Re: [Freesurfer] retinotopy question

hi lars, i just checked with doug, and he agreed that, since your stimulus is periodic, 'sfa-sess' can do the job provided that you specify that the analysis should be carried out using a block design. so, for example, if the TR is 2 sec, and since each of your conditions lasts 20 TRs per epoch

Re: [Freesurfer] make_average-subject

Hi Lars, it looks like no input subjects are defined. Bruce On Wed, 27 Jun 2007, Lars M. Rimol wrote: Hi, Trying to run make_average_subject but getting an error message. Any idea what may be wrong? Thank you! Lars M. Rimol make_average_surface --fsgd /space/emc1/3/data/TOP/Analysis_lmr/

[Freesurfer] make_average-subject

Hi, Trying to run make_average_subject but getting an error message. Any idea what may be wrong? Thank you! Lars M. Rimol make_average_surface --fsgd /space/emc1/3/data/TOP/Analysis_lmr/TOPtest.fsgdf --out /space/emc1/3/data/TOP/Analysis_lmr/average_TOPtest $Id: make_average_surface,v 1.27.2.2

[Freesurfer] OASIS Freesurfer Data

Hi folks- The Freesurfer processing of the OASIS cross-sectional data set is now available for download via anonymous FTP. The whole set will also be available at the OASIS website in the coming weeks. Check out www.oasis-brains.org for more information on the OASIS project. Download inst

Re: [Freesurfer] Making labels from the commandline

Hi Doug, I see what you mean now. mri_cor2label should do it. Thanks again. Cheers, -Morgan Doug Greve wrote: No, use mri_cor2label to create the label file. I think the 2nd example matches what you want to do. doug Morgan Hough wrote: Hi Doug, Thanks for the ftp fix. I have downloaded

Re: [Freesurfer] Making labels from the commandline

No, use mri_cor2label to create the label file. I think the 2nd example matches what you want to do. doug Morgan Hough wrote: Hi Doug, Thanks for the ftp fix. I have downloaded these fine now. I don't see a use case for making a label in mri_binarize's help. When I project the volumes to s

Re: [Freesurfer] Making labels from the commandline

Hi Doug, Thanks for the ftp fix. I have downloaded these fine now. I don't see a use case for making a label in mri_binarize's help. When I project the volumes to surfaces I actually save them as nifti files so I can keep using avwmaths++ when I want to. What I think I am missing now is the w

Re: [Freesurfer] Making labels from the commandline

Sorry, should be accessible now. To do what you need, you can just run mri_binarize on the output (or input) of vol2surf. I've put an uptodate copy of mri_binarize there too. doug Morgan Hough wrote: Thanks Doug, I am having some trouble downloading this but the tksurfer interface suffices

Re: [Freesurfer] problem to save images

The RGB format is an old Irix format, I think. The UNIX/Linux program 'convert' should be able to convert it to a jpeg for you. On Wed, Jun 27, 2007 at 12:34:44PM -0400, Wang, Xin wrote: > Hello, group > I have problems to save the display in TKsurfer. I tried 'Save RGB > as', but I could not ope

Re: [Freesurfer] Making labels from the commandline

Thanks Doug, I am having some trouble downloading this but the tksurfer interface suffices for now. I would still be interested in making a label from a volumetric projection as this is something I can foresee being useful for other things as well. Is there anyway to do this after a mri_vol2

[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] 3D volume generation, ROI selection, subvolume analysis

Good morning, We have been working on Slicer and have been able to read in our stack of images. I can view them at the desired cross-sections by moving the three planes at will. But now we would like to be able to generate a 3D volume (in this case a rectangular prism) that contains all of the

Re: [Freesurfer] retinotopy question

thanks Jon, i didn't know that a simple block design analysis is possible to compute the visual area boundaries... (which is the reason why I tried to fit it into the standard sfa-sess analysis)... could you explain me (shortly) what to do than with my data regards, Lars. -design info: 8hz f

[Freesurfer] (no subject)

  hi ,I have solved the the probelm.Now, I have some new question, just as belows:1  In the GUI interface, I can't type the letters ,I don't know why?2 when I choose the volume in the Morphometric-Measure, the Qdec runs error. how to solve it ? the screenshot on the attachment.3 In the term

[Freesurfer] (no subject)

  hi ,I have solved the the probelm.Now, I have some new question, just as belows:1  In the GUI interface, I can't type the letters ,I don't know why?2 when I choose the volume in the Morphometric-Measure, the Qdec runs error. how to solve it ? the screenshot on the attachment.3 In the term