Re: [Freesurfer] FSL to FreeSurfer registration
Hi Michael, while fslmaths has an option to do 2D smoothing, this is still only smoothing in a slice of the volume and has the same problems as 3D smoothing (ie, smoothing across tissue types and sulci). The 2D that FS implements with mris_volsmooth is along the cortical surface, which is unrelated to the volume axes. So, unfortunately, you do still have to do two analyses if you want a volume-based analysis with smoothing. doug Michael Scheel wrote: Hi Estephan, you don't necessarily have to rerun the full 1st level Analysis in total. What you have to find out is which of your volumes is the one that example_func is created from. Normally this should be the middle timepoint fmri image of your functional run (e.g. if you have 99 volumes then number 45 will be taken as example_func) that's the default if you haven't specified it otherwise. You can use fslroi as a command to extract this volume for the above example e.g.: fslroi input_fmri.nii.gz middle_volume.nii.gz 44 1 (fslroi starts counting from 0 thats why it is 44 instead of 45) 2D and 3D smoothing can also be done with fslmaths see the -s and the -kernel option Best, Michael On 23-Sep-09, at 6:52 PM, Douglas N Greve wrote: Estephan Moana wrote: So what I need to do is to run the 1st level FEAT as usual for the FSL pipeline, and repeat this analysis for FS with the only difference been to set the Spatial smoothing FWHM to zero on the pre-stats tab of the FEAT GUI? yes Also, can you explain if this smoothing on the FEAT GUI is the 3D you refer to? And how 2D smoothing is accomplished? Yes, this the 3D smoothing. 2D smoothing on the raw data is more difficult inside of feat. You'd have to use MC and then run mris_volsmooth (FS program) outside of FEAT, then pass FEAT the preprocessed data and tell it not to do MC or smoothing. Thank you. Estephan Douglas N Greve wrote: The example_func does not actually get smoothed, so smoothing itself will not affect the registration. 3D smoothing will smooth values from WM and CSF into gray and from across sulci into functionally distinct regions. For this reason we recommend not using 3D smoothing (or doing 2D smoothing on the surface). Unfortunately, this requires two different analyses. doug Estephan Moana wrote: Hello all, I took the FS course last June at the OHBM in San Francisco, and am now playing with it to get to know it better. One of the slides on the talk about FSL-FS integration mentioned that the input data (from FEAT) for the reg-feat2anat command should have not been smoothed prior to registering to FS. Considering that FEAT 1st level analysis has a default of 5mm spatial smoothing (and that's what I used on my data), it seems counterintuitive to need to run a 1st level analysis again so the output files are not spatially smoothed. So my questions are: 1) having the example_func file spatially smoothed will necessarily hinder a proper registration to the FS anatomical?; 2) if so, should I re-run all my FEAT 1st level analysis without smoothing or is there any other way? I know this is quite a beginners question, but I could not find the answers on the FS FAQ or the mailing list archives. I appreciate any light on this. Regards, Estephan Moana, DDS Graduate Student Oral Biology PhD Program - Neurobiology track School of Dentistry, UNC- Chapel Hill 2140 Old Dental Building, CB# 7455 Chapel Hill, NC 27599 Phone: (919) 966-5680 Fax: (919) 966-5339 Cell: (612) 702-3295 mo...@email.unc.edu mailto:mo...@email.unc.edu ___ 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 gr...@nmr.mgh.harvard.edu 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 -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu 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] FSL to FreeSurfer registration
Thanks for you input Michael. For some reason, I only saw your answer after Dougla's response. Assuming that I do not want to do volume-based analysis and just want nice pics of my blobs over a 3D brain, would Michael's suggestion work? If so, what is the next step after using fslroi, as the input for reg-feat2anat is a feat directory (an not a single example_func file)? An unrelated question: is there a way to get the FreeSurfer mailing list via a RSS feed? This would be help decrease the amount of emails in my inbox... Thanks again. Estephan ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] FSL to FreeSurfer registration
Estephan Moana wrote: Thanks for you input Michael. For some reason, I only saw your answer after Dougla's response. Assuming that I do not want to do volume-based analysis and just want nice pics of my blobs over a 3D brain, would Michael's suggestion work? If so, what is the next step after using fslroi, as the input for reg-feat2anat is a feat directory (an not a single example_func file)? At what level do you want pics? The group or individual level? If the group (after Flame1 or Flame2), then you can skip smoothing the raw data and just smooth prior to group analysis. If the individual level, then smoothing the raw data will affect the maps. You cannot use fslmaths to do cortical 2D smoothing. An unrelated question: is there a way to get the FreeSurfer mailing list via a RSS feed? This would be help decrease the amount of emails in my inbox... Thanks again. Estephan -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu 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] FSL to FreeSurfer registration
Estephan, I can ask our IT people about an RSS feed. Another option is to turn-on digest mode under the mailing list options. Freesurfer emails would arrive in once-a-day bundles. https://mail.nmr.mgh.harvard.edu/mailman/options/freesurfer Nick On Thu, 2009-09-24 at 12:35 -0400, Estephan Moana wrote: Thanks for you input Michael. For some reason, I only saw your answer after Dougla's response. Assuming that I do not want to do volume-based analysis and just want nice pics of my blobs over a 3D brain, would Michael's suggestion work? If so, what is the next step after using fslroi, as the input for reg-feat2anat is a feat directory (an not a single example_func file)? An unrelated question: is there a way to get the FreeSurfer mailing list via a RSS feed? This would be help decrease the amount of emails in my inbox... Thanks again. Estephan ___ 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] FSL to FreeSurfer registration
