Re: [Freesurfer] mz3 for freesurfer brain render
External Email - Use Caution Hi Douglas, I would like to plot some values (z-scores) of ROI (grey matter) that are from freesurfer atlas and would like render them on the brain (freesurfer atlas) using surf ice. Is there .mz3 for the Desikan-Killarny atlas? Thanks k On Fri, Jun 5, 2020, 1:09 PM Douglas N. Greve wrote: > I don't know what you are asking for. Can you elaboraet? > > On 6/5/2020 10:41 AM, Kate Marvel wrote: > > External Email - Use Caution > > Hi Freesurfer team, > > I would like to do a brain render using freesurfer ROIs. Is there .mz3 > file for freesurfer brain atlas? > > Thanks, > -- > kate > > ___ > 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 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] mz3 for freesurfer brain render
External Email - Use Caution Hi Freesurfer team, I would like to do a brain render using freesurfer ROIs. Is there .mz3 file for freesurfer brain atlas? Thanks, -- kate ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] code for estimating volume
External Email - Use Caution Hi Iglesias, I would like to learn the two ways for estimating volumes mentioned in another post, see below. Please send me the codes in Freesurfer to do this. Thank you, Kate -- Forwarded message - From: Iglesias Gonzalez, Juan E. Date: Wed, Apr 8, 2020, 10:43 AM Subject: Re: [Freesurfer] Hippocampal subfields To: Freesurfer support list Dear Ioana, This is tricky because the volumes are computed from soft segmentations, which are not the ones you’re editing. In general, editing outputs is a bad idea; it may be better to simply discard the cases for which quality control fails. Having said that: if you want to use corrected cases, you could compute volumes by simply summing the number of voxels with each label, and multiplying by the volume of a voxel (which is 1/27=0.03703703703 cubic mm). But if you do this, then you need to compute the volume this way for all cases, including the ones you didn’t edit (you don’t want to mix 2 ways of estimating volumes). Cheers, /Eugenio Juan Eugenio Iglesias Senior research fellow CMIC (UCL), MGH (HMS) and CSAIL (MIT) http://www.jeiglesias.com *From: * on behalf of ioana cracana *Reply-To: *Freesurfer support list *Date: *Wednesday, April 8, 2020 at 04:59 *To: *"freesurfer@nmr.mgh.harvard.edu" *Subject: *[Freesurfer] Hippocampal subfields *External Email - Use Caution* Hello, I'm doing a study about hippocampal atrophy and I'm using the Segmentation of Hippocampal subfields tool. There were some minor errors and I edited them using Freeview, voxel edit tool. I would like to generate a new [lr]h.hippoSfVolumes-T1.v10.txt file using the edited [lr]h.hippoSfLabels-T1.v10.mgz in order to see the new results. What command do i have to use? Is there another way to edit the hippocampal subfields?And how do i see the results? I'm using Freesurfer v6.0.0. on macOS Mojave. Thanks, Ioana ___ 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] hippocampus subfield segmentation using Siemen and GE scans
