[Freesurfer] functional overlay onto the occiptal patch with fieldsign
Hi Dear FreeSurfers, I'm using the new version of FreeSurfer to process retinotopic data. I can view the finial results of eccen, polar and fieldsign on the occiptal patch. Now I want to overlay another block designed activations onto the fieldsign patch with file---load overlay--select the corresponding fsig_000.bfloat---select register.dat---OK, but actually no activations appeared on the patch altough the fsig_000.bfloat can be shown on the overlay layer. Would smeone let me know how to overlay the functional activations onto the retinotopic patch? Thanks in advance! Lei ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] roisummary and FIR
Hi, I am running roisummary with an FIR analysis with a 25s timewindow, 5s prestim and TR=2.5s. I In the summary output I receive 10 nestpercond but shouldn't I receive 11 with these parameters? timecourse: -5.0 -2.5 0.0 2.5 5.0 7.5 10.0 12.5 15.0 17.5 20.0 timepoint: 01 2 3 4 56789 10 I did not mask the roi. If I should only receive 10 nestpercond which timepoint is left out? Thanks in advance. Cameron ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] functional overlay onto the occiptal patch with fieldsign
Are you sure the viewing threshold is set correctly for that data? Check out the View->Configure->Overlay dialog box and try changing the values. On Wed, Oct 04, 2006 at 03:22:54PM +0200, [EMAIL PROTECTED] wrote: > Hi Dear FreeSurfers, > > I'm using the new version of FreeSurfer to process retinotopic data. I can > view the finial results of eccen, polar and fieldsign on the occiptal > patch. > Now I want to overlay another block designed activations onto the fieldsign > patch with file---load overlay--select the corresponding > fsig_000.bfloat---select register.dat---OK, but actually no activations > appeared on the patch altough the fsig_000.bfloat can be shown on the > overlay layer. > Would smeone let me know how to overlay the functional activations onto the > retinotopic patch? > > Thanks in advance! > > Lei > > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > -- Kevin Teich ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] roisummary and FIR
Hi Cameron, there's no missing time point, that window does cover 25 sec as the last time point covers 20-22.5. doug Cameron Ellis wrote: Hi, I am running roisummary with an FIR analysis with a 25s timewindow, 5s prestim and TR=2.5s. I In the summary output I receive 10 nestpercond but shouldn't I receive 11 with these parameters? timecourse: -5.0 -2.5 0.0 2.5 5.0 7.5 10.0 12.5 15.0 17.5 20.0 timepoint: 01 2 3 4 56789 10 I did not mask the roi. If I should only receive 10 nestpercond which timepoint is left out? Thanks in advance. Cameron ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center [EMAIL PROTECTED] Phone Number: 617-724-2358 Fax: 617-726-7422 In order to help us help you, please follow the steps in: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] roisummary and FIR
I THINK your last timepoint shld be 17.5 which covers from 17.5 - 20 and makes the timewindow 25 sec. so, yu will have 10 timepoints in total. Balaji Cameron Ellis > Hi, > I am running roisummary with an FIR analysis with a 25s timewindow, 5s > prestim and TR=2.5s. I In the summary output I receive 10 nestpercond but > shouldn't I receive 11 with these parameters? > > timecourse: -5.0 -2.5 0.0 2.5 5.0 7.5 10.0 12.5 15.0 17.5 20.0 > timepoint: 01 2 3 4 56789 10 > > I did not mask the roi. If I should only receive 10 nestpercond which > timepoint is left out? Thanks in advance. > Cameron > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > --- Balaji M Lakshmanan M.S. Research Technologist Mass. General Hospital (East) e-mail: [EMAIL PROTECTED] Phone: 617-726-9189 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] corrupted curvature file
Dear all, One of our subjects have a corrupted curvature file(lh.curv) due to some overwriting. This subject was reconstructed using older version of freesurfer. I would like to know which step/command should I rerun in order to retrieve this file. Thanks in advance, Balaji ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] corrupted curvature file
Hi Balaji, from the surf dir mris_curvature -a 10 -w ./lh.white mv lh.white.H lh.curv should do it Bruce On Wed, 4 Oct 2006, Balaji Lakshmanan wrote: Dear all, One of our subjects have a corrupted curvature file(lh.curv) due to some overwriting. This subject was reconstructed using older version of freesurfer. I would like to know which step/command should I rerun in order to retrieve this file. Thanks in advance, Balaji ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] corrupted curvature file
Hi Balaji, I just modified mri_surf2surf to be able to store the output in curv format, just use --tfmt curv doug Bruce Fischl wrote: Hi Balaji, from the surf dir mris_curvature -a 10 -w ./lh.white mv lh.white.H lh.curv should do it Bruce On Wed, 4 Oct 2006, Balaji Lakshmanan wrote: Dear all, One of our subjects have a corrupted curvature file(lh.curv) due to some overwriting. This subject was reconstructed using older version of freesurfer. I would like to know which step/command should I rerun in order to retrieve this file. Thanks in advance, Balaji ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center [EMAIL PROTECTED] Phone Number: 617-724-2358 Fax: 617-726-7422 In order to help us help you, please follow the steps in: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