Estaphan, It turns out the freesurfer mailing list does support RSS feeds: http://www.mail-archive.com/freesur...@surfer.nmr.mgh.harvard.edu/maillist.xml Nick On Thu, 2009-09-24 at 13:25 -0400, Nick Schmansky wrote: Estephan, I can ask our IT people about an RSS feed. Another option is to turn-on digest mode under the mailing list options. Freesurfer emails would arrive in once-a-day bundles. https://mail.nmr.mgh.harvard.edu/mailman/options/freesurfer Nick On Thu, 2009-09-24 at 12:35 -0400, Estephan Moana wrote: Thanks for you input Michael. For some reason, I only saw your answer after Dougla's response. Assuming that I do not want to do volume-based analysis and just want nice pics of my blobs over a 3D brain, would Michael's suggestion work? If so, what is the next step after using fslroi, as the input for reg-feat2anat is a feat directory (an not a single example_func file)? An unrelated question: is there a way to get the FreeSurfer mailing list via a RSS feed? This would be help decrease the amount of emails in my inbox... Thanks again. Estephan ___ 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 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] FSL to FreeSurfer registration
Thanks Nick, this helps a lot! Estephan Nick Schmansky wrote: Estaphan, It turns out the freesurfer mailing list does support RSS feeds: http://www.mail-archive.com/freesur...@surfer.nmr.mgh.harvard.edu/maillist.xml Nick On Thu, 2009-09-24 at 13:25 -0400, Nick Schmansky wrote: Estephan, I can ask our IT people about an RSS feed. Another option is to turn-on digest mode under the mailing list options. Freesurfer emails would arrive in once-a-day bundles. https://mail.nmr.mgh.harvard.edu/mailman/options/freesurfer Nick On Thu, 2009-09-24 at 12:35 -0400, Estephan Moana wrote: Thanks for you input Michael. For some reason, I only saw your answer after Dougla's response. Assuming that I do not want to do volume-based analysis and just want nice pics of my blobs over a 3D brain, would Michael's suggestion work? If so, what is the next step after using fslroi, as the input for reg-feat2anat is a feat directory (an not a single example_func file)? An unrelated question: is there a way to get the FreeSurfer mailing list via a RSS feed? This would be help decrease the amount of emails in my inbox... Thanks again. Estephan ___ 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 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] FSL to FreeSurfer registration
The example_func does not actually get smoothed, so smoothing itself will not affect the registration. 3D smoothing will smooth values from WM and CSF into gray and from across sulci into functionally distinct regions. For this reason we recommend not using 3D smoothing (or doing 2D smoothing on the surface). Unfortunately, this requires two different analyses. doug Estephan Moana wrote: Hello all, I took the FS course last June at the OHBM in San Francisco, and am now playing with it to get to know it better. One of the slides on the talk about FSL-FS integration mentioned that the input data (from FEAT) for the reg-feat2anat command should have not been smoothed prior to registering to FS. Considering that FEAT 1st level analysis has a default of 5mm spatial smoothing (and that's what I used on my data), it seems counterintuitive to need to run a 1st level analysis again so the output files are not spatially smoothed. So my questions are: 1) having the example_func file spatially smoothed will necessarily hinder a proper registration to the FS anatomical?; 2) if so, should I re-run all my FEAT 1st level analysis without smoothing or is there any other way? I know this is quite a beginners question, but I could not find the answers on the FS FAQ or the mailing list archives. I appreciate any light on this. Regards, Estephan Moana, DDS Graduate Student Oral Biology PhD Program - Neurobiology track School of Dentistry, UNC- Chapel Hill 2140 Old Dental Building, CB# 7455 Chapel Hill, NC 27599 Phone: (919) 966-5680 Fax: (919) 966-5339 Cell: (612) 702-3295 mo...@email.unc.edu mailto:mo...@email.unc.edu ___ 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 gr...@nmr.mgh.harvard.edu 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
[Freesurfer] FSL to FreeSurfer registration
Hello all, I took the FS course last June at the OHBM in San Francisco, and am now playing with it to get to know it better. One of the slides on the talk about FSL-FS integration mentioned that the input data (from FEAT) for the reg-feat2anat command should have not been smoothed prior to registering to FS. Considering that FEAT 1st level analysis has a default of 5mm spatial smoothing (and that's what I used on my data), it seems counterintuitive to need to run a 1st level analysis again so the output files are not spatially smoothed. So my questions are: 1) having the example_func file spatially smoothed will necessarily hinder a proper registration to the FS anatomical?; 2) if so, should I re-run all my FEAT 1st level analysis without smoothing or is there any other way? I know this is quite a beginners question, but I could not find the answers on the FS FAQ or the mailing list archives. I appreciate any light on this. Regards, Estephan Moana, DDS Graduate Student Oral Biology PhD Program - Neurobiology track School of Dentistry, UNC- Chapel Hill 2140 Old Dental Building, CB# 7455 Chapel Hill, NC 27599 Phone: (919) 966-5680 Fax: (919) 966-5339 Cell: (612) 702-3295 mo...@email.unc.edu ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
