Re: [Freesurfer] freesurfer output
thanks a lot for your help best, hessam On Sun, Sep 24, 2017 at 6:51 PM, Bruce Fischl wrote: > Hi Hessam > > yes, check the stats subdir for each subject (e.g. stats/aseg.stats) > > cheers > Bruuce > On Sun, > 24 Sep 2017, Z Hessam wrote: > > > > > Hello FreeSurfer Developers, > > > > I can't access numerical value of each volume after segmentation of MRI > images. > > > > how can i access that? does "freesurfer" produce such value for each > segment? > > > > Best, > > > > Hessam > > > > > ___ > 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.
Re: [Freesurfer] cortical/subcortical volume based analysis
Hi Paul if you use a property (like gm) to drive intersubject registration it then becomes difficult to also analyze it. If your warp was truly perfect you could just analyze the properties of the warp, but even then it is hard to localize effects (e.g. if you changed the smoothness of the warp field would the effect move somewhere else?). If the warp is not perfect then some of the effect is in your warp and some in the residual anatomical differences. There are lots of caveats like this you have to worry about. It's the reason we drive our spherical warp with the ?h.white surface. It is invariant to gm atrophy and so can be used to assess it without worrying about this kind of thing cheers Bruce On Fri, 13 Oct 2017, miracle ozzoude wrote: Hello Bruce, Thank you for the response. I meant the latter ( making maps etc). I want to do something similar to the subcortical volume based analysis on PETSurfer page however, on freesurfer T1. Freesurfer doesn't perform VBM hence, why should there be a problem with interpretation? Best, Miracle Sent from my BlackBerry 10 smartphone. Original Message From: Bruce Fischl Sent: Friday, October 13, 2017 6:53 PM To: Freesurfer support list Reply To: Freesurfer support list Subject: Re: [Freesurfer] cortical/subcortical volume based analysis Hi Paul we typically do this type of analysis by looking at scatter plots of structure volumes (e.g. hippocampus). Alternatively, you can make maps, but that opens up all the problems/difficulties of interpretation of VBM. Which did you mean? cheers Bruce On Fri, 13 Oct 2017, miracle ozzoude wrote: Hello FreeSurfer experts, I want to perform a whole brain volume based group analysis for cortical and subcortical regions. That's something very similar to surface based group analysis for cortical thickness however, for volume. Is there a tutorial on how to do it? if yes, please can i get the link. If not, please can someone direct me how to go about doing it? My goal is to perform a group comparison between control and PD patients based on volume. Thank you very much. Best, Paul ___ 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 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] cortical/subcortical volume based analysis
Hello Bruce, Thank you very much. Can I still general cortical and subcortical maps with the Spherical warp of r/lh.white surface? If yes, please what are the steps to achieve this? can I still analyze it with mri_glm? Best, Paul Sent from my BlackBerry 10 smartphone. Original Message From: Bruce Fischl Sent: Saturday, October 14, 2017 11:27 AM To: Freesurfer support list Reply To: Freesurfer support list Subject: Re: [Freesurfer] cortical/subcortical volume based analysis Hi Paul if you use a property (like gm) to drive intersubject registration it then becomes difficult to also analyze it. If your warp was truly perfect you could just analyze the properties of the warp, but even then it is hard to localize effects (e.g. if you changed the smoothness of the warp field would the effect move somewhere else?). If the warp is not perfect then some of the effect is in your warp and some in the residual anatomical differences. There are lots of caveats like this you have to worry about. It's the reason we drive our spherical warp with the ?h.white surface. It is invariant to gm atrophy and so can be used to assess it without worrying about this kind of thing cheers Bruce On Fri, 13 Oct 2017, miracle ozzoude wrote: > Hello Bruce, > > Thank you for the response. I meant the