External Email - Use Caution Thank you so much Iglesias. kate On Tue, Apr 7, 2020, 9:48 AM Iglesias Gonzalez, Juan E. < jiglesiasgonza...@mgh.harvard.edu> wrote: > It should be fine but please make sure you correct by scanner in > subsequent analyses. > > Cheers, > > /Eugenio > > > > > > Juan Eugenio Iglesias > > Senior research fellow > > CMIC (UCL), MGH (HMS) and CSAIL (MIT) > > http://www.jeiglesias.com > > > > > > > > *From: * on behalf of Kate Marvel > > *Reply-To: *Freesurfer support list > *Date: *Tuesday, April 7, 2020 at 06:26 > *To: *Freesurfer support list > *Subject: *[Freesurfer] hippocampus subfield segmentation using Siemen > and GE scans > > > > *External Email - Use Caution* > > Hi Freesurfer Community, > > > > I have run Hippocampus subfield segmentation using scans from GE and > Siemens. The field of view (FOV) for GE and Siemens are different, with FOV > of 8 and 9 respectively. Will this affect the analysis since they have > different FOV? > > > > Thanks, > > > > Kate > ___ > 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] hippocampus subfield segmentation using Siemen and GE scans
External Email - Use Caution Hi Freesurfer Community, I have run Hippocampus subfield segmentation using scans from GE and Siemens. The field of view (FOV) for GE and Siemens are different, with FOV of 8 and 9 respectively. Will this affect the analysis since they have different FOV? Thanks, Kate ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] how to calculate the ROI volumes of grey matter using Desikan atlas
External Email - Use Caution Hi Thomas, Thanks for this. k On Sun, Mar 15, 2020, 8:51 AM Thomas Yeo wrote: > External Email - Use Caution > > Hi Kate, > > The Desikan ROI volumes should be in the ?h.aparc.stats file after you run > recon-all. See Section 4.2 here ( > https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/AnatomicalROI#IndividualStatsfiles). > > > Regards, > Thomas > > On Sun, Mar 15, 2020 at 7:22 PM Kate Marvel wrote: > >> External Email - Use Caution >> >> >> Hi Freesurfer community, >> >> I would like to know how to compute the >> ROI volumes of grey matter using Desikan atlas? Is there a threshold >> value set for this? is it 0.2? >> >> Thanks >> >> kate >> ___ >> 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] how to calculate the ROI volumes of grey matter using Desikan atlas
External Email - Use Caution Hi Freesurfer community, I would like to know how to compute the ROI volumes of grey matter using Desikan atlas? Is there a threshold value set for this? is it 0.2? Thanks kate ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Which FDG-PET file to use for PETSufer?
External Email - Use Caution Thank you very much Douglas for the information. Kate On Mon, Feb 24, 2020 at 2:44 PM Douglas N. Greve wrote: > what are those three? The same data just oriented in a differeent way? If > so, then it does not matter as long as the orientation info is correct. > Load one into freeview to assure that the cor view actually shows up as > cor, etc. One thing you will not be able to check is whether there is a > left-right flip > > On 2/24/2020 3:30 PM, Kate Marvel wrote: > > External Email - Use Caution > Hi FreeSurfer Users, > > I would like to perform PET analysis using PETSurfer and I have the > following FDG-PET NIfTI files below: > > 1. TRANSAXIAL_BRAIN_3D_FDG_IR_CTAC+Time-TMGX.nii > > 2. SAGITTAL_BRAIN_3D_FDG_IR_CTAC+Time-TMGX.nii > > 3. CORONAL_BRAIN_3D_FDG_IR_CTAC+Time-TMGX.nii > > Which of the 3 NIfTI files above should one use for the PETSurfer? > > Thank you. > > -- > kate > > ___ > 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 -- kate ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] Which FDG-PET file to use for PETSufer?
