Re: [Freesurfer] number of vertices
Thanks! That number helps. Just want to get an approx. number in general. Best, Daniel -- Daniel Yang, Ph.D. Yale Child Study Center E-mail: daniel.yj.y...@yale.edu On 2/29/16, 11:52 AM, "freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Bruce Fischl" <freesurfer-boun...@nmr.mgh.harvard.edu on behalf of fis...@nmr.mgh.harvard.edu> wrote: >it's usually a bit less than that - aroudn 140K or so >Bruce > >On Mon, 29 Feb 2016, >Yang, Daniel wrote: > >> Hi Bruce, >> >> Is it okay to say that it is approximately 160,000 vertices per >> hemisphere? I found the answer from a paper >> >>(https://urldefense.proofpoint.com/v2/url?u=http-3A__www.ncbi.nlm.nih.gov >>_pmc_articles_PMC3824100_pdf_fnhum-2D07-2D00722.pdf=AwIBAg=-dg2m7zWuu >>DZ0MUcV7Sdqw=vhD8z919MORXy6GkKdTAw3V58rxzUZGOKpGXPDgqUHY=z_5IoiYhMwET >>NcHWHhQzvAvNmllYCkZY02MMWkBOj_A=0bpC-Abjox4A5ZgIdt-inwG08b5S26qYBdABg43 >>hTTo= >> ). >> >> Best, >> Daniel >> >> >___ >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 >https://urldefense.proofpoint.com/v2/url?u=http-3A__www.partners.org_compl >ianceline=AwIBAg=-dg2m7zWuuDZ0MUcV7Sdqw=vhD8z919MORXy6GkKdTAw3V58rxz >UZGOKpGXPDgqUHY=z_5IoiYhMwETNcHWHhQzvAvNmllYCkZY02MMWkBOj_A=584YcScp1G >pXgup8GDXIom4Jyraa7qyQVMN6VEMpdkg= . 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] number of vertices
Dear FreeSurfer experts, Can you please indicate the number of vertices FreeSurfer use in each hemisphere to reconstruct the brain (e.g., cortical thickness)? Is there a fixed number or an approx. number? Many thanks, Daniel -- Daniel Yang, Ph.D. Yale Child Study Center E-mail: daniel.yj.y...@yale.edu ___ 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] number of vertices
Hi Bruce, Is it okay to say that it is approximately 160,000 vertices per hemisphere? I found the answer from a paper (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3824100/pdf/fnhum-07-00722.pdf ). Best, Daniel -- Daniel Yang, Ph.D. Yale Child Study Center E-mail: daniel.yj.y...@yale.edu On 2/29/16, 11:42 AM, "freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Bruce Fischl" <freesurfer-boun...@nmr.mgh.harvard.edu on behalf of fis...@nmr.mgh.harvard.edu> wrote: >Hi Daniel > >the number of vertices will vary depending on the surface area and >geometry >of the white matter for each hemisphere. > >cheers >Bruce > > >On Mon, 29 Feb 2016, Yang, Daniel wrote: > >> Dear FreeSurfer experts, >> >> Can you please indicate the number of vertices FreeSurfer use in each >>hemisphere to reconstruct the brain (e.g., cortical >> thickness)? Is there a fixed number or an approx. number? >> >> Many thanks, >> Daniel >> >> -- >> Daniel Yang, Ph.D. >> Yale Child Study Center >> E-mail: daniel.yj.y...@yale.edu >> ___ 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_convert and image orientation
Just to note for people who are interested: It does seem that when voxel-to-ras determinant > 0, then the file is neurological. -- Daniel Yang, Ph.D. Yale Child Study Center E-mail: daniel.yj.y...@yale.edu On 1/26/16, 10:09 PM, "Yang, Daniel" <daniel.yj.y...@yale.edu> wrote: >Thanks so much, I see that voxel-to-ras determinant is -1 in my file, so >it’s most likely to be radiological. > >Just curious, so determinant > 0 means neurological then? > >Daniel > > >-- >Daniel Yang, Ph.D. >Yale Child Study Center > >E-mail: daniel.yj.y...@yale.edu > > > > >On 1/26/16, 4:26 PM, "freesurfer-boun...@nmr.mgh.harvard.edu on behalf of >Douglas N Greve" <freesurfer-boun...@nmr.mgh.harvard.edu on behalf of >gr...@nmr.mgh.harvard.edu> wrote: > >>If the determinant is less than 0, then it is radiological (probably it >>will be radiological). >> >>On 01/26/2016 04:20 PM, Yang, Daniel wrote: >>> Dear Doug, >>> >>> Thanks for your reply. Is it possible to upload the raw DICOM to a >>>server >>> so that you can see if mri_convert is making the orientation in the >>>output >>> NII file neurological? I just want to make sure what my image >>>orientation >>> is and how mri_convert interacts with it. >>> >>> Many thanks! >>> Daniel >>> >>> >> >>-- >>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 >>https://urldefense.proofpoint.com/v2/url?u=http-3A__www.partners.org_comp >>l >>ianceline=AwIBAg=-dg2m7zWuuDZ0MUcV7Sdqw=vhD8z919MORXy6GkKdTAw3V58rx >>z >>UZGOKpGXPDgqUHY=WLltv6OcAkXClyk0AkG4dpyu2SPQluAJ6oEiH94MutM=TD-7P7Mmd >>H >>yxRXXCDN_76DHGG7ZDDwckhxJfe-wp-cU= . 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] mri_convert and image orientation
Dear Doug, Thanks for your reply. Is it possible to upload the raw DICOM to a server so that you can see if mri_convert is making the orientation in the output NII file neurological? I just want to make sure what my image orientation is and how mri_convert interacts with it. Many thanks! Daniel -- Daniel Yang, Ph.D. Yale Child Study Center E-mail: daniel.yj.y...@yale.edu On 1/25/16, 1:47 PM, "freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Douglas N Greve" <freesurfer-boun...@nmr.mgh.harvard.edu on behalf of gr...@nmr.mgh.harvard.edu> wrote: >not necessarily. For FSL, the determinant must be less than 0 (see >mri_info output). Having said that, even if the det<0, it may still show >up funny in fslview > >On 01/25/2016 12:11 PM, Yang, Daniel wrote: >> Dear FreeSurfer experts, >> >> I find that mri_convert will convert DICOM of structural scan to >> neurological orientation by default. >> >> For example, mri_convert --in_type dicom --out_type mii > the DICOM directory> >> >> Thus, the NII may need to be swapped in x for use in FSL. >> >> In this the case? >> >> Many thanks, >> Daniel >> >> -- >> Daniel Yang, Ph.D. >> Yale Child Study Center >> E-mail: daniel.yj.y...@yale.edu >> >> >> ___ >> 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 >https://urldefense.proofpoint.com/v2/url?u=http-3A__www.partners.org_compl >ianceline=AwIBAg=-dg2m7zWuuDZ0MUcV7Sdqw=vhD8z919MORXy6GkKdTAw3V58rxz >UZGOKpGXPDgqUHY=vPCUh0LHBB0FFqxEXa3WMuAGE7_uhojBsOWMI4IcGCE=hHbJW-rVbK >tbdsFRHLaY0s9EKUtssTAJmRyP2VVqzUE= . 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] mri_convert and image orientation
Thanks so much, I see that voxel-to-ras determinant is -1 in my file, so it’s most likely to be radiological. Just curious, so determinant > 0 means neurological then? Daniel -- Daniel Yang, Ph.D. Yale Child Study Center E-mail: daniel.yj.y...@yale.edu On 1/26/16, 4:26 PM, "freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Douglas N Greve" <freesurfer-boun...@nmr.mgh.harvard.edu on behalf of gr...@nmr.mgh.harvard.edu> wrote: >If the determinant is less than 0, then it is radiological (probably it >will be radiological). > >On 01/26/2016 04:20 PM, Yang, Daniel wrote: >> Dear Doug, >> >> Thanks for your reply. Is it possible to upload the raw DICOM to a >>server >> so that you can see if mri_convert is making the orientation in the >>output >> NII file neurological? I just want to make sure what my image >>orientation >> is and how mri_convert interacts with it. >> >> Many thanks! >> Daniel >> >> > >-- >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 >https://urldefense.proofpoint.com/v2/url?u=http-3A__www.partners.org_compl >ianceline=AwIBAg=-dg2m7zWuuDZ0MUcV7Sdqw=vhD8z919MORXy6GkKdTAw3V58rxz >UZGOKpGXPDgqUHY=WLltv6OcAkXClyk0AkG4dpyu2SPQluAJ6oEiH94MutM=TD-7P7MmdH >yxRXXCDN_76DHGG7ZDDwckhxJfe-wp-cU= . 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] mri_convert and image orientation
Dear FreeSurfer experts, I find that mri_convert will convert DICOM of structural scan to neurological orientation by default. For example, mri_convert --in_type dicom --out_type mii Thus, the NII may need to be swapped in x for use in FSL. In this the case? Many thanks, Daniel -- Daniel Yang, Ph.D. Yale Child Study Center E-mail: daniel.yj.y...@yale.edu ___ 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] TalX TalY TalZ
Thanks, Doug! Got it. So FreeSurfer registers the individual scans to the MNI305 atlas but mri_surfcluster reports approx. Talairach coordinates with the default option: —fixmni I was a little bit confused because this website (https://surfer.nmr.mgh.harvard.edu/fswiki/CoordinateSystems) says that the following: "Note on Talairach: FreeSurfer<https://surfer.nmr.mgh.harvard.edu/fswiki/FreeSurfer> does not report true "Talairach" coordinates. The coordinates listed unter "Talairach" are actually based on Matthew Brett's 10/8/98 non-linear transform from MNI305 space (see http://www.mrc-cbu.cam.ac.uk/Imaging/mnispace.html). FreeSurfer<https://surfer.nmr.mgh.harvard.edu/fswiki/FreeSurfer> also reports "Talairach MNI" coordinates. These are MNI305 space.” If my understanding is correct, by default, the “Talairach” coordinates reported by mri_surfcluster (with —fixmni) are non-linear transformation from the MNI305 space; they are approx. Talairach coord as you suggested. And If I ever use —nofixmni, then it is what is internally used by FreeSurfer, the MNI305 space, or the "Talairach MNI” coordinates. Is the understanding above correct? Thanks! -- Daniel Yang, Ph.D. Yale Child Study Center E-mail: daniel.yj.y...@yale.edu From: <freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>> on behalf of Douglas Greve <gr...@nmr.mgh.harvard.edu<mailto:gr...@nmr.mgh.harvard.edu>> Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>> Date: Wednesday, November 11, 2015 at 11:01 AM To: "freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>" <freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>> Subject: Re: [Freesurfer] TalX TalY TalZ If you use --fixmni, then they are reported in approximate talairach space On 11/11/15 10:08 AM, Yang, Daniel wrote: Dear FreeSurfer Experts, Are these coordinates reported in mri_surfcluster in MNI305 space? (with —fixmni) Thanks, Daniel -- Daniel Yang, Ph.D. Yale Child Study Center E-mail: daniel.yj.y...@yale.edu<mailto:daniel.yj.y...@yale.edu> ___ 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 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] TalX TalY TalZ
Dear FreeSurfer Experts, Are these coordinates reported in mri_surfcluster in MNI305 space? (with —fixmni) Thanks, Daniel -- Daniel Yang, Ph.D. Yale Child Study Center E-mail: daniel.yj.y...@yale.edu ___ 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_surfcluster statistics and label question
Thanks! The F.mgh works well, and it also increases precision as converting from the exponent itself is less precise. -- Daniel Yang, Ph.D. Yale Child Study Center E-mail: daniel.yj.y...@yale.edu On 11/9/15, 10:57 PM, "freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Douglas Greve" <freesurfer-boun...@nmr.mgh.harvard.edu on behalf of gr...@nmr.mgh.harvard.edu> wrote: >There should be a t.mgh file there (or maybe F.mgh). You can just pull >the value out of the vertex out of that. > >On 11/9/15 6:46 PM, Yang, Daniel wrote: >> Hi Doug, >> >> Got it! Sorry that I keep forgetting this. So it’s an exponent >>statistic. >> >> The reviewers asked for a statistic and df. I think I can convert it to >>a >> Z-statistic so it’s more “conventional”. >> >> I also noticed that qdec provides a df when I set up the model. It is >> valid to use that df to derive the t-statistic? >> >> Best, >> Daniel >> > >___ >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 >https://urldefense.proofpoint.com/v2/url?u=http-3A__www.partners.org_compl >ianceline=AwIGaQ=-dg2m7zWuuDZ0MUcV7Sdqw=vhD8z919MORXy6GkKdTAw3V58rxz >UZGOKpGXPDgqUHY=0RrRr1_vfqKidnHFsGCektDHjSDuECMNGanFYSOjE8w=Go4hBLGpzA >KSdkn0TGgNfAvJpyToUgrusCYlC8IFuAY= . 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] convert label to mgh
Dear FreeSurfer Experts, Is it possible to convert a label file to a surface-based mgh file? Could you please provide an example (e.g., on a white surface)? Best, Daniel -- Daniel Yang, Ph.D. Yale Child Study Center E-mail: daniel.yj.y...@yale.edu ___ 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] mri_surfcluster statistics and label question
Dear FreeSurfer experts, In the output mri_surfcluster (e.g., https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysisClusterSummary), what is the statistics behind the Max? Is it either t-statistic (if only 1 line of contrast) or F-statistic (if two lines of contrast), but not Z-statistics? Also, I notice that the annotation is picking only one of the anatomical regions in which the cluster is located. Is it possible to tell all the anatomical regions that a label has? Thanks, Daniel -- Daniel Yang, Ph.D. Yale Child Study Center E-mail: daniel.yj.y...@yale.edu ___ 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] convert label to mgh
Hi Doug, Thanks a lot! The --outmask option appears to be working well!! Best, Daniel -- Daniel Yang, Ph.D. Yale Child Study Center E-mail: daniel.yj.y...@yale.edu On 11/9/15, 1:47 PM, "freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Douglas N Greve" <freesurfer-boun...@nmr.mgh.harvard.edu on behalf of gr...@nmr.mgh.harvard.edu> wrote: >use mri_label2label with the --mask option > >On 11/09/2015 01:34 PM, Yang, Daniel wrote: >> Dear FreeSurfer Experts, >> >> Is it possible to convert a label file to a surface-based mgh file? >> Could you please provide an example (e.g., on a white surface)? >> >> Best, >> Daniel >> -- >> Daniel Yang, Ph.D. >> Yale Child Study Center >> E-mail: daniel.yj.y...@yale.edu >> >> >> ___ >> 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 >https://urldefense.proofpoint.com/v2/url?u=http-3A__www.partners.org_compl >ianceline=AwIBAg=-dg2m7zWuuDZ0MUcV7Sdqw=vhD8z919MORXy6GkKdTAw3V58rxz >UZGOKpGXPDgqUHY=Kr91S3CtdbKsoaxf82Rfxr2bZFg9YfCZZ0pXvsVVPDE=XWnWWKLBt8 >zJAFoKWkwdoWZB3ADPCwh_q5na-xaPmmY= . 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] mri_surfcluster statistics and label question
Hi Doug, Got it! Sorry that I keep forgetting this. So it’s an exponent statistic. The reviewers asked for a statistic and df. I think I can convert it to a Z-statistic so it’s more “conventional”. I also noticed that qdec provides a df when I set up the model. It is valid to use that df to derive the t-statistic? Best, Daniel -- Daniel Yang, Ph.D. Yale Child Study Center E-mail: daniel.yj.y...@yale.edu On 11/9/15, 6:02 PM, "freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Douglas N Greve" <freesurfer-boun...@nmr.mgh.harvard.edu on behalf of gr...@nmr.mgh.harvard.edu> wrote: > > >On 11/09/2015 10:51 AM, Yang, Daniel wrote: >> Dear FreeSurfer experts, >> >> In the output mri_surfcluster (e.g., >> >>https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysisCluster >>Summary), >> what is the statistics behind the Max? >> >> Is it either t-statistic (if only 1 line of contrast) or F-statistic >> (if two lines of contrast), but not Z-statistics? >it is the maximum of the abs(-log10(p)) ___ 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] Curvilinear interaction with age