latter ( making maps etc). I want to > do something similar to the subcortical volume based analysis on PETSurfer > page however, on freesurfer T1. Freesurfer doesn't perform VBM hence, why > should there be a problem with interpretation? > > Best, > Miracle > > Sent from my BlackBerry 10 smartphone. > Original Message > From: Bruce Fischl > Sent: Friday, October 13, 2017 6:53 PM > To: Freesurfer support list > Reply To: Freesurfer support list > Subject: Re: [Freesurfer] cortical/subcortical volume based analysis > > Hi Paul > > we typically do this type of analysis by looking at scatter plots of > structure volumes (e.g. hippocampus). Alternatively, you can make maps, > but that opens up all the problems/difficulties of interpretation of VBM. > Which did you mean? > cheers > Bruce > > On Fri, 13 Oct 2017, miracle ozzoude wrote: > >> Hello FreeSurfer experts, >> I want to perform a whole brain volume based group analysis for cortical and >> subcortical regions. >> That's something very similar to surface based group analysis for cortical >> thickness however, for >> volume. Is there a tutorial on how to do it? if yes, please can i get the >> link. If not, please can >> someone direct me how to go about doing it? My goal is to perform a group >> comparison between control >> and PD patients based on volume. Thank you very much. >> >> Best, >> Paul >> >> > > ___ > 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 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] cortical/subcortical volume based analysis
Hi Paul I guess you could use CVS for this. cheers Bruce On Sat, 14 Oct 2017, miracle ozzoude wrote: Hello Bruce, Thank you very much. Can I still general cortical and subcortical maps with the Spherical warp of r/lh.white surface? If yes, please what are the steps to achieve this? can I still analyze it with mri_glm? Best, Paul Sent from my BlackBerry 10 smartphone. Original Message From: Bruce Fischl Sent: Saturday, October 14, 2017 11:27 AM To: Freesurfer support list Reply To: Freesurfer support list Subject: Re: [Freesurfer] cortical/subcortical volume based analysis Hi Paul if you use a property (like gm) to drive intersubject registration it then becomes difficult to also analyze it. If your warp was truly perfect you could just analyze the properties of the warp, but even then it is hard to localize effects (e.g. if you changed the smoothness of the warp field would the effect move somewhere else?). If the warp is not perfect then some of the effect is in your warp and some in the residual anatomical differences. There are lots of caveats like this you have to worry about. It's the reason we drive our spherical warp with the ?h.white surface. It is invariant to gm atrophy and so can be used to assess it without worrying about this kind of thing cheers Bruce On Fri, 13 Oct 2017, miracle ozzoude wrote: Hello Bruce, Thank you for the response. I meant the latter ( making maps etc). I want to do something similar to the subcortical volume based analysis on PETSurfer page however, on freesurfer T1. Freesurfer doesn't perform VBM hence, why should there be a problem with interpretation? Best, Miracle Sent from my BlackBerry 10 smartphone. Original Message From: Bruce Fischl Sent: Friday, October 13, 2017 6:53 PM To: Freesurfer support list Reply To: Freesurfer support list Subject: Re: [Freesurfer] cortical/subcortical volume based analysis Hi Paul we typically do this type of analysis by looking at scatter plots of structure volumes (e.g. hippocampus). Alternatively, you can make maps, but that opens up all the problems/difficulties of interpretation of VBM. Which did you mean? cheers Bruce On Fri, 13 Oct 2017, miracle ozzoude wrote: Hello FreeSurfer experts, I want to perform a whole brain volume based group analysis for cortical and subcortical regions. That's something very similar to surface based group analysis for cortical thickness however, for volume. Is there a tutorial on how to do it? if yes, please can i get the link. If not, please can someone direct me how to go about doing it? My goal is to perform a group comparison between control and PD patients based on volume. Thank you very much. Best, Paul ___ 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 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] lta_convert does not produce ITK transforms that are correctly applied by antsApplyTransforms