External Email - Use Caution Hi FreeSurfer Users, I would like to perform PET analysis using PETSurfer and I have the following FDG-PET NIfTI files below: 1. TRANSAXIAL_BRAIN_3D_FDG_IR_CTAC+Time-TMGX.nii 2. SAGITTAL_BRAIN_3D_FDG_IR_CTAC+Time-TMGX.nii 3. CORONAL_BRAIN_3D_FDG_IR_CTAC+Time-TMGX.nii Which of the 3 NIfTI files above should one use for the PETSurfer? Thank you. -- kate ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] how to convert the registered file (.lta) into NIfTI format in PETsurfer
External Email - Use Caution Hi Bruce, Thank you very much Bruce. Kate On Mon, Feb 24, 2020 at 8:50 AM Bruce Fischl wrote: > Hi Kate > > the .lta format is for a linear registration (in ascii). YOu can just cat > it to see the contents - it is not a PET image (which will be stored in > .mgz or .nii). mri_convert or mri_vol2vol can be used to apply the > registration and/or change the output format (if you specify file.nii or > file.nii.gz it will write in Nifti) > > cheers > Bruce > > > On Mon, 24 Feb 2020, Kate Marvel wrote: > > > > > External Email - Use Caution > > > > Hi Douglas, > > Is there a way to save the registered PET image in NIfTi format instead > of > > .lta? > > > > Kate > > > > On Mon, Feb 24, 2020 at 8:26 AM Douglas N. Greve > > > wrote: > > Not sure what you are trying to do. An lta file is a matrix and > > nifti is a format for storing images. > > > > On 2/21/2020 7:52 AM, Kate Marvel wrote: > > > > External Email - Use Caution > > > > Hi All, > > How do you convert the registered file (.lta) into NIfTI format > > in PETsurfer. > > > > Thanks, > > > > > > ___ > > 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 > > > > > > > > -- > > kate > > > >___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- kate ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] how to convert the registered file (.lta) into NIfTI format in PETsurfer
External Email - Use Caution Hi Douglas, Is there a way to save the registered PET image in NIfTi format instead of .lta? Kate On Mon, Feb 24, 2020 at 8:26 AM Douglas N. Greve wrote: > Not sure what you are trying to do. An lta file is a matrix and nifti is a > format for storing images. > > On 2/21/2020 7:52 AM, Kate Marvel wrote: > > External Email - Use Caution > Hi All, > > How do you convert the registered file (.lta) into NIfTI format in > PETsurfer. > > Thanks, > > > ___ > 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 -- kate ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] how to convert the registered file (.lta) into NIfTI format in PETsurfer
External Email - Use Caution Hi All, How do you convert the registered file (.lta) into NIfTI format in PETsurfer. Thanks, ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] how to perform No Partial Volume Correction for PET using PETSURFER
External Email - Use Caution Sorry for that. psf is zero. Thank you very much Douglas. Kate On Thu, Feb 20, 2020 at 3:55 PM Douglas N. Greve wrote: > yes, they are, thought I don't know why you include "psf6" in the output > folder. > > On 2/20/2020 3:36 PM, Kate Marvel wrote: > > External Email - Use Caution > Dear All, > > I would like to perform no partial volume correction of PET using > PETSURFER. > The steps followed in doing this is shown below: > > gtmseg --s Patient_1 > > mri_concat Patient_1_pet.nii.gz --mean --o > Patient_1_pet_tac_vol_mean.nii.gz > > mri_coreg --s Patient_1 --mov Patient_1_pet_tac_vol_mean.nii.gz --reg > Patient_1_pet_registration.lta --threads 4 > > mri_gtmpvc --i Patient_1_pet.nii.gz --reg Patient_1_pet_registration.lta > --no-tfe --psf 0 --seg gtmseg.mgz --o Patient_1_gtmpvc.output.psf6 > > I would like to know whether these steps suffices for a no partial volume > correction. > > Thanks. > -- > kate > > ___ > 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 -- kate ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] how to perform No Partial Volume Correction for PET using PETSURFER
External Email - Use Caution Dear All, I would like to perform no partial volume correction of PET using PETSURFER. The steps followed in doing this is shown below: gtmseg --s Patient_1 mri_concat Patient_1_pet.nii.gz --mean --o Patient_1_pet_tac_vol_mean.nii.gz mri_coreg --s Patient_1 --mov Patient_1_pet_tac_vol_mean.nii.gz --reg Patient_1_pet_registration.lta --threads 4 mri_gtmpvc --i Patient_1_pet.nii.gz --reg Patient_1_pet_registration.lta --no-tfe --psf 0 --seg gtmseg.mgz --o Patient_1_gtmpvc.output.psf6 I would like to know whether these steps suffices for a no partial volume correction. Thanks. -- kate ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] what is the argument for arguments for symmetric Geometric Transfer Matrix and two-compartment model (Meltzer Method) in the PETsurfer ?
