[Freesurfer] Creation of V1 mask in volume
Dear freesurfer experts, I am trying to create a V1 mask in volume, based on the V1 label, in fsaverage space. I use the following command: mri_label2vol --label /Applications/freesurfer/subjects/fsaverage/label/rh.V1.label --temp /Applications/freesurfer/subjects/fsaverage/mri/orig.mgz --hemi rh --identity --o v1volume.nii When I check out the output (in freeview, I load orig,mgz and v1volume.nii as a mask), V1 as defined in v1volume.nii seems to be mislocated. I am surprised since I would think that I use the proper inputs ; or is my command line somehow wrong? Thank you very much, Florence ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] Transformation between spaces
Hi Matt, I follow-up on your suggestion of running MELODIC in surface. I am unsure about the registration files that I should use (I guess that they should be surface files?), notably for the Main Structural Images and the Standard Space. I am sorry if this sounds like a naive question. Thank you very much, Florence 2017-10-09 22:28 GMT-04:00 Matt Glasser <m...@ma-tea.com>: > The latest version of melodic is compatible with CIFTI data (e.g. From the > HCP). > > Peace, > > Matt. > > From: <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Florence > Campana <campana.flore...@gmail.com> > Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu> > Date: Monday, October 9, 2017 at 9:25 PM > To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu> > Subject: [Freesurfer] Transformation between spaces > > Hi Matt, > > Thank you for your quick input ; I did not try yet to use melodic, it > seems indeed to be the most straightforward solution, I will try it, thank > you again! > > Florence > > Le lundi 9 octobre 2017, Matt Glasser <m...@ma-tea.com> a écrit : > >> I’d note that you can run the group ICA on surface data in surface space >> pretty easily using melodic, which would avoid the issue that Doug mentions. >> >> Peace, >> >> Matt. >> >> From: <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Douglas >> Greve <gr...@nmr.mgh.harvard.edu> >> Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu> >> Date: Monday, October 9, 2017 at 7:20 PM >> To: <freesurfer@nmr.mgh.harvard.edu> >> Subject: Re: [Freesurfer] Transformation between spaces >> >> >> How did you get your ICA analysis into MNI305 (or MNI152) space? You're >> ICA intergroup comparisons will only be as good as that space -- how you >> get it onto the surface from there is not so important. You can run >> recon-all on the MNI152, sample the ICA maps onto the surface, then use the >> surface-based registration to map it to fsaverage. >> >> On 10/9/17 7:20 PM, Florence Campana wrote: >> >> Dear freesurfer experts, >> >> I ran a spatial ICA in volume and would like to visualize the components >> in surface in order to assess the overlap between the independent >> components and my ROI (defined on surface). However after reading this >> paper, https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2862732/, I am >> concerned with transformations between the MNI 305 space and the surface >> space without totally understanding the nature of the distortions >> unfortunately. Would you mind explaining it briefly to me and let me know >> whether you think that the transformation of the components from the MNI305 >> space to the surface will lead to distorted results in the case of our >> spatial overlap estimates? (in which case I can define the ROI in volume >> and conduct all the analyses in volume). >> >> Thank you very much, >> Florence Campana >> >> >> ___ >> Freesurfer mailing >> listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> >> ___ Freesurfer mailing list >> freesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.e >> du/mailman/listinfo/freesurfer The information in this e-mail is >> intended only for the person to whom it is addressed. If you believe this >> e-mail was sent to you in error and the e-mail contains patient >> information, please contact the Partners Compliance HelpLine at >> http://www.partners.org/complianceline . If the e-mail was sent to you >> in error but does not contain patient information, please contact the >> sender and properly dispose of the e-mail. >> > ___ Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard. > edu/mailman/listinfo/freesurfer The information in this e-mail is > intended only for the person to whom it is addressed. If you believe this > e-mail was sent to you in error and the e-mail contains patient > information, please contact the Partners Compliance HelpLine at > http://www.partners.org/complianceline . If the e-mail was sent to you in > error but does not contain patient information, please contact the sender > and properly dispose of the e-mail. > > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > The inf
[Freesurfer] Transformation between spaces
