[Freesurfer] Kurtosis and Skewness
Hi FS experts, I was wondering whether there is a tool to measure the kurtosis and skewness of an ROI. (For instance would the mri_kurtosis.m script under the FS home directory be the best option for the measurement of kurtosis?) Thanks in advance, Panos ___ 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] Kurtosis and Skewness
Thanks a lot Doug! Additionally, I've been trying to calculate the curvature of an ROI extracted from a CT scan. Is there a way to do that in Freesurfer even though this ROI is not part of an MRI? (I was playing with mris_anatomical_stats and mris_curvature_stats but have been unsuccessful so far since I could not find a way to convert this file into a surface/curvature file). Thank you for your time, Panos > Yes. I've attached mri_skew.m as well. There are several ways to > estimate kurtosis, make sure mri_kurtosis is doing what you want. > > On 04/22/2015 01:48 PM, pfot...@nmr.mgh.harvard.edu wrote: >> Hi FS experts, >> >> I was wondering whether there is a tool to measure the kurtosis and >> skewness of an ROI. (For instance would the mri_kurtosis.m script under >> the FS home directory be the best option for the measurement of >> kurtosis?) >> >> Thanks in advance, >> Panos >> ___ >> 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 ___ 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] mris_preproc - srcsubjreg
I'm actually curious about this as well! Best, Panos > Hi Doug, still wondering about this - thanks! > > > From: freesurfer-boun...@nmr.mgh.harvard.edu > [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Makaretz, Sara > Johanna [smakar...@mgh.harvard.edu] > Sent: Tuesday, May 24, 2016 16:23 > To: Freesurfer support list > Subject: [Freesurfer] mris_preproc - srcsubjreg > > Hi Doug, I¹m curious why the newer mris_preproc does not use sphere.reg as > the default srcsurfreg when the target is not fsaverage - see below > > Thanks for any info! (not urgent) > > > On 2016-5-24, 11:30, "Z K" wrote: > >>Good question, and I dont know the answer. mris_preproc is Dougs baby so >>I suggest just posting this question to the list with "mris_preproc" in >>the subject, and I bet he will give you the answer. >> >>-Zeke >> >>On 05/23/2016 10:31 PM, Makaretz, Sara Johanna wrote: >>> Hi Zeke, >>> >>> I am running some surface glms where targ is a patient surface. The >>> help >>> says --target TargetSubject (requires ?h.TargetSubject.sphere.reg), and >>> I was getting errors because dev-default mris_preproc wanted >>> mri_surf2surf to have srcsurfreg = >>> $SUBJECTS_DIR/$srcsubject/surf/$h.$TARGSUBJ.sphere.reg >>> >>> But mris_preproc in 5.3 let me do target = patient surface with no >>> extra >>> surf reg files or extra flags to get mri_surf2surf to use srcsurfreg = >>> $SUBJECTS_DIR/$srcsubject/surf/$h.sphere.reg >>> >>> I had been running this with 5.3: >>> mris_preproc\ >>> --target $TARGSUBJ\ >>> --hemi lh\ >>> --meas thickness\ >>> --fsgd file.fsgd\ >>> --out lh.output.mgh >>> >>> And I was about to email freesurfer@nmr but "for fun" tried adding >>> --surfreg sphere.reg which got mris_surf2surf to use the right reg >>> files. So now I'm selfishly trying to figure this out - do you know >>> what >>> prompted the switch from sphere.reg "opt-out" to sphere.reg "opt-in"? >>> Aka why sphere.reg is non-default when the target is non-fsaverage? Did >>> that make sense? I know there must be some reason, so I really want to >>> know a bit more so I can stay sane when old scripts break. >>> >>> Thanks for any info! Sorry to bother you! >>> Sara >>> >>> >>> >>> >>> >>> >>> Outputs from the FS-dev one: >>> >>> $Id: mris_preproc,v 1.76 2015/12/09 20:02:53 zkaufman Exp $ >>> >>> Src lh $TARGSUBJ.sphere.reg >>> Trg lh sphere.reg >>> >>> mri_surf2surf --srcsubject $SRCSUBJ --srchemi lh --srcsurfreg >>> $TARGSUBJ.sphere.reg --trgsubject $TARGSUBJ --trghemi lh --trgsurfreg >>> sphere.reg --etcetcetc >>> >>> ERROR can't find $SUBJECTS_DIR/$SRCSUBJ/surf/$TARGSUBJ.sphere.reg >>> because I never made it >>> >>> >>> >>> Outputs from the FS-dev one with fsaverage as the targ subj: >>> >>> $Id: mris_preproc,v 1.76 2015/12/09 20:02:53 zkaufman Exp $ >>> >>> Src lh sphere.reg >>> Trg lh sphere.reg >>> >>> mri_surf2surf --srcsubject $SRCSUBJ --srchemi lh --srcsurfreg >>> sphere.reg >>> --trgsubject fsaverage --trghemi lh --trgsurfreg sphere.reg --etcetcetc >>> >>> mris_preproc finds everything, runs no problem >>> >>> >>> >>> Outputs from the FS-5.3 one: >>> >>> $Id: mris_preproc,v 1.59.2.4 2012/12/06 16:06:52 mreuter Exp $ >>> >>> Src lh sphere.reg >>> Trg lh sphere.reg >>> >>> mri_surf2surf --srcsubject $SRCSUBJ --srchemi lh --srcsurfreg >>> sphere.reg >>> --trgsubject $TARGSUBJ --trghemi lh --trgsurfreg sphere.reg --etcetcetc >>> >>> mris_preproc exits with no errors because everything exists >>> >>> >>> >>> > > > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] Freeview question
Hello FS Community, Lately, whenever I am trying to use freeview I get the following error message: freeview.bin: error while loading shared libraries: libvtkverdict.so.5.6: cannot open shared object file: No such file or directory Exit 127 The error started showing up after the cluster went down. I was wondering whether there was a way to fix this since I don't have admin privileges (and hence can't sudo). Thanks in advance, Panos ___ 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] Freeview question
Yes, that worked Thank you. > Have you tried rebooting your computer? > > Best, > Ruopeng > >> On Jul 12, 2016, at 3:14 PM, pfot...@nmr.mgh.harvard.edu wrote: >> >> Hello FS Community, >> Lately, whenever I am trying to use freeview I get the following error >> message: >> >> freeview.bin: error while loading shared libraries: >> libvtkverdict.so.5.6: >> cannot open shared object file: No such file or directory >> Exit 127 >> >> The error started showing up after the cluster went down. I was >> wondering >> whether there was a way to fix this since I don't have admin privileges >> (and hence can't sudo). >> >> Thanks in advance, >> Panos >> ___ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> > > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] mri_volcluster question
Hi FS Community, I am using the mri_volcluster command but for some reason the --sumfile shows up as an unknown flag. Is there another way to get a summary text file? (I am using FS 5.3 stable.) Thank you for your time! Best, Panos ___ 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] Surface doesn't match error