Hi, I've used `bbregister` to generate a transform `bold2T1.lta` from `bold.nii` to `T1.mgz` (assume we have a `T1.nii` as well for the sake of ANTs). The following produces a well-aligned output: mri_convert --apply_transform bold2T1.lta bold.nii bold_space-T1.nii As does the following: lta_convert --inlta bold2T1.lta --outfsl bold2T1.mat c3d_affine_tool -ref T1.nii -src bold.nii bold2T1.mat -fsl2ras -oitk bold2T1.txt antsApplyTransforms -i bold.nii -r T1.nii -o bold_space-T1.nii -t bold2T1.txt However, if one skips the FSL step, the registration is quite far off: lta_convert --inlta bold2T1.lta --outitk bold2T1.txt antsApplyTransforms -i bold.nii -r T1.nii -o bold_space-T1.nii -t bold2T1.txt Comparing the ITK transform files: LTA-FSL-ITK #Insight Transform File V1.0 #Transform 0 Transform: MatrixOffsetTransformBase_double_3_3 Parameters: 0.9895096215486424 0.011126830936108464 -0.00042204653562094823 -0.01079971161879626 0.872329255299452 -0.42602926756857834 -0.004755964529051335 0.42420535065804454 0.8878552541301569 -1.3066136395454464 -45.60342165876236 -43.10584860730749 FixedParameters: 0 0 0 LTA-ITK #Insight Transform File V1.0 #Transform 0 Transform: AffineTransform_double_3_3 Parameters: 0.98950976133346558 0.011126830242574215 -0.00042204943019896746 -0.010799713432788849 0.87232941389083862 -0.42602935433387756 -0.0047559700906276703 0.42420542240142822 0.88785547018051147 -2.2848172187805176 -2.9065067768096924 11.744022369384766 FixedParameters: 0 0 0 To 5 significant digits, these are the same, except the last three (translation) parameters. And the `AffineTransform_double_3_3` is different from `MatrixOffsetTransformBase_double_3_3`, though I'm not sure whether this has any effect. Here is the original LTA: type = 1 # LINEAR_RAS_TO_RAS nxforms = 1 mean = 0. 0. 0. sigma = 1. 1 4 4 1.010462999343872e+00 -1.063966564834118e-02 4.625014495104551e-03 -2.332115173339844e+00 1.228639855980873e-02 9.293417930603027e-01 -4.459420144557953e-01 2.507942199707031e+00 4.575361963361502e-04 4.440840482711792e-01 9.132194519042969e-01 -1.201664733886719e+01 0.000e+00 0.000e+00 0.000e+00 9.98807907104e-01 src volume info valid = 1 # volume info valid filename = /scratch/fmriprep_wf/single_subject_02_wf/func_preproc_task_short_wf/bold_reg_wf/bbreg_wf/bbregister/uni_masked_xform.nii.gz volume = 64 64 34 voxelsize = 3.125e+00 3.125e+00 4.000e+00 xras = -1.000e+00 0.000e+00 0.000e+00 yras = 0.000e+00 1.000e+00 0.000e+00 zras = 0.000e+00 0.000e+00 1.000e+00 cras = -1.090248107910156e+00 -1.071614074707031e+01 1.619928741455078e+01 dst volume info valid = 1 # volume info valid filename = /scratch/fmriprep_wf/single_subject_02_wf/anat_preproc_wf/t1_merge/sub-02_T1w_template.nii.gz volume = 160 192 192 voxelsize = 1.000e+00 1.33015441895e+00 1.33015441895e+00 xras = 1.000e+00 0.000e+00 0.000e+00 yras = 0.000e+00 1.000e+00 0.000e+00 zras = 0.000e+00 0.000e+00 1.000e+00 cras = -3.000e+00 2.69482421875e+00 -8.30517578125e+00 subject sub-02 fscale 0.10 If it would be useful, I can provide any relevant images for testing. -- Chris Markiewicz Center for Reproducible Neuroscience Stanford University ___ 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] cortical/subcortical volume based analysis
Hello Bruce, Thank you for the response. I was able to look into CVS command and I wrote a command on how to register each subjects to cvs_avg35_inMNI152 template using the following: mri_cvs_register --mov subID --mni /Application/freesurfer/subjects/cvs_avg35_inMNI152/T1.mgz --step1 --step2 --step3 --outdir $SUBJECTS_DIR/$subID/cvs --asegfname aparc+aseg --openmp 8. Do i need to use the T1 in the mri folder or mri.2mm folder when performing mri_cvs_register? My next goals are to: 1) sample the volumes created using mri_cvs_register to the cvs_avg35_inMNI152 template using mri_vol2vol -reg . -which of the outputs from mri_cvs_register should i use to