Hi Matt, Thank you for your quick input ; I did not try yet to use melodic, it seems indeed to be the most straightforward solution, I will try it, thank you again! Florence Le lundi 9 octobre 2017, Matt Glasser <m...@ma-tea.com <javascript:_e(%7B%7D,'cvml','m...@ma-tea.com');>> a écrit : > I’d note that you can run the group ICA on surface data in surface space > pretty easily using melodic, which would avoid the issue that Doug mentions. > > Peace, > > Matt. > > From: <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Douglas Greve > <gr...@nmr.mgh.harvard.edu> > Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu> > Date: Monday, October 9, 2017 at 7:20 PM > To: <freesurfer@nmr.mgh.harvard.edu> > Subject: Re: [Freesurfer] Transformation between spaces > > > How did you get your ICA analysis into MNI305 (or MNI152) space? You're > ICA intergroup comparisons will only be as good as that space -- how you > get it onto the surface from there is not so important. You can run > recon-all on the MNI152, sample the ICA maps onto the surface, then use the > surface-based registration to map it to fsaverage. > > On 10/9/17 7:20 PM, Florence Campana wrote: > > Dear freesurfer experts, > > I ran a spatial ICA in volume and would like to visualize the components > in surface in order to assess the overlap between the independent > components and my ROI (defined on surface). However after reading this > paper, https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2862732/, I am > concerned with transformations between the MNI 305 space and the surface > space without totally understanding the nature of the distortions > unfortunately. Would you mind explaining it briefly to me and let me know > whether you think that the transformation of the components from the MNI305 > space to the surface will lead to distorted results in the case of our > spatial overlap estimates? (in which case I can define the ROI in volume > and conduct all the analyses in volume). > > Thank you very much, > Florence Campana > > > ___ > Freesurfer mailing > listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > ___ Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.e > du/mailman/listinfo/freesurfer The information in this e-mail is intended > only for the person to whom it is addressed. If you believe this e-mail was > sent to you in error and the e-mail contains patient information, please > contact the Partners Compliance HelpLine at http://www.partners.org/compli > anceline . If the e-mail was sent to you in error but does not contain > patient information, please contact the sender and properly dispose of the > e-mail. > ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] Transformation between spaces
Dear freesurfer experts, I ran a spatial ICA in volume and would like to visualize the components in surface in order to assess the overlap between the independent components and my ROI (defined on surface). However after reading this paper, https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2862732/, I am concerned with transformations between the MNI 305 space and the surface space without totally understanding the nature of the distortions unfortunately. Would you mind explaining it briefly to me and let me know whether you think that the transformation of the components from the MNI305 space to the surface will lead to distorted results in the case of our spatial overlap estimates? (in which case I can define the ROI in volume and conduct all the analyses in volume). Thank you very much, Florence Campana ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] PCA and v.gmh
Thank you very much, Doug, it works indeed with your command! I am also curious about your advices to run the PCA on surface on resting state data (I know that mri_glmfit is not designed for that, but wonder there is a way to specify a contrast matrix and a design matrix such that the residuals are equal to the initial signal in order to run the PCA on my input resting state signal?). Thank you very much, Florence 2017-10-04 9:41 GMT-04:00 Douglas Greve <gr...@nmr.mgh.harvard.edu>: > what command are you using to view the data? It should be something like > > tksurferfv fsaverage lh inflated -ov v.mgh -fminmax .0001 .1 > > On 10/3/17 4:27 PM, Florence Campana wrote: > > > Dear freesurfers, > > I contact you since I ran a PCA with mri_glmfit. I do not manage to load > the output v.mgh as an overlay as suggested in the documentation, which > makes me wonder what is wrong. The output file or me loading it? > > For clarification, I ran the command: mri_glmfit --surf fsaverage lh --y > fmcpr.siemens.sm4.fsaverage.lh.nii.gz --pca --osgm --glmdir > /Users/Florence/Documents/test_glm_pca to run the PCA in surface. > > v.mgh is of size 1*163842(nb of vertices)*1*300 (number of components). > On the one hand, the output seems to make sense (its size, and the values > are centered around 0), on the other hand I do not understand why I do not > see anything when I load it as an overlay in tksurfer, despite modifying > the thresholds and color parameters etc. Or should I then save separately > each spatial component contained in v.mgh, and load each of them as one > overlay? > I would also like to specify that my input data > (fmcpr.siemens.sm4.fsaverage.lh.nii.gz) are of size 1*163842(nb of > vertices)*1*300 (time points). This is the data from a single subject for > now (before getting group data via mris_preproc) and I am not sure of > whether it has the proper format. Indeed, it is specified that —y is the “path > to input file with each frame being a separate input”. I do not understand > what it means: does frame refer to one time point, and should I then have > 300 input files (which seems a lot!)