[Freesurfer] citation for smoothing method

Hi, I have a question about citation for smoothing methods. In the following link, http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/FslFeatFreeSurfer there are statement " This data was smoothed in the volume at 5mm, but when preparing for a group surface-based analysis, we recommend tha

[Freesurfer] mris_preproc error

processed. > doug > > > > On 05/30/2012 02:53 PM, YUMI MAEDA wrote: >> HI, >> I figured out, one of the cope file had problem... >> YUMI >> >> HI, >> I am trying to see difference in groupmap between 2 time-point within 1 >> group with glmfit.

[Freesurfer] [Fwd: mri_glmfit error]

HI, I figured out, one of the cope file had problem... YUMI HI, I am trying to see difference in groupmap between 2 time-point within 1 group with glmfit. I followed the instruction"PairedAnalysis". mris_preproc --paired-diff mri_glmfit --surf fsaverage "$hemi" --y "$hemi"_cope1_"$grp".sm"$

[Freesurfer] mri_glmfit error

HI, I am trying to see difference in groupmap between 2 time-point within 1 group with glmfit. I followed the instruction"PairedAnalysis". mris_preproc --paired-diff mri_glmfit --surf fsaverage "$hemi" --y "$hemi"_cope1_"$grp".sm"$fwhmsrc".mgh --yffxvar "$hemi"_varcope1_"$grp".sm"$fwhmsrc".m

[Freesurfer] mask from sig.mgh

Hi, I want to make a mask file from the output file of mri_glmfit, sig.mgh. will you show me how to get it? thank you. YUMI ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The info

[Freesurfer] norm.mgz

Hi, I had 2 bad blocks in freesurfer/subject/mri/norm.mgz on my disk drive. I had to delete mri/norm.mgz. Is there any way that I can just creat norm.mgz? or do I need to do recon-all? thank you. YUMI ___ Freesurfer mailing list Freesurfer@nmr.mgh.

Re: [Freesurfer] time course within ROI

when I want to get the timecourse from vertex number, what is the option name can I use? YUMI > > Yes, that is correct. You can have it produce one time course with --id 1 > doug > > YUMI MAEDA wrote: >> Doug, >> thank you very much. I tried with --ctab-out >>

Re: [Freesurfer] time course within ROI

to get a color table that indicates > which column belongs to which region. > doug > > YUMI MAEDA wrote: >> HI, >> I am trying to get timecourse from each subject within a ROI >> with GUI as follows, >> in tksurfer GUI, >> Tools > timecourse > Write sum

[Freesurfer] time course within ROI

HI, I am trying to get timecourse from each subject within a ROI with GUI as follows, in tksurfer GUI, Tools > timecourse > Write summary of marked vetices/label, I would like to do it command line, would you tell me what line I can use? I tried to use mri_segstats --i ./filtered_func_data.nii -

Re: [Freesurfer] inter vertex distance

Yes, I will ask him more information. yumi > did Rudolpha's answer work for you? > On Wed, 29 Dec 2010, YUMI MAEDA wrote: > >> Bruce, >> I meant the distance of 2 nodes along the surface. >> >> YUMI >> >> >>> do you mean on along

[Freesurfer] problem with tksurfer

Dear Freesurfers, I am experiencing a strange problem with tksurfer: lately I seem to be unable to manually enter (using the keyboard) the Vertex Index in the GUI, either on the main window or in the "Tool>Select Vertex number" window. Oddly enough, while I cannot enter numbers, I can PASTE them (

[Freesurfer] inter vertex distance

HI, I am wondering if there is a way to calculate inter vertex distance on fsaverage surface with freesurfer. thanks for your help. YUMI ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/frees

[Freesurfer] left right reversal

Hi, I am trying to do left right reversal of surface by following this link, http://surfer.nmr.mgh.harvard.edu/fswiki/LeftRightReversal?highlight=(reversal)|(Left)|(right) after recon-all -subcortseg -s LRflipped-subject", I tried to check the result with tksurfer with 'tksurfer LRflipped-subject

[Freesurfer] Left Right reversal

Hi, I am trying to do left right reversal of surface with the instruction of this link below. http://surfer.nmr.mgh.harvard.edu/fswiki/LeftRightReversal?highlight=(reversal)|(Left)|(right) After recon-all -subcortseg -s LRflipped-subject, I tried to see the result with this command , 'tksurfer LR

[Freesurfer] feat registration to standard space

lose but completely wrong. Is there any requirement for the cordination of example_func.nii ? Or other issue? I appreciate any help & advice. YUMI MAEDA ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mail

[Freesurfer] GLM analysis on individual surface

HI, I am trying to do GLM analysis on individual surface data. I found the online documentation about group feat on surface but I could not find how to do first-level feat on surface. Thank you for any information. YUMI ___ Freesurfer mailing list Fr