Re: [Freesurfer] freeview command line generic overlay colormap question
Dear all, I am currently trying to automatically generate Freesurfer screenshots and, to this purpose, I need to change the color scale of the surface overlay to "Color Wheel - Inverse" and with specific min and max threshold. Looking for a way to achieve this, I found this thread with similar request, but unfortunately no solution was posted. Thus Heath (who kindly replied to my email) suggested to re-post the question to the entire FreeSurfer community. So far I am able only to set the min max threshold with the following command: freeview -f $SUBJECTS_DIR/subj01/surf/lh.inflated:overlay=/pathToOverlay/MyOverlay.mgh:overlay_threshold=-10,10 Does anybody know the command line to set the overlay color scale to "Color Wheel (Inverse)"? Thank you! Any help is very much appreciated! Best regards, Anna - Anna Gardumi Department of Cognitive Neuroscience | Faculty of Psychology & Neuroscience | Maastricht University Postal address: PO Box 616, 6200MD, Maastricht, The Nederlands Visiting address: Oxfordlaan 55, room 2.012, 6229EV anna.gard...@maastrichtuniversity.nl ___ 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] mri_vol2surf Averaging with exclusion of specific values
Thanks a lot for your prompt reply and suggestion! -Original Message- From: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Douglas Greve Sent: donderdag 4 februari 2016 17:01 To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] mri_vol2surf Averaging with exclusion of specific values Hi Anna, don't use --projfrac-avg as that will average the values over the ribbon (and so give non-integer results). Just use --projfrac On 2/4/16 9:07 AM, Gardumi Anna (PSYCHOLOGY) wrote: > Dear all, > > I have checked the result of projecting a map from volume to surface with > nearest neighbor "interpolation" with the following command: > > mri_vol2surf --mov DiscreteMap.nii --reg $REGMAT --hemi lh > --projfrac-avg 0 1 0.2 --interp nearest --o > DiscreteMap_InFS_projAvg02_SurfLh.mgh > > and the resulting map does contain additional values which were not present > in the original volume map (I used a map with discrete values so that it is > easy to check for). Therefore, it seems to me that there should be at some > point of the projection pipeline an interpolation/averaging procedure. Could > you, please, clarify me where this interpolation/averaging take place when > using the option "--interp nearest" or whether I am making a mistake in the > command line? > > I still hope to be able to average across the cortex depth excluding from > such averaging voxels with a specific value (e.g. 0, which would represent > voxels for which the map is not defined). Is this possible? > > Finally, I would like to automatize taking screenshots of the resulting > surface maps. I am using the following script: > freeview -f DiscreteMap_SurfLh.mgh:overlay_threshold=-10,10 -cam > Azimuth -35 Zoom 1.5 Elevation 5 Roll 0 -ss test How can I set the colormap > to "Color Wheel" option "Inverse" (i.e. low to high values = blue to red) via > command line? > > Thank you in advance for your help! > Anna > > -Original Message- > From: Gardumi Anna (PSYCHOLOGY) > Sent: maandag 1 februari 2016 17:57 > To: 'Freesurfer support list' > Subject: RE: [Freesurfer] mri_vol2surf Averaging with exclusion of > specific values > > Thank you for your reply. > > I am then a bit confused because I thought each surface value was the result > of a two-step procedure: > 1) sampling of the values along the normal to the surface at the > points specified by the option --projfrac-avg min max del; with such > values computed according the chosen interpolation method (nearest by > default or specified by --interp nearest/trilinear); > 2) averaging of the value obtained from point 1) Is this correct? > > What I would like is the following: > 1) sampling along the normal at the nearest voxel to each point > defined by --projfrac-avg min max del (I will obtain for example five > values, let's say [1 0 1 2 2]) > 2) averaging these values excluding from the mean points having a > specific value (e.g. 0 so that I would obtain as a mean value 1.5, and > not 1.2) > > I hope this clarify my point. > > -Original Message- > From: freesurfer-boun...