? > > Thank you very much, > > Florence > > > ___ > Freesurfer mailing > listfreesur...@nmr.mgh.harvard.eduhttps://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 > > > The information in this e-mail is intended only for the person to whom it > is > addressed. If you believe this e-mail was sent to you in error and the > e-mail > contains patient information, please contact the Partners Compliance > HelpLine at > http://www.partners.org/complianceline . If the e-mail was sent to you in > error > but does not contain patient information, please contact the sender and > properly > dispose of the e-mail. > > ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] PCA and v.gmh
Dear freesurfers, I contact you since I ran a PCA with mri_glmfit. I do not manage to load the output v.mgh as an overlay as suggested in the documentation, which makes me wonder what is wrong. The output file or me loading it? For clarification, I ran the command: mri_glmfit --surf fsaverage lh --y fmcpr.siemens.sm4.fsaverage.lh.nii.gz --pca --osgm --glmdir /Users/Florence/Documents/test_glm_pca to run the PCA in surface. v.mgh is of size 1*163842(nb of vertices)*1*300 (number of components). On the one hand, the output seems to make sense (its size, and the values are centered around 0), on the other hand I do not understand why I do not see anything when I load it as an overlay in tksurfer, despite modifying the thresholds and color parameters etc. Or should I then save separately each spatial component contained in v.mgh, and load each of them as one overlay? I would also like to specify that my input data (fmcpr.siemens.sm4.fsaverage.lh.nii.gz) are of size 1*163842(nb of vertices)*1*300 (time points). This is the data from a single subject for now (before getting group data via mris_preproc) and I am not sure of whether it has the proper format. Indeed, it is specified that —y is the “path to input file with each frame being a separate input”. I do not understand what it means: does frame refer to one time point, and should I then have 300 input files (which seems a lot!)? Thank you very much, Florence ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] converting vertex numbers in .label files to R, A, S coordinates
Hi Doug, Thank you for your reply. I computed the tkRAS coordinates using the formula TkRAS = Torig*[C R S 1]’. It returns me coordinates such as: [113, -119,88], [105, -103, 96]. I wonder whether such tkRAS coordinates are normal since in label files obtained by saving ROI upon a certain threshold in tksurfer, the coordinates seem fairly different: non integers, and in different ranges e.g. [-36.806 -18.293 64.462], [-21.393 -61.263 8.910]) etc. However, when I create a label file (via write_label.m) with -1 in the first column and with the TkRAS coordinates that I computed in the columns 2,3,4 , and then via tksurfer load this label and then save the selected label, I obtain a new label with R A S coordinates as [34.198 -48.599 29.835], [35.364 -45.689 31.179], i.e. similar to the one that I have in my ROI label files. Could you please help me to figure out what my tkRAS values (e.g.[113, -119,88], [105, -103, 96) correspond to, versus the ones returned by tksurfer ([34.198 -48.599 29.835], [35.364 -45.689 31.179])? I hope that it makes sense. Thank you so much! Florence *From:* Douglas Greve <gr...@nmr.mgh.harvard.edu> *Date:* July 24, 2017 at 4:06:25 PM EDT *To:* <freesurfer@nmr.mgh.harvard.edu> *Subject:* *Re: [Freesurfer] converting vertex numbers in .label files to R, A, S coordinates* *Reply-To:* Freesurfer support list <freesurfer@nmr.mgh.harvard.edu> Try using mri_label2label with the --paint option. I think the vertex numbers need to be -1 (not random numbers). You will also need to convert the RAS to "tkregisterRAS", one of our internal coordinate systems. See https://surfer.nmr.mgh.harvard.edu/fswiki/CoordinateSystems, you'll need to do the inverse of case #1. On 7/19/17 12:28 PM, Li Guo wrote: *Dear Freesurfer experts,* *My question concerns the .label files and the correspondence between the vertex numbers (in the first column) and the R,A,S coordinates.* *I have the R,A,S coordinates of voxels that I want to display on the surface. For this purpose, I created a label file with the R,A,S coordinates (col 2,3,4) and random vertex ID in the col 1 (since I do not know what is the vertex ID for a given R,A,S coordinate). I displayed the content of the label file via tksurfer. However, tksurfer reads vertex ID, not R,A,S coordinates. * *I wonder whether anyone knows about a function computing the vertex ID based on the R,A,S coordinates, or an alternative solution to represent the vertices on the surface based on the voxel coordinates--and the registration file I assume?* *Thank you very much!* *Best* *Li Guo & Florence Campana* ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