Hi FS Community, I have been using control points and adding wm voxels in the wm.mgz volume of a subject, in order to fix the reconstruction, and after doing so for a number of times, when I tried to run the command: tkmedit brainmask.mgz -aux wm.mgz -surfs the following message popped up: Reading 574 control points... Converting main surface: 100% done. Converting main surface: 100% done. mrisReadTriangleFile(/cluster/ichresearch/Petechial/MEG/1424_02042011_CTh_fixed/surf/lh.pial): surface doesn't match /cluster/ichresearch/Petechial/MEG/1424_02042011_CTh_fixed/surf/lh.white No such file or directory mrisReadTriangleFile failed. No such file or directory Converting main surface: 100% done. Converting main surface: 100% done. Converting pial surface: 100% done. Reading 574 control points... Reading /usr/local/freesurfer/stable5_3_0/tktools/tkm_common.tcl Reading /usr/local/freesurfer/stable5_3_0/tktools/tkm_wrappers.tcl Reading /usr/local/freesurfer/stable5_3_0/lib/tcl/fsgdfPlot.tcl Reading /usr/local/freesurfer/stable5_3_0/tktools/tkUtils.tcl % and after tkmedit loads, the lh.pial is not shown. I ran mris_euler_number on lh.pial and lh.white and they are both equal to 2 as they should. I was wondering whether you happen to know why is this happening and how to fix it. (I am using FS 5.3) Thank you for your time! Best, Panos ___ 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] Surface doesn't match error
Thanks Bruce! Panos > Hi Panos > > that means that you reran one of the surfaces but not the other. Try > running recon-all -make all, which should check to see if the > surfaces/volumes are up-to-date and rebuild them if needed. Note that > having an euler number of 2 doesn't mean the surfaces match, they also > need > to have the same number of edges, vertices and faces. > > cheers > Bruce > > > On Wed, 25 Sep > 2013, pfot...@nmr.mgh.harvard.edu wrote: > >> Hi FS Community, >> >> I have been using control points and adding wm voxels in the wm.mgz >> volume >> of a subject, in order to fix the reconstruction, and after doing so for >> a >> number of times, when I tried to run the command: >> >> tkmedit brainmask.mgz -aux wm.mgz -surfs >> >> the following message popped up: >> >> Reading 574 control points... >> Converting main surface: 100% done. >> Converting main surface: 100% done. >> mrisReadTriangleFile(/cluster/ichresearch/Petechial/MEG/1424_02042011_CTh_fixed/surf/lh.pial): >> surface doesn't match >> /cluster/ichresearch/Petechial/MEG/1424_02042011_CTh_fixed/surf/lh.white >> >> No such file or directory >> mrisReadTriangleFile failed. >> >> No such file or directory >> Converting main surface: 100% done. >> Converting main surface: 100% done. >> Converting pial surface: 100% done. >> Reading 574 control points... >> Reading /usr/local/freesurfer/stable5_3_0/tktools/tkm_common.tcl >> Reading /usr/local/freesurfer/stable5_3_0/tktools/tkm_wrappers.tcl >> Reading /usr/local/freesurfer/stable5_3_0/lib/tcl/fsgdfPlot.tcl >> Reading /usr/local/freesurfer/stable5_3_0/tktools/tkUtils.tcl >> % >> >> >> and after tkmedit loads, the lh.pial is not shown. I ran >> mris_euler_number >> on lh.pial and lh.white and they are both equal to 2 as they should. >> >> I was wondering whether you happen to know why is this happening and how >> to fix it. (I am using FS 5.3) >> >> Thank you for your time! >> >> Best, >> Panos >> ___ >> 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] Conversion question
Hi FS Community, I was wondering whether there is a way to convert a FLOAT type niftii file to an INT type niftii file. Thanks in advance! Best, Panos ___ 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_volcluster question
I see, thanks Doug! > It is --sum, not --sumfile > doug > > > On 09/25/2013 12:44 PM, pfot...@nmr.mgh.harvard.edu wrote: >> Hi FS Community, >> >> I am using the mri_volcluster command but for some reason the --sumfile >> shows up as an unknown flag. Is there another way to get a summary text >> file? >> (I am using FS 5.3 stable.) >> Thank you for your time! >> >> Best, >> Panos >> ___ >> 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 > > > ___ 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] Binary mask of the pons
Hi FS Community, I was wondering whether there is a way to get a binary mask of the pons. Thanks in advance, Panos ___ 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] Binary stats
Hi FS Community, I have a binary mask and have used the mri_volcluster command to come up with different clusters and their volumes based on that binary mask. However, I was wondering if it would be possible to come up with the sum of the sizes (in mm3) of all the different clusters that come out of the sum file as well. I could do it by writing a script that reads the separate values from the summary file output of the mri_volcluster and then adding them, but I was wondering whether there was an easier way. Thanks in advance, Panos ___ 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] Questions regarding stats file
Hi, I am using FS v5.3 and I had two questions regarding the calculation of cortical thickness in the stats files: 1) Is the average cortical thickness of each structure (i.e. precuneus) calculated by averaging the cortical thickness values of each location in that structure? 2) Is the mean thickness calculated in the *h.aparc.stats (or in the other aparc stats files) calculated by averaging the cortical thickness values of all the structures in that hemisphere, or by using a weighted average of the cortical thicknesses of the structures included in that hemisphere? Thanks, Panos ___ 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] Questions regarding stats file
Hi Doug, Thanks for your response. In addition, as it it mentioned in the wiki page the total white matter volume is volume inside the white surface minus anything that is not WM. Would it be correct to say that even though the total white matter volume calculation is based on a surface-based volume calculation, the calculation of the volume of any structure enclosed that is not WM, is computed based on a volume-based volume calculation? Thanks, Panos > > On 11/12/2013 11:26 AM, pfot...@nmr.mgh.harvard.edu wrote: >> Hi, >> >> I am using FS v5.3 and I had two questions regarding the calculation of >> cortical thickness in the stats files: >> >> 1) Is the average cortical thickness of each structure (i.e. precuneus) >> calculated by averaging the cortical thickness values of each location >> in >> that structure? > Yes >> >> 2) Is the mean thickness calculated in the *h.aparc.stats (or in the >> other >> aparc stats files) calculated by averaging the cortical thickness values >> of all the structures in that hemisphere, or by using a weighted average >> of the cortical thicknesses of the structures included in that >> hemisphere? > It is the mean over all vertices without regard to structure > doug >> >> >> Thanks, >> Panos >> ___ >> 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 > > > ___ 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] Questions regarding stats file