Thanks so much for your help! -- Daniel Yang, Ph.D. Yale Child Study Center E-mail: daniel.yj.y...@yale.edu On 11/6/15, 9:23 PM, "freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Martin Reuter" <freesurfer-boun...@nmr.mgh.harvard.edu on behalf of mreu...@nmr.mgh.harvard.edu> wrote: >Hi Daniel, > >you can always specify your own design matrix X in mri_glmfit. So just >create those columns, fit and test. Of course you need to make sure that >the order of subjects in Y is identical with the one used in X. > >Cheers, Martin > >On 11/06/2015 06:14 PM, Yang, Daniel wrote: >> Dear FreeSurfer experts, >> >> I have a group variable (X) with two levels and I want to test if there >>is a curvilinear interaction with age (Z). Can this be tested in >>FreeSurfer? >> >> Specifically, the model would be >> >> Y = b0 + b1X + b2Z + b3Z*Z + b4X*Z + b5X*Z*Z + error >> >> I want to test b5 while controlling for b0-b4. >> >> Many thanks! >> Daniel >> ___ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> > >-- >Martin Reuter, PhD >Assistant Professor of Radiology, Harvard Medical School >Assistant Professor of Neurology, Harvard Medical School >A.A.Martinos Center for Biomedical Imaging >Massachusetts General Hospital >Research Affiliate, CSAIL, MIT >Phone: +1-617-724-5652 >Web : >https://urldefense.proofpoint.com/v2/url?u=http-3A__reuter.mit.edu=AwIBA >g=-dg2m7zWuuDZ0MUcV7Sdqw=vhD8z919MORXy6GkKdTAw3V58rxzUZGOKpGXPDgqUHY >=cb9CorGJuJmEK4aPCmFuaMdl2fQb1F9u09ewaw0BJp8=ab1OEzviyC2H214Ar7pPsOizune >Nf70N_HSA6GFF4gs= > >___ >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 >https://urldefense.proofpoint.com/v2/url?u=http-3A__www.partners.org_compl >ianceline=AwIBAg=-dg2m7zWuuDZ0MUcV7Sdqw=vhD8z919MORXy6GkKdTAw3V58rxz >UZGOKpGXPDgqUHY=cb9CorGJuJmEK4aPCmFuaMdl2fQb1F9u09ewaw0BJp8=9RthKtMjgu >qEGVWRB4PMDWnDdltdzCG2x7QjEwnI4iU= . 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] Curvilinear interaction with age
Dear FreeSurfer experts, I have a group variable (X) with two levels and I want to test if there is a curvilinear interaction with age (Z). Can this be tested in FreeSurfer? Specifically, the model would be Y = b0 + b1X + b2Z + b3Z*Z + b4X*Z + b5X*Z*Z + error I want to test b5 while controlling for b0-b4. Many thanks! Daniel ___ 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] aparcstats2table
Dear FreeSurfer Experts, When I perform aparcstats2table —meas area, does it get it pial.area or white area? I believe it is the pial.area, but this is not documented. If yes, what can I obtain white area via aparcstats2table? Thanks, Daniel -- Daniel Yang, Ph.D. Yale Child Study Center E-mail: daniel.yj.y...@yale.edu ___ 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] how to obtain individual's pial_lgi value
Hi all, Found an answer here: https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2014-March/036542.html It works for me! Best, Daniel From:> on behalf of Daniel Yang > Reply-To: Freesurfer support list > Date: Wednesday, November 4, 2015 at 3:30 PM To: Freesurfer support list > Subject: [Freesurfer] how to obtain individual's pial_lgi value Dear FreeSurfer Experts, When I specify --measure pial_lgi, aparcstats2table says it’s an invalid option. Could you please advise how I can obtain an individual’s pial_lgi value, give a label? Many thanks! Daniel ___ 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] how to obtain individual's pial_lgi value
Dear FreeSurfer Experts, When I specify --measure pial_lgi, aparcstats2table says it’s an invalid option. Could you please advise how I can obtain an individual’s pial_lgi value, give a label? Many thanks! Daniel ___ 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] stat/math tools for MGH file
Dear FreeSurfer experts, I have a number of *.cluster.mgh files and I would like to calculate their difference and peak coordinate etc like in fslmaths or fslstats in FSL. For example, given two images, I want to know the brain regions in image1 but not in image2. Could you please recommend the general command line tools I can use for these purposes? Many thanks, Daniel ___ 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] stat/math tools for MGH file
Hi Bruce, Yes, that’s perfect! Thanks for the reply!! :) Best, Daniel On 11/2/15, 8:48 PM, "freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Bruce Fischl" <freesurfer-boun...@nmr.mgh.harvard.edu on behalf of fis...@nmr.mgh.harvard.edu> wrote: >Hi Daniel > >you can always convert to nifti via: > >mri_convert cluster.mgh cluster.nii > >and you will be able to use the FSL tools > >cheers >Bruce > > >On Tue, 3 Nov 2015, Yang, Daniel >wrote: > >> Dear FreeSurfer experts, >> >> I have a number of *.cluster.mgh files and I would like to calculate >>their >> difference and peak coordinate etc like in fslmaths or fslstats in FSL. >> >> For example, given two images, I want to know the brain regions in >>image1 >> but not in image2. >> >> Could you please recommend the general command line tools I can use for >> these purposes? >> >> Many thanks, >> Daniel >> >> >> >> >___ >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 >https://urldefense.proofpoint.com/v2/url?u=http-3A__www.partners.org_compl >ianceline=AwIBAg=-dg2m7zWuuDZ0MUcV7Sdqw=vhD8z919MORXy6GkKdTAw3V58rxz >UZGOKpGXPDgqUHY=xYv-TPUIzaxdOU0_l0VVahSrl6jSBd6Rbsb4dfB0Jak=uRT7WmDS-H >I2mX7rEaBPdsfzQTjJgPVdORtlxQzhgvw= . 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] how to obtain sulcal depth in a given region for a specific subject
Thanks so much for your help!! - Daniel On 8/6/15, 3:06 PM, freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Bruce Fischl freesurfer-boun...@nmr.mgh.harvard.edu on behalf of fis...@nmr.mgh.harvard.edu wrote: ignore grayvol, the other two will be the mean and standard deviation of the sulc cheers Bruce On Thu, 6 Aug 2015, Yang, Daniel wrote: Hi Bruce, Thanks so much! From the output of mris_anatomical_stats, I can see that it affects the following three variables: GrayVol ThickAvg ThickStd When sulc is used instead of thickness, do you know what the meaning of these three variables is changed to? Many thanks, Daniel On 8/6/15, 1:35 PM, freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Bruce Fischl freesurfer-boun...@nmr.mgh.harvard.edu on behalf of fis...@nmr.mgh.harvard.edu wrote: sure, you can use mris_anatomical_stats with the label (-l) and specify sulc instead of thickness on the command line Bruce On Thu, 6 Aug 2015, Yang, Daniel wrote: Dear FreeSurfer Experts, Is there a way to obtain sulcal depth in a given region (label) for a particular subject? Many thanks! Daniel ___ 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 https://urldefense.proofpoint.com/v2/url?u=http-3A__www.partners.org_com pl iancelined=AwIBAgc=-dg2m7zWuuDZ0MUcV7Sdqwr=vhD8z919MORXy6GkKdTAw3V58r xz UZGOKpGXPDgqUHYm=xyE0RdUufB5jqZcisLNchEsdjJ5ZrxPKb_nS1NUHf6As=f9y2eo81 NI x6DddRv7BfTBuLWMoaGFQAWMNMlqXCD7se= . 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 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 https://urldefense.proofpoint.com/v2/url?u=http-3A__www.partners.org_compl iancelined=AwIBAgc=-dg2m7zWuuDZ0MUcV7Sdqwr=vhD8z919MORXy6GkKdTAw3V58rxz UZGOKpGXPDgqUHYm=MGg2posyaqsYcBQNPMfU8se8ukFgyZ7f-Oe0LQdl9aAs=yl0bAVXLDZ -FAqiDaW-T036lJiy1KcmDmqmve98TXQce= . 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] how to obtain sulcal depth in a given region for a specific subject
Dear FreeSurfer Experts, Is there a way to obtain sulcal depth in a given region (label) for a particular subject? Many thanks! Daniel ___ 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] how to obtain sulcal depth in a given region for a specific subject
Hi Bruce, Thanks so much! From the output of mris_anatomical_stats, I can see that it affects the following three variables: GrayVol ThickAvg ThickStd When sulc is used instead of thickness, do you know what the meaning of these three variables is changed to? Many thanks, Daniel On 8/6/15, 1:35 PM, freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Bruce Fischl freesurfer-boun...@nmr.mgh.harvard.edu on behalf of fis...@nmr.mgh.harvard.edu wrote: sure, you can use mris_anatomical_stats with the label (-l) and specify sulc instead of thickness on the command line Bruce On Thu, 6 Aug 2015, Yang, Daniel wrote: Dear FreeSurfer Experts, Is there a way to obtain sulcal depth in a given region (label) for a particular subject? Many thanks! Daniel ___ 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 https://urldefense.proofpoint.com/v2/url?u=http-3A__www.partners.org_compl iancelined=AwIBAgc=-dg2m7zWuuDZ0MUcV7Sdqwr=vhD8z919MORXy6GkKdTAw3V58rxz UZGOKpGXPDgqUHYm=xyE0RdUufB5jqZcisLNchEsdjJ5ZrxPKb_nS1NUHf6As=f9y2eo81NI x6DddRv7BfTBuLWMoaGFQAWMNMlqXCD7se= . 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] visualize subcortical areas in tksurfer?
Thanks, Bruce!! Daniel On Feb 23, 2015, at 8:23 AM, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: Hi Daniel I wouldn't advise this - you will miss most of the activation unless it happens to be right next to where the surface runs adjacent to the structure of interest. For subcortical structures you are better off showing the results in slices. cheers Bruce On Mon, 23 Feb 2015, Yang, Daniel wrote: Hi Bruce, Thanks for the reply. My main question is how to best visualize subcortical activation in a figure. Sometimes we do see some subcortical activation (like the attached, which is a random search) (if the attachment does not work, please see the examplehere: https://urldefense.proofpoint.com/v2/url?u=http-3A__www.frontiersin.org_files_Articles_18483_fnhum-2D06-2D00021-2DHTML_d=AwIDaQc=-dg2m7zWuuDZ0MUcV7Sdqwr=vhD8z919MORXy6GkKdTAw3V58rxzUZGOKpGXPDgqUHYm=FY2aLrzWyEp88KG_1MRXz7kOCWAb3NfLU7iRz6Ftg_4s=AsAyDkBwKH1FHSCReHATnZnHPXl7wm3478H1viSUbpce= image_m/fnhum-06-00021-g003.jpg). Is it okay to visualize such subcortical activation via tksurfer? If not, could you please recommend a method to visualize subcortical activation? Sincerely, Daniel On 2/20/15, 9:06 AM, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: HI Daniel no, that won't work. Vol2surf samples a volume to an existig surface and none of the subcortical structures will be anywere near the cortical surface. You would need to run mri_tessellate on each subcortical label that you want to generate a surface for, but I'm still not sure what you are trying to do. cheers Bruce On Fri, 20 Feb 2015, Yang, Daniel wrote: Hi Bruce, Thanks! and yes, I used mri_vol2surf to convert subcortical region as a volume file to surface (mgh file) and then visualize it with tksurfer. According to what you said, this is still valid, right? Best, Daniel On 2/19/15, 5:59 PM, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: Hi Daniel no, tksurfer visualizes surfaces exclusively, and the subcortical structures are volumetric by and large. You could tesselate their surface and view it in tksurfer, or just use tkmediit or freeview. cheers Bruce On Thu, 19 Feb 2015, Yang, Daniel wrote: Dear FreeSurfer experts, I find that tksurfer allows me to visualize subcortical areas such as hippocampus. The visualization looks valid to me. Can tksurfer be used in this way? Thanks!! Daniel ___ 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 https://urldefense.proofpoint.com/v2/url?u=http-3A__www.partners.org_compl iancelined=AwIBAgc=-dg2m7zWuuDZ0MUcV7Sdqwr=vhD8z919MORXy6GkKdTAw3V58rxz UZGOKpGXPDgqUHYm=GwXYm_UFsMTK666w58RNVUgITnGz6y7wSvA4OWe3VDIs=X6YOsg4F5k hF6_1eRhIIXjcpNfRIveb8xbtz9jVs7Rke= . 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 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 https://urldefense.proofpoint.com/v2/url?u=http-3A__www.partners.org_compli ancelined=AwIBAgc=-dg2m7zWuuDZ0MUcV7Sdqwr=vhD8z919MORXy6GkKdTAw3V58rxzUZ GOKpGXPDgqUHYm=cue78znVQSK09ZAzgx1bpMEP_Q1FH_tPiP6u951nI6Is=FTUF8bxfkijut U0D90a6nXk4E6QXECVzI7RktBWSD04e= . 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 https://urldefense.proofpoint.com/v2/url?u=http-3A__www.partners.org_compliancelined=AwIBAgc=-dg2m7zWuuDZ0MUcV7Sdqwr=vhD8z919MORXy6GkKdTAw3V58rxzUZGOKpGXPDgqUHYm=FY2aLrzWyEp88KG_1MRXz7kOCWAb3NfLU7iRz6Ftg_4s=ezWokB_ADNk3taLpmFv9QYfWH3gqVBCuqJA-NL9WIT8e= . If the e-mail was sent to you in error but does
Re: [Freesurfer] visualize subcortical areas in tksurfer?
Hi Bruce, Thanks for the reply. My main question is how to best visualize subcortical activation in a figure. Sometimes we do see some subcortical activation (like the attached, which is a random search) (if the attachment does not work, please see the example here: http://www.frontiersin.org/files/Articles/18483/fnhum-06-00021-HTML/image_m/fnhum-06-00021-g003.jpg). Is it okay to visualize such subcortical activation via tksurfer? If not, could you please recommend a method to visualize subcortical activation? Sincerely, Daniel On 2/20/15, 9:06 AM, Bruce Fischl fis...@nmr.mgh.harvard.edumailto:fis...@nmr.mgh.harvard.edu wrote: HI Daniel no, that won't work. Vol2surf samples a volume to an existig surface and none of the subcortical structures will be anywere near the cortical surface. You would need to run mri_tessellate on each subcortical label that you want to generate a surface for, but I'm still not sure what you are trying to do. cheers Bruce On Fri, 20 Feb 2015, Yang, Daniel wrote: Hi Bruce, Thanks! and yes, I used mri_vol2surf to convert subcortical region as a volume file to surface (mgh file) and then visualize it with tksurfer. According to what you said, this is still valid, right? Best, Daniel On 2/19/15, 5:59 PM, Bruce Fischl fis...@nmr.mgh.harvard.edumailto:fis...@nmr.mgh.harvard.edu wrote: Hi Daniel no, tksurfer visualizes surfaces exclusively, and the subcortical structures are volumetric by and large. You could tesselate their surface and view it in tksurfer, or just use tkmediit or freeview. cheers Bruce On Thu, 19 Feb 2015, Yang, Daniel wrote: Dear FreeSurfer experts, I find that tksurfer allows me to visualize subcortical areas such as hippocampus. The visualization looks valid to me. Can tksurfer be used in this way? Thanks!! Daniel ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto: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 https://urldefense.proofpoint.com/v2/url?u=http-3A__www.partners.org_compl iancelined=AwIBAgc=-dg2m7zWuuDZ0MUcV7Sdqwr=vhD8z919MORXy6GkKdTAw3V58rxz UZGOKpGXPDgqUHYm=GwXYm_UFsMTK666w58RNVUgITnGz6y7wSvA4OWe3VDIs=X6YOsg4F5k hF6_1eRhIIXjcpNfRIveb8xbtz9jVs7Rke= . 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.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto: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 https://urldefense.proofpoint.com/v2/url?u=http-3A__www.partners.org_compliancelined=AwIBAgc=-dg2m7zWuuDZ0MUcV7Sdqwr=vhD8z919MORXy6GkKdTAw3V58rxzUZGOKpGXPDgqUHYm=cue78znVQSK09ZAzgx1bpMEP_Q1FH_tPiP6u951nI6Is=FTUF8bxfkijutU0D90a6nXk4E6QXECVzI7RktBWSD04e= . 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] extract individual label from Destrieux Atlas
Dear FreeSurfer experts, The following command works but how do I get the labels from —a2009s ? mri_annotation2label --a2005s --subject fsaverage --hemi rh --outdir . What is the difference between a2005s and a2009s? Thanks! Daniel ___ 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] extract individual label from Destrieux Atlas
Thanks!! From: Douglas Greve gr...@nmr.mgh.harvard.edumailto:gr...@nmr.mgh.harvard.edu Reply-To: Freesurfer support list freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu Date: Thursday, February 19, 2015 at 3:18 PM To: freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] extract individual label from Destrieux Atlas Use --annotation a2009s.aparc On 2/19/15 8:34 PM, Yang, Daniel wrote: Dear FreeSurfer experts, The following command works but how do I get the labels from —a2009s ? mri_annotation2label --a2005s --subject fsaverage --hemi rh --outdir . What is the difference between a2005s and a2009s? Thanks! Daniel ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@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] visualize subcortical areas in tksurfer?
Dear FreeSurfer experts, I find that tksurfer allows me to visualize subcortical areas such as hippocampus. The visualization looks valid to me. Can tksurfer be used in this way? Thanks!! Daniel ___ 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] visualize subcortical areas in tksurfer?