External Email - Use Caution Thank your very much Douglas for the information. Much appreciated. On Tue, Jan 28, 2020 at 1:12 PM Greve, Douglas N.,Ph.D. < dgr...@mgh.harvard.edu> wrote: > The symmetric GTM is the default (the non-sym is not implemented). > > I highly recommend that you don't use melzter (which is why I did not have > docs for it:). But if you must run it, add --melzter BinThresh MaskThresh > nDilations > BinThresh is used to create a binary mask by thresholding the WM+GM tissue > fraction maps at BinThresh. This is a number between 0 and 1 > nDilations is the number of times that the binary mask is dilated to > expand it a bit (don't use more than 2) > MaskThresh - the binarized mask is smoothed and then divided into the PET > image to do the correction. Voxels whose smoothed value is less than > MaskThresh is set to 0. MaskThresh should be between 0 and 1 > > this is all kind of messy and unprincipled and the results are very > sensitive to the values you set above . which is why I avoid it. > > On 1/27/2020 9:23 PM, Kate Marvel wrote: > > External Email - Use Caution > Thanks Douglas. > > I checked the mri_gtmpvc --help command but the arguments for symmetric > Geometric Transfer Matrix and two-component model (Meltzer) > are missing. See the output below: > > USAGE: mri_gtmpvc > >--i inputvol : source data to PVC > --frame F : only process 0-based frame F from inputvol >--psf psfmm : scanner PSF FWHM in mm >--seg segfile : anatomical segmentation to define regions for GTM >--reg reg.lta : LTA registration file that maps anatomical to PET >--regheader : assume input and seg share scanner space >--o outdir: output directory > >--mask volfile : ignore areas outside of the mask (in input vol space) >--auto-mask FWHM thresh : automatically compute mask >--no-reduce-fov : do not reduce FoV to encompass automask >--C contrast.mtx : univariate contrast to test (ascii text file) > >--default-seg-merge : default schema for merging ROIs >--merge-hypos : merge left and right hypointensites into to ROI >--merge-cblum-wm-gyri : cerebellum WM gyri back into cerebellum WM >--tt-reduce : reduce segmentation to that of a tissue type >--replace Id1 Id2 : replace seg Id1 with seg Id2 >--replace-file : file with a list of Ids to replace >--reg-identity : assume that input is in anatomical space >--rescale Id1 : specify reference region(s) used to rescale > (default is pons) >--no-rescale : do not global rescale such that mean of reference > region is scaleref >--scale-refval refval : scale such that mean in reference region is > refval > >--no-tfe : do not correction for tissue fraction effect (with --psf 0 > turns off PVC entirely) >--rbv : perform RBV PVC >--rbv-res voxsize : set RBV voxel resolution (good for when standard > res takes too much memory) >--mg gmthresh RefId1 RefId2 ...: perform Mueller-Gaertner PVC, gmthresh > is min gm pvf bet 0 and 1 >--mg-ref-cerebral-wm : set MG RefIds to 2 and 41 >--mg-ref-lobes-wm : set MG RefIds to those for lobes when using wm > subseg >--mgx gmxthresh : GLM-based Mueller-Gaertner PVC, gmxthresh is min gm > pvf bet 0 and 1 >--km-ref RefId1 RefId2 ... : compute reference TAC for KM as mean of > given RefIds >--km-hb RefId1 RefId2 ... : compute HiBinding TAC for KM as mean of > given RefIds >--ss bpc scale dcf : steady-state analysis spec blood plasma > concentration, unit scale > and decay correction factor. You must also spec --km-ref. Turns off > rescaling > >--X : save X matrix in matlab4 format as X.mat (it will be big) >--y : save y matrix in matlab4 format as y.mat >--beta : save beta matrix in matlab4 format as beta.mat >--X0 : save X0 matrix in matlab4 format as X0.mat (it will be big) >--save-input : saves rescaled input as input.rescaled.nii.gz >--save-eres : saves residual error >--save-yhat : saves yhat >--save-yhat-with-noise seed nreps : saves yhat with noise, seed < 0 for > TOD >--save-yhat-full-fov : saves yhat in full FoV (if FoV was reduced) >--save-yhat0 : saves yhat prior to smoothing > >--synth gtmbeta C R S MBs seed nreps : synthesize volume with gtmbeta > as input >spec all other inputs the same; CRS are PSF for col, row, slice, > MBs motion blur slope >seed=0 for no noise, -1 for TOD seed. Turns on VFC for synth >but returns it to its specified value for analysis >--synth-only : exit after doing synthesis (implies --synth-save) >--synth-save : with --synth saves synthesized volume to > outd
Re: [Freesurfer] what is the argument for arguments for symmetric Geometric Transfer Matrix and two-compartment model (Meltzer Method) in the PETsurfer ?