Great, thanks Doug! Panos > > yes > > > On 11/12/2013 03:21 PM, pfot...@nmr.mgh.harvard.edu wrote: >> Hi Doug, >> >> Thanks for your response. In addition, as it it mentioned in the wiki >> page >> the total white matter volume is volume inside the white surface minus >> anything that is not WM. Would it be correct to say that even though the >> total white matter volume calculation is based on a surface-based volume >> calculation, the calculation of the volume of any structure enclosed >> that >> is not WM, is computed based on a volume-based volume calculation? >> >> Thanks, >> Panos >> >>> On 11/12/2013 11:26 AM, pfot...@nmr.mgh.harvard.edu wrote: Hi, I am using FS v5.3 and I had two questions regarding the calculation of cortical thickness in the stats files: 1) Is the average cortical thickness of each structure (i.e. precuneus) calculated by averaging the cortical thickness values of each location in that structure? >>> Yes 2) Is the mean thickness calculated in the *h.aparc.stats (or in the other aparc stats files) calculated by averaging the cortical thickness values of all the structures in that hemisphere, or by using a weighted average of the cortical thicknesses of the structures included in that hemisphere? >>> It is the mean over all vertices without regard to structure >>> doug Thanks, Panos ___ 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 >>> >>> >>> >> ___ >> 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 > > > ___ 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] Units of coordinates in freeview
Hi FS experts, When I open a file with freeview, are the coordinates reported in the third row under Cursor (right under RAS and TkReg RAS) in mm? Thank you for your time, Panos ___ 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] Units of coordinates in freeview
Hi Bruce, Yes, I have already resampled my images into 1mm isometric voxel size, so all of the three reported coordinates must be in mm right? Thanks, Panos > the RAS and TkRegRAS are mm, the voxel coords are not (unless your > acquisition is 1mm isotropic) > > cheers > Bruce > > > On Tue, 3 Dec 2013, pfot...@nmr.mgh.harvard.edu wrote: > >> Hi FS experts, >> >> When I open a file with freeview, are the coordinates reported in the >> third row under Cursor (right under RAS and TkReg RAS) in mm? >> >> Thank you for your time, >> Panos >> ___ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> >> > > > ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] Units of coordinates in freeview
Great, thanks Bruce! Panos > yes, they should be > On Tue, 3 Dec 2013, pfot...@nmr.mgh.harvard.edu wrote: > >> Hi Bruce, >> >> Yes, I have already resampled my images into 1mm isometric voxel size, >> so >> all of the three reported coordinates must be in mm right? >> >> Thanks, >> Panos >> >>> the RAS and TkRegRAS are mm, the voxel coords are not (unless your >>> acquisition is 1mm isotropic) >>> >>> cheers >>> Bruce >>> >>> >>> On Tue, 3 Dec 2013, pfot...@nmr.mgh.harvard.edu wrote: >>> Hi FS experts, When I open a file with freeview, are the coordinates reported in the third row under Cursor (right under RAS and TkReg RAS) in mm? Thank you for your time, Panos ___ 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] FDR question
Hi FS community, I am doing a cortical thickness comparison between a diseased and a healthy group. After running the mri_glmfit command for both hemispheres, I project the uncorrected significance map and there are a number of significant clusters showing (if you consider the p value to be at most 0.05). However, instead of using the clusterwise Correction for Multiple Comparisons, I wanted to use FDR to see what the results would look like, and I had a few questions regarding the whole process: 1) Is Tksurfer the only tool in FS that I can apply the FDR correction with, or are there any other ways? 2) In Tksurfer, I tried using the "Set Threshold Using FDR" tool, and when I set the rate from 0.88 to 0.87 it bumps down the minimum threshold from 1.37 to 3.24 hence resulting in no significant clusters for rates less than 0.88. Does that sound normal? Thanks in advance! Panos ___ 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] QDEC Error
Hi FS community, After I open QDEC, when I try to load my qdec data table, QDEC crashes for some reason. The error message that comes out at the terminal is: Returned Error on line 1: missing close-brace Stack trace: missing close-brace while executing ".vtkKWLoadSaveDialog5.vtkKWFileBrowserWidget0.vtkKWSplitFrame0.vtkKWFrame2.vtkKWSplitFrame0.vtkKWFrame0.vtkKWDirectoryExplorer0.vtkKWTreeWithScrollbar..." X Error of failed request: BadAlloc (insufficient resources for operation) Major opcode of failed request: 53 (X_CreatePixmap) Serial number of failed request: 611512 Current serial number in output stream: 611810 Exit 1 I was wondering whether you know why is this happening. I am using FS v5.3 and my OS is Linux Centos 6.5. Thanks in advance, Panos ___ 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] FDR question
Hi FS community, I was wondering if anyone had a chance to give this a look. Thanks in advance, Panos > Hi FS community, > > I am doing a cortical thickness comparison between a diseased and a > healthy group. After running the mri_glmfit command for both hemispheres, > I project the uncorrected significance map and there are a number of > significant clusters showing (if you consider the p value to be at most > 0.05). However, instead of using the clusterwise Correction for Multiple > Comparisons, I wanted to use FDR to see what the results would look like, > and I had a few questions regarding the whole process: > > 1) Are Tksurfer and QDEC the only tools in FS that I can apply the FDR correction > with, or are there any other ways? > > 2) In Tksurfer, I tried using the "Set Threshold Using FDR" tool, and when > I set the rate from 0.88 to 0.87 it bumps up the minimum threshold from > 1.37 to 3.24 hence resulting in no significant clusters for rates less > than 0.88. Does that sound normal? > > Thanks in advance! > Panos > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] FDR question