Hi Bruce, Thanks! and yes, I used mri_vol2surf to convert subcortical region as a volume file to surface (mgh file) and then visualize it with tksurfer. According to what you said, this is still valid, right? Best, Daniel On 2/19/15, 5:59 PM, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: Hi Daniel no, tksurfer visualizes surfaces exclusively, and the subcortical structures are volumetric by and large. You could tesselate their surface and view it in tksurfer, or just use tkmediit or freeview. cheers Bruce On Thu, 19 Feb 2015, Yang, Daniel wrote: Dear FreeSurfer experts, I find that tksurfer allows me to visualize subcortical areas such as hippocampus. The visualization looks valid to me. Can tksurfer be used in this way? Thanks!! Daniel ___ 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 https://urldefense.proofpoint.com/v2/url?u=http-3A__www.partners.org_compl iancelined=AwIBAgc=-dg2m7zWuuDZ0MUcV7Sdqwr=vhD8z919MORXy6GkKdTAw3V58rxz UZGOKpGXPDgqUHYm=GwXYm_UFsMTK666w58RNVUgITnGz6y7wSvA4OWe3VDIs=X6YOsg4F5k hF6_1eRhIIXjcpNfRIveb8xbtz9jVs7Rke= . 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] mri_label2label results
Dear all, I found that mri_label2label generates different results, depending on whether the software’s platform is MacOS Lion or CentOS 6. Is this possible? Thanks! Daniel ___ 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_label2label results
Ah, it¹s FreeSurfer 5.3 ‹ Release Date 15 May 2013. Do you mean that the FreeSurfer 5.3 was updated after 05/15/2013? Thanks, Daniel On 6/19/14, 7:55 PM, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: what version are you using? I think this is a bug we fixed a few months ago. Or another one Bruce On Thu, 19 Jun 2014, Yang, Daniel wrote: Dear all, I found that mri_label2label generates different results, depending on whether the software¹s platform is MacOS Lion or CentOS 6. Is this possible? Thanks! Daniel ___ 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_label2label results
I just tried a few different versions of FreeSurfer. Here are the results: 1. FreeSurfer-5.3 (Linux, CentOS 6, Release: 05/15/2013) 2. FreeSurfer-5.3 (Darwin, Lion, Release: 05/15/2013) 3. FreeSurfer-dev (Linux, CentOS 6, 06/19/2014) 4. FreeSurfer-dev (Darwin, Lion, 06/19/2014) I am comparing the results of mri_label2label and then mris_anatomical_stats here. The results of 3 and 4 are the same The results of 1 and 2 are different The results of 1 and 3 are different The results or 2 and 4 are different In my testing, I used an arbitrary label file and here is detail information of area, volume, thickness, thicknessstd, meancurv, gauscurv, foldind, and curvind 1: 1261.0,4900.0,2.763,0.818,0.145,0.048,28.0,3.7 2: 1109.0,4343.0,2.761,0.798,0.15,0.046,23.0,2.8 3: 1261.0,4900.0,2.763,0.818,0.132,0.032,22.0,2.3 4: 1261.0,4900.0,2.763,0.818,0.132,0.032,22.0,2.3 What should we do here? Is the difference between 1 and 3 trivial? Thanks! Daniel On 6/19/14, 8:13 PM, Yang, Daniel yung-jui.y...@yale.edumailto:yung-jui.y...@yale.edu wrote: Ah, it¹s FreeSurfer 5.3 ‹ Release Date 15 May 2013. Do you mean that the FreeSurfer 5.3 was updated after 05/15/2013? Thanks, Daniel On 6/19/14, 7:55 PM, Bruce Fischl fis...@nmr.mgh.harvard.edumailto:fis...@nmr.mgh.harvard.edu wrote: what version are you using? I think this is a bug we fixed a few months ago. Or another one Bruce On Thu, 19 Jun 2014, Yang, Daniel wrote: Dear all, I found that mri_label2label generates different results, depending on whether the software¹s platform is MacOS Lion or CentOS 6. Is this possible? Thanks! Daniel ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto: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] mri_label2label results
Thanks! Is there a list of bug fixed (after release) somewhere? Should we use the development version instead? Please tell me that it is only mri_label2label that has a bug … On 6/19/14, 9:08 PM, Bruce Fischl fis...@nmr.mgh.harvard.edumailto:fis...@nmr.mgh.harvard.edu wrote: I think it was a bug we fixed after the release. We can send you new versions on those operating systems and you can try them out. Zeke: can you get Daniel new versions of mri_label2label? thanks Bruce On Fri, 20 Jun 2014, Yang, Daniel wrote: Ah, it¹s FreeSurfer 5.3 ‹ Release Date 15 May 2013. Do you mean that the FreeSurfer 5.3 was updated after 05/15/2013? Thanks, Daniel On 6/19/14, 7:55 PM, Bruce Fischl fis...@nmr.mgh.harvard.edumailto:fis...@nmr.mgh.harvard.edu wrote: what version are you using? I think this is a bug we fixed a few months ago. Or another one Bruce On Thu, 19 Jun 2014, Yang, Daniel wrote: Dear all, I found that mri_label2label generates different results, depending on whether the software¹s platform is MacOS Lion or CentOS 6. Is this possible? Thanks! Daniel ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto: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] mri_label2label results
That is great to know! I personally feel that there should be some sort of autoupdate function or patch file list in FreeSurfer so that when a bug like this is fixed, FreeSurfer can be updated automatically or we can apply the patch from the website. I think the one currently released should be FreeSurfer 5.3.1, with this bug fixed. This bug could have invalidated the research results to some extent if one is retrieving ROI-based stats manually, I feel. Many major software tend to have bugs after release, like SPSS, so this should be a routine... These are just my two cents. Daniel On Jun 19, 2014, at 10:20 PM, Bruce Fischl fis...@nmr.mgh.harvard.edumailto:fis...@nmr.mgh.harvard.edu wrote: Yes, it was only mri_label2label has that bug On Jun 19, 2014, at 10:14 PM, Yang, Daniel yung-jui.y...@yale.edumailto:yung-jui.y...@yale.edu wrote: Thanks! Is there a list of bug fixed (after release) somewhere? Should we use the development version instead? Please tell me that it is only mri_label2label that has a bug … On 6/19/14, 9:08 PM, Bruce Fischl fis...@nmr.mgh.harvard.edumailto:fis...@nmr.mgh.harvard.edu wrote: I think it was a bug we fixed after the release. We can send you new versions on those operating systems and you can try them out. Zeke: can you get Daniel new versions of mri_label2label? thanks Bruce On Fri, 20 Jun 2014, Yang, Daniel wrote: Ah, it¹s FreeSurfer 5.3 ‹ Release Date 15 May 2013. Do you mean that the FreeSurfer 5.3 was updated after 05/15/2013? Thanks, Daniel On 6/19/14, 7:55 PM, Bruce Fischl fis...@nmr.mgh.harvard.edumailto:fis...@nmr.mgh.harvard.edu wrote: what version are you using? I think this is a bug we fixed a few months ago. Or another one Bruce On Thu, 19 Jun 2014, Yang, Daniel wrote: Dear all, I found that mri_label2label generates different results, depending on whether the software¹s platform is MacOS Lion or CentOS 6. Is this possible? Thanks! Daniel ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto: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] subcortical segment NIFTI files
Hi Doug, Could you show us the full command of performing such a registration? Very curious! Thanks. Best, Daniel From: Douglas Greve gr...@nmr.mgh.harvard.edumailto:gr...@nmr.mgh.harvard.edu Reply-To: Freesurfer support list freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu Date: Tuesday, June 17, 2014 at 4:30 AM To: freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] subcortical segment NIFTI files Also curious, what is $FREESURFER_HOME/average/mni152.register.dat created? I performed a registration between the MNI305 (ie, fsaverage) and the MNI152 to get this file doug Thanks! Daniel From: Douglas Greve gr...@nmr.mgh.harvard.edumailto:gr...@nmr.mgh.harvard.edu Reply-To: Freesurfer support list freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu Date: Monday, June 16, 2014 at 12:32 PM To: freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] subcortical segment NIFTI files sorry, don't use the mri.2mm/aseg.mgz use the one from mri/ The --inv take the inverse so it maps in the right direction On 6/16/14 6:16 PM, Yang, Daniel wrote: Hi Doug, The way you are referring is to convert from MNI152 to MNI305? But I wanted to do the opposite. You can see that the right_amygdala.mgz I have as the input is already in the MNI305 space? mri_binarize --i ${FREESURFER_HOME}/subjects/fsaverage/mri.2mm/aseg.mgz --o right_amygdala.mgz --match 54 If I use $FREESURFER_HOME/average/mni152.register.dat instead of reg.2mm.mni152.dat, the product does not look right. Thanks, Daniel From: Douglas Greve gr...@nmr.mgh.harvard.edumailto:gr...@nmr.mgh.harvard.edu Reply-To: Freesurfer support list freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu Date: Monday, June 16, 2014 at 11:43 AM To: freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] subcortical segment NIFTI files That is not the right registration. Use $FREESURFER_HOME/average/mni152.register.dat instead of reg.2mm.mni152.dat specify right_amyg as the --targ and MNI152 as --mov and add --inv and spec --interp nearest doug On 6/16/14 3:13 PM, Yang, Daniel wrote: Hi Doug, I am trying to obtain FreeSurfer aseg label NIFTI files in the MNI152 2mm space. The code posted below, for example, generate the right amygdala in the MNI152 2mm space. I am a little bit confused why my code is viewed as not doing sensible things. In that mri_vol2vol command, the right_amygdala.mgz is in MNI305 2mm space, thus I use the reg.2mm.mni152.dat to transform to MNI152 2mm space. Could you tell me which part is wrong? Thanks, Daniel From: Douglas Greve gr...@nmr.mgh.harvard.edumailto:gr...@nmr.mgh.harvard.edu Reply-To: Freesurfer support list freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu Date: Monday, June 16, 2014 at 8:16 AM To: freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] subcortical segment NIFTI files Sorry, I was trying to find out what it is you are trying to do, not what your command line is. The command may run, it is not doing anything intelligible, ie, it appears to be using the 2mm reg from fsaverage/mni305 with the 2mm mni152, which does not make sense doug On 6/16/14 1:38 PM, Yang, Daniel wrote: It appears that Email in Plaint Text makes the command line look ugly. Here is a cleaner view. These two should provide the right amygdala as the anatomical ROI in MNI152 2mm space. mri_binarize --i ${FREESURFER_HOME}/subjects/fsaverage/mri.2mm/aseg.mgz --o right_amygdala.mgz --match 54 mri_vol2vol --mov right_amygdala.mgz --targ ${FSLDIR}/data/standard/MNI152_T1_2mm_brain.nii.gz —reg ${FREESURFER_HOME}/subjects/fsaverage/mri.2mm/reg.2mm.mni152.dat --o right_amygdala.nii.gz If you run them, you will see what they do. They work for me. Again, my next question is, where can I find reg.1mm.mni152.dat? Or how can I generate one? Thanks! On 6/16/14, 3:51 AM, Douglas Greve gr...@nmr.mgh.harvard.edumailto:gr...@nmr.mgh.harvard.edu wrote: Sorry, what are you trying to do with that vol2vol command? The command line is surely wrong ... On 6/16/14 5:57 AM, Yang, Daniel wrote: Thanks! I see that mri_binarize + mri_vol2vol is what I wanted. I am able to obtain, for example, the right amygdala, using the following commands: mri_binarize --i ${FREESURFER_HOME}/subjects/fsaverage/mri.2mm/aseg.mgz --o right_amygdala.mgz --match 54 mri_vol2vol --mov right_amygdala.mgz --targ ${FSLDIR}/data/standard/MNI152_T1_2mm_brain.nii.gz --reg ${FREESURFER_HOME}/subjects/fsaverage/mri.2mm/reg.2mm.mni152.dat --o right_amygdala.nii.gz rm
Re: [Freesurfer] subcortical segment NIFTI files
Hi Doug, Thanks! I ran this: bbregister --mov $FSLDIR/data/standard/MNI152_T1_1mm_brain.nii.gz --s fsaverage --t1 --reg 1mmreg.dat --init-fsl And obtained the following: fsaverage 1.00 1.00 0.15 9.999634623527527e-01 -4.681387450546026e-03 7.184753660112619e-03 1.294338703155518e+00 -7.163462694734335e-03 4.548550583422184e-03 9.999641776084900e-01 -1.810301017761230e+01 -4.713898524641991e-03 -9.999790787696838e-01 4.514861386269331e-03 -1.897199630737305e+01 0 0 0 1 round Which is a little bit different from mni152.register.dat: fsaverage 1.00 1.00 0.15 9.975314e-01 -7.324822e-03 1.760415e-02 9.570923e-01 -1.296475e-02 -9.262221e-03 9.970638e-01 -1.781596e+01 -1.459537e-02 -1.000945e+00 2.444772e-03 -1.854964e+01 0 0 0 1 tkregister I am curious about this transformation because I want to transform BrainVoyager Talairach brain template to another common space. Two questions: 1. Why are the two different? Is one better than the one, or the difference is trivial? Is it okay to use the one I generated myself? What “tweaks” were done in mni152.register.dat? 2. I see that there are multiple options in bbregister. For example, is it better to use --nearest? Thanks! Daniel From: Douglas Greve gr...@nmr.mgh.harvard.edumailto:gr...@nmr.mgh.harvard.edu Reply-To: Freesurfer support list freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu Date: Tuesday, June 17, 2014 at 7:15 AM To: freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] subcortical segment NIFTI files I think I just ran something like bbregister --mov MNI152_T1_2mm.nii.gz --s fsaverage --t1 --reg reg.dat --init-fsl Maybe I tweeked it manually On 6/17/14 1:10 PM, Yang, Daniel wrote: Hi Doug, Could you show us the full command of performing such a registration? Very curious! Thanks. Best, Daniel From: Douglas Greve gr...@nmr.mgh.harvard.edumailto:gr...@nmr.mgh.harvard.edu Reply-To: Freesurfer support list freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu Date: Tuesday, June 17, 2014 at 4:30 AM To: freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] subcortical segment NIFTI files Also curious, what is $FREESURFER_HOME/average/mni152.register.dat created? I performed a registration between the MNI305 (ie, fsaverage) and the MNI152 to get this file doug Thanks! Daniel From: Douglas Greve gr...@nmr.mgh.harvard.edumailto:gr...@nmr.mgh.harvard.edu Reply-To: Freesurfer support list freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu Date: Monday, June 16, 2014 at 12:32 PM To: freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] subcortical segment NIFTI files sorry, don't use the mri.2mm/aseg.mgz use the one from mri/ The --inv take the inverse so it maps in the right direction On 6/16/14 6:16 PM, Yang, Daniel wrote: Hi Doug, The way you are referring is to convert from MNI152 to MNI305? But I wanted to do the opposite. You can see that the right_amygdala.mgz I have as the input is already in the MNI305 space? mri_binarize --i ${FREESURFER_HOME}/subjects/fsaverage/mri.2mm/aseg.mgz --o right_amygdala.mgz --match 54 If I use $FREESURFER_HOME/average/mni152.register.dat instead of reg.2mm.mni152.dat, the product does not look right. Thanks, Daniel From: Douglas Greve gr...@nmr.mgh.harvard.edumailto:gr...@nmr.mgh.harvard.edu Reply-To: Freesurfer support list freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu Date: Monday, June 16, 2014 at 11:43 AM To: freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] subcortical segment NIFTI files That is not the right registration. Use $FREESURFER_HOME/average/mni152.register.dat instead of reg.2mm.mni152.dat specify right_amyg as the --targ and MNI152 as --mov and add --inv and spec --interp nearest doug On 6/16/14 3:13 PM, Yang, Daniel wrote: Hi Doug, I am trying to obtain FreeSurfer aseg label NIFTI files in the MNI152 2mm space. The code posted below, for example, generate the right amygdala in the MNI152 2mm space. I am a little bit confused why my code is viewed as not doing sensible things. In that mri_vol2vol command, the right_amygdala.mgz is in MNI305 2mm space, thus I use the reg.2mm.mni152.dat to transform to MNI152 2mm space. Could you tell me which part is wrong? Thanks, Daniel From: Douglas Greve gr...@nmr.mgh.harvard.edumailto:gr...@nmr.mgh.harvard.edu Reply-To: Freesurfer support list freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu Date: Monday, June 16, 2014 at 8:16 AM To: freesurfer
Re: [Freesurfer] subcortical segment NIFTI files
Thanks! Does bbregister use orig.mgz in --s? If yes, I guess I should use MNI152_T1_1mm.nii.gz instead, since it has skull, like $FREESURFER_HOME/subjects/fsaverage/mri/orig.mgz. Daniel From: Douglas Greve gr...@nmr.mgh.harvard.edumailto:gr...@nmr.mgh.harvard.edu Reply-To: Freesurfer support list freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu Date: Tuesday, June 17, 2014 at 10:51 AM To: freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] subcortical segment NIFTI files They look pretty similar. I doubt that there will be much practical difference. On 6/17/14 3:08 PM, Yang, Daniel wrote: Hi Doug, Thanks! I ran this: bbregister --mov $FSLDIR/data/standard/MNI152_T1_1mm_brain.nii.gz --s fsaverage --t1 --reg 1mmreg.dat --init-fsl And obtained the following: fsaverage 1.00 1.00 0.15 9.999634623527527e-01 -4.681387450546026e-03 7.184753660112619e-03 1.294338703155518e+00 -7.163462694734335e-03 4.548550583422184e-03 9.999641776084900e-01 -1.810301017761230e+01 -4.713898524641991e-03 -9.999790787696838e-01 4.514861386269331e-03 -1.897199630737305e+01 0 0 0 1 round Which is a little bit different from mni152.register.dat: fsaverage 1.00 1.00 0.15 9.975314e-01 -7.324822e-03 1.760415e-02 9.570923e-01 -1.296475e-02 -9.262221e-03 9.970638e-01 -1.781596e+01 -1.459537e-02 -1.000945e+00 2.444772e-03 -1.854964e+01 0 0 0 1 tkregister I am curious about this transformation because I want to transform BrainVoyager Talairach brain template to another common space. Two questions: 1. Why are the two different? Is one better than the one, or the difference is trivial? Is it okay to use the one I generated myself? What “tweaks” were done in mni152.register.dat? 2. I see that there are multiple options in bbregister. For example, is it better to use --nearest? Thanks! Daniel From: Douglas Greve gr...@nmr.mgh.harvard.edumailto:gr...@nmr.mgh.harvard.edu Reply-To: Freesurfer support list freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu Date: Tuesday, June 17, 2014 at 7:15 AM To: freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] subcortical segment NIFTI files I think I just ran something like bbregister --mov MNI152_T1_2mm.nii.gz --s fsaverage --t1 --reg reg.dat --init-fsl Maybe I tweeked it manually On 6/17/14 1:10 PM, Yang, Daniel wrote: Hi Doug, Could you show us the full command of performing such a registration? Very curious! Thanks. Best, Daniel From: Douglas Greve gr...@nmr.mgh.harvard.edumailto:gr...@nmr.mgh.harvard.edu Reply-To: Freesurfer support list freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu Date: Tuesday, June 17, 2014 at 4:30 AM To: freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] subcortical segment NIFTI files Also curious, what is $FREESURFER_HOME/average/mni152.register.dat created? I performed a registration between the MNI305 (ie, fsaverage) and the MNI152 to get this file doug Thanks! Daniel From: Douglas Greve gr...@nmr.mgh.harvard.edumailto:gr...@nmr.mgh.harvard.edu Reply-To: Freesurfer support list freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu Date: Monday, June 16, 2014 at 12:32 PM To: freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] subcortical segment NIFTI files sorry, don't use the mri.2mm/aseg.mgz use the one from mri/ The --inv take the inverse so it maps in the right direction On 6/16/14 6:16 PM, Yang, Daniel wrote: Hi Doug, The way you are referring is to convert from MNI152 to MNI305? But I wanted to do the opposite. You can see that the right_amygdala.mgz I have as the input is already in the MNI305 space? mri_binarize --i ${FREESURFER_HOME}/subjects/fsaverage/mri.2mm/aseg.mgz --o right_amygdala.mgz --match 54 If I use $FREESURFER_HOME/average/mni152.register.dat instead of reg.2mm.mni152.dat, the product does not look right. Thanks, Daniel From: Douglas Greve gr...@nmr.mgh.harvard.edumailto:gr...@nmr.mgh.harvard.edu Reply-To: Freesurfer support list freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu Date: Monday, June 16, 2014 at 11:43 AM To: freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] subcortical segment NIFTI files That is not the right registration. Use $FREESURFER_HOME/average/mni152.register.dat instead of reg.2mm.mni152.dat specify right_amyg as the --targ and MNI152 as --mov and add --inv and spec --interp nearest doug On 6/16/14 3:13
Re: [Freesurfer] subcortical segment NIFTI files
It appears that Email in Plaint Text makes the command line look ugly. Here is a cleaner view. These two should provide the right amygdala as the anatomical ROI in MNI152 2mm space. mri_binarize --i ${FREESURFER_HOME}/subjects/fsaverage/mri.2mm/aseg.mgz --o right_amygdala.mgz --match 54 mri_vol2vol --mov right_amygdala.mgz --targ ${FSLDIR}/data/standard/MNI152_T1_2mm_brain.nii.gz —reg ${FREESURFER_HOME}/subjects/fsaverage/mri.2mm/reg.2mm.mni152.dat --o right_amygdala.nii.gz If you run them, you will see what they do. They work for me. Again, my next question is, where can I find reg.1mm.mni152.dat? Or how can I generate one? Thanks! On 6/16/14, 3:51 AM, Douglas Greve gr...@nmr.mgh.harvard.edumailto:gr...@nmr.mgh.harvard.edu wrote: Sorry, what are you trying to do with that vol2vol command? The command line is surely wrong ... On 6/16/14 5:57 AM, Yang, Daniel wrote: Thanks! I see that mri_binarize + mri_vol2vol is what I wanted. I am able to obtain, for example, the right amygdala, using the following commands: mri_binarize --i ${FREESURFER_HOME}/subjects/fsaverage/mri.2mm/aseg.mgz --o right_amygdala.mgz --match 54 mri_vol2vol --mov right_amygdala.mgz --targ ${FSLDIR}/data/standard/MNI152_T1_2mm_brain.nii.gz --reg ${FREESURFER_HOME}/subjects/fsaverage/mri.2mm/reg.2mm.mni152.dat --o right_amygdala.nii.gz rm right_amygdala.mgz One question: I don’t see a file like reg.1mm.mni152.dat. How do I obtain a similar file in MNI152 1mm space, based on ${FREESURFER_HOME}/subjects/fsaverage/mri/aseg.mgz ― I think this is a 1mm file? Best, Daniel On 6/15/14, 10:58 PM, Bruce Fischl fis...@nmr.mgh.harvard.edumailto:fis...@nmr.mgh.harvard.edu wrote: mri_vol2vol with the transforms/talairach.xfm as the transform should do the trick. Make sure that the resample type is nearest neighbor Cheers Bruce On Jun 15, 2014, at 10:28 PM, Yang, Daniel yung-jui.y...@yale.edumailto:yung-jui.y...@yale.edu wrote: Hi Bruce, Sorry, I wasn¹t clear. It¹s great to know that the FreeSurfer is very flexible. I meant to obtain the aseg individual label files in MNI152 space as NIfTI files, for example, the different parts of the CC. Could you please point me to the right direction, as to what tool I should use for this purpose (preferably a command line tool, rather than a visualization tool)? Best, Daniel On 6/15/14, 10:16 PM, Bruce Fischl fis...@nmr.mgh.harvard.edumailto:fis...@nmr.mgh.harvard.edu wrote: Hi Daniel Any of our tools can write nifti if you give the output volume the extension .nii or .nii.gz Cheers Bruce On Jun 15, 2014, at 5:54 PM, Yang, Daniel yung-jui.y...@yale.edumailto:yung-jui.y...@yale.edu wrote: Dear all, While it is possible to obtain NIfTI files for cortical parcellation using mri_annotation2label, I am running if it is possible to obtain NIfTI files associated with aseg parts? Thanks! Daniel ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto: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.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto: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