External Email - Use Caution Thanks Douglas. I checked the mri_gtmpvc --help command but the arguments for symmetric Geometric Transfer Matrix and two-component model (Meltzer) are missing. See the output below: USAGE: mri_gtmpvc --i inputvol : source data to PVC --frame F : only process 0-based frame F from inputvol --psf psfmm : scanner PSF FWHM in mm --seg segfile : anatomical segmentation to define regions for GTM --reg reg.lta : LTA registration file that maps anatomical to PET --regheader : assume input and seg share scanner space --o outdir: output directory --mask volfile : ignore areas outside of the mask (in input vol space) --auto-mask FWHM thresh : automatically compute mask --no-reduce-fov : do not reduce FoV to encompass automask --C contrast.mtx : univariate contrast to test (ascii text file) --default-seg-merge : default schema for merging ROIs --merge-hypos : merge left and right hypointensites into to ROI --merge-cblum-wm-gyri : cerebellum WM gyri back into cerebellum WM --tt-reduce : reduce segmentation to that of a tissue type --replace Id1 Id2 : replace seg Id1 with seg Id2 --replace-file : file with a list of Ids to replace --reg-identity : assume that input is in anatomical space --rescale Id1 : specify reference region(s) used to rescale (default is pons) --no-rescale : do not global rescale such that mean of reference region is scaleref --scale-refval refval : scale such that mean in reference region is refval --no-tfe : do not correction for tissue fraction effect (with --psf 0 turns off PVC entirely) --rbv : perform RBV PVC --rbv-res voxsize : set RBV voxel resolution (good for when standard res takes too much memory) --mg gmthresh RefId1 RefId2 ...: perform Mueller-Gaertner PVC, gmthresh is min gm pvf bet 0 and 1 --mg-ref-cerebral-wm : set MG RefIds to 2 and 41 --mg-ref-lobes-wm : set MG RefIds to those for lobes when using wm subseg --mgx gmxthresh : GLM-based Mueller-Gaertner PVC, gmxthresh is min gm pvf bet 0 and 1 --km-ref RefId1 RefId2 ... : compute reference TAC for KM as mean of given RefIds --km-hb RefId1 RefId2 ... : compute HiBinding TAC for KM as mean of given RefIds --ss bpc scale dcf : steady-state analysis spec blood plasma concentration, unit scale and decay correction factor. You must also spec --km-ref. Turns off rescaling --X : save X matrix in matlab4 format as X.mat (it will be big) --y : save y matrix in matlab4 format as y.mat --beta : save beta matrix in matlab4 format as beta.mat --X0 : save X0 matrix in matlab4 format as X0.mat (it will be big) --save-input : saves rescaled input as input.rescaled.nii.gz --save-eres : saves residual error --save-yhat : saves yhat --save-yhat-with-noise seed nreps : saves yhat with noise, seed < 0 for TOD --save-yhat-full-fov : saves yhat in full FoV (if FoV was reduced) --save-yhat0 : saves yhat prior to smoothing --synth gtmbeta C R S MBs seed nreps : synthesize volume with gtmbeta as input spec all other inputs the same; CRS are PSF for col, row, slice, MBs motion blur slope seed=0 for no noise, -1 for TOD seed. Turns on VFC for synth but returns it to its specified value for analysis --synth-only : exit after doing synthesis (implies --synth-save) --synth-save : with --synth saves synthesized volume to outdir/synth.nii.gz --threads N : use N threads (with Open MP) --max-threads : use the maximum allowable