achieve? final_CVSmorphed_toTEMPLATE_norm.mgz,final_CVSmorph_toTEMPLATE.m3z, or final_CVSmorphed_toTEMPLATE_aseg.mgz 2)Use a cortical+subcortical mask from cvs_avg35_inMNI152 to smooth the output from mri_vol2vol. - How can I create the cortical mask from the cvs_avg35_inMNI152/mri.2mm folder? This is because the folder already has a subcortical mask and I want to create a cortical mask, combine both (using mri_merge) and use it to smooth with 8mm. 3) Lastly, use mri_concat to combine the smoothened maps in order to perform group level analysis on them. - when performing mri_glmfit on the combined maps, i don't need to specify the --surf fsaverage and lh/rh flags because it is a volume based analysis and it was done on MNI template not fsaverage? Thank you very much Best, Paul On Sat, Oct 14, 2017 at 12:38 PM, Bruce Fischl wrote: > Hi Paul > > I guess you could use CVS for this. > > cheers > Bruce > > On Sat, 14 Oct 2017, miracle ozzoude wrote: > > Hello Bruce, >> >> Thank you very much. Can I still general cortical and subcortical maps >> with the Spherical warp of r/lh.white surface? If yes, please what are the >> steps to achieve this? can I still analyze it with mri_glm? >> >> Best, >> Paul >> >> Sent from my BlackBerry 10 smartphone. >> Original Message >> From: Bruce Fischl >> Sent: Saturday, October 14, 2017 11:27 AM >> To: Freesurfer support list >> Reply To: Freesurfer support list >> Subject: Re: [Freesurfer] cortical/subcortical volume based analysis >> >> Hi Paul >> >> if you use a property (like gm) to drive intersubject registration it then >> becomes difficult to also analyze it. If your warp was truly perfect you >> could just analyze the properties of the warp, but even then it is hard to >> localize effects (e.g. if you changed the smoothness of the warp field >> would the effect move somewhere else?). If the warp is not perfect then >> some of the effect is in your warp and some in the residual anatomical >> differences. There are lots of caveats like this you have to worry about. >> It's the reason we drive our spherical warp with the ?h.white surface. It >> is invariant to gm atrophy and so can be used to assess it without >> worrying >> about this kind of thing >> >> cheers >> Bruce >> >> >> >> On Fri, 13 Oct 2017, miracle ozzoude wrote: >> >> Hello Bruce, >>> >>> Thank you for the response. I meant the latter ( making maps etc). I >>> want to do something similar to the subcortical volume based analysis on >>> PETSurfer page however, on freesurfer T1. Freesurfer doesn't perform VBM >>> hence, why should there be a problem with interpretation? >>> >>> Best, >>> Miracle >>> >>> Sent from my BlackBerry 10 smartphone. >>> Original Message >>> From: Bruce Fischl >>> Sent: Friday, October 13, 2017 6:53 PM >>> To: Freesurfer support list >>> Reply To: Freesurfer support list >>> Subject: Re: [Freesurfer] cortical/subcortical volume based analysis >>> >>> Hi Paul >>> >>> we typically do this type of analysis by looking at scatter plots of >>> structure volumes (e.g. hippocampus). Alternatively, you can make maps, >>> but that opens up all the problems/difficulties of interpretation of VBM. >>> Which did you mean? >>> cheers >>> Bruce >>> >>> On Fri, 13 Oct 2017, miracle ozzoude wrote: >>> >>> Hello FreeSurfer experts, I want to perform a whole brain volume based group analysis for cortical and subcortical regions. That's something very similar to surface based group analysis for cortical thickness however, for volume. Is there a tutorial on how to do it? if yes, please can i get the link. If not, please can someone direct me how to go about doing it? My goal is to perform a group comparison between control and PD patients based on volume. Thank you very much. Best, Paul >>> ___ >>> 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
[Freesurfer] How to obtain a label for Custom ROI mask
Dear all, I have custom ROI mask ( MNI Space ) that i have prepared from Jülich atlas , I would be like to obtain corresponding surface label file, Could you please guide me necessary the steps that i have to follow inorder to obtain corresponding label for my mask. Thanks Vasudev ___ 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.