Re: [Freesurfer] subcortical segment NIFTI files
Hi Doug, I am trying to obtain FreeSurfer aseg label NIFTI files in the MNI152 2mm space. The code posted below, for example, generate the right amygdala in the MNI152 2mm space. I am a little bit confused why my code is viewed as not doing sensible things. In that mri_vol2vol command, the right_amygdala.mgz is in MNI305 2mm space, thus I use the reg.2mm.mni152.dat to transform to MNI152 2mm space. Could you tell me which part is wrong? Thanks, Daniel From: Douglas Greve gr...@nmr.mgh.harvard.edumailto:gr...@nmr.mgh.harvard.edu Reply-To: Freesurfer support list freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu Date: Monday, June 16, 2014 at 8:16 AM To: freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] subcortical segment NIFTI files Sorry, I was trying to find out what it is you are trying to do, not what your command line is. The command may run, it is not doing anything intelligible, ie, it appears to be using the 2mm reg from fsaverage/mni305 with the 2mm mni152, which does not make sense doug On 6/16/14 1:38 PM, Yang, Daniel wrote: It appears that Email in Plaint Text makes the command line look ugly. Here is a cleaner view. These two should provide the right amygdala as the anatomical ROI in MNI152 2mm space. mri_binarize --i ${FREESURFER_HOME}/subjects/fsaverage/mri.2mm/aseg.mgz --o right_amygdala.mgz --match 54 mri_vol2vol --mov right_amygdala.mgz --targ ${FSLDIR}/data/standard/MNI152_T1_2mm_brain.nii.gz —reg ${FREESURFER_HOME}/subjects/fsaverage/mri.2mm/reg.2mm.mni152.dat --o right_amygdala.nii.gz If you run them, you will see what they do. They work for me. Again, my next question is, where can I find reg.1mm.mni152.dat? Or how can I generate one? Thanks! On 6/16/14, 3:51 AM, Douglas Greve gr...@nmr.mgh.harvard.edumailto:gr...@nmr.mgh.harvard.edu wrote: Sorry, what are you trying to do with that vol2vol command? The command line is surely wrong ... On 6/16/14 5:57 AM, Yang, Daniel wrote: Thanks! I see that mri_binarize + mri_vol2vol is what I wanted. I am able to obtain, for example, the right amygdala, using the following commands: mri_binarize --i ${FREESURFER_HOME}/subjects/fsaverage/mri.2mm/aseg.mgz --o right_amygdala.mgz --match 54 mri_vol2vol --mov right_amygdala.mgz --targ ${FSLDIR}/data/standard/MNI152_T1_2mm_brain.nii.gz --reg ${FREESURFER_HOME}/subjects/fsaverage/mri.2mm/reg.2mm.mni152.dat --o right_amygdala.nii.gz rm right_amygdala.mgz One question: I don’t see a file like reg.1mm.mni152.dat. How do I obtain a similar file in MNI152 1mm space, based on ${FREESURFER_HOME}/subjects/fsaverage/mri/aseg.mgz ― I think this is a 1mm file? Best, Daniel On 6/15/14, 10:58 PM, Bruce Fischl fis...@nmr.mgh.harvard.edumailto:fis...@nmr.mgh.harvard.edu wrote: mri_vol2vol with the transforms/talairach.xfm as the transform should do the trick. Make sure that the resample type is nearest neighbor Cheers Bruce On Jun 15, 2014, at 10:28 PM, Yang, Daniel yung-jui.y...@yale.edumailto:yung-jui.y...@yale.edu wrote: Hi Bruce, Sorry, I wasn¹t clear. It¹s great to know that the FreeSurfer is very flexible. I meant to obtain the aseg individual label files in MNI152 space as NIfTI files, for example, the different parts of the CC. Could you please point me to the right direction, as to what tool I should use for this purpose (preferably a command line tool, rather than a visualization tool)? Best, Daniel On 6/15/14, 10:16 PM, Bruce Fischl fis...@nmr.mgh.harvard.edumailto:fis...@nmr.mgh.harvard.edu wrote: Hi Daniel Any of our tools can write nifti if you give the output volume the extension .nii or .nii.gz Cheers Bruce On Jun 15, 2014, at 5:54 PM, Yang, Daniel yung-jui.y...@yale.edumailto:yung-jui.y...@yale.edu wrote: Dear all, While it is possible to obtain NIfTI files for cortical parcellation using mri_annotation2label, I am running if it is possible to obtain NIfTI files associated with aseg parts? Thanks! Daniel ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto: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
Re: [Freesurfer] subcortical segment NIFTI files
Hi Doug, The way you are referring is to convert from MNI152 to MNI305? But I wanted to do the opposite. You can see that the right_amygdala.mgz I have as the input is already in the MNI305 space? mri_binarize --i ${FREESURFER_HOME}/subjects/fsaverage/mri.2mm/aseg.mgz --o right_amygdala.mgz --match 54 If I use $FREESURFER_HOME/average/mni152.register.dat instead of reg.2mm.mni152.dat, the product does not look right. Thanks, Daniel From: Douglas Greve gr...@nmr.mgh.harvard.edumailto:gr...@nmr.mgh.harvard.edu Reply-To: Freesurfer support list freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu Date: Monday, June 16, 2014 at 11:43 AM To: freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] subcortical segment NIFTI files That is not the right registration. Use $FREESURFER_HOME/average/mni152.register.dat instead of reg.2mm.mni152.dat specify right_amyg as the --targ and MNI152 as --mov and add --inv and spec --interp nearest doug On 6/16/14 3:13 PM, Yang, Daniel wrote: Hi Doug, I am trying to obtain FreeSurfer aseg label NIFTI files in the MNI152 2mm space. The code posted below, for example, generate the right amygdala in the MNI152 2mm space. I am a little bit confused why my code is viewed as not doing sensible things. In that mri_vol2vol command, the right_amygdala.mgz is in MNI305 2mm space, thus I use the reg.2mm.mni152.dat to transform to MNI152 2mm space. Could you tell me which part is wrong? Thanks, Daniel From: Douglas Greve gr...@nmr.mgh.harvard.edumailto:gr...@nmr.mgh.harvard.edu Reply-To: Freesurfer support list freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu Date: Monday, June 16, 2014 at 8:16 AM To: freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] subcortical segment NIFTI files Sorry, I was trying to find out what it is you are trying to do, not what your command line is. The command may run, it is not doing anything intelligible, ie, it appears to be using the 2mm reg from fsaverage/mni305 with the 2mm mni152, which does not make sense doug On 6/16/14 1:38 PM, Yang, Daniel wrote: It appears that Email in Plaint Text makes the command line look ugly. Here is a cleaner view. These two should provide the right amygdala as the anatomical ROI in MNI152 2mm space. mri_binarize --i ${FREESURFER_HOME}/subjects/fsaverage/mri.2mm/aseg.mgz --o right_amygdala.mgz --match 54 mri_vol2vol --mov right_amygdala.mgz --targ ${FSLDIR}/data/standard/MNI152_T1_2mm_brain.nii.gz —reg ${FREESURFER_HOME}/subjects/fsaverage/mri.2mm/reg.2mm.mni152.dat --o right_amygdala.nii.gz If you run them, you will see what they do. They work for me. Again, my next question is, where can I find reg.1mm.mni152.dat? Or how can I generate one? Thanks! On 6/16/14, 3:51 AM, Douglas Greve gr...@nmr.mgh.harvard.edumailto:gr...@nmr.mgh.harvard.edu wrote: Sorry, what are you trying to do with that vol2vol command? The command line is surely wrong ... On 6/16/14 5:57 AM, Yang, Daniel wrote: Thanks! I see that mri_binarize + mri_vol2vol is what I wanted. I am able to obtain, for example, the right amygdala, using the following commands: mri_binarize --i ${FREESURFER_HOME}/subjects/fsaverage/mri.2mm/aseg.mgz --o right_amygdala.mgz --match 54 mri_vol2vol --mov right_amygdala.mgz --targ ${FSLDIR}/data/standard/MNI152_T1_2mm_brain.nii.gz --reg ${FREESURFER_HOME}/subjects/fsaverage/mri.2mm/reg.2mm.mni152.dat --o right_amygdala.nii.gz rm right_amygdala.mgz One question: I don’t see a file like reg.1mm.mni152.dat. How do I obtain a similar file in MNI152 1mm space, based on ${FREESURFER_HOME}/subjects/fsaverage/mri/aseg.mgz ― I think this is a 1mm file? Best, Daniel On 6/15/14, 10:58 PM, Bruce Fischl fis...@nmr.mgh.harvard.edumailto:fis...@nmr.mgh.harvard.edu wrote: mri_vol2vol with the transforms/talairach.xfm as the transform should do the trick. Make sure that the resample type is nearest neighbor Cheers Bruce On Jun 15, 2014, at 10:28 PM, Yang, Daniel yung-jui.y...@yale.edumailto:yung-jui.y...@yale.edu wrote: Hi Bruce, Sorry, I wasn¹t clear. It¹s great to know that the FreeSurfer is very flexible. I meant to obtain the aseg individual label files in MNI152 space as NIfTI files, for example, the different parts of the CC. Could you please point me to the right direction, as to what tool I should use for this purpose (preferably a command line tool, rather than a visualization tool)? Best, Daniel On 6/15/14, 10:16 PM, Bruce Fischl fis...@nmr.mgh.harvard.edumailto:fis...@nmr.mgh.harvard.edu wrote: Hi Daniel Any of our tools can write nifti if you give the output volume the extension .nii or .nii.gz Cheers Bruce On Jun 15, 2014, at 5:54 PM, Yang, Daniel yung-jui.y...@yale.edumailto:yung-jui.y...@yale.edu wrote: Dear
Re: [Freesurfer] subcortical segment NIFTI files
Hi Doug, I see. It works well. Just curious, when should we use reg.2mm.mni152.dat then? Also curious, what is $FREESURFER_HOME/average/mni152.register.dat created? Thanks! Daniel From: Douglas Greve gr...@nmr.mgh.harvard.edumailto:gr...@nmr.mgh.harvard.edu Reply-To: Freesurfer support list freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu Date: Monday, June 16, 2014 at 12:32 PM To: freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] subcortical segment NIFTI files sorry, don't use the mri.2mm/aseg.mgz use the one from mri/ The --inv take the inverse so it maps in the right direction On 6/16/14 6:16 PM, Yang, Daniel wrote: Hi Doug, The way you are referring is to convert from MNI152 to MNI305? But I wanted to do the opposite. You can see that the right_amygdala.mgz I have as the input is already in the MNI305 space? mri_binarize --i ${FREESURFER_HOME}/subjects/fsaverage/mri.2mm/aseg.mgz --o right_amygdala.mgz --match 54 If I use $FREESURFER_HOME/average/mni152.register.dat instead of reg.2mm.mni152.dat, the product does not look right. Thanks, Daniel From: Douglas Greve gr...@nmr.mgh.harvard.edumailto:gr...@nmr.mgh.harvard.edu Reply-To: Freesurfer support list freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu Date: Monday, June 16, 2014 at 11:43 AM To: freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] subcortical segment NIFTI files That is not the right registration. Use $FREESURFER_HOME/average/mni152.register.dat instead of reg.2mm.mni152.dat specify right_amyg as the --targ and MNI152 as --mov and add --inv and spec --interp nearest doug On 6/16/14 3:13 PM, Yang, Daniel wrote: Hi Doug, I am trying to obtain FreeSurfer aseg label NIFTI files in the MNI152 2mm space. The code posted below, for example, generate the right amygdala in the MNI152 2mm space. I am a little bit confused why my code is viewed as not doing sensible things. In that mri_vol2vol command, the right_amygdala.mgz is in MNI305 2mm space, thus I use the reg.2mm.mni152.dat to transform to MNI152 2mm space. Could you tell me which part is wrong? Thanks, Daniel From: Douglas Greve gr...@nmr.mgh.harvard.edumailto:gr...@nmr.mgh.harvard.edu Reply-To: Freesurfer support list freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu Date: Monday, June 16, 2014 at 8:16 AM To: freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] subcortical segment NIFTI files Sorry, I was trying to find out what it is you are trying to do, not what your command line is. The command may run, it is not doing anything intelligible, ie, it appears to be using the 2mm reg from fsaverage/mni305 with the 2mm mni152, which does not make sense doug On 6/16/14 1:38 PM, Yang, Daniel wrote: It appears that Email in Plaint Text makes the command line look ugly. Here is a cleaner view. These two should provide the right amygdala as the anatomical ROI in MNI152 2mm space. mri_binarize --i ${FREESURFER_HOME}/subjects/fsaverage/mri.2mm/aseg.mgz --o right_amygdala.mgz --match 54 mri_vol2vol --mov right_amygdala.mgz --targ ${FSLDIR}/data/standard/MNI152_T1_2mm_brain.nii.gz —reg ${FREESURFER_HOME}/subjects/fsaverage/mri.2mm/reg.2mm.mni152.dat --o right_amygdala.nii.gz If you run them, you will see what they do. They work for me. Again, my next question is, where can I find reg.1mm.mni152.dat? Or how can I generate one? Thanks! On 6/16/14, 3:51 AM, Douglas Greve gr...@nmr.mgh.harvard.edumailto:gr...@nmr.mgh.harvard.edu wrote: Sorry, what are you trying to do with that vol2vol command? The command line is surely wrong ... On 6/16/14 5:57 AM, Yang, Daniel wrote: Thanks! I see that mri_binarize + mri_vol2vol is what I wanted. I am able to obtain, for example, the right amygdala, using the following commands: mri_binarize --i ${FREESURFER_HOME}/subjects/fsaverage/mri.2mm/aseg.mgz --o right_amygdala.mgz --match 54 mri_vol2vol --mov right_amygdala.mgz --targ ${FSLDIR}/data/standard/MNI152_T1_2mm_brain.nii.gz --reg ${FREESURFER_HOME}/subjects/fsaverage/mri.2mm/reg.2mm.mni152.dat --o right_amygdala.nii.gz rm right_amygdala.mgz One question: I don’t see a file like reg.1mm.mni152.dat. How do I obtain a similar file in MNI152 1mm space, based on ${FREESURFER_HOME}/subjects/fsaverage/mri/aseg.mgz ― I think this is a 1mm file? Best, Daniel On 6/15/14, 10:58 PM, Bruce Fischl fis...@nmr.mgh.harvard.edumailto:fis...@nmr.mgh.harvard.edu wrote: mri_vol2vol with the transforms/talairach.xfm as the transform should do the trick. Make sure that the resample type is nearest neighbor Cheers Bruce On Jun 15, 2014, at 10:28 PM, Yang, Daniel yung-jui.y
[Freesurfer] subcortical segment NIFTI files
Dear all, While it is possible to obtain NIfTI files for cortical parcellation using mri_annotation2label, I am running if it is possible to obtain NIfTI files associated with aseg parts? Thanks! Daniel ___ 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] subcortical segment NIFTI files
Hi Bruce, Sorry, I wasn¹t clear. It¹s great to know that the FreeSurfer is very flexible. I meant to obtain the aseg individual label files in MNI152 space as NIfTI files, for example, the different parts of the CC. Could you please point me to the right direction, as to what tool I should use for this purpose (preferably a command line tool, rather than a visualization tool)? Best, Daniel On 6/15/14, 10:16 PM, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: Hi Daniel Any of our tools can write nifti if you give the output volume the extension .nii or .nii.gz Cheers Bruce On Jun 15, 2014, at 5:54 PM, Yang, Daniel yung-jui.y...@yale.edu wrote: Dear all, While it is possible to obtain NIfTI files for cortical parcellation using mri_annotation2label, I am running if it is possible to obtain NIfTI files associated with aseg parts? Thanks! Daniel ___ 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 mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] subcortical segment NIFTI files
Thanks! I see that mri_binarize + mri_vol2vol is what I wanted. I am able to obtain, for example, the right amygdala, using the following commands: mri_binarize --i ${FREESURFER_HOME}/subjects/fsaverage/mri.2mm/aseg.mgz --o right_amygdala.mgz --match 54 mri_vol2vol --mov right_amygdala.mgz --targ ${FSLDIR}/data/standard/MNI152_T1_2mm_brain.nii.gz --reg ${FREESURFER_HOME}/subjects/fsaverage/mri.2mm/reg.2mm.mni152.dat --o right_amygdala.nii.gz rm right_amygdala.mgz One question: I don’t see a file like reg.1mm.mni152.dat. How do I obtain a similar file in MNI152 1mm space, based on ${FREESURFER_HOME}/subjects/fsaverage/mri/aseg.mgz ― I think this is a 1mm file? Best, Daniel On 6/15/14, 10:58 PM, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: mri_vol2vol with the transforms/talairach.xfm as the transform should do the trick. Make sure that the resample type is nearest neighbor Cheers Bruce On Jun 15, 2014, at 10:28 PM, Yang, Daniel yung-jui.y...@yale.edu wrote: Hi Bruce, Sorry, I wasn¹t clear. It¹s great to know that the FreeSurfer is very flexible. I meant to obtain the aseg individual label files in MNI152 space as NIfTI files, for example, the different parts of the CC. Could you please point me to the right direction, as to what tool I should use for this purpose (preferably a command line tool, rather than a visualization tool)? Best, Daniel On 6/15/14, 10:16 PM, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: Hi Daniel Any of our tools can write nifti if you give the output volume the extension .nii or .nii.gz Cheers Bruce On Jun 15, 2014, at 5:54 PM, Yang, Daniel yung-jui.y...@yale.edu wrote: Dear all, While it is possible to obtain NIfTI files for cortical parcellation using mri_annotation2label, I am running if it is possible to obtain NIfTI files associated with aseg parts? Thanks! Daniel ___ 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 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] reg.1mm.mni152.dat
Dear all, While there is the file ${FREESURFER_HOME}/subjects/fsaverage/mri.2mm/reg.2mm.mni152.dat, there is no such file as: ${FREESURFER_HOME}/subjects/fsaverage/mri/reg.1mm.mni152.dat or ${FREESURFER_HOME}/subjects/fsaverage/mri/transforms/reg.1mm.mni152.dat ? I am wondering how we can create the reg.1mm.mni152.dat file? Thanks! Daniel ___ 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] Frontal WM volume
Dear FreeSurfer group, If I want to extract frontal WM volume, is it something doable in FreeSurfer? Much obliged, Daniel ___ 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] Frontal WM volume
Hi Doug, Do you mean wmparc.stats? If yes, that is my understanding of the only way (so far) to estimate WM volume by FreeSurfer too, and you already told me (before) that it is only 5mm from white surface down into the brain center, correct?? I don't have a better way to do this so far. If there is another way to get those WM volume by area other than wmparc.stats, can you let me know too? Best, Daniel On 5/14/14 5:58 PM, Douglas N Greve gr...@nmr.mgh.harvard.edumailto:gr...@nmr.mgh.harvard.edu wrote: You can choose the areas that you want to define frontal from wmparc.mgz and add up the volumes. If you have another way to define frontal, then you'd have to tell us what that is. doug On 05/14/2014 05:37 PM, Yang, Daniel wrote: Dear FreeSurfer group, If I want to extract frontal WM volume, is it something doable in FreeSurfer? Much obliged, Daniel ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto: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.edumailto: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.edumailto: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] MeanThickness
Dear FreeSurfer Experts, I would like to extract the mean thickness for each subject, and I can see that in the lh.aparc.stats, there are three lines. For example: # Measure Cortex, NumVert, Number of Vertices, 107414, unitless # Measure Cortex, WhiteSurfArea, White Surface Total Area, 73280.4, mm^2 # Measure Cortex, MeanThickness, Mean Thickness, 2.56763, mm I am wondering what command I can run with aparcstats2table or mris_calc to retrieve these three pieces of information for each subject? And is the MeanThickness across the whole brain supposed to be (lh + rh)/2? Best, Daniel -- Daniel (Yung-Jui) Yang, Ph.D. Postdoctoral Researcher Yale Child Study Center New Haven, CT Tel: (203) 737-5454 E-mail: yung-jui.y...@yale.edu ___ 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] MeanThickness
Thanks! Instead of aparcstats2table, I just used grep and awk to retrieve those directly from the ?h.aparc.stats, and then I calculated the mean_thickness = ((lh_mean_thickness * lh_white_surface_area ) + (rh_mean_thickness * rh_white_surface_area)) / (lh_white_surface_area + rh_white_surface_area)... Best, Daniel -- Daniel (Yung-Jui) Yang, Ph.D. Postdoctoral Researcher Yale Child Study Center New Haven, CT Tel: (203) 737-5454 E-mail: yung-jui.y...@yale.edu On 3/30/14 2:40 PM, Douglas Greve gr...@nmr.mgh.harvard.edumailto:gr...@nmr.mgh.harvard.edu wrote: I think aparcstats2table automatically includes these measures. Can you check? And, yes, mean thickness can be computed as (lh+rh)/2 doug On 3/30/14 12:58 PM, Yang, Daniel wrote: Dear FreeSurfer Experts, I would like to extract the mean thickness for each subject, and I can see that in the lh.aparc.stats, there are three lines. For example: # Measure Cortex, NumVert, Number of Vertices, 107414, unitless # Measure Cortex, WhiteSurfArea, White Surface Total Area, 73280.4, mm^2 # Measure Cortex, MeanThickness, Mean Thickness, 2.56763, mm I am wondering what command I can run with aparcstats2table or mris_calc to retrieve these three pieces of information for each subject? And is the MeanThickness across the whole brain supposed to be (lh + rh)/2? Best, Daniel -- Daniel (Yung-Jui) Yang, Ph.D. Postdoctoral Researcher Yale Child Study Center New Haven, CT Tel: (203) 737-5454 E-mail: yung-jui.y...@yale.edumailto:yung-jui.y...@yale.edu ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@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.
