Yes sorry. I meant without resampling. In that case, I will just re-run as you suggested. Thanks for your help!
________________________________ From: freesurfer-boun...@nmr.mgh.harvard.edu <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Douglas N. Greve <dgr...@mgh.harvard.edu> Sent: Monday, May 7, 2018 1:44:55 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] fmriprep to fsfast interface I'm not sure what you mean to apply the tal without a registration. Do you mean without resampling? We don't have anything that will do that for a 12dof registration. On 05/04/2018 05:11 PM, Boggess, Matthew Jozsef wrote: > > Hello, > > > I just wanted to follow up on this again. Is there any way to > transform functional data (already in T1 space) to tal space directly? > Something like passing an identity registration matrix to mri_vol2vol > or another command that would apply the tal transform without a > registration? > > > If not, I will just try re-registering as you suggested, but I am > hoping to minimize the extra processing steps. > > > Thanks, > > Matt > > ------------------------------------------------------------------------ > *From:* freesurfer-boun...@nmr.mgh.harvard.edu > <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Boggess, Matthew > Jozsef <mbogg...@mgh.harvard.edu> > *Sent:* Friday, April 20, 2018 8:13:11 AM > *To:* freesurfer@nmr.mgh.harvard.edu > *Subject:* Re: [Freesurfer] fmriprep to fsfast interface > > Thank you for the response! > > > I'm interested primarily in tal space, but potentially native as well. > For tal space, is there no easy way to just directly transform the > data into tal space or provide an identity matrix for the registration? > > ------------------------------------------------------------------------ > *From:* freesurfer-boun...@nmr.mgh.harvard.edu > <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Douglas Greve > <dgr...@mgh.harvard.edu> > *Sent:* Tuesday, April 17, 2018 12:01:46 PM > *To:* freesurfer@nmr.mgh.harvard.edu > *Subject:* Re: [Freesurfer] fmriprep to fsfast interface > > sorry for the delay, see below > > > On 4/14/18 10:00 AM, Boggess, Matthew Jozsef wrote: >> >> Hello, >> >> >> I just wanted to follow up to see if anyone could help with any of my >> questions, particularly # 1. >> >> >> Thank you! >> >> Matt Boggess >> >> ------------------------------------------------------------------------ >> *From:* freesurfer-boun...@nmr.mgh.harvard.edu >> <mailto:freesurfer-boun...@nmr.mgh.harvard.edu> >> <freesurfer-boun...@nmr.mgh.harvard.edu> >> <mailto:freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Boggess, >> Matthew Jozsef <mbogg...@mgh.harvard.edu> >> <mailto:mbogg...@mgh.harvard.edu> >> *Sent:* Thursday, April 5, 2018 8:02:07 AM >> *To:* freesurfer@nmr.mgh.harvard.edu >> <mailto:freesurfer@nmr.mgh.harvard.edu> >> *Subject:* [Freesurfer] fmriprep to fsfast interface >> Hello, >> >> I've been working on taking the outputs of the fmriprep >> BOLD preprocessing tool >> (https://fmriprep.readthedocs.io/en/latest/index.html) and coercing >> them into the fsfast structure so that first levels can be run with >> mkanalysis-sess and selxavg3b-sess. It's been a bit trickier than >> anticipated and I was hoping to get some help verifying my current >> approach (attached to this email). >> >> Question 1: >> >> fmriprep outputs the preprocessed BOLD data in the T1 space (mni305 >> is not an option). However, the typical spatial normalization >> workflow uses a registration matrix from the bold to T1 to transform >> to talairach. Is there a way to do this transformation without having >> to specify a registration matrix given the functional data is already >> in the T1 space? My current approach is to use mri_convert with the >> --apply_transform flag pointing to the talairach.xfm registration >> matrix in the subject's recon folder, but I am not sure if this is a >> reasonable workaround. > Do you want to analyze it in the native T1 space or in talairach > space? If native, then when you run mkanalysis-sess you can bypass the > preprocessing by directly specifying the stem of the functional data > you want to process (-funcstem). If tal space, then I think it should > work out of the box (it would recalc the registration, but that > should be ok). >> >> Question 2: >> >> fsfast normally calculates the global mean value of the raw data to >> be used for intensity normalization. However, with fmriprep I only >> have access to the preprocessed data in T1 space. Would extracting >> the global mean value for intensity normalization from the >> preprocessed BOLD in T1 space be valid? > Yes >> >> Question 3: >> >> Is there a way to do first levels in the native subcortical space? If >> so, what is the filename structure expected (maybe mni305.2mm gets >> replaced with the subject name as with the surface data)? I've only >> seen examples transforming to mni305 space, but ideally an option >> would be to just transfer the preprocessed BOLD in T1 space and run >> first levels staying in the native T1 space. > See above. >> >> Thanks for your help! >> >> Matt >> >> >> >> >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu <mailto: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
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