number of threads for this computer --max-threads-minus-1 : use one less than the maximum allowable number of threads for this computer --sd SUBJECTS_DIR --vg-thresh thrshold : threshold for 'ERROR: LTAconcat(): LTAs 0 and 1 do not match' --gdiag diagno : set diagnostic level --debug turn on debugging --checkopts don't run anything, just check options and exit --help print out information on how to use this program --version print out version and exit Thanks, On Mon, Jan 27, 2020 at 6:03 PM Greve, Douglas N.,Ph.D. < dgr...@mgh.harvard.edu> wrote: > Run it with --help. Also look at the PETsurfer wiki page for typical usage > > On 1/27/2020 3:54 PM, Kate Marvel wrote: > > External Email - Use Caution > Hi Freesurfer community, > > I would like to know the arguments to use for symmetric Geometric Transfer > Matrix and two-compartment model (Meltzer Method) in the petsurfer > command "mri_gtmpvc". > > Thank you, > > -- > kate > > ___ > 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] what is the argument for arguments for symmetric Geometric Transfer Matrix and two-compartment model (Meltzer Method) in the PETsurfer ?
External Email - Use Caution Hi Freesurfer community, I would like to know the arguments to use for symmetric Geometric Transfer Matrix and two-compartment model (Meltzer Method) in the petsurfer command "mri_gtmpvc". Thank you, -- kate ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] how to include Schaefer atlas into freesurfer and compute surface statistics
External Email - Use Caution Thank you very much! Much appreciated Prof Leo. On Tue, Jan 14, 2020, 6:46 PM Thomas Yeo wrote: > Hi Kate, > > You can see the instructions here: > https://github.com/ThomasYeoLab/CBIG/tree/master/stable_projects/brain_parcellation/Schaefer2018_LocalGlobal/Parcellations/project_to_individual > > The gcs files will be incorporated into freesurfer at some point. > Aihuiping (cc-ed) will attach the gcs files in the next email. > > Thanks, > Thomas > > On Wed, Jan 15, 2020 at 7:40 AM Kate Marvel wrote: > >> Dear Freesurfer team, >> >> I would like to include Schaefer atlas into freesurfer. The Schaefer >> atlas can be found in the link below: >> >> >> https://github.com/ThomasYeoLab/CBIG/tree/master/stable_projects/brain_parcellation/Schaefer2018_LocalGlobal/Parcellations/FreeSurfer5.3 >> >> My question is how can I integrate the atlas in the freesurfer so that I >> can run recon-all and calculate the statistics using Schaefer >> parcellations, just like aparc_DK40 or aparc_a2009s atlases already >> pre-installed in freesurfer >> >> >> Thank you, >> >> -- >> kate >> > ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] how to include Schaefer atlas into freesurfer and compute surface statistics
External Email - Use Caution Dear Freesurfer team, I would like to include Schaefer atlas into freesurfer. The Schaefer atlas can be found in the link below: https://github.com/ThomasYeoLab/CBIG/tree/master/stable_projects/brain_parcellation/Schaefer2018_LocalGlobal/Parcellations/FreeSurfer5.3 My question is how can I integrate the atlas in the freesurfer so that I can run recon-all and calculate the statistics using Schaefer parcellations, just like aparc_DK40 or aparc_a2009s atlases already pre-installed in freesurfer Thank you, -- kate ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