Re: [Freesurfer] WM vol as measure
Dear all, I notice that there is a file called wmparc_stats.txt http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/AnatomicalROI#Tableofwhitematterparcellationvolumes Is it possible to get corresponding WM info for a given label? Best, Daniel -- Daniel (Yung-Jui) Yang, Ph.D. Postdoctoral Researcher Yale Child Study Center New Haven, CT Tel: (203) 737-5454 E-mail: yung-jui.y...@yale.edu On 3/2/14 7:18 PM, Yang, Daniel yung-jui.y...@yale.edumailto:yung-jui.y...@yale.edu wrote: Dear FreeSurfer Experts, FS provides thickness as the DV in qdec and mri-glmfit. Do you know how I can have WM vol as the DV in these tools with the same GLM model? For example, I want to test the WM regions that is most strongly positively correlated with a given factor. Thanks! Daniel ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto: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] WM vol as measure
Thanks, Doug! But that is about using wmparc.stats as IV or continuous/covariate variables. I would like to use WM vol as the DV (measure). -- Daniel (Yung-Jui) Yang, Ph.D. Postdoctoral Researcher Yale Child Study Center New Haven, CT Tel: (203) 737-5454 E-mail: yung-jui.y...@yale.edu On 3/3/14 12:58 PM, Douglas N Greve gr...@nmr.mgh.harvard.edumailto:gr...@nmr.mgh.harvard.edu wrote: you can just add them into your qdec file (from wmparc.stats) doug On 03/02/2014 07:18 PM, Yang, Daniel wrote: Dear FreeSurfer Experts, FS provides thickness as the DV in qdec and mri-glmfit. Do you know how I can have WM vol as the DV in these tools with the same GLM model? For example, I want to test the WM regions that is most strongly positively correlated with a given factor. Thanks! Daniel ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto: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.edumailto: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.edumailto: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] WM vol as measure
Hi Doug, I am able to find wmparc.stats in stats. It shows WM vol based on pre-defined ROIs. However, do you know how can we generate corresponding WM vol for a given label (not the D-K ROIs)? I'd like to use WM vol as DV but are limited to pre-defined ROIs. Best, Daniel -- Daniel (Yung-Jui) Yang, Ph.D. Postdoctoral Researcher Yale Child Study Center New Haven, CT Tel: (203) 737-5454 E-mail: yung-jui.y...@yale.edu On 3/3/14 1:14 PM, Douglas N Greve gr...@nmr.mgh.harvard.edumailto:gr...@nmr.mgh.harvard.edu wrote: It should be there if the recon did not fail. The file is called wmparc.stats (not wmparc_stats.txt) On 03/03/2014 01:07 PM, Yang, Daniel wrote: Thanks, Doug! But that is about using wmparc.stats as IV or continuous/covariate variables. I would like to use WM vol as the DV (measure). -- Daniel (Yung-Jui) Yang, Ph.D. Postdoctoral Researcher Yale Child Study Center New Haven, CT Tel: (203) 737-5454 E-mail: _yung-jui.yang@yale.edu_mailto:_yung-jui.yang@yale.edu_ On 3/3/14 12:58 PM, Douglas N Greve gr...@nmr.mgh.harvard.edumailto:gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu wrote: you can just add them into your qdec file (from wmparc.stats) doug On 03/02/2014 07:18 PM, Yang, Daniel wrote: Dear FreeSurfer Experts, FS provides thickness as the DV in qdec and mri-glmfit. Do you know how I can have WM vol as the DV in these tools with the same GLM model? For example, I want to test the WM regions that is most strongly positively correlated with a given factor. Thanks! Daniel ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu mailto: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.edumailto:gr...@nmr.mgh.harvard.edu mailto: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.edumailto:Freesurfer@nmr.mgh.harvard.edu mailto: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. -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edumailto: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.
Re: [Freesurfer] WM vol as measure
Sorry, I wasn't clear. It's a cortical label that I manually created, based on the pial surface. Is it possible to generate the corresponding WM vol based on a new label (not pre-defined)? -- Daniel (Yung-Jui) Yang, Ph.D. Postdoctoral Researcher Yale Child Study Center New Haven, CT Tel: (203) 737-5454 E-mail: yung-jui.y...@yale.edu On 3/3/14 2:17 PM, Douglas N Greve gr...@nmr.mgh.harvard.edumailto:gr...@nmr.mgh.harvard.edu wrote: I don't understand. What label do you have? Do you mean a WM label or a cortical label that you want to find the WM under? On 03/03/2014 02:12 PM, Yang, Daniel wrote: Hi Doug, I am able to find wmparc.stats in stats. It shows WM vol based on pre-defined ROIs. However, do you know how can we generate corresponding WM vol for a given label (not the D-K ROIs)? I'd like to use WM vol as DV but are limited to pre-defined ROIs. Best, Daniel -- Daniel (Yung-Jui) Yang, Ph.D. Postdoctoral Researcher Yale Child Study Center New Haven, CT Tel: (203) 737-5454 E-mail: _yung-jui.yang@yale.edu_mailto:_yung-jui.yang@yale.edu_ On 3/3/14 1:14 PM, Douglas N Greve gr...@nmr.mgh.harvard.edumailto:gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu wrote: It should be there if the recon did not fail. The file is called wmparc.stats (not wmparc_stats.txt) On 03/03/2014 01:07 PM, Yang, Daniel wrote: Thanks, Doug! But that is about using wmparc.stats as IV or continuous/covariate variables. I would like to use WM vol as the DV (measure). -- Daniel (Yung-Jui) Yang, Ph.D. Postdoctoral Researcher Yale Child Study Center New Haven, CT Tel: (203) 737-5454 E-mail: _yung-jui.yang@yale.edu_mailto:_yung-jui.yang@yale.edu_ mailto:_yung-jui.yang@yale.edu_ On 3/3/14 12:58 PM, Douglas N Greve gr...@nmr.mgh.harvard.edumailto:gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu%3E wrote: you can just add them into your qdec file (from wmparc.stats) doug On 03/02/2014 07:18 PM, Yang, Daniel wrote: Dear FreeSurfer Experts, FS provides thickness as the DV in qdec and mri-glmfit. Do you know how I can have WM vol as the DV in these tools with the same GLM model? For example, I want to test the WM regions that is most strongly positively correlated with a given factor. Thanks! Daniel ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu mailto: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.edumailto:gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu mailto: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.edumailto:Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu mailto: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. -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edumailto:gr...@nmr.mgh.harvard.edu mailto: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
Re: [Freesurfer] WM vol as measure
Sounds like a lot of work, but thanks for your reply. By the way, the wm vol generated this way is 5mm from white surface into the center of the brain, correct? Thus, it is not necessarily the complete WM vol underneath the label? Daniel -- Daniel (Yung-Jui) Yang, Ph.D. Postdoctoral Researcher Yale Child Study Center New Haven, CT Tel: (203) 737-5454 E-mail: yung-jui.y...@yale.edu On 3/3/14 2:48 PM, Douglas N Greve gr...@nmr.mgh.harvard.edumailto:gr...@nmr.mgh.harvard.edu wrote: yes, but not easily. You will have to create an annotation with your new label in it (and any other label for the other parts of cortex) (probably using mris_label2annot), then run mri_aparc2aseg to generate a new wmparc-style volume, then run mri_segstats. You can look in the recon-all.log file for example command lines for mri_aparc2aseg (used to generate the wmparc.mgz) doug On 03/03/2014 02:31 PM, Yang, Daniel wrote: Sorry, I wasn't clear. It's a cortical label that I manually created, based on the pial surface. Is it possible to generate the corresponding WM vol based on a new label (not pre-defined)? -- Daniel (Yung-Jui) Yang, Ph.D. Postdoctoral Researcher Yale Child Study Center New Haven, CT Tel: (203) 737-5454 E-mail: _yung-jui.yang@yale.edu_mailto:_yung-jui.yang@yale.edu_ On 3/3/14 2:17 PM, Douglas N Greve gr...@nmr.mgh.harvard.edumailto:gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu wrote: I don't understand. What label do you have? Do you mean a WM label or a cortical label that you want to find the WM under? On 03/03/2014 02:12 PM, Yang, Daniel wrote: Hi Doug, I am able to find wmparc.stats in stats. It shows WM vol based on pre-defined ROIs. However, do you know how can we generate corresponding WM vol for a given label (not the D-K ROIs)? I'd like to use WM vol as DV but are limited to pre-defined ROIs. Best, Daniel -- Daniel (Yung-Jui) Yang, Ph.D. Postdoctoral Researcher Yale Child Study Center New Haven, CT Tel: (203) 737-5454 E-mail: _yung-jui.yang@yale.edu_mailto:_yung-jui.yang@yale.edu_ mailto:_yung-jui.yang@yale.edu_ On 3/3/14 1:14 PM, Douglas N Greve gr...@nmr.mgh.harvard.edumailto:gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu%3E wrote: It should be there if the recon did not fail. The file is called wmparc.stats (not wmparc_stats.txt) On 03/03/2014 01:07 PM, Yang, Daniel wrote: Thanks, Doug! But that is about using wmparc.stats as IV or continuous/covariate variables. I would like to use WM vol as the DV (measure). -- Daniel (Yung-Jui) Yang, Ph.D. Postdoctoral Researcher Yale Child Study Center New Haven, CT Tel: (203) 737-5454 E-mail: _yung-jui.yang@yale.edu_mailto:_yung-jui.yang@yale.edu_ mailto:_yung-jui.yang@yale.edu_ mailto:_yung-jui.yang@yale.edu_ On 3/3/14 12:58 PM, Douglas N Greve gr...@nmr.mgh.harvard.edumailto:gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu%3E mailto:gr...@nmr.mgh.harvard.edu%3E%3E wrote: you can just add them into your qdec file (from wmparc.stats) doug On 03/02/2014 07:18 PM, Yang, Daniel wrote: Dear FreeSurfer Experts, FS provides thickness as the DV in qdec and mri-glmfit. Do you know how I can have WM vol as the DV in these tools with the same GLM model? For example, I want to test the WM regions that is most strongly positively correlated with a given factor. Thanks! Daniel ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr
[Freesurfer] WM vol as measure
Dear FreeSurfer Experts, FS provides thickness as the DV in qdec and mri-glmfit. Do you know how I can have WM vol as the DV in these tools with the same GLM model? For example, I want to test the WM regions that is most strongly positively correlated with a given factor. Thanks! Daniel ___ 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] WM vol as measure
Hi FreeSurfers, A related question (I can't find the answers on the FS website): what's jacobian_white (as a measure)? Thanks! Daniel -- Daniel (Yung-Jui) Yang, Ph.D. Postdoctoral Researcher Yale Child Study Center New Haven, CT Tel: (203) 737-5454 E-mail: yung-jui.y...@yale.edu On 3/2/14 7:18 PM, Yang, Daniel yung-jui.y...@yale.edumailto:yung-jui.y...@yale.edu wrote: Dear FreeSurfer Experts, FS provides thickness as the DV in qdec and mri-glmfit. Do you know how I can have WM vol as the DV in these tools with the same GLM model? For example, I want to test the WM regions that is most strongly positively correlated with a given factor. Thanks! Daniel ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto: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] two labels in tksurfer/freeview?
Dear FreeSurfer experts, Is it possible to display two labels in tksurfer or freeview, where one label is outlined with a certain color and the other label is filled with a different color? I want to show two labels, one is within the other one. If yes, could you please tell me the specific steps..? thanks a lot! Daniel -- Daniel (Yung-Jui) Yang, Ph.D. Postdoctoral Researcher Yale Child Study Center New Haven, CT Tel: (203) 737-5454 E-mail: yung-jui.y...@yale.edu ___ 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] two labels in tksurfer/freeview?
Doug, Thanks for your reply! In the annotation, can one of the label be just outlined and the other filled? I would really appreciate if you could provide a step-by-step example for this one… esp. how to create the colorLUT in this case... Best, Daniel -- Daniel (Yung-Jui) Yang, Ph.D. Postdoctoral Researcher Yale Child Study Center New Haven, CT Tel: (203) 737-5454 E-mail: yung-jui.y...@yale.edu On 2/26/14 5:14 PM, Douglas N Greve gr...@nmr.mgh.harvard.edumailto:gr...@nmr.mgh.harvard.edu wrote: I'm not sure about freeview, but you cannot do it in tksurfer. You can take your two labels and create an annotation with mris_label2annot (you get to specify the color) doug On 02/26/2014 05:12 PM, Yang, Daniel wrote: Dear FreeSurfer experts, Is it possible to display two labels in tksurfer or freeview, where one label is outlined with a certain color and the other label is filled with a different color? I want to show two labels, one is within the other one. If yes, could you please tell me the specific steps..? thanks a lot! Daniel -- Daniel (Yung-Jui) Yang, Ph.D. Postdoctoral Researcher Yale Child Study Center New Haven, CT Tel: (203) 737-5454 E-mail: _yung-jui.yang@yale.edu_mailto:_yung-jui.yang@yale.edu_ ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto: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.edumailto: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.edumailto: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] two labels in tksurfer/freeview?
Thanks for both of you for the helps! I also find a 3rd solution: convert one of the labels to mgh and thus use it as overlay and use the other one as label in freeview. Doug: Creating an outlined label sounds pretty cool. I wonder whether either erosion or dilution would do the trick … some sort of tricky conjunction. Bruce: thanks!! -- Daniel (Yung-Jui) Yang, Ph.D. Postdoctoral Researcher Yale Child Study Center New Haven, CT Tel: (203) 737-5454 E-mail: yung-jui.y...@yale.edu On 2/26/14 5:52 PM, Bruce Fischl fis...@nmr.mgh.harvard.edumailto:fis...@nmr.mgh.harvard.edu wrote: the other thing you could do is draw a path in tksurfer and have it be the outline, then load the inner label and display it as filled On Wed, 26 Feb 2014, Douglas N Greve wrote: No, you'd have to modify the label itself to exclude the center (and create an outline). I don't have any code to do this. For the other stuff, look at the help for mris_label2annot --help doug On 02/26/2014 05:35 PM, Yang, Daniel wrote: Doug, Thanks for your reply! In the annotation, can one of the label be just outlined and the other filled? I would really appreciate if you could provide a step-by-step example for this one… esp. how to create the colorLUT in this case... Best, Daniel -- Daniel (Yung-Jui) Yang, Ph.D. Postdoctoral Researcher Yale Child Study Center New Haven, CT Tel: (203) 737-5454 E-mail: _yung-jui.yang@yale.edu_mailto:_yung-jui.yang@yale.edu_ On 2/26/14 5:14 PM, Douglas N Greve gr...@nmr.mgh.harvard.edumailto:gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu wrote: I'm not sure about freeview, but you cannot do it in tksurfer. You can take your two labels and create an annotation with mris_label2annot (you get to specify the color) doug On 02/26/2014 05:12 PM, Yang, Daniel wrote: Dear FreeSurfer experts, Is it possible to display two labels in tksurfer or freeview, where one label is outlined with a certain color and the other label is filled with a different color? I want to show two labels, one is within the other one. If yes, could you please tell me the specific steps..? thanks a lot! Daniel -- Daniel (Yung-Jui) Yang, Ph.D. Postdoctoral Researcher Yale Child Study Center New Haven, CT Tel: (203) 737-5454 E-mail: _yung-jui.yang@yale.edu_mailto:_yung-jui.yang@yale.edu_ mailto:_yung-jui.yang@yale.edu_ ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu mailto: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.edumailto:gr...@nmr.mgh.harvard.edu mailto: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.edumailto:Freesurfer@nmr.mgh.harvard.edu mailto: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] two labels in tksurfer/freeview?
Thanks, Bruce! That is neat!! -- Daniel (Yung-Jui) Yang, Ph.D. Postdoctoral Researcher Yale Child Study Center New Haven, CT Tel: (203) 737-5454 E-mail: yung-jui.y...@yale.edu On 2/26/14 7:03 PM, Bruce Fischl fis...@nmr.mgh.harvard.edumailto:fis...@nmr.mgh.harvard.edu wrote: that's a good way to do it. You don't even need to save it as an mgz. You can just do tools-labels-copy label stats to overlay, then delete the label and you have an overlay from it (assuming the label-stat field is not zero) On Thu, 27 Feb 2014, Yang, Daniel wrote: Thanks for both of you for the helps! I also find a 3rd solution: convert one of the labels to mgh and thus use it as overlay and use the other one as label in freeview. Doug: Creating an outlined label sounds pretty cool. I wonder whether either erosion or dilution would do the trick … some sort of tricky conjunction. Bruce: thanks!! -- Daniel (Yung-Jui) Yang, Ph.D. Postdoctoral Researcher Yale Child Study Center New Haven, CT Tel: (203) 737-5454 E-mail: yung-jui.y...@yale.edumailto:yung-jui.y...@yale.edu On 2/26/14 5:52 PM, Bruce Fischl fis...@nmr.mgh.harvard.edumailto:fis...@nmr.mgh.harvard.edu wrote: the other thing you could do is draw a path in tksurfer and have it be the outline, then load the inner label and display it as filled On Wed, 26 Feb 2014, Douglas N Greve wrote: No, you'd have to modify the label itself to exclude the center (and create an outline). I don't have any code to do this. For the other stuff, look at the help for mris_label2annot --help doug On 02/26/2014 05:35 PM, Yang, Daniel wrote: Doug, Thanks for your reply! In the annotation, can one of the label be just outlined and the other filled? I would really appreciate if you could provide a step-by-step example for this one… esp. how to create the colorLUT in this case... Best, Daniel -- Daniel (Yung-Jui) Yang, Ph.D. Postdoctoral Researcher Yale Child Study Center New Haven, CT Tel: (203) 737-5454 E-mail: _yung-jui.yang@yale.edu_mailto:_yung-jui.yang@yale.edu_ On 2/26/14 5:14 PM, Douglas N Greve gr...@nmr.mgh.harvard.edumailto:gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu wrote: I'm not sure about freeview, but you cannot do it in tksurfer. You can take your two labels and create an annotation with mris_label2annot (you get to specify the color) doug On 02/26/2014 05:12 PM, Yang, Daniel wrote: Dear FreeSurfer experts, Is it possible to display two labels in tksurfer or freeview, where one label is outlined with a certain color and the other label is filled with a different color? I want to show two labels, one is within the other one. If yes, could you please tell me the specific steps..? thanks a lot! Daniel -- Daniel (Yung-Jui) Yang, Ph.D. Postdoctoral Researcher Yale Child Study Center New Haven, CT Tel: (203) 737-5454 E-mail: _yung-jui.yang@yale.edu_mailto:_yung-jui.yang@yale.edu_ mailto:_yung-jui.yang@yale.edu_ ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu mailto: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.edumailto:gr...@nmr.mgh.harvard.edu mailto: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.edumailto:Freesurfer@nmr.mgh.harvard.edu mailto: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
Re: [Freesurfer] two labels in tksurfer/freeview?