@nmr.mgh.harvard.edu > [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Douglas N > Greve > Sent: maandag 1 februari 2016 17:14 > To: freesurfer@nmr.mgh.harvard.edu > Subject: Re: [Freesurfer] mri_vol2surf Averaging with exclusion of > specific values > > By default, the projection is done using nearest neighbor "interpolation", so > there is no averaging. Is this what you mean? > > On 02/01/2016 09:53 AM, Gardumi Anna (PSYCHOLOGY) wrote: >> Dear FreeSurfer expert, >> >> I would like to project my maps from the "original" functional space >> (2.5mm iso, same format as COPE images from FSL) to inflated >> FreeSurfer surfaces (created from 1.0mm MPRAGE image with recon-all >> pipeline) excluding voxels with a specific value (e.g. 0) from the >> averaging procedure of the projection. The reason for this is that I >> have non-continuous maps (i.e. map values are defined only for some >> voxels; voxels for which map value is not defined will have 0 as >> value). Is there a way to perform the projection excluding voxels >> with a specific value from the averaging of the projection? >> >> Thank you in advance for any help! >> >> Anna >> >> As complementary information: >> >> My maps have discrete values (between -10 and 10) and at the moment I >> am using the following command: >> >> mri_vol2surf --mov DiscreteMap.nii --reg $REGMAT --hemi lh >> --projfrac-avg 0 1 0.2 --interp
Re: [Freesurfer] mri_vol2surf Averaging with exclusion of specific values
Dear all, I have checked the result of projecting a map from volume to surface with nearest neighbor "interpolation" with the following command: mri_vol2surf --mov DiscreteMap.nii --reg $REGMAT --hemi lh --projfrac-avg 0 1 0.2 --interp nearest --o DiscreteMap_InFS_projAvg02_SurfLh.mgh and the resulting map does contain additional values which were not present in the original volume map (I used a map with discrete values so that it is easy to check for). Therefore, it seems to me that there should be at some point of the projection pipeline an interpolation/averaging procedure. Could you, please, clarify me where this interpolation/averaging take place when using the option "--interp nearest" or whether I am making a mistake in the command line? I still hope to be able to average across the cortex depth excluding from such averaging voxels with a specific value (e.g. 0, which would represent voxels for which the map is not defined). Is this possible? Finally, I would like to automatize taking screenshots of the resulting surface maps. I am using the following script: freeview -f DiscreteMap_SurfLh.mgh:overlay_threshold=-10,10 -cam Azimuth -35 Zoom 1.5 Elevation 5 Roll 0 -ss test How can I set the colormap to "Color Wheel" option "Inverse" (i.e. low to high values = blue to red) via command line? Thank you in advance for your help! Anna -Original Message- From: Gardumi Anna (PSYCHOLOGY) Sent: maandag 1 februari 2016 17:57 To: 'Freesurfer support list' Subject: RE: [Freesurfer] mri_vol2surf Averaging with exclusion of specific values Thank you for your reply. I am then a bit confused because I thought each surface value was the result of a two-step procedure: 1) sampling of the values along the normal to the surface at the points specified by the option --projfrac-avg min max del; with such values computed according the chosen interpolation method (nearest by default or specified by --interp nearest/trilinear); 2) averaging of the value obtained from point 1) Is this correct? What I would like is the following: 1) sampling along the normal at the nearest voxel to each point defined by --projfrac-avg min max del (I will obtain for example five values, let's say [1 0 1 2 2]) 2) averaging these values excluding from the mean points having a specific value (e.g. 0 so that I would obtain as a mean value 1.5, and not 1.2) I hope this clarify my point. -Original Message- From: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Douglas N Greve Sent: maandag 1 februari 2016 17:14 To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] mri_vol2surf Averaging with exclusion of specific values By default, the projection is done using nearest neighbor "interpolation", so there is no averaging. Is this what you mean? On 02/01/2016 09:53 AM, Gardumi Anna (PSYCHOLOGY) wrote: > > Dear FreeSurfer expert, > > I would like to project my maps from the "original" functional space > (2.5mm iso, same format as COPE images from FSL) to inflated > FreeSurfer surfaces (created from 1.0mm MPRAGE image with recon-all > pipeline) excluding voxels with a specific value (e.g. 0) from the > averaging procedure of the projection. The reason for this is that I > have non-continuous maps (i.e. map values are defined only for some > voxels; voxels for which map value is not defined will have 0 as > value). Is there a way to perform the projection excluding voxels with > a specific value from the averaging of the projection? > > Thank you in advance for any help! > > Anna > > As complementary information: > > My maps have discrete values (between -10 and 10) and at the moment I > am using the following command: > > mri_vol2surf --mov DiscreteMap.nii --reg $REGMAT --hemi lh > --projfrac-avg 0 1 0.2 --interp nearest --o DiscreteMap > _InFS_projAvg02_SurfLh.mgh > > However, in this way the resulting surface map will have values biased > by including in the average also the 0 values which in reality > represents voxels not included in the map. > > > > ___ > 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 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in thi
