[Freesurfer] fast-selxavg3 error: input to SVD must not contain NaN or Inf

Dear experts, I run selxavg3-sess for retinotopy analysis and get the error below: Input to SVD must not contain NaN or Inf Error in cond (line 39) s = svd(A) Error in fast_selxavg3(line 254) XCond = cond(XtX) I am also sending the log file and Xtmp.mat. Hope to get the help. Thank you very much

Re: [Freesurfer] Convert surface Labels From FreeSurfer to Volumetric Masks for FSL (both in subject's space)

for further analysis to that data? Thanks in advance! Mingxia Zhang On Sun, Jun 7, 2015 at 4:13 PM, zhang mingxia wrote: > Dear experts, > > I saw a lot of people have posted this issue, but it's not exactly the > same as what I met. Hopefully some one would reply me. > &g

[Freesurfer] Convert surface Labels From FreeSurfer to Volumetric Masks for FSL (both in subject's space)

Dear experts, I saw a lot of people have posted this issue, but it's not exactly the same as what I met. Hopefully some one would reply me. What I have done is running recon-all on each subject's structural data and manually getting some labels as the ROIs. My further analysis is extract the valu

[Freesurfer] The colorwheel of rtview

Dear Freesurfer experts, I posted my question before, but didn't get any answer. I really hope to get the answer! I did the retinotopy analysis with the guide of freesurfer and viewed the results by rtview. How could I get the colorwheel with which I can define the visual area? I also really want

[Freesurfer] The phase of angle.nii.gz

Dear Freesurfer experts, I saw you answered one email the phase for "polar" is -pi to pi. Could you please expain how the phase represent the location on retina? For example, in my retinotopic experiment, the wedge rotate counterclockwise (start from right horizontal), I wonder how the phase rotat

Re: [Freesurfer] Delineation of the Retinotopic Visual Areas

appreciated! Mingxia zhang On Wed, May 20, 2015 at 6:15 PM, zhang mingxia wrote: > Dear Freesurfer experts, > > > > I did the retinotopic mapping analysis followed by > https://surfer.nmr.mgh.harvard.edu/fswiki/FsFastIndividualRetinotopyAnalysis > and view the results by rtview re

[Freesurfer] Delineation of the Retinotopic Visual Areas

Dear Freesurfer experts, I did the retinotopic mapping analysis followed by https://surfer.nmr.mgh.harvard.edu/fswiki/FsFastIndividualRetinotopyAnalysis and view the results by rtview recommended by you. e.g., for subject s03: rtview --s s03 --rh --polar --real polar/real.nii.gz --imag polar/

Re: [Freesurfer] retinotopy analysis viewing problem in Freesurfer 5

nd imag components > > > On 12/11/2014 05:09 AM, zhang mingxia wrote: > > Thank you very much! > > > > The map opened by rtview seems correct. As a new learner of > > retinotopic analysis, I have one more basic quesion: What do the three > > files (imag.

Re: [Freesurfer] retinotopy analysis viewing problem in Freesurfer 5

, Douglas N Greve wrote: > > On 12/08/2014 09:19 PM, zhang mingxia wrote: > > Hi Doug, > > > > I followed this guide: > > > https://surfer.nmr.mgh.harvard.edu/fswiki/FsFastIndividualRetinotopyAnalysis > . > > I used "tksurfer-sess" to view. Does &q

Re: [Freesurfer] retinotopy analysis viewing problem in Freesurfer 5

rfer@nmr.mgh.harvard.edu/msg21512.html. How can I get a standard color? Thanks again! Mingxia On Tue, Dec 9, 2014 at 12:07 AM, Douglas N Greve wrote: > > I'm not sure what you are asking for. Do you see significant activation > in the visual cortex? What command are you running to

Re: [Freesurfer] retinotopy analysis viewing problem in Freesurfer 5

I saw Doug recommended rtview, But I can't access this website: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/rtview. On Mon, Dec 8, 2014 at 6:48 AM, zhang mingxia wrote: > Dear freesurfer experts, > > I used Freesurfer 5 to do the retinotopic analysis follo

[Freesurfer] retinotopy analysis viewing problem in Freesurfer 5

Dear freesurfer experts, I used Freesurfer 5 to do the retinotopic analysis followed by https://surfer.nmr.mgh.harvard.edu/fswiki/FsFastIndividualRetinotopyAnalysis. However, finally I didn't get a red, green and blue map as I expected. This is the first time for me to analyze retinotopic data. I

Re: [Freesurfer] error from selxavg3-sess: matlab:commond not found, ERROR:fast_selxavg3() failed\n

Hi Fischl, Thank you. I have resolved the problem by adding the matlab in my path. Mingxia On Tue, Dec 2, 2014 at 9:14 PM, Bruce Fischl wrote: > what happens when you type: > > which matlab > > cheers > Bruce > > On Tue, 2 Dec 2014, zhang mingxia wrote: > > I in