By the way, what command can I use to erode a label/mgh..? -- Daniel (Yung-Jui) Yang, Ph.D. Postdoctoral Researcher Yale Child Study Center New Haven, CT Tel: (203) 737-5454 E-mail: yung-jui.y...@yale.edu On 2/26/14 7:03 PM, Bruce Fischl fis...@nmr.mgh.harvard.edumailto:fis...@nmr.mgh.harvard.edu wrote: that's a good way to do it. You don't even need to save it as an mgz. You can just do tools-labels-copy label stats to overlay, then delete the label and you have an overlay from it (assuming the label-stat field is not zero) On Thu, 27 Feb 2014, Yang, Daniel wrote: Thanks for both of you for the helps! I also find a 3rd solution: convert one of the labels to mgh and thus use it as overlay and use the other one as label in freeview. Doug: Creating an outlined label sounds pretty cool. I wonder whether either erosion or dilution would do the trick … some sort of tricky conjunction. Bruce: thanks!! -- Daniel (Yung-Jui) Yang, Ph.D. Postdoctoral Researcher Yale Child Study Center New Haven, CT Tel: (203) 737-5454 E-mail: yung-jui.y...@yale.edumailto:yung-jui.y...@yale.edu On 2/26/14 5:52 PM, Bruce Fischl fis...@nmr.mgh.harvard.edumailto:fis...@nmr.mgh.harvard.edu wrote: the other thing you could do is draw a path in tksurfer and have it be the outline, then load the inner label and display it as filled On Wed, 26 Feb 2014, Douglas N Greve wrote: No, you'd have to modify the label itself to exclude the center (and create an outline). I don't have any code to do this. For the other stuff, look at the help for mris_label2annot --help doug On 02/26/2014 05:35 PM, Yang, Daniel wrote: Doug, Thanks for your reply! In the annotation, can one of the label be just outlined and the other filled? I would really appreciate if you could provide a step-by-step example for this one… esp. how to create the colorLUT in this case... Best, Daniel -- Daniel (Yung-Jui) Yang, Ph.D. Postdoctoral Researcher Yale Child Study Center New Haven, CT Tel: (203) 737-5454 E-mail: _yung-jui.yang@yale.edu_mailto:_yung-jui.yang@yale.edu_ On 2/26/14 5:14 PM, Douglas N Greve gr...@nmr.mgh.harvard.edumailto:gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu wrote: I'm not sure about freeview, but you cannot do it in tksurfer. You can take your two labels and create an annotation with mris_label2annot (you get to specify the color) doug On 02/26/2014 05:12 PM, Yang, Daniel wrote: Dear FreeSurfer experts, Is it possible to display two labels in tksurfer or freeview, where one label is outlined with a certain color and the other label is filled with a different color? I want to show two labels, one is within the other one. If yes, could you please tell me the specific steps..? thanks a lot! Daniel -- Daniel (Yung-Jui) Yang, Ph.D. Postdoctoral Researcher Yale Child Study Center New Haven, CT Tel: (203) 737-5454 E-mail: _yung-jui.yang@yale.edu_mailto:_yung-jui.yang@yale.edu_ mailto:_yung-jui.yang@yale.edu_ ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu mailto: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.edumailto:gr...@nmr.mgh.harvard.edu mailto: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.edumailto:Freesurfer@nmr.mgh.harvard.edu mailto: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
Re: [Freesurfer] two labels in tksurfer/freeview?
Thanks, Bruce! I also found in tksurfer -- Tools -- Labels -- Erode/Dilate Selected Label ! -- Daniel (Yung-Jui) Yang, Ph.D. Postdoctoral Researcher Yale Child Study Center New Haven, CT Tel: (203) 737-5454 E-mail: yung-jui.y...@yale.edu On 2/26/14 8:02 PM, Bruce Fischl fis...@nmr.mgh.harvard.edumailto:fis...@nmr.mgh.harvard.edu wrote: mri_morphology for the .mgz for the label you can do it in tksurfer in the tools-label menu or use mri_label2label (at least I put it in the dev version, not sure if it is released yet) On Thu, 27 Feb 2014, Yang, Daniel wrote: By the way, what command can I use to erode a label/mgh..? -- Daniel (Yung-Jui) Yang, Ph.D. Postdoctoral Researcher Yale Child Study Center New Haven, CT Tel: (203) 737-5454 E-mail: yung-jui.y...@yale.edumailto:yung-jui.y...@yale.edu On 2/26/14 7:03 PM, Bruce Fischl fis...@nmr.mgh.harvard.edumailto:fis...@nmr.mgh.harvard.edu wrote: that's a good way to do it. You don't even need to save it as an mgz. You can just do tools-labels-copy label stats to overlay, then delete the label and you have an overlay from it (assuming the label-stat field is not zero) On Thu, 27 Feb 2014, Yang, Daniel wrote: Thanks for both of you for the helps! I also find a 3rd solution: convert one of the labels to mgh and thus use it as overlay and use the other one as label in freeview. Doug: Creating an outlined label sounds pretty cool. I wonder whether either erosion or dilution would do the trick … some sort of tricky conjunction. Bruce: thanks!! -- Daniel (Yung-Jui) Yang, Ph.D. Postdoctoral Researcher Yale Child Study Center New Haven, CT Tel: (203) 737-5454 E-mail: yung-jui.y...@yale.edumailto:yung-jui.y...@yale.edu On 2/26/14 5:52 PM, Bruce Fischl fis...@nmr.mgh.harvard.edumailto:fis...@nmr.mgh.harvard.edu wrote: the other thing you could do is draw a path in tksurfer and have it be the outline, then load the inner label and display it as filled On Wed, 26 Feb 2014, Douglas N Greve wrote: No, you'd have to modify the label itself to exclude the center (and create an outline). I don't have any code to do this. For the other stuff, look at the help for mris_label2annot --help doug On 02/26/2014 05:35 PM, Yang, Daniel wrote: Doug, Thanks for your reply! In the annotation, can one of the label be just outlined and the other filled? I would really appreciate if you could provide a step-by-step example for this one… esp. how to create the colorLUT in this case... Best, Daniel -- Daniel (Yung-Jui) Yang, Ph.D. Postdoctoral Researcher Yale Child Study Center New Haven, CT Tel: (203) 737-5454 E-mail: _yung-jui.yang@yale.edu_mailto:_yung-jui.yang@yale.edu_ On 2/26/14 5:14 PM, Douglas N Greve gr...@nmr.mgh.harvard.edumailto:gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu wrote: I'm not sure about freeview, but you cannot do it in tksurfer. You can take your two labels and create an annotation with mris_label2annot (you get to specify the color) doug On 02/26/2014 05:12 PM, Yang, Daniel wrote: Dear FreeSurfer experts, Is it possible to display two labels in tksurfer or freeview, where one label is outlined with a certain color and the other label is filled with a different color? I want to show two labels, one is within the other one. If yes, could you please tell me the specific steps..? thanks a lot! Daniel -- Daniel (Yung-Jui) Yang, Ph.D. Postdoctoral Researcher Yale Child Study Center New Haven, CT Tel: (203) 737-5454 E-mail: _yung-jui.yang@yale.edu_mailto:_yung-jui.yang@yale.edu_ mailto:_yung-jui.yang@yale.edu_ ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu mailto: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.edumailto:gr...@nmr.mgh.harvard.edu mailto: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.edumailto:Freesurfer@nmr.mgh.harvard.edu mailto: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
[Freesurfer] continusous x continuous interaction?
Dear FreeSurfer Experts, In the example here: http://surfer.nmr.mgh.harvard.edu/fswiki/Fsgdf1G2V, it describes the testing of the main effects of two continuous variables. In order to test the interaction effect, I think we can form an interaction term like age x weight as the third covariate, that is, Regressor1: All ones. Codes intercept/mean for Main Regressor2: age for each subject. Codes age slope for Main Regressor3: weight for each subject. Codes weight slope for Main Regressor4: age x weight for each subject. Codes age x weight interaction effect and then specify a contrast [0 0 0 1]? Is that the way to go? Best, Daniel -- Daniel (Yung-Jui) Yang, Ph.D. Postdoctoral Researcher Yale Child Study Center New Haven, CT Tel: (203) 737-5454 E-mail: yung-jui.y...@yale.edu ___ 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] interpretation of a 3-way interaction
Thanks, Doug! I guess in order to interpret the interaction correctly, I would need to extract the thickness value and plot the interaction. Best, Daniel -- Daniel (Yung-Jui) Yang, Ph.D. Postdoctoral Researcher Yale Child Study Center New Haven, CT Tel: (203) 737-5454 E-mail: yung-jui.y...@yale.edu On 2/20/14 2:57 PM, Douglas N Greve gr...@nmr.mgh.harvard.edumailto:gr...@nmr.mgh.harvard.edu wrote: The basic contrast is (PM-PF)-(CM-CF) If that is positive, then it will be red, otherwise blue This opens up a lot of possibilities as to what is driving the interaction, so it is hard to come up with a sentence like the one you are trying to state doug On 02/20/2014 02:25 PM, Yang, Daniel wrote: Dear FreeSurfers, I have two discrete and binary factors (Dx: patients vs. controls; Sex: female vs. male), one continuous variable (Age), one nuisance factor (IQ). If there is a 3-way interaction of Dx x Sex x Age, regressing out IQ, is the following interpretation correct? Red/yellow: In females (vs. males), the Age effect of cortical thickening is stronger in patients (vs. controls). Blue/cyan: In females (vs. males), the Age effect of cortical thinning is stronger in patients (vs. controls). Note. by stronger, I mean greater magnitude without sign. Thanks, Daniel ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto: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.edumailto: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.edumailto: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] ocn?
Dear FreeSurfers, I obtained a file from cluster analysis, called cache.th20.pos.sig.ocn.mgh Can you tell me what OCN stand for? And what is this file for? I tried to view it but was unable to see anything. Best, Daniel -- Daniel (Yung-Jui) Yang, Ph.D. Postdoctoral Researcher Yale Child Study Center New Haven, CT Tel: (203) 737-5454 E-mail: yung-jui.y...@yale.edu ___ 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] interpretation of a 3-way interaction
Dear FreeSurfers, I have two discrete and binary factors (Dx: patients vs. controls; Sex: female vs. male), one continuous variable (Age), one nuisance factor (IQ). If there is a 3-way interaction of Dx x Sex x Age, regressing out IQ, is the following interpretation correct? Red/yellow: In females (vs. males), the Age effect of cortical thickening is stronger in patients (vs. controls). Blue/cyan: In females (vs. males), the Age effect of cortical thinning is stronger in patients (vs. controls). Note. by stronger, I mean greater magnitude without sign. Thanks, Daniel ___ 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] interaction between two covariates in qdec?
Dear FreeSurfer Experts, In this webpage (http://surfer.nmr.mgh.harvard.edu/fswiki/FsgdExamples), it says Two Groups (1 Factor, Two Levels), Two Covariates. DODS only. QDEC-able. However, I cannot select more than one covariate in qdec. Any suggestion? I'm using qdec in Mac, FreeSurfer 5.3. Thanks! Daniel -- Daniel (Yung-Jui) Yang, Ph.D. Postdoctoral Researcher Yale Child Study Center New Haven, CT Tel: (203) 737-5454 E-mail: yung-jui.y...@yale.edu ___ 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] interaction between two covariates in qdec?
Sorry, I've found an answer to this here: https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg32928.html Daniel -- Daniel (Yung-Jui) Yang, Ph.D. Postdoctoral Researcher Yale Child Study Center New Haven, CT Tel: (203) 737-5454 E-mail: yung-jui.y...@yale.edu On 2/19/14 6:47 PM, Yang, Daniel yung-jui.y...@yale.edumailto:yung-jui.y...@yale.edu wrote: Dear FreeSurfer Experts, In this webpage (http://surfer.nmr.mgh.harvard.edu/fswiki/FsgdExamples), it says Two Groups (1 Factor, Two Levels), Two Covariates. DODS only. QDEC-able. However, I cannot select more than one covariate in qdec. Any suggestion? I'm using qdec in Mac, FreeSurfer 5.3. Thanks! Daniel -- Daniel (Yung-Jui) Yang, Ph.D. Postdoctoral Researcher Yale Child Study Center New Haven, CT Tel: (203) 737-5454 E-mail: yung-jui.y...@yale.edumailto:yung-jui.y...@yale.edu ___ 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] Contrasts and regressors involving two binary factors, 1 covariate, and 1 nuisance factor
Got it! I guess we may work around by specifying weighted contrast like [ 0.1 0.2 0.3 0.4 ] ? -- Daniel (Yung-Jui) Yang, Ph.D. Postdoctoral Researcher Yale Child Study Center New Haven, CT Tel: (203) 737-5454 E-mail: yung-jui.y...@yale.edu On 2/18/14 11:25 PM, Douglas Greve gr...@nmr.mgh.harvard.edumailto:gr...@nmr.mgh.harvard.edu wrote: Let's say you have four groups with 10 20 30 40 (100 total). The first group would get a weight of .25 where it only had 10% of the total. I don't think there is any way around this. On 2/18/14 4:07 PM, Yang, Daniel wrote: Doug, sorry, I am not sure I can fully understand. Do you mean the results are weighted MORE toward groups with smaller sample sizes (than groups with larger sample sizes)? -- Daniel (Yung-Jui) Yang, Ph.D. Postdoctoral Researcher Yale Child Study Center New Haven, CT Tel: (203) 737-5454 E-mail: yung-jui.y...@yale.edumailto:yung-jui.y...@yale.edu On 2/18/14 2:13 PM, Douglas N Greve gr...@nmr.mgh.harvard.edumailto:gr...@nmr.mgh.harvard.edu wrote: It will tend to weight smaller groups by a proportion greater than the number of subjects in the group. On 02/18/2014 01:58 PM, Yang, Daniel wrote: Thanks Doug! One follow-up question: since it's [0.25 0.25 0.25 0.25], would the effect be biased toward large sample sizes in one of the groups (versus the other groups)? Or, does FreeSurfer qdec take care of the unequal cell, in a possible way analogous to using Type III SS in the traditional ANOVA? Best, Daniel -- Daniel (Yung-Jui) Yang, Ph.D. Postdoctoral Researcher Yale Child Study Center New Haven, CT Tel: (203) 737-5454 E-mail: _yung-jui.yang@yale.edu_mailto:_yung-jui.yang@yale.edu_ On 2/18/14 1:30 PM, Douglas N Greve gr...@nmr.mgh.harvard.edumailto:gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edumailto:gr...@nmr.mgh.harvard.edu%3E wrote: That looks right to me doug On 02/18/2014 10:08 AM, Yang, Daniel wrote: Dear FreeSurfer experts, I have two binary factors (F1: F1L1 F1L2; F2: F2L1 F2L2), 1 covariate (COV), and 1 nuisance factor (NUI). I want to make sense of some specification of the regressors and contrasts. Because they are not described in http://surfer.nmr.mgh.harvard.edu/fswiki/Fsgdf4G1V, I post my understanding below. Can you let me know if it is correct? This model using the DODS method will have 12 regressors: Regressor1: 1's for F1L1 F2L1, 0 otherwise (i.e., offset for Group 1) Regressor2: 1's for F1L1 F2L2, 0 otherwise (i.e, offset for Group 2) Regressor3: 1's for F1L2 F2L1, 0 otherwise (i.e., offset for Group 3) Regressor4: 1's for F1L2 F2L2, 0 otherwise (i.e., offset for Group 4) Regressor5: COV for Group1 subjects, 0 otherwise (i.e., COV slope for Group 1) Regressor6: COV for Group2 subjects, 0 otherwise (i.e., COV slope for Group 2) Regressor7: COV for Group3 subjects, 0 otherwise (i.e., COV slope for Group 3) Regressor8: COV for Group4 subjects, 0 otherwise (i.e., COV slope for Group 4) Regressor9: NUI for Group1 subjects, 0 otherwise (i.e., NUI slope for Group 1) Regressor10: NUI for Group2 subjects, 0 otherwise (i.e., NUI slope for Group 2) Regressor11: NUI for Group3 subjects, 0 otherwise (i.e., NUI slope for Group 3) Regressor12: NUI for Group4 subjects, 0 otherwise (i.e., NUI slope for Group 4) Description1: Does the correlation between thickness and COV, accounting for F1 and F2, differ from 0? Nuisance factors: NUI Contrast1: [0 0 0 0 0.25 0.25 0.25 0.25 0 0 0 0] Best, Daniel -- Daniel (Yung-Jui) Yang, Ph.D. Postdoctoral Researcher Yale Child Study Center New Haven, CT Tel: (203) 737-5454 E-mail: _yung-jui.yang@yale.edu_mailto:_yung-jui.yang@yale.edu_ mailto:_yung-jui.yang@yale.edu_ ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu mailto: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.edumailto:gr...@nmr.mgh.harvard.edu mailto: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.htmlhttp://www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve
[Freesurfer] Contrasts and regressors involving two binary factors, 1 covariate, and 1 nuisance factor
Dear FreeSurfer experts, I have two binary factors (F1: F1L1 F1L2; F2: F2L1 F2L2), 1 covariate (COV), and 1 nuisance factor (NUI). I want to make sense of some specification of the regressors and contrasts. Because they are not described in http://surfer.nmr.mgh.harvard.edu/fswiki/Fsgdf4G1V, I post my understanding below. Can you let me know if it is correct? This model using the DODS method will have 12 regressors: Regressor1: 1's for F1L1 F2L1, 0 otherwise (i.e., offset for Group 1) Regressor2: 1's for F1L1 F2L2, 0 otherwise (i.e, offset for Group 2) Regressor3: 1's for F1L2 F2L1, 0 otherwise (i.e., offset for Group 3) Regressor4: 1's for F1L2 F2L2, 0 otherwise (i.e., offset for Group 4) Regressor5: COV for Group1 subjects, 0 otherwise (i.e., COV slope for Group 1) Regressor6: COV for Group2 subjects, 0 otherwise (i.e., COV slope for Group 2) Regressor7: COV for Group3 subjects, 0 otherwise (i.e., COV slope for Group 3) Regressor8: COV for Group4 subjects, 0 otherwise (i.e., COV slope for Group 4) Regressor9: NUI for Group1 subjects, 0 otherwise (i.e., NUI slope for Group 1) Regressor10: NUI for Group2 subjects, 0 otherwise (i.e., NUI slope for Group 2) Regressor11: NUI for Group3 subjects, 0 otherwise (i.e., NUI slope for Group 3) Regressor12: NUI for Group4 subjects, 0 otherwise (i.e., NUI slope for Group 4) Description1: Does the correlation between thickness and COV, accounting for F1 and F2, differ from 0? Nuisance factors: NUI Contrast1: [0 0 0 0 0.25 0.25 0.25 0.25 0 0 0 0] Best, Daniel -- Daniel (Yung-Jui) Yang, Ph.D. Postdoctoral Researcher Yale Child Study Center New Haven, CT Tel: (203) 737-5454 E-mail: yung-jui.y...@yale.edu ___ 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] Contrasts and regressors involving two binary factors, 1 covariate, and 1 nuisance factor