Hi Doug and Martin, Thanks both for your replies! Doug, I would normally set the FDR to something close to .05 but when this value didn't give me any significant clusters for my analysis, I was trying to find which value was the min one that gave significant clusters just out of curiosity, and this value happened to be 0.88. But I wasn't going to actually use this value for my analysis. It just surprised that for such a high fdr threshold, the min -log(p) value increased so much, hence excluding every uncorrected significant cluster for any fdr threshold less than 0.88. Best, Panos > Hi Panos, > > also the LME tools (matlab) have tools for FDR correction: > > /lme_mass_FDR/ (Original Benjamini and Hochberg FDR procedure) > > /lme_mass_FDR2/ (A more powerful two-stage FDR procedure: > > "Adaptive Linear Step-up Procedures that control the False > Discovery Rate" Benjamini, Krieger, Yekutieli ) > > > Best, Martin > > On 02/10/2014 03:28 PM, pfot...@nmr.mgh.harvard.edu wrote: >> Hi FS community, >> >> I was wondering if anyone had a chance to give this a look. >> >> Thanks in advance, >> Panos >> >> >>> Hi FS community, >>> >>> I am doing a cortical thickness comparison between a diseased and a >>> healthy group. After running the mri_glmfit command for both >>> hemispheres, >>> I project the uncorrected significance map and there are a number of >>> significant clusters showing (if you consider the p value to be at most >>> 0.05). However, instead of using the clusterwise Correction for >>> Multiple >>> Comparisons, I wanted to use FDR to see what the results would look >>> like, >>> and I had a few questions regarding the whole process: >>> >>> 1) Are Tksurfer and QDEC the only tools in FS that I can apply the FDR >> correction >>> with, or are there any other ways? >>> >>> 2) In Tksurfer, I tried using the "Set Threshold Using FDR" tool, and >>> when >>> I set the rate from 0.88 to 0.87 it bumps up the minimum threshold from >>> 1.37 to 3.24 hence resulting in no significant clusters for rates less >>> than 0.88. Does that sound normal? >>> >>> Thanks in advance! >>> Panos >>> ___ >>> 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 >> >> > > -- > Martin Reuter, Ph.D. > Assistant in Neuroscience - Massachusetts General Hospital > Instructor in Neurology - Harvard Medical School > MGH / HMS / MIT > > A.A.Martinos Center for Biomedical Imaging > 149 Thirteenth Street, Suite 2301 > Charlestown, MA 02129 > > Phone: +1-617-724-5652 > Email: > mreu...@nmr.mgh.harvard.edu > reu...@mit.edu > Web : http://reuter.mit.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] FDR question
I see. Thanks for your input! Panos > > This kind of thing can happen, especially when there is not much > activity in the map > doug > > On 02/11/2014 12:02 PM, pfot...@nmr.mgh.harvard.edu wrote: >> Hi Doug and Martin, >> >> Thanks both for your replies! >> >> Doug, I would normally set the FDR to something close to .05 but when >> this >> value didn't give me any significant clusters for my analysis, I was >> trying to find which value was the min one that gave significant >> clusters >> just out of curiosity, and this value happened to be 0.88. But I wasn't >> going to actually use this value for my analysis. It just surprised that >> for such a high fdr threshold, the min -log(p) value increased so much, >> hence excluding every uncorrected significant cluster for any fdr >> threshold less than 0.88. >> >> Best, >> Panos >> >>> Hi Panos, >>> >>> also the LME tools (matlab) have tools for FDR correction: >>> >>> /lme_mass_FDR/ (Original Benjamini and Hochberg FDR procedure) >>> >>> /lme_mass_FDR2/ (A more powerful two-stage FDR procedure: >>> >>> "Adaptive Linear Step-up Procedures that control the False >>> Discovery Rate" Benjamini, Krieger, Yekutieli ) >>> >>> >>> Best, Martin >>> >>> On 02/10/2014 03:28 PM, pfot...@nmr.mgh.harvard.edu wrote: Hi FS community, I was wondering if anyone had a chance to give this a look. Thanks in advance, Panos > Hi FS community, > > I am doing a cortical thickness comparison between a diseased and a > healthy group. After running the mri_glmfit command for both > hemispheres, > I project the uncorrected significance map and there are a number of > significant clusters showing (if you consider the p value to be at > most > 0.05). However, instead of using the clusterwise Correction for > Multiple > Comparisons, I wanted to use FDR to see what the results would look > like, > and I had a few questions regarding the whole process: > > 1) Are Tksurfer and QDEC the only tools in FS that I can apply the > FDR correction > with, or are there any other ways? > > 2) In Tksurfer, I tried using the "Set Threshold Using FDR" tool, and > when > I set the rate from 0.88 to 0.87 it bumps up the minimum threshold > from > 1.37 to 3.24 hence resulting in no significant clusters for rates > less > than 0.88. Does that sound normal? > > Thanks in advance! > Panos > ___ > 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 >>> -- >>> Martin Reuter, Ph.D. >>> Assistant in Neuroscience - Massachusetts General Hospital >>> Instructor in Neurology - Harvard Medical School >>> MGH / HMS / MIT >>> >>> A.A.Martinos Center for Biomedical Imaging >>> 149 Thirteenth Street, Suite 2301 >>> Charlestown, MA 02129 >>> >>> Phone: +1-617-724-5652 >>> Email: >>> mreu...@nmr.mgh.harvard.edu >>> reu...@mit.edu >>> Web : http://reuter.mit.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 > > > ___ 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] Group Analysis Questions
Hi FS community, I had a few questions regarding my understanding of the group analysis in FS: 1) If I use an fsgd file with Two Groups (One Factor/Two Levels), No Covariates, and my contrast matrix is [1 -1], do the resulting clusters (if any) show the regional significant differences between the two groups by comparing just the means of the values that I am comparing? For instance, if I'm comparing cortical thickness between a diseased and a control group, is this going to give me the clusters where the Diseased subjects' (no age included in the fsgd file, just the two groups) mean/regional cortical thickness differs significantly from the controls'? In other words, is a 50 yo subject's mean/regional cortical thickness going to be treated the same as a 80 yo subject's? 2) Now suppose that I would like to control for age. Then I'm assuming that I need to create an fsgd file with two Groups (One Factor/Two Levels) and One Covariate (age). Similarly, if I would want to visualize the differences in the regional values of cortical thickness between the two groups but after they have been controlled/adjusted for age, what contrast matrix should I use? Normally I would use [0 0 1 -1] but this will give me the significant differences in the age slopes not the mean values, unless I am missing something here. Thanks in advance for your help and sorry for the lengthy message. Best, Panos ___ 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] Group Analysis Questions
