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
[Freesurfer] fsgd and contrast matrix
Hi, I would like to study cortical thickness in a cohort of patient with respect to MMSE and CDR. I prepared a fsgd file where I have both MMSE and CDR listed: GroupDescriptorFile 1 Title Mytitle Class Male Class Female Variable Age Variable MMSE Variable CDR Class Ctrl Class MCI Input subject1 Male 70 27 0.5 MCI Input subject2 Female 65 28 0 Ctrl My design matrix should thus have 4*(3+1)=16 columns/regressors. I am puzzeled a bit, how would I set the contrast matrix to study only correlation of thickness with MMSE, while ignoring CDR. Or should I have a separate fsgd file? Thanks, Martin ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] Labels for the auditory cortex
Dear developers, I was wondering if you would have labels for the Broadman areas corresponding to the auditory cortex for the fsaverage subject. Thank you, Nasim ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] fsgd and contrast matrix
Just set the CDR-related slope components in the contrast matrix to 0. If you truly believe that the CDR has no effect, then you can create a new fsgd without CDR as a variable. This will improve both DOF and efficiency. doug Martin Kavec wrote: Hi, I would like to study cortical thickness in a cohort of patient with respect to MMSE and CDR. I prepared a fsgd file where I have both MMSE and CDR listed: GroupDescriptorFile 1 Title Mytitle Class Male Class Female Variable Age Variable MMSE Variable CDR Class Ctrl Class MCI Input subject1 Male 70 27 0.5 MCI Input subject2 Female 65 28 0 Ctrl My design matrix should thus have 4*(3+1)=16 columns/regressors. I am puzzeled a bit, how would I set the contrast matrix to study only correlation of thickness with MMSE, while ignoring CDR. Or should I have a separate fsgd file? Thanks, Martin ___ 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] fsgd and contrast matrix
Thanks, Dough. On Thursday 24 September 2009 21:31:34 Douglas N Greve wrote: Just set the CDR-related slope components in the contrast matrix to 0. If you truly believe that the CDR has no effect, then you can create a new fsgd without CDR as a variable. No no, I believe that the CDR has an effect, I just want to see whether the atrophy areas correlated with CDR and MMSE differ. Thanks, Martin This will improve both DOF and efficiency. doug Martin Kavec wrote: Hi, I would like to study cortical thickness in a cohort of patient with respect to MMSE and CDR. I prepared a fsgd file where I have both MMSE and CDR listed: GroupDescriptorFile 1 Title Mytitle Class Male Class Female Variable Age Variable MMSE Variable CDR Class Ctrl Class MCI Input subject1 Male 70 27 0.5 MCI Input subject2 Female 65 28 0 Ctrl My design matrix should thus have 4*(3+1)=16 columns/regressors. I am puzzeled a bit, how would I set the contrast matrix to study only correlation of thickness with MMSE, while ignoring CDR. Or should I have a separate fsgd file? Thanks, Martin ___ 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] cortex.label stats
what is no longer there? The cortex.label should be there, then you'd use your cmd below to compute the stats file. doug Dankner, Nathan (NIH/NIMH) [F] wrote: Hi all, In past versions, I have been using this command to generate average cortical thickness across the cortex: Mris_anatomical_stats -l (hemi).cortex.label -f (id)/stats/(hemi).cortex.stats (id) (hemi) However, I have noticed that in version 4.5 the cortex.stats files are no longer in the stats folder. Are they somewhere else, or is there a different method which I should now use to compute these statistics? ___ 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] hippocampus volume difference
Hi, there, I use the following matlab code to find right and left hippocampus in aseg.mgz %% filename = 'case_1/mri/aseg.mgz'; [vol, M, mr_parms, volsz] = load_mgh(filename); hippo_left = find( (vol 16.99) (vol 17.01) ); hippo_right = find( (vol 52.99) (vol 53.01) ); %%% I found size(hippo_left, 1) = 3075; size(hippo_right, 1) = 3237; However, the value I found in aseg.mgz is 3162 3162.0 Left-Hippocampus 3390 3390.0 Right-Hippocampus Why these values are different (3075 3162, 3237 3390)? Thanks a lot! Guang _ Hotmail® has ever-growing storage! Don’t worry about storage limits. http://windowslive.com/Tutorial/Hotmail/Storage?ocid=TXT_TAGLM_WL_HM_Tutorial_Storage_062009___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] hippocampus volume difference
When we compute the aseg.stats, we include partial volume correction, we don't just count up the voxels in hippo. doug Guang Zeng wrote: Hi, there, I use the following matlab code to find right and left hippocampus in aseg.mgz %% filename = 'case_1/mri/aseg.mgz'; [vol, M, mr_parms, volsz] = load_mgh(filename); hippo_left = find( (vol 16.99) (vol 17.01) ); hippo_right = find( (vol 52.99) (vol 53.01) ); %%% I found size(hippo_left, 1) = 3075; size(hippo_right, 1) = 3237; However, the value I found in aseg.mgz is 3162 3162.0 Left-Hippocampus 3390 3390.0 Right-Hippocampus Why these values are different (3075 3162, 3237 3390)? Thanks a lot! Guang Hotmail® has ever-growing storage! Don’t worry about storage limits. Check it out. http://windowslive.com/Tutorial/Hotmail/Storage?ocid=TXT_TAGLM_WL_HM_Tutorial_Storage_062009 ___ 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 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] how to use mri_surf2surf
you have to register one to another using bbregister, fslregister, or spmregister. You can then run mri_surf2surf specifying --sval-xyz surfname and specifying --tval-xyz to get and output surface (instead of a scaler file). You will also have to spec the registration you created above with --reg (or --reg-inv). Note that the number of vertices will be different, but you should still be able to load it into tksurfer. doug Guang Zeng wrote: Hi, there, mri_surf2surf resamples one CorticalSurface http://surfer.nmr.mgh.harvard.edu/fswiki/CorticalSurface onto another. If I have two subjects from different time points (tp1 and tp2), I'd like to compare the FreeSurfer analyzed surface data. For example, could I use mri_surf2surf to resample the white matter surface of tp1 onto tp2, so I can overlay the white matter surface of tp2 to tp1 using tkmedit? Thanks! guang Hotmail® has ever-growing storage! Don’t worry about storage limits. Check it out. http://windowslive.com/Tutorial/Hotmail/Storage?ocid=TXT_TAGLM_WL_HM_Tutorial_Storage_062009 ___ 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] how to use mri_surf2surf
Hi Guang, If you have the same subject and two timepoints, you might want to look at the longitudinal stream. Martin On Sep 23, 2009, at 17:52, Guang Zeng freesurfer...@hotmail.com wrote: Hi, there, mri_surf2surf resamples one CorticalSurface onto another. If I have two subjects from different time points (tp1 and tp2), I'd like to compare the FreeSurfer analyzed surface data. For example, could I use mri_surf2surf to resample the white matter surface of tp1 onto tp2, so I can overlay the white matter surface of tp2 to tp1 using tkmedit? Thanks! guang Hotmail® has ever-growing storage! Don’t worry about storage limits. Check it out. ___ 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
