freesurfer] questions about longitudinal analysis

Hi, groups, I noticed the updates of longitudinal analysis in the new version of Freesurfer. However, I still have a couple of questions about the goal of longitudinal analysis. 1. The goal of longitudinal analysis is to detect the atrophy (thinning), but the transformation in the registration

RE: [Freesurfer] tksurfer display problems

We did for one node, and going to up-grade the rest. A simple answer to your question is to up-grade any node you want to run tksurfer. Help it helps. Xin From: Siddharth Srivastava [mailto:[EMAIL PROTECTED] Sent: Wed 11/19/2008 6:37 PM To: Wang, Xin Subject

RE: [Freesurfer] reg-feat2anat failed

12/15/2008 1:09 PM To: Wang, Xin Cc: freesurfer Subject: Re: [Freesurfer] reg-feat2anat failed Hi Xin, the problem is that neither the sform nor the qform are valid. Did the message below not appear when you ran tkmedit? WARNING: neither NIfTI-1 qform or sform are valid WARNING: your volume

RE: [Freesurfer] reg-feat2anat failed

PM To: Wang, Xin Cc: freesurfer Subject: Re: [Freesurfer] reg-feat2anat failed There is a flag in the nifti header saying whether the qform or sform are valid, and it looks like your scripts do not set this flag. You can use mri_convert (the freesurfer program). This will create valid files

RE: [Freesurfer] Problem with post-spm registered data

Sorry for asking same question here again. I asked Dung before holiday about the criteria of good registration of fMRI and thickness map. http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg08913.html I paste m

RE: [Freesurfer] questions about region-wise analysis data

I want to ask a related question: We study group differences between patients and controls, and correlations of symptoms and thickness in patients only. We would like to display (and extract) the common regions between two analyses in ONE figure. Which template can we use? We created two sets of

[Freesurfer] smoothing size

Hello, Freesurfer group, Could you tell me the default size of smoothing extents (kernel?) of smooth1 and smooth2 in the auto-recon-all? How can I change the size with mris_smooth in the auto-recon-all flow? And why does the smoothing not affect the thickness measure? Thank you in advance, X

RE: [Freesurfer] reg-feat2anat failed

in tkregister2 when I zoomed in. How can I see other parts of the target and movable pictures? Thank you, Xin Wang From: Douglas N Greve [mailto:gr...@nmr.mgh.harvard.edu] Sent: Tue 1/13/2009 4:19 PM To: Wang, Xin Subject: Re: [Freesurfer] reg-feat2anat

RE: [Freesurfer] reg-feat2anat failed

the coronal view of orig). I am still struggle with same questions as before. I appreciate any suggestion. Thank you, Xin Wang From: Wang, Xin Sent: Tue 1/13/2009 4:36 PM To: Douglas N Greve Cc: freesurfer Subject: RE: [Freesurfer] reg-feat2anat failed Sorry

[Freesurfer] more info about bbregister

Hello, Dr. Greve, I am using bbregister to register the BOLD to T1. The --help does not provide any imformation about how it works. What are the difference from bbregister to flirt (fslregister)? more information about --intvol also needed. For example, the format of intvol.reg (.mat or .bat?)

[Freesurfer] questions about SPM surfrend

Dear Dr. Kahn, I have a few question about your surfrend. I attended Freesurfer workshop a month ago, but I did not know your SPM surfrend tool at that time. So I send you this email to seek your help. 1) could you give some details about the surfrend? I am interested in the procedures and c

[Freesurfer] need T-values

Hello, Freesurfer group, I need T values instead of F values for a one-sample T test GLM. How can I convert the values in F.mgh or sig.mgh (for 12 subjects one group no factor) to T values and overlay them on the surface? I found the similar questions in the following emails posted on freesu

[Freesurfer] How to project fMRI activity of entire depth of cortex on to surface

Hello, Freesurfer group, The mri_vol2surf only register the fMRI activity at a certain depth of cortex, as specisfied by -projecfrac, to the cortical surface. mri_surf2surf does the same thing. I want to identify any cortical region have activation during the task, therefore, I need to project

RE: [Freesurfer] How to project fMRI activity of entire depth of cortex on to surface

or mris_surf2surf during the surface-based group analysis? Xin From: Douglas N Greve [mailto:gr...@nmr.mgh.harvard.edu] Sent: Thu 3/5/2009 11:25 AM To: Wang, Xin Cc: freesurfer Subject: Re: [Freesurfer] How to project fMRI activity of entire depth of cortex

RE: [Freesurfer] How to project fMRI activity of entire depth of cortex on to surface

...@nmr.mgh.harvard.edu] Sent: Thu 3/5/2009 1:01 PM To: Wang, Xin Cc: freesurfer Subject: Re: [Freesurfer] How to project fMRI activity of entire depth of cortex on to surface Wang, Xin wrote: > Thank you, Dr. Greve. > > Does _-projfrac-max 0 1_ register the maximal P value cross entir

[Freesurfer] active volume of surface-based analysis

Hello, Freesurfer group, In the tutorial of surface-based fMRI analysis, the active volume are calculated from the entire depth of an given active vertex. I do not think it is the best way to measure it since no all activities occupy the entire depth of cortex. A logical way to get accurate acti

[Freesurfer] group analysis of large data sets

Hello, FreeSurfer Group, What is the maximal matrix size for glm_fit process? How to use FreeSurfer for group analyses of more than 2000 subjects, 128 variables, and 128 Classes? Thank you. Xin ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.ed

Re: [Freesurfer] group analysis of large data sets

On 03/26/2017 07:54 PM, Wang, Xin wrote: > > Hello, FreeSurfer Group, > > What is the maximal matrix size for glm_fit process? > > How to use FreeSurfer for group analyses of more than 2000 subjects, > 128 variables,

[Freesurfer] glmfit: matrix error

Hello, FreeSurfer group, When I ran glmfit I got the following error massage. I standardize ages but the problem remains. Any other suggestions? Alternatively, is there any way to by-pass this design checking step? Thank you very much. Xin ERROR: matrix is ill

[Freesurfer] Job posting: SRA at UCSD

External Email - Use Caution Hi there, Could you help to post this job advertisement for our lab as below, please? Thank you so much. Please let me know if you need more. Best, Xin Wang Imaging Researcher This position will work a hybrid schedule which includes a combination o

[Freesurfer] Job posting: SRA at UCSD

External Email - Use Caution Imaging Researcher University of California, San Diego. Apply in Institution’s website (https://secure-web.cisco.com/1SDJQkDq6j9d8jlPgTY38dMqz5jAkszVSyrb5fr9lxdmTS2UQdtxkDv6psRu-rVLopDpJxd3C2OzndVaWjjBAWNWNoHwbdsmVrkmbosaIxM_ZWGCvQPe0IjSMG7l3jTtjO0NPUq