Hi Doug, Thank you for your response. Concerning scenario 2, I believe I have some hard time understanding the term intercept. If I'm not mistaken the intercept represents the cortical thickness at "age 0." The resulting clusters by using a design matrix of [1 -1 0 0] will give me the areas where the intercept is significantly different between the Diseased group and the healthy group. Are those clusters the same clusters that have a different mean regional cortical thickness in Diseased versus Healthy subjects after controlling for age, or are those two completely different things? Thanks again, Panos > > On 02/25/2014 02:07 PM, pfot...@nmr.mgh.harvard.edu wrote: >> Hi FS community, >> >> I had a few questions regarding my understanding of the group analysis >> in FS: >> >> 1) If I use an fsgd file with Two Groups (One Factor/Two Levels), No >> Covariates, and my contrast matrix is [1 -1], do the resulting clusters >> (if any) show the regional significant differences between the two >> groups >> by comparing just the means of the values that I am comparing? For >> instance, if I'm comparing cortical thickness between a diseased and a >> control group, is this going to give me the clusters where the Diseased >> subjects' (no age included in the fsgd file, just the two groups) >> mean/regional cortical thickness differs significantly from the >> controls'? >> In other words, is a 50 yo subject's mean/regional cortical thickness >> going to be treated the same as a 80 yo subject's? > Yes, just a simple two-group t-test. >> >> 2) Now suppose that I would like to control for age. Then I'm assuming >> that I need to create an fsgd file with two Groups (One Factor/Two >> Levels) >> and One Covariate (age). Similarly, if I would want to visualize the >> differences in the regional values of cortical thickness between the two >> groups but after they have been controlled/adjusted for age, what >> contrast >> matrix should I use? Normally I would use [0 0 1 -1] but this will give >> me >> the significant differences in the age slopes not the mean values, >> unless >> I am missing something here. > Correct, that will give you the difference in age/thickness slopes. You > could do [1 -1 0 0] to give you the difference in intercepts. A better > way, is to first look for differences in the slopes. If you do not find > any, then rerun with DOSS with a contrast of [1 -1 0]. By using a DOSS, > the difference in intercept is always constant regardless of age (as > opposed to DODS). > doug >> >> Thanks in advance for your help and sorry for the lengthy message. >> >> Best, >> Panos >> ___ >> 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 > > > ___ 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] Group Analysis Questions
That's great. Thanks a lot for your help, Doug! > > Those are the same things. The way you control for age is to compute a > value for both groups at the same age (eg, age=0). If you demean the > age, then the difference will be at age=meanage. With DOSS, the > difference is always the same regardless of age (which makes it more > interpretable) > doug > > > On 02/25/2014 03:00 PM, pfot...@nmr.mgh.harvard.edu wrote: >> Hi Doug, >> >> Thank you for your response. >> Concerning scenario 2, I believe I have some hard time understanding the >> term intercept. If I'm not mistaken the intercept represents the >> cortical >> thickness at "age 0." The resulting clusters by using a design matrix of >> [1 -1 0 0] will give me the areas where the intercept is significantly >> different between the Diseased group and the healthy group. >> >> Are those clusters the same clusters that have a different mean >> regional >> cortical thickness in Diseased versus Healthy subjects after controlling >> for age, or are those two completely different things? >> >> >> Thanks again, >> Panos >> >>> On 02/25/2014 02:07 PM, pfot...@nmr.mgh.harvard.edu wrote: Hi FS community, I had a few questions regarding my understanding of the group analysis in FS: 1) If I use an fsgd file with Two Groups (One Factor/Two Levels), No Covariates, and my contrast matrix is [1 -1], do the resulting clusters (if any) show the regional significant differences between the two groups by comparing just the means of the values that I am comparing? For instance, if I'm comparing cortical thickness between a diseased and a control group, is this going to give me the clusters where the Diseased subjects' (no age included in the fsgd file, just the two groups) mean/regional cortical thickness differs significantly from the controls'? In other words, is a 50 yo subject's mean/regional cortical thickness going to be treated the same as a 80 yo subject's? >>> Yes, just a simple two-group t-test. 2) Now suppose that I would like to control for age. Then I'm assuming that I need to create an fsgd file with two Groups (One Factor/Two Levels) and One Covariate (age). Similarly, if I would want to visualize the differences in the regional values of cortical thickness between the two groups but after they have been controlled/adjusted for age, what contrast matrix should I use? Normally I would use [0 0 1 -1] but this will give me the significant differences in the age slopes not the mean values, unless I am missing something here. >>> Correct, that will give you the difference in age/thickness slopes. You >>> could do [1 -1 0 0] to give you the difference in intercepts. A better >>> way, is to first look for differences in the slopes. If you do not find >>> any, then rerun with DOSS with a contrast of [1 -1 0]. By using a DOSS, >>> the difference in intercept is always constant regardless of age (as >>> opposed to DODS). >>> doug Thanks in advance for your help and sorry for the lengthy message. Best, Panos ___ 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 >>> >>> >>> >> ___ >> 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 > > > ___ 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 y