Re: [Freesurfer] error from selxavg3-sess: matlab:commond not found, ERROR:fast_selxavg3() failed\n

I installed matlab and set path of $FREESURFER_HOME/matlab and $FREESURFER_HOME/fsfast/toolbox into matlab, but also got the error. What else should I do? Thank you for your always support! On Tue, Dec 2, 2014 at 10:08 AM, zhang mingxia wrote: > Dear freesurfer experts, > > I got t

Re: [Freesurfer] error from selxavg3-sess: matlab:commond not found, ERROR:fast_selxavg3() failed\n

Does it mean i need to install matlab? On Tue, Dec 2, 2014 at 10:08 AM, zhang mingxia wrote: > Dear freesurfer experts, > > I got this error when I analysis the retinotopic data by this code: > selxavg3-sess -a rtopy.self.lh -sf sessid > > The version of freesurfer is v5.1

[Freesurfer] error from selxavg3-sess: matlab:commond not found, ERROR:fast_selxavg3() failed\n

Dear freesurfer experts, I got this error when I analysis the retinotopic data by this code: selxavg3-sess -a rtopy.self.lh -sf sessid The version of freesurfer is v5.1.0. What does this error mean? What should I do? Thank you for your support! Mingxia __

[Freesurfer] A question of preproc-sess -fsd

Dear Freesurfer experts, Could you please give me more detail of "-fsd"? It is asked to "specify a functional subdirectory with -fsd" when i preprocess the functional data. If, for example, the current directory is /home/Proj, the f.nii is in /home/Proj/sess01/bold/002/ and /home/Proj/sess01/bold/

[Freesurfer] How to extract subjects' volume based on mask from spm?

Dear Freesurfer experts, I analyzed functional data by spm and made a mask (analyze format). I have also run recon-all of structural data. My question is: how to extract mean volume (from structural data) of the mask(from spm)? I only extracted volume(or thickness) of ROI of a label edited by my

[Freesurfer] How to create a circle ROI centered at certain coordinate?

Dear Freesurfer experts, Recently, I was creating ROI. But I just knew how to create it manually as this website introduce: http://surfer.nmr.mgh.harvard.edu/fswiki/tksurfer_labeledit. Does Freesurfer provide the way to create ROI by using of certain coordinate? That is, if I know the MNI or Talai

[Freesurfer] How can I get the mean thickness of the significant cluster

Dear Freesurfer experts, I have done the whole brain analysis and get some significant clusters. How can I get the mean thickness of these clusters of every subject? Thank you very much. Mingxia Zhang ___ Freesurfer mailing list Freesurfer@nmr.mgh.harv

[Freesurfer] [freesurfer] Is there any way to get the image from Tksurfer with white background?

Hi dear freesurfer experts, I am making pictures for publication. The images saving from Tksurfer are black backgrounds. Is there any way to save the image with white background? Thank you very much Mingxia Zhang ___ Freesurfer mailing list Freesurfer@

[Freesurfer] Can I do multiple comparison correction in one area (not whole brain)

Dear Freesurfer experts, Can freesurfer do multiple comparison correction in part of the brain (not the whole brain)? How can it do? Thank you very much in advance. Mingxia ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh

[Freesurfer] [freesurfer] How do we know the size of manual drawn ROI

Dear freesurfer experts, I have drawn a ROI manually. However, there is only vertex information (How many vertices of the ROI). How can i get the size information (mm2) of the ROI. Thank you very much Mingxia ___ Freesurfer mailing list Freesurfer@nmr.

[Freesurfer] About ROI edit

Hi, every one, I have a question about ROI edit. Is there a way with which we can define spherical ROIs with exact radius. Now, I just know the manual method. But I want to define a ROI with exact Talairach Coordinate and radius. Are there bottons when I input Talairach Coordinate and radius in t

Re: [Freesurfer] mri_glmfit-sim error

Thank you very much!! On Wed, Jan 4, 2012 at 11:55 PM, zhang mingxia wrote: > Hi, every one, > > I just run the flag mri_glmfit-sim for Surface-based Correction for > Multiple Comparisons as below: > > mri_glmfit-sim \ > --glmdir lh.Chinese_fastreading_thickness.glmdi

[Freesurfer] mri_glmfit-sim error

Hi, every one, I just run the flag mri_glmfit-sim for Surface-based Correction for Multiple Comparisons as below: mri_glmfit-sim \ --glmdir lh.Chinese_fastreading_thickness.glmdir \ --cache neg 1.3 \ --cwpvalthresh .025 lh.Chinese_fastreading_thickness.glmdir is the pre-cached simulation result