Thanks Doug! One follow-up question: since it's [0.25 0.25 0.25 0.25], would the effect be biased toward large sample sizes in one of the groups (versus the other groups)? Or, does FreeSurfer qdec take care of the unequal cell, in a possible way analogous to using Type III SS in the traditional ANOVA? Best, Daniel -- Daniel (Yung-Jui) Yang, Ph.D. Postdoctoral Researcher Yale Child Study Center New Haven, CT Tel: (203) 737-5454 E-mail: yung-jui.y...@yale.edu On 2/18/14 1:30 PM, Douglas N Greve gr...@nmr.mgh.harvard.edumailto:gr...@nmr.mgh.harvard.edu wrote: That looks right to me doug On 02/18/2014 10:08 AM, Yang, Daniel wrote: Dear FreeSurfer experts, I have two binary factors (F1: F1L1 F1L2; F2: F2L1 F2L2), 1 covariate (COV), and 1 nuisance factor (NUI). I want to make sense of some specification of the regressors and contrasts. Because they are not described in http://surfer.nmr.mgh.harvard.edu/fswiki/Fsgdf4G1V, I post my understanding below. Can you let me know if it is correct? This model using the DODS method will have 12 regressors: Regressor1: 1's for F1L1 F2L1, 0 otherwise (i.e., offset for Group 1) Regressor2: 1's for F1L1 F2L2, 0 otherwise (i.e, offset for Group 2) Regressor3: 1's for F1L2 F2L1, 0 otherwise (i.e., offset for Group 3) Regressor4: 1's for F1L2 F2L2, 0 otherwise (i.e., offset for Group 4) Regressor5: COV for Group1 subjects, 0 otherwise (i.e., COV slope for Group 1) Regressor6: COV for Group2 subjects, 0 otherwise (i.e., COV slope for Group 2) Regressor7: COV for Group3 subjects, 0 otherwise (i.e., COV slope for Group 3) Regressor8: COV for Group4 subjects, 0 otherwise (i.e., COV slope for Group 4) Regressor9: NUI for Group1 subjects, 0 otherwise (i.e., NUI slope for Group 1) Regressor10: NUI for Group2 subjects, 0 otherwise (i.e., NUI slope for Group 2) Regressor11: NUI for Group3 subjects, 0 otherwise (i.e., NUI slope for Group 3) Regressor12: NUI for Group4 subjects, 0 otherwise (i.e., NUI slope for Group 4) Description1: Does the correlation between thickness and COV, accounting for F1 and F2, differ from 0? Nuisance factors: NUI Contrast1: [0 0 0 0 0.25 0.25 0.25 0.25 0 0 0 0] Best, Daniel -- Daniel (Yung-Jui) Yang, Ph.D. Postdoctoral Researcher Yale Child Study Center New Haven, CT Tel: (203) 737-5454 E-mail: _yung-jui.yang@yale.edu_mailto:_yung-jui.yang@yale.edu_ ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto: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.edumailto: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.edumailto: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] Contrasts and regressors involving two binary factors, 1 covariate, and 1 nuisance factor
Doug, sorry, I am not sure I can fully understand. Do you mean the results are weighted MORE toward groups with smaller sample sizes (than groups with larger sample sizes)? -- Daniel (Yung-Jui) Yang, Ph.D. Postdoctoral Researcher Yale Child Study Center New Haven, CT Tel: (203) 737-5454 E-mail: yung-jui.y...@yale.edu On 2/18/14 2:13 PM, Douglas N Greve gr...@nmr.mgh.harvard.edumailto:gr...@nmr.mgh.harvard.edu wrote: It will tend to weight smaller groups by a proportion greater than the number of subjects in the group. On 02/18/2014 01:58 PM, Yang, Daniel wrote: Thanks Doug! One follow-up question: since it's [0.25 0.25 0.25 0.25], would the effect be biased toward large sample sizes in one of the groups (versus the other groups)? Or, does FreeSurfer qdec take care of the unequal cell, in a possible way analogous to using Type III SS in the traditional ANOVA? Best, Daniel -- Daniel (Yung-Jui) Yang, Ph.D. Postdoctoral Researcher Yale Child Study Center New Haven, CT Tel: (203) 737-5454 E-mail: _yung-jui.yang@yale.edu_mailto:_yung-jui.yang@yale.edu_ On 2/18/14 1:30 PM, Douglas N Greve gr...@nmr.mgh.harvard.edumailto:gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu wrote: That looks right to me doug On 02/18/2014 10:08 AM, Yang, Daniel wrote: Dear FreeSurfer experts, I have two binary factors (F1: F1L1 F1L2; F2: F2L1 F2L2), 1 covariate (COV), and 1 nuisance factor (NUI). I want to make sense of some specification of the regressors and contrasts. Because they are not described in http://surfer.nmr.mgh.harvard.edu/fswiki/Fsgdf4G1V, I post my understanding below. Can you let me know if it is correct? This model using the DODS method will have 12 regressors: Regressor1: 1's for F1L1 F2L1, 0 otherwise (i.e., offset for Group 1) Regressor2: 1's for F1L1 F2L2, 0 otherwise (i.e, offset for Group 2) Regressor3: 1's for F1L2 F2L1, 0 otherwise (i.e., offset for Group 3) Regressor4: 1's for F1L2 F2L2, 0 otherwise (i.e., offset for Group 4) Regressor5: COV for Group1 subjects, 0 otherwise (i.e., COV slope for Group 1) Regressor6: COV for Group2 subjects, 0 otherwise (i.e., COV slope for Group 2) Regressor7: COV for Group3 subjects, 0 otherwise (i.e., COV slope for Group 3) Regressor8: COV for Group4 subjects, 0 otherwise (i.e., COV slope for Group 4) Regressor9: NUI for Group1 subjects, 0 otherwise (i.e., NUI slope for Group 1) Regressor10: NUI for Group2 subjects, 0 otherwise (i.e., NUI slope for Group 2) Regressor11: NUI for Group3 subjects, 0 otherwise (i.e., NUI slope for Group 3) Regressor12: NUI for Group4 subjects, 0 otherwise (i.e., NUI slope for Group 4) Description1: Does the correlation between thickness and COV, accounting for F1 and F2, differ from 0? Nuisance factors: NUI Contrast1: [0 0 0 0 0.25 0.25 0.25 0.25 0 0 0 0] Best, Daniel -- Daniel (Yung-Jui) Yang, Ph.D. Postdoctoral Researcher Yale Child Study Center New Haven, CT Tel: (203) 737-5454 E-mail: _yung-jui.yang@yale.edu_mailto:_yung-jui.yang@yale.edu_ mailto:_yung-jui.yang@yale.edu_ ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu mailto: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.edumailto:gr...@nmr.mgh.harvard.edu mailto: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.edumailto:Freesurfer@nmr.mgh.harvard.edu mailto: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
[Freesurfer] one factor with three levels in qdec?
Dear FreeSurfer creators and experts, I am trying to run qdec with one discrete with three levels (i.e., https://surfer.nmr.mgh.harvard.edu/fswiki/Fsgdf3G0V) but there is some error message: ERROR: no contrasts specified. Error in Analyze: command failed: mri_glmfit --y … I am wondering if three levels a discrete factor are currently supported in qdec in FS 5.3? Thanks! Daniel -- Daniel (Yung-Jui) Yang, Ph.D. Postdoctoral Researcher Yale Child Study Center New Haven, CT Tel: (203) 737-5454 E-mail: yung-jui.y...@yale.edu ___ 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] one factor with three levels in qdec?
Hi Doug, Thanks, I see. That really helps a lot. I will try to use the command line version. Best, Daniel -- Daniel (Yung-Jui) Yang, Ph.D. Postdoctoral Researcher Yale Child Study Center New Haven, CT Tel: (203) 737-5454 E-mail: yung-jui.y...@yale.edu On 2/16/14 7:13 PM, Douglas Greve gr...@nmr.mgh.harvard.edumailto:gr...@nmr.mgh.harvard.edu wrote: sorry, you cannot have three levels in qdec (two max). You will need to use the command line stream (ie, create a FSGD file and consrast files, run mris_preproc, mri_surf2surf to smooth, mri_glmfit, and mri_glmfit-sim). See the wiki for more details. doug On 2/16/14 4:53 PM, Yang, Daniel wrote: Dear FreeSurfer creators and experts, I am trying to run qdec with one discrete with three levels (i.e., https://surfer.nmr.mgh.harvard.edu/fswiki/Fsgdf3G0V) but there is some error message: ERROR: no contrasts specified. Error in Analyze: command failed: mri_glmfit --y … I am wondering if three levels a discrete factor are currently supported in qdec in FS 5.3? Thanks! Daniel -- Daniel (Yung-Jui) Yang, Ph.D. Postdoctoral Researcher Yale Child Study Center New Haven, CT Tel: (203) 737-5454 E-mail: yung-jui.y...@yale.edumailto:yung-jui.y...@yale.edu ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@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] Interaction test
Dear FreeSurfer developers and experts, If I have a binary factor (Group1: patients, Group2: controls) and a continuous variable (age), I know I can follow Contrast2 in the following wiki to test the interaction effect. http://surfer.nmr.mgh.harvard.edu/fswiki/Fsgdf2G1V Contrast2: [0 0 1 -1] tests if Age slope in patients (Group1) controls (Group2), and if Age slope_Group1 - Age slope_Group2 0, I can see red/yellow. For example, cortical thickening is accelerated in patients (vs. controls). I am wondering how I can test for whether cortical thinning is accelerated in patients (vs. controls)? Here, the slope for Age would be negative. And if cortical thinning is accelerated in Group1 (vs. Group2), I should observe Age slope_Group1 Age slope_Group2, that is, Age slope_Group1 - Age slope_Group2 0, thus, I should expect to see blue/cyan? Best, Daniel -- Daniel (Yung-Jui) Yang, Ph.D. Postdoctoral Researcher Yale Child Study Center New Haven, CT Tel: (203) 737-5454 E-mail: yung-jui.y...@yale.edu ___ 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] MPRAGE SNR
Dear FreeSurfer Experts, Is there a way to estimate the SNR in MPRAGE scans besides using wm-anat-snr ? For examples, I read that SNR is improved in multiecho MPRAGE and I am wondering how that is computed? Thanks! Daniel ___ 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] rh or lh?
Thanks! Got you. If only there can be a header/meta info/tag added into mgh -- that would be great. I believe it can help prevent errors and improve processing efficiency :) Best, Daniel -- Yung-Jui Daniel Yang, PhD Postdoctoral Researcher Yale Child Study Center New Haven, CT (203) 737-5454 On 10/1/13 7:55 PM, Douglas N Greve gr...@nmr.mgh.harvard.edumailto:gr...@nmr.mgh.harvard.edu wrote: Not really. If this is an individual subject, you can look at the number of vertices and see whether it matches lh or rh. For fsaverage, the number of vertices is the same for lh and rh. On 10/01/2013 07:45 PM, Yang, Daniel wrote: Dear FreeSurfer Experts, Is there a program that can automatically judge whether a mgh is in the rh or lh? Thanks! Daniel -- Yung-Jui Daniel Yang, PhD Postdoctoral Researcher Yale Child Study Center New Haven, CT (203) 737-5454 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto: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.edumailto: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.edumailto: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] overlay mni152 activation -- difference between tksurfer and freeview
Hi Doug, Just checking again, because I haven't heard from you. So the purpose is to use mri_vol2surf is convert MNI152 to a FreeSurfer (MNI305) mgh file. I am not sure about the correct register.dat to use. The mni152.register.dat is for MNI305 - MNI152 though. I'm assuming that there exists some sort of inverse mni152.register.dat somewhere? Thanks! Daniel -- Yung-Jui Daniel Yang, PhD Postdoctoral Researcher Yale Child Study Center New Haven, CT (203) 737-5454 On 9/27/13 6:44 AM, Yang, Daniel yung-jui.y...@yale.edumailto:yung-jui.y...@yale.edu wrote: Thanks Doug! Because it maps from a MNI152 space to the FreeSurfer average space, do you know what register.dat I can use? Is it some sort of inverse mni152.register.dat? Thanks! Daniel -- Yung-Jui Daniel Yang, PhD Postdoctoral Researcher Yale Child Study Center New Haven, CT (203) 737-5454 On 9/26/13 12:26 PM, Douglas N Greve gr...@nmr.mgh.harvard.edumailto:gr...@nmr.mgh.harvard.edu wrote: They might be sampling to different surfaces. To make sure they show the same exact thing, try mapping the data to the surface with mri_vol2surf doug On 09/25/2013 08:31 AM, Yang, Daniel wrote: Dear FreeSurfer Experts, I am trying to visualize fMRI activation (generated from fsl) on the fsaverage inflated surface, using mni152.register.dat. It's odd that I find the results to be slightly different between tksurfer and freeview. However, I made sure that I am using the same threshold... Judging from fslview, I think the result with freeview is more accurate -- is it due to tksurfer loading orig.mgz by default, and free view loading something else? Thanks! Daniel -- Yung-Jui Daniel Yang, PhD Postdoctoral Researcher Yale Child Study Center New Haven, CT (203) 737-5454 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto: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.edumailto: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.edumailto: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] overlay mni152 activation -- difference between tksurfer and freeview
Hi Doug, I understand. But the end product turned out to be a much smaller brain … so I thought there is something wrong. What should I do here? Thanks! Daniel -- Yung-Jui Daniel Yang, PhD Postdoctoral Researcher Yale Child Study Center New Haven, CT (203) 737-5454 On 10/1/13 6:00 PM, Douglas N Greve gr...@nmr.mgh.harvard.edumailto:gr...@nmr.mgh.harvard.edu wrote: The way the software is set up, you should use mni152.register.dat with mri_vol2surf to map mni152 volumes to the fsaverage (ie MNI305) surfaces doug On 10/01/2013 05:49 PM, Yang, Daniel wrote: Hi Doug, Just checking again, because I haven't heard from you. So the purpose is to use mri_vol2surf is convert MNI152 to a FreeSurfer (MNI305) mgh file. I am not sure about the correct register.dat to use. The mni152.register.dat is for MNI305 - MNI152 though. I'm assuming that there exists some sort of inverse mni152.register.dat somewhere? Thanks! Daniel -- Yung-Jui Daniel Yang, PhD Postdoctoral Researcher Yale Child Study Center New Haven, CT (203) 737-5454 On 9/27/13 6:44 AM, Yang, Daniel yung-jui.y...@yale.edumailto:yung-jui.y...@yale.edu mailto:yung-jui.y...@yale.edu wrote: Thanks Doug! Because it maps from a MNI152 space to the FreeSurfer average space, do you know what register.dat I can use? Is it some sort of inverse mni152.register.dat? Thanks! Daniel -- Yung-Jui Daniel Yang, PhD Postdoctoral Researcher Yale Child Study Center New Haven, CT (203) 737-5454 On 9/26/13 12:26 PM, Douglas N Greve gr...@nmr.mgh.harvard.edumailto:gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu wrote: They might be sampling to different surfaces. To make sure they show the same exact thing, try mapping the data to the surface with mri_vol2surf doug On 09/25/2013 08:31 AM, Yang, Daniel wrote: Dear FreeSurfer Experts, I am trying to visualize fMRI activation (generated from fsl) on the fsaverage inflated surface, using mni152.register.dat. It's odd that I find the results to be slightly different between tksurfer and freeview. However, I made sure that I am using the same threshold... Judging from fslview, I think the result with freeview is more accurate -- is it due to tksurfer loading orig.mgz by default, and free view loading something else? Thanks! Daniel -- Yung-Jui Daniel Yang, PhD Postdoctoral Researcher Yale Child Study Center New Haven, CT (203) 737-5454 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu mailto: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.edumailto:gr...@nmr.mgh.harvard.edu mailto: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.edumailto:Freesurfer@nmr.mgh.harvard.edu mailto: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.edumailto: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.edumailto: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
[Freesurfer] rh or lh?
Dear FreeSurfer Experts, Is there a program that can automatically judge whether a mgh is in the rh or lh? Thanks! Daniel -- Yung-Jui Daniel Yang, PhD Postdoctoral Researcher Yale Child Study Center New Haven, CT (203) 737-5454 ___ 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] overlay mni152 activation -- difference between tksurfer and freeview
Thanks Doug! Because it maps from a MNI152 space to the FreeSurfer average space, do you know what register.dat I can use? Is it some sort of inverse mni152.register.dat? Thanks! Daniel -- Yung-Jui Daniel Yang, PhD Postdoctoral Researcher Yale Child Study Center New Haven, CT (203) 737-5454 On 9/26/13 12:26 PM, Douglas N Greve gr...@nmr.mgh.harvard.edumailto:gr...@nmr.mgh.harvard.edu wrote: They might be sampling to different surfaces. To make sure they show the same exact thing, try mapping the data to the surface with mri_vol2surf doug On 09/25/2013 08:31 AM, Yang, Daniel wrote: Dear FreeSurfer Experts, I am trying to visualize fMRI activation (generated from fsl) on the fsaverage inflated surface, using mni152.register.dat. It's odd that I find the results to be slightly different between tksurfer and freeview. However, I made sure that I am using the same threshold... Judging from fslview, I think the result with freeview is more accurate -- is it due to tksurfer loading orig.mgz by default, and free view loading something else? Thanks! Daniel -- Yung-Jui Daniel Yang, PhD Postdoctoral Researcher Yale Child Study Center New Haven, CT (203) 737-5454 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto: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.edumailto: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.edumailto: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] overlay mni152 activation -- difference between tksurfer and freeview
Dear FreeSurfer Experts, I am trying to visualize fMRI activation (generated from fsl) on the fsaverage inflated surface, using mni152.register.dat. It's odd that I find the results to be slightly different between tksurfer and freeview. However, I made sure that I am using the same threshold... Judging from fslview, I think the result with freeview is more accurate -- is it due to tksurfer loading orig.mgz by default, and free view loading something else? Thanks! Daniel -- Yung-Jui Daniel Yang, PhD Postdoctoral Researcher Yale Child Study Center New Haven, CT (203) 737-5454 ___ 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] label stats?
Dear all, I wanted to add that I would to obtain the stats associated with fsaverage. When I used mris_anatomical_stats on fsaverage, it gave me a warning message: could not read fsaverage/mri/wm.mgz Thanks! Daniel -- Yung-Jui Daniel Yang, PhD Postdoctoral Researcher Yale Child Study Center New Haven, CT (203) 737-5454 On 9/23/13 3:40 PM, Yang, Daniel yung-jui.y...@yale.edumailto:yung-jui.y...@yale.edu wrote: Dear FreeSurfer Experts, Is there a way to use command line to obtain the stats (e.g., area) for a given label? Thanks! Daniel -- Yung-Jui Daniel Yang, PhD Postdoctoral Researcher Yale Child Study Center New Haven, CT (203) 737-5454 ___ 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] label stats?
Dear FreeSurfer Experts, Is there a way to use command line to obtain the stats (e.g., area) for a given label? Thanks! Daniel -- Yung-Jui Daniel Yang, PhD Postdoctoral Researcher Yale Child Study Center New Haven, CT (203) 737-5454 ___ 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] label stats?
Hi Bruce, I am sorry. I wasn't clear.. I wanted to obtain the label stats associated with fsaverage. I also just read this earlier message: http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg10441.html Are things different now -- is there an easy way to obtain fsaverage's stats with the standard labels? They will serve as a relative basis for comparison only. Thanks! Daniel -- Yung-Jui Daniel Yang, PhD Postdoctoral Researcher Yale Child Study Center New Haven, CT (203) 737-5454 On 9/23/13 4:37 PM, Bruce Fischl fis...@nmr.mgh.harvard.edumailto:fis...@nmr.mgh.harvard.edu wrote: Hi Daniel you can give it to mris_anatomical_stats with the -l label command cheers Bruce On Mon, 23 Sep 2013, Yang, Daniel wrote: Dear FreeSurfer Experts, Is there a way to use command line to obtain the stats (e.g., area) for a given label? Thanks! Daniel -- Yung-Jui Daniel Yang, PhD Postdoctoral Researcher Yale Child Study Center New Haven, CT (203) 737-5454 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] break down a label?
Dear FreeSurfer Experts, If I have a label that spans across multiple anatomical regions, is it possible to automatically break it down according to aparc.annot? Thanks! Daniel -- Yung-Jui Daniel Yang, PhD Postdoctoral Researcher Yale Child Study Center New Haven, CT (203) 737-5454 ___ 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] break down a label?