Re: [Freesurfer] Group Analysis Questions
Hi Doug, I was wondering about something. If I have an fsgd file that has no variable set (just the 2 groups: Diseased and Control) do I need to include the DefaultVariable line at the end of the file? Thanks, Panos > That's great. Thanks a lot for your help, Doug! > > >> >> Those are the same things. The way you control for age is to compute a >> value for both groups at the same age (eg, age=0). If you demean the >> age, then the difference will be at age=meanage. With DOSS, the >> difference is always the same regardless of age (which makes it more >> interpretable) >> doug >> >> >> On 02/25/2014 03:00 PM, pfot...@nmr.mgh.harvard.edu wrote: >>> Hi Doug, >>> >>> Thank you for your response. >>> Concerning scenario 2, I believe I have some hard time understanding >>> the >>> term intercept. If I'm not mistaken the intercept represents the >>> cortical >>> thickness at "age 0." The resulting clusters by using a design matrix >>> of >>> [1 -1 0 0] will give me the areas where the intercept is significantly >>> different between the Diseased group and the healthy group. >>> >>> Are those clusters the same clusters that have a different mean >>> regional >>> cortical thickness in Diseased versus Healthy subjects after >>> controlling >>> for age, or are those two completely different things? >>> >>> >>> Thanks again, >>> Panos >>> On 02/25/2014 02:07 PM, pfot...@nmr.mgh.harvard.edu wrote: > Hi FS community, > > I had a few questions regarding my understanding of the group > analysis > in FS: > > 1) If I use an fsgd file with Two Groups (One Factor/Two Levels), No > Covariates, and my contrast matrix is [1 -1], do the resulting > clusters > (if any) show the regional significant differences between the two > groups > by comparing just the means of the values that I am comparing? For > instance, if I'm comparing cortical thickness between a diseased and > a > control group, is this going to give me the clusters where the > Diseased > subjects' (no age included in the fsgd file, just the two groups) > mean/regional cortical thickness differs significantly from the > controls'? > In other words, is a 50 yo subject's mean/regional cortical thickness > going to be treated the same as a 80 yo subject's? Yes, just a simple two-group t-test. > 2) Now suppose that I would like to control for age. Then I'm > assuming > that I need to create an fsgd file with two Groups (One Factor/Two > Levels) > and One Covariate (age). Similarly, if I would want to visualize the > differences in the regional values of cortical thickness between the > two > groups but after they have been controlled/adjusted for age, what > contrast > matrix should I use? Normally I would use [0 0 1 -1] but this will > give > me > the significant differences in the age slopes not the mean values, > unless > I am missing something here. Correct, that will give you the difference in age/thickness slopes. You could do [1 -1 0 0] to give you the difference in intercepts. A better way, is to first look for differences in the slopes. If you do not find any, then rerun with DOSS with a contrast of [1 -1 0]. By using a DOSS, the difference in intercept is always constant regardless of age (as opposed to DODS). doug > Thanks in advance for your help and sorry for the lengthy message. > > Best, > Panos > ___ > 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 >>> ___ >>> 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 >> Free
Re: [Freesurfer] Group Analysis Questions
I see. Thank you > no, that is only for plotting > > On 03/03/2014 03:18 PM, pfot...@nmr.mgh.harvard.edu wrote: >> Hi Doug, >> >> I was wondering about something. If I have an fsgd file that has no >> variable set (just the 2 groups: Diseased and Control) do I need to >> include the DefaultVariable line at the end of the file? >> >> Thanks, >> Panos >> >>> That's great. Thanks a lot for your help, Doug! >>> >>> Those are the same things. The way you control for age is to compute a value for both groups at the same age (eg, age=0). If you demean the age, then the difference will be at age=meanage. With DOSS, the difference is always the same regardless of age (which makes it more interpretable) doug On 02/25/2014 03:00 PM, pfot...@nmr.mgh.harvard.edu wrote: > Hi Doug, > > Thank you for your response. > Concerning scenario 2, I believe I have some hard time understanding > the > term intercept. If I'm not mistaken the intercept represents the > cortical > thickness at "age 0." The resulting clusters by using a design matrix > of > [1 -1 0 0] will give me the areas where the intercept is > significantly > different between the Diseased group and the healthy group. > >Are those clusters the same clusters that have a different mean > regional > cortical thickness in Diseased versus Healthy subjects after > controlling > for age, or are those two completely different things? > > > Thanks again, > Panos > >> On 02/25/2014 02:07 PM, pfot...@nmr.mgh.harvard.edu wrote: >>> Hi FS community, >>> >>> I had a few questions regarding my understanding of the group >>> analysis >>> in FS: >>> >>> 1) If I use an fsgd file with Two Groups (One Factor/Two Levels), >>> No >>> Covariates, and my contrast matrix is [1 -1], do the resulting >>> clusters >>> (if any) show the regional significant differences between the two >>> groups >>> by comparing just the means of the values that I am comparing? For >>> instance, if I'm comparing cortical thickness between a diseased >>> and >>> a >>> control group, is this going to give me the clusters where the >>> Diseased >>> subjects' (no age included in the fsgd file, just the two groups) >>> mean/regional cortical thickness differs significantly from the >>> controls'? >>> In other words, is a 50 yo subject's mean/regional cortical >>> thickness >>> going to be treated the same as a 80 yo subject's? >> Yes, just a simple two-group t-test. >>> 2) Now suppose that I would like to control for age. Then I'm >>> assuming >>> that I need to create an fsgd file with two Groups (One Factor/Two >>> Levels) >>> and One Covariate (age). Similarly, if I would want to visualize >>> the >>> differences in the regional values of cortical thickness between >>> the >>> two >>> groups but after they have been controlled/adjusted for age, what >>> contrast >>> matrix should I use? Normally I would use [0 0 1 -1] but this will >>> give >>> me >>> the significant differences in the age slopes not the mean values, >>> unless >>> I am missing something here. >> Correct, that will give you the difference in age/thickness slopes. >> You >> could do [1 -1 0 0] to give you the difference in intercepts. A >> better >> way, is to first look for differences in the slopes. If you do not >> find >> any, then rerun with DOSS with a contrast of [1 -1 0]. By using a >> DOSS, >> the difference in intercept is always constant regardless of age (as >> opposed to DODS). >> doug >>> Thanks in advance for your help and sorry for the lengthy message. >>> >>> Best, >>> Panos >>> ___ >>> 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 >> >> >> > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > -- Douglas N. Greve, Ph.D. MGH