Re: [Freesurfer] mri_vol2surf Averaging with exclusion of specific values
Thank you for your reply. I am then a bit confused because I thought each surface value was the result of a two-step procedure: 1) sampling of the values along the normal to the surface at the points specified by the option --projfrac-avg min max del; with such values computed according the chosen interpolation method (nearest by default or specified by --interp nearest/trilinear); 2) averaging of the value obtained from point 1) Is this correct? What I would like is the following: 1) sampling along the normal at the nearest voxel to each point defined by --projfrac-avg min max del (I will obtain for example five values, let's say [1 0 1 2 2]) 2) averaging these values excluding from the mean points having a specific value (e.g. 0 so that I would obtain as a mean value 1.5, and not 1.2) I hope this clarify my point. -Original Message- From: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Douglas N Greve Sent: maandag 1 februari 2016 17:14 To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] mri_vol2surf Averaging with exclusion of specific values By default, the projection is done using nearest neighbor "interpolation", so there is no averaging. Is this what you mean? On 02/01/2016 09:53 AM, Gardumi Anna (PSYCHOLOGY) wrote: > > Dear FreeSurfer expert, > > I would like to project my maps from the "original" functional space > (2.5mm iso, same format as COPE images from FSL) to inflated > FreeSurfer surfaces (created from 1.0mm MPRAGE image with recon-all > pipeline) excluding voxels with a specific value (e.g. 0) from the > averaging procedure of the projection. The reason for this is that I > have non-continuous maps (i.e. map values are defined only for some > voxels; voxels for which map value is not defined will have 0 as > value). Is there a way to perform the projection excluding voxels with > a specific value from the averaging of the projection? > > Thank you in advance for any help! > > Anna > > As complementary information: > > My maps have discrete values (between -10 and 10) and at the moment I > am using the following command: > > mri_vol2surf --mov DiscreteMap.nii --reg $REGMAT --hemi lh > --projfrac-avg 0 1 0.2 --interp nearest --o DiscreteMap > _InFS_projAvg02_SurfLh.mgh > > However, in this way the resulting surface map will have values biased > by including in the average also the 0 values which in reality > represents voxels not included in the map. > > > > ___ > 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 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ___ 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
[Freesurfer] mri_vol2surf Averaging with exclusion of specific values
Dear FreeSurfer expert, I would like to project my maps from the "original" functional space (2.5mm iso, same format as COPE images from FSL) to inflated FreeSurfer surfaces (created from 1.0mm MPRAGE image with recon-all pipeline) excluding voxels with a specific value (e.g. 0) from the averaging procedure of the projection. The reason for this is that I have non-continuous maps (i.e. map values are defined only for some voxels; voxels for which map value is not defined will have 0 as value). Is there a way to perform the projection excluding voxels with a specific value from the averaging of the projection? Thank you in advance for any help! Anna As complementary information: My maps have discrete values (between -10 and 10) and at the moment I am using the following command: mri_vol2surf --mov DiscreteMap.nii --reg $REGMAT --hemi lh --projfrac-avg 0 1 0.2 --interp nearest --o DiscreteMap _InFS_projAvg02_SurfLh.mgh However, in this way the resulting surface map will have values biased by including in the average also the 0 values which in reality represents voxels not included in the map. ___ 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.