Hi Bruce, Cool! This works nicely! Thanks so much! Best, Daniel -- Yung-Jui Daniel Yang, PhD Postdoctoral Researcher Yale Child Study Center New Haven, CT (203) 737-5454 On 9/22/13 10:07 AM, Bruce Fischl fis...@nmr.mgh.harvard.edumailto:fis...@nmr.mgh.harvard.edu wrote: Hi Daniel you could do this in tksurfer, but I don't think there is a commandline facility for it (although you could write a matlab script to do so). In tksurfer, I would: 1. Load the label. 2. Copy label statistics to overlay 3. Delete the label 4. Load the parcellation you want to use 5. Use the custom fill with up to functional threshold and up to different labels check (not sure of the exact wording). 6. Left click in a region that you want, and click fill. 7. Save the label. 8. Right click to unselect and go to 6 until you are done with all the subregions cheers Bruce On Sun, 22 Sep 2013, Yang, Daniel wrote: Dear FreeSurfer Experts, If I have a label that spans across multiple anatomical regions, is it possible to automatically break it down according to aparc.annot? Thanks! Daniel -- Yung-Jui Daniel Yang, PhD Postdoctoral Researcher Yale Child Study Center New Haven, CT (203) 737-5454 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] dilate a label?
Hi FreeSurfer Experts, Is it possible to dilate a label using command line? Thanks! Daniel -- Yung-Jui Daniel Yang, PhD Postdoctoral Researcher Yale Child Study Center New Haven, CT (203) 737-5454 ___ 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] dilate a label?
Hi Bruce, That's cool! Thanks so much! Best, Daniel -- Yung-Jui Daniel Yang, PhD Postdoctoral Researcher Yale Child Study Center New Haven, CT (203) 737-5454 On 9/22/13 9:24 PM, Bruce Fischl fis...@nmr.mgh.harvard.edumailto:fis...@nmr.mgh.harvard.edu wrote: Hi Daniel, yes, mri_label2label will do this, at least the current dev version and maybe 5.3: mri_label2label | grep dilate --dilate Ndilate the label N times before writing cheers Bruce On Mon, 23 Sep 2013, Yang, Daniel wrote: Hi FreeSurfer Experts, Is it possible to dilate a label using command line? Thanks! Daniel -- Yung-Jui Daniel Yang, PhD Postdoctoral Researcher Yale Child Study Center New Haven, CT (203) 737-5454 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] dilate a label?
It seems that only in dev version, mri_label2label supports dilation. But I find that in 5.3, mris_label_calc is able to perform dilation too! Best, Daniel -- Yung-Jui Daniel Yang, PhD Postdoctoral Researcher Yale Child Study Center New Haven, CT (203) 737-5454 On 9/22/13 9:38 PM, Yang, Daniel yung-jui.y...@yale.edumailto:yung-jui.y...@yale.edu wrote: Hi Bruce, That's cool! Thanks so much! Best, Daniel -- Yung-Jui Daniel Yang, PhD Postdoctoral Researcher Yale Child Study Center New Haven, CT (203) 737-5454 On 9/22/13 9:24 PM, Bruce Fischl fis...@nmr.mgh.harvard.edumailto:fis...@nmr.mgh.harvard.edu wrote: Hi Daniel, yes, mri_label2label will do this, at least the current dev version and maybe 5.3: mri_label2label | grep dilate --dilate Ndilate the label N times before writing cheers Bruce On Mon, 23 Sep 2013, Yang, Daniel wrote: Hi FreeSurfer Experts, Is it possible to dilate a label using command line? Thanks! Daniel -- Yung-Jui Daniel Yang, PhD Postdoctoral Researcher Yale Child Study Center New Haven, CT (203) 737-5454 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] TALx coordinates
Hi Doug, I'm looking at the $FREESURFER_HOME/average/mni152.register.dat and I can see some relation with the formula you provided. It appears that y and z are swapped, and the offsets are all different. Do you know why they are so? By the way, is there a way I can ask mri_surfcluster to read mni152.register.dat? fsaverage 1.00 1.00 0.15 9.975314e-01 -7.324822e-03 1.760415e-02 9.570923e-01 -1.296475e-02 -9.262221e-03 9.970638e-01 -1.781596e+01 -1.459537e-02 -1.000945e+00 2.444772e-03 -1.854964e+01 0 0 0 1 tkregister Thanks a lot! Daniel -- Yung-Jui Daniel Yang, PhD Postdoctoral Researcher Yale Child Study Center New Haven, CT (203) 737-5454 On 9/15/13 3:53 PM, Douglas Greve gr...@nmr.mgh.harvard.edumailto:gr...@nmr.mgh.harvard.edu wrote: That converts from MNI305 to MNI152 without going through the talairach itself. When FS computes Tal coords, it does so nonlinearly. doug On 9/11/13 12:08 PM, Yang, Daniel wrote: Hi Doug, It's pretty awesome. So accordingly, MNI152x = (0.9975) MNI305x + (-0.0073) MNI305y + (0.0176) MNI305z + (-0.0429) * 1 MNI152y = (0.0146) MNI305x + (1.0009) MNI305y + (-0.0024) MNI305z + (1.5496) * 1 MNI152z = (-0.0130) MNI305 + (-0.0093) MNI305y + (0.9971) MNI305z + (1.1840) * 1 The last row of the M (i.e., [-0.0429 1.5496 1.1840]') looks like some sort of offset to me, correct? In other words, we are obtaining MNI305 first, Freesurfer convert that to TAL by default (question: is it done linearly or non-linearly?), and then we can manually convert it to MNI152 also. Thanks so much! Daniel -- Yung-Jui Daniel Yang, PhD Postdoctoral Researcher Yale Child Study Center New Haven, CT (203) 737-5454 On 9/10/13 6:52 PM, Douglas N Greve gr...@nmr.mgh.harvard.edumailto:gr...@nmr.mgh.harvard.edu wrote: Hi Yang, I've computed a matrix that should do the trick. If you are in matlab, then M = [0.9975 -0.00730.0176 -0.0429 0.01461.0009 -0.00241.5496 -0.0130 -0.00930.99711.1840 0 0 01.] P305 = [MNI305x MNI305y MNI305z 1]'; P152 = M*P305 Can you give this a shot and see if it makes sense? It will probably be hard to tell since the matrix is pretty close to identity. doug On 09/10/2013 05:17 PM, Yang, Daniel wrote: Thanks, Doug. I am really hoping to get MNI152 (because I also use fsl). Are MNI305 and MNI152 the same? How can I obtain MNI152 coordinates? Best, Daniel -- Yung-Jui Daniel Yang, PhD Postdoctoral Researcher Yale Child Study Center New Haven, CT (203) 737-5454 On 9/10/13 5:14 PM, Douglas N Greve gr...@nmr.mgh.harvard.edumailto:gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edumailto:gr...@nmr.mgh.harvard.edu%3E wrote: It is an estimate of Tal coords from the MNI305. See http://imaging.mrc-cbu.cam.ac.uk/imaging/MniTalairach If you want MNI305, run mri_surfcluster with --nofixmni doug On 09/10/2013 05:08 PM, Yang, Daniel wrote: Hi all, The output of mri_surfcluster --sum shows TalX TalY TalZ. I am wondering if they are based on the Talairach system or some sort of MNI-Talairach system. If the latter, can you tell me something more about it? Like a webpage that describes its relationship between the MNI152 or the Talairach system? I find it confusing because mri_surfcluster said: INFO: fixing MNI talairach coordinates Thanks! Daniel -- Yung-Jui Daniel Yang, PhD Postdoctoral Researcher Yale Child Study Center New Haven, CT (203) 737-5454 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu mailto: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.edumailto:gr...@nmr.mgh.harvard.edu mailto: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.htmlhttp://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.edumailto:Freesurfer@nmr.mgh.harvard.edu mailto: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
Re: [Freesurfer] TALx coordinates
Thanks, Doug!! That sounds good. I think if FreeSurfer can include MNI152 output option in its next release, that would be awesome! Best, Daniel On Sep 15, 2013, at 3:54 PM, Douglas Greve gr...@nmr.mgh.harvard.edumailto:gr...@nmr.mgh.harvard.edu wrote: That converts from MNI305 to MNI152 without going through the talairach itself. When FS computes Tal coords, it does so nonlinearly. doug On 9/11/13 12:08 PM, Yang, Daniel wrote: Hi Doug, It's pretty awesome. So accordingly, MNI152x = (0.9975) MNI305x + (-0.0073) MNI305y + (0.0176) MNI305z + (-0.0429) * 1 MNI152y = (0.0146) MNI305x + (1.0009) MNI305y + (-0.0024) MNI305z + (1.5496) * 1 MNI152z = (-0.0130) MNI305 + (-0.0093) MNI305y + (0.9971) MNI305z + (1.1840) * 1 The last row of the M (i.e., [-0.0429 1.5496 1.1840]') looks like some sort of offset to me, correct? In other words, we are obtaining MNI305 first, Freesurfer convert that to TAL by default (question: is it done linearly or non-linearly?), and then we can manually convert it to MNI152 also. Thanks so much! Daniel -- Yung-Jui Daniel Yang, PhD Postdoctoral Researcher Yale Child Study Center New Haven, CT (203) 737-5454 On 9/10/13 6:52 PM, Douglas N Greve gr...@nmr.mgh.harvard.edumailto:gr...@nmr.mgh.harvard.edu wrote: Hi Yang, I've computed a matrix that should do the trick. If you are in matlab, then M = [0.9975 -0.00730.0176 -0.0429 0.01461.0009 -0.00241.5496 -0.0130 -0.00930.99711.1840 0 0 01.] P305 = [MNI305x MNI305y MNI305z 1]'; P152 = M*P305 Can you give this a shot and see if it makes sense? It will probably be hard to tell since the matrix is pretty close to identity. doug On 09/10/2013 05:17 PM, Yang, Daniel wrote: Thanks, Doug. I am really hoping to get MNI152 (because I also use fsl). Are MNI305 and MNI152 the same? How can I obtain MNI152 coordinates? Best, Daniel -- Yung-Jui Daniel Yang, PhD Postdoctoral Researcher Yale Child Study Center New Haven, CT (203) 737-5454 On 9/10/13 5:14 PM, Douglas N Greve gr...@nmr.mgh.harvard.edumailto:gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edumailto:gr...@nmr.mgh.harvard.edu%3E wrote: It is an estimate of Tal coords from the MNI305. See http://imaging.mrc-cbu.cam.ac.uk/imaging/MniTalairach If you want MNI305, run mri_surfcluster with --nofixmni doug On 09/10/2013 05:08 PM, Yang, Daniel wrote: Hi all, The output of mri_surfcluster --sum shows TalX TalY TalZ. I am wondering if they are based on the Talairach system or some sort of MNI-Talairach system. If the latter, can you tell me something more about it? Like a webpage that describes its relationship between the MNI152 or the Talairach system? I find it confusing because mri_surfcluster said: INFO: fixing MNI talairach coordinates Thanks! Daniel -- Yung-Jui Daniel Yang, PhD Postdoctoral Researcher Yale Child Study Center New Haven, CT (203) 737-5454 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu mailto: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.edumailto:gr...@nmr.mgh.harvard.edu mailto: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.htmlhttp://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.edumailto:Freesurfer@nmr.mgh.harvard.edu mailto: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. -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edumailto: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
[Freesurfer] Maximum significance
Hi all, I performed cluster analyses and obtained several clusters, which are indicated by the corresponding maximum significance levels. For example, cluster one -- 4.00, and cluster two -- 4.00. Then I did a conjunction analysis to see their overlap, and then did a mri_surfcluster to get the clusters from the overlap. Then I observed that I have TalX TalY TalZ for each cluster in the overlap -- my question is, how does mri_surfcluster determine those coordinates? Since the whole cluster might have the same significance level everywhere? Thanks, Daniel ___ 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] z-scores versus raw_age for correction in GLM_FIT or qdec
Just my two cents: I think the age should be mean-centered; otherwise, the meaning of the other variables need to be interpreted as age = 0 (rather than mean age = 0). In general, I believe in qdec or mri_glmfit, the effects of Class variable are interpreted as 0 on the continuous/nuisance variables. Best, Daniel -- Yung-Jui Daniel Yang, PhD Postdoctoral Researcher Yale Child Study Center New Haven, CT (203) 737-5454 On 9/11/13 1:13 PM, Erik Lindberg erikoloflindb...@gmail.commailto:erikoloflindb...@gmail.com wrote: Dear Douglas, attached you´ll find the two y.fsgd file from the analysis run in GLM_FIT. the results are completely different (the z-score converted age produces a believable result, while the result correcting with raw age scores seems completely wrong. best regards Olof ___ 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] Interpretation of red/blue clusters in group analysis
you can refer to this post: http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg31297.html -- Yung-Jui Daniel Yang, PhD Postdoctoral Researcher Yale Child Study Center New Haven, CT (203) 737-5454 On 9/12/13 9:04 AM, Anita van Loenhoud acvanloenh...@gmail.commailto:acvanloenh...@gmail.com wrote: Hi FreeSurfers, I'm doing an analysis with two groups: patients and controls. When I look at Does the average thickness differ between 1 (patients) and 2 (controls)?, I can see blue (negative) and red (positive) correlations. I know that it means that in some cases, the patients have a higher cortical thickness compared to the controls, and in others it's the other way around. But which is which? Since most of the clusters are blue, I assume that blue means: patients have a lower cortical thickness compared to controls, and red means: patients have a higher cortical thickness compared to controls. Is this correct? How does FreeSurfer decide which group to use as the 'reference group' (i.e. the group to which the other group is compared)? Thanks, Anita ___ 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] mri_annotation2annotation?
Hi all, I know I can use mri_label2label and then mris_anatomical_stats -l to obtain the label-based cortical thickness for each individual subject. I also know that there is a tool called mri_annotation2label. But is there a way to convert annotation to each individual subject, so that I can use mris_anatomical_stats -a to obtain the annotation-based cortical thickness for each individual subject? Many thanks! Daniel -- Yung-Jui Daniel Yang, PhD Postdoctoral Researcher Yale Child Study Center New Haven, CT (203) 737-5454 ___ 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] TALx coordinates
Hi Doug, It's pretty awesome. So accordingly, MNI152x = (0.9975) MNI305x + (-0.0073) MNI305y + (0.0176) MNI305z + (-0.0429) * 1 MNI152y = (0.0146) MNI305x + (1.0009) MNI305y + (-0.0024) MNI305z + (1.5496) * 1 MNI152z = (-0.0130) MNI305 + (-0.0093) MNI305y + (0.9971) MNI305z + (1.1840) * 1 The last row of the M (i.e., [-0.0429 1.5496 1.1840]') looks like some sort of offset to me, correct? In other words, we are obtaining MNI305 first, Freesurfer convert that to TAL by default (question: is it done linearly or non-linearly?), and then we can manually convert it to MNI152 also. Thanks so much! Daniel -- Yung-Jui Daniel Yang, PhD Postdoctoral Researcher Yale Child Study Center New Haven, CT (203) 737-5454 On 9/10/13 6:52 PM, Douglas N Greve gr...@nmr.mgh.harvard.edumailto:gr...@nmr.mgh.harvard.edu wrote: Hi Yang, I've computed a matrix that should do the trick. If you are in matlab, then M = [0.9975 -0.00730.0176 -0.0429 0.01461.0009 -0.00241.5496 -0.0130 -0.00930.99711.1840 0 0 01.] P305 = [MNI305x MNI305y MNI305z 1]'; P152 = M*P305 Can you give this a shot and see if it makes sense? It will probably be hard to tell since the matrix is pretty close to identity. doug On 09/10/2013 05:17 PM, Yang, Daniel wrote: Thanks, Doug. I am really hoping to get MNI152 (because I also use fsl). Are MNI305 and MNI152 the same? How can I obtain MNI152 coordinates? Best, Daniel -- Yung-Jui Daniel Yang, PhD Postdoctoral Researcher Yale Child Study Center New Haven, CT (203) 737-5454 On 9/10/13 5:14 PM, Douglas N Greve gr...@nmr.mgh.harvard.edumailto:gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu wrote: It is an estimate of Tal coords from the MNI305. See http://imaging.mrc-cbu.cam.ac.uk/imaging/MniTalairach If you want MNI305, run mri_surfcluster with --nofixmni doug On 09/10/2013 05:08 PM, Yang, Daniel wrote: Hi all, The output of mri_surfcluster --sum shows TalX TalY TalZ. I am wondering if they are based on the Talairach system or some sort of MNI-Talairach system. If the latter, can you tell me something more about it? Like a webpage that describes its relationship between the MNI152 or the Talairach system? I find it confusing because mri_surfcluster said: INFO: fixing MNI talairach coordinates Thanks! Daniel -- Yung-Jui Daniel Yang, PhD Postdoctoral Researcher Yale Child Study Center New Haven, CT (203) 737-5454 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu mailto: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.edumailto:gr...@nmr.mgh.harvard.edu mailto: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.edumailto:Freesurfer@nmr.mgh.harvard.edu mailto: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. -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edumailto: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
Re: [Freesurfer] convert .mgh to .label?
Gotcha, so you mean run mri_concat --conjunct on the original .mgh files first, and then use mri_surfcluster to extract labels from the finalized .mgh. By the way, mri_annotation2label works like a charm! -- Yung-Jui Daniel Yang, PhD Postdoctoral Researcher Yale Child Study Center New Haven, CT (203) 737-5454 On 9/9/13 6:40 PM, Douglas N Greve gr...@nmr.mgh.harvard.edumailto:gr...@nmr.mgh.harvard.edu wrote: You cannot. You will have to do the conjunction on the cluster sig files, then extract a label from that. On 09/09/2013 06:30 PM, Yang, Daniel wrote: Thanks so much! I used the cluster analysis, I will look for the .annot there. I am also performing a conjunction analysis. One question I have is that can I perform mri_concat on those label files? I wanted to obtain the thickness value from the regions from the conjunction analysis. Thanks! Daniel On Sep 9, 2013, at 3:08 PM, Douglas N Greve gr...@nmr.mgh.harvard.edumailto:gr...@nmr.mgh.harvard.edu wrote: If you have run the correction for multiple comparisons, there should be an annotation (.annot) file in the QDEC output directory (in the contrast folder). You can convert that into labels using mri_annotation2label. Otherwise use Gari's suggestion. doug On 09/09/2013 03:00 PM, Garikoitz Lerma-Usabiaga wrote: Hi Daniel, you can use mri_surfcluster. br, Gari On Mon, Sep 9, 2013 at 8:25 PM, Yang, Daniel yung-jui.y...@yale.edumailto:yung-jui.y...@yale.edu mailto:yung-jui.y...@yale.edu wrote: Dear all, Is there a way to convert .mgh to .label? My .mgh is a ROI file from qdec-based group analysis and I don't want to draw the ROIs manually. Thanks! Daniel -- Yung-Jui Daniel Yang, PhD Postdoctoral Researcher Yale Child Study Center New Haven, CT (203) 737-5454 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu mailto: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.edumailto: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.edumailto: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.edumailto: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.edumailto: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] TALx coordinates
Hi all, The output of mri_surfcluster --sum shows TalX TalY TalZ. I am wondering if they are based on the Talairach system or some sort of MNI-Talairach system. If the latter, can you tell me something more about it? Like a webpage that describes its relationship between the MNI152 or the Talairach system? I find it confusing because mri_surfcluster said: INFO: fixing MNI talairach coordinates Thanks! Daniel -- Yung-Jui Daniel Yang, PhD Postdoctoral Researcher Yale Child Study Center New Haven, CT (203) 737-5454 ___ 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.