[Freesurfer] Group Analysis Age slopes
Hi Doug, I ran a group analysis comparing a trait between two groups (Diseased vs Controls) with one continuous variable (age), with the following design matrices [1 -1 0 0] and [0 0 1 -1]. When I loaded the significance map and the descriptor file, the age slope of the trait in Controls was positive whereas the age slope of the trait in the Diseased cases was negative. Therefore, comparing the intercept between the two groups does not really give that much info, since the slopes are of opposite sign. What do you believe would be the best course of action in order to compare the age-corrected traits: 1) instead of age=0 maybe comparing the groups at age=mean? 2) or going with a DOSS model? Thank you for your time, Panos ___ 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] Group Analysis Age slopes
Hi Doug, Thanks for your reply. Yes there were areas of significant difference reported in the age slopes maps, after the mri_glmfit command was run. However, I haven't checked to see yet whether there are surviving clusters after correction for multiple comparisons. I see, yes that definitely makes sense especially since the slopes have an opposite sign. However I still had a couple questions: 1) If I did want to look at what the age-corrected trait looked like when compared between the Diseased and Healthy groups at age=mean instead of age=0, what would I need to do? 2) When not including the age in the fsgd file and using a design matrix of [1 -1] I get the significant differences between the average trait in the diseased cases vs the average trait in the control cases. Is there a way to get a summary file with the actual averages along with the significance maps? Thanks a lot for your help! Panos > > Was the difference in the age slopes significant? Ie, and interaction > between age and group. If so, then you have to proceed with caution (at > least one statistician told me not to proceed at at:) because the > difference in the intercepts between the two groups will depend on age > making it very difficult to interpret. At the age where the lines > intercept, there will be no difference > doug > > > On 03/07/2014 02:57 PM, pfot...@nmr.mgh.harvard.edu wrote: >> Hi Doug, >> >> I ran a group analysis comparing a trait between two groups (Diseased vs >> Controls) with one continuous variable (age), with the following design >> matrices [1 -1 0 0] and [0 0 1 -1]. When I loaded the significance map >> and >> the descriptor file, the age slope of the trait in Controls was positive >> whereas the age slope of the trait in the Diseased cases was negative. >> Therefore, comparing the intercept between the two groups does not >> really >> give that much info, since the slopes are of opposite sign. What do you >> believe would be the best course of action in order to compare the >> age-corrected traits: >> 1) instead of age=0 maybe comparing the groups at age=mean? >> 2) or going with a DOSS model? >> >> Thank you for your time, >> Panos >> ___ >> 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 > > > ___ 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] Group Analysis Age slopes
Hi Doug, Thanks for your reply. Just to be clear, I need to ask some trivial questions: 1) I need to do that subtraction in the fsgd file right? (In which case there will be negative numbers as well) 2) I ran the analysis and the resulting significant clusters when looking at the results of [1 -1 0 0] look very similar to the ones that I got when I ran the analysis without accounting for age (that is an fsgd file with no age included and a design matrix of [1 -1]), but not that similar to the results that I got when looking at age=0. That makes sense, right? Thank you for your time, Panos > > On 03/07/2014 07:46 PM, pfot...@nmr.mgh.harvard.edu wrote: >> Hi Doug, >> >> Thanks for your reply. Yes there were areas of significant difference >> reported in the age slopes maps, after the mri_glmfit command was run. >> However, I haven't checked to see yet whether there are surviving >> clusters >> after correction for multiple comparisons. I see, yes that definitely >> makes sense especially since the slopes have an opposite sign. However I >> still had a couple questions: >> >> 1) If I did want to look at what the age-corrected trait looked like >> when >> compared between the Diseased and Healthy groups at age=mean instead of >> age=0, what would I need to do? > Subtract the mean age (computed across all subjects regardless of group) > from the age of each subject >> >> 2) When not including the age in the fsgd file and using a design matrix >> of [1 -1] I get the significant differences between the average trait in >> the diseased cases vs the average trait in the control cases. Is there a >> way to get a summary file with the actual averages along with the >> significance maps? > If you run mri_glmfit-sim it will produce a lot of summaries. Run it > with --help to see if what you want is there > doug >> >> Thanks a lot for your help! >> Panos >> >>> Was the difference in the age slopes significant? Ie, and interaction >>> between age and group. If so, then you have to proceed with caution (at >>> least one statistician told me not to proceed at at:) because the >>> difference in the intercepts between the two groups will depend on age >>> making it very difficult to interpret. At the age where the lines >>> intercept, there will be no difference >>> doug >>> >>> >>> On 03/07/2014 02:57 PM, pfot...@nmr.mgh.harvard.edu wrote: Hi Doug, I ran a group analysis comparing a trait between two groups (Diseased vs Controls) with one continuous variable (age), with the following design matrices [1 -1 0 0] and [0 0 1 -1]. When I loaded the significance map and the descriptor file, the age slope of the trait in Controls was positive whereas the age slope of the trait in the Diseased cases was negative. Therefore, comparing the intercept between the two groups does not really give that much info, since the slopes are of opposite sign. What do you believe would be the best course of action in order to compare the age-corrected traits: 1) instead of age=0 maybe comparing the groups at age=mean? 2) or going with a DOSS model? Thank you for your time, Panos ___ 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 >>> >>> >>> >> ___ >> 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 > > > ___ 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
[Freesurfer] Longitudinal Analysis Questions
Hi FS community, I am using FS 5.3 to do a longitudinal analysis on some data of mine. I have manually edited some of the reconstructed scans (i.e. addition of control points and white voxels) where the reconstruction was not as precise: 1) Is the base template created from the recon-all -base command in the wiki preserving those edits or do I need to reapply them in the base template? I know that this has been answered for previous versions of FS but I was wondering whether anything has changed in more recent versions. 2) Is it ok to run the longitudinal analysis described in the wiki when my subjects have an unequal number of timepoints (i.e. one person has 3 different timepoints, whereas another one has five) or should they all have the same number of timepoints? Thanks in advance! Best, Panos ___ 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] Longitudinal Analysis Questions
Hi Martin, Thanks for your reply! Yes, that definitely makes sense. I had an additional probably elementary question: I tried to reconstruct the base after I added some control points to it, using the command recon-all -autorecon2-cp -autorecon3 -subjid but the following error pops up: ERROR: It appears that this subject ID is an existing base/template from longitudinal processing (-base). Please make sure you pass all necessary flags. For example, if you are trying to re-run a -base: \' -base -tp ... \' Exit 1 In order to reconstruct the base do I need to run again the command that created the base in the first place and then add the flag -autorecon2-cp -autorecon3 that is: recon-all -autorecon2-cp -autorecon3 -base -tp -tp ... -tp -all ? Thanks in advance, Panos > Hi Panos, > > 1. you need to edit the base. That is actually more important than > editing the individual (cross) time points from the first stage, > especially when the edits are supposed to improve the surface. The > reason is that the surface is taken from the base to initialize all time > points in the -long step. So accurate surfaces, brainmasks and talairach > transforms are very important in the base. > > 2. Yes, that is generally OK. It would be bad if one group has only 3 > time points the other 5 though, but if that is relatively balanced > across your groups, you'll be fine. > > Best, Martin > > > On 03/28/2014 03:43 PM, pfot...@nmr.mgh.harvard.edu wrote: >> Hi FS community, >> >> I am using FS 5.3 to do a longitudinal analysis on some data of mine. I >> have manually edited some of the reconstructed scans (i.e. addition of >> control points and white voxels) where the reconstruction was not as >> precise: >> >> 1) Is the base template created from the recon-all -base command in the >> wiki preserving those edits or do I need to reapply them in the base >> template? I know that this has been answered for previous versions of FS >> but I was wondering whether anything has changed in more recent >> versions. >> >> 2) Is it ok to run the longitudinal analysis described in the wiki when >> my >> subjects have an unequal number of timepoints (i.e. one person has 3 >> different timepoints, whereas another one has five) or should they all >> have the same number of timepoints? >> Thanks in advance! >> >> Best, >> Panos >> ___ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> > > -- > Martin Reuter, Ph.D. > > Instructor in Neurology >Harvard Medical School > Assistant in Neuroscience >Dept. of Radiology, Massachusetts General Hospital >Dept. of Neurology, Massachusetts General Hospital > Research Affiliate >Computer Science and Artificial Intelligence Lab, >Dept. of Electrical Engineering and Computer Science, >Massachusetts Institute of Technology > > A.A.Martinos Center for Biomedical Imaging > 149 Thirteenth Street, Suite 2301 > Charlestown, MA 02129 > > Phone: +1-617-724-5652 > Email: > mreu...@nmr.mgh.harvard.edu > reu...@mit.edu > Web : http://reuter.mit.edu > > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] Longitudinal Analysis Questions
Hi Martin, That sounds great. Thanks for your time! Panos > Hi Panos > Yes, except you would not pass the -all flag as you don't want to rerun > everything: > > recon-all -base -tp -tp ... -tp > -autorecon2-cp -autorecon3 > > Best, Martin > > On 04/01/2014 01:41 PM, pfot...@nmr.mgh.harvard.edu wrote: >> Hi Martin, >> >> Thanks for your reply! Yes, that definitely makes sense. I had an >> additional probably elementary question: I tried to reconstruct the base >> after I added some control points to it, using the command >> recon-all -autorecon2-cp -autorecon3 -subjid >> >> but the following error pops up: >> >> ERROR: It appears that this subject ID is an existing >> base/template from longitudinal processing (-base). >> Please make sure you pass all necessary flags. >> For example, if you are trying to re-run a -base: >> >> \' -base -tp ... \' >> >> Exit 1 >> >> >> In order to reconstruct the base do I need to run again the command that >> created the base in the first place and then add the flag -autorecon2-cp >> -autorecon3 that is: >> >> recon-all -autorecon2-cp -autorecon3 -base -tp >> >> -tp ... -tp -all ? >> >> Thanks in advance, >> Panos >> >>> Hi Panos, >>> >>> 1. you need to edit the base. That is actually more important than >>> editing the individual (cross) time points from the first stage, >>> especially when the edits are supposed to improve the surface. The >>> reason is that the surface is taken from the base to initialize all >>> time >>> points in the -long step. So accurate surfaces, brainmasks and >>> talairach >>> transforms are very important in the base. >>> >>> 2. Yes, that is generally OK. It would be bad if one group has only 3 >>> time points the other 5 though, but if that is relatively balanced >>> across your groups, you'll be fine. >>> >>> Best, Martin >>> >>> >>> On 03/28/2014 03:43 PM, pfot...@nmr.mgh.harvard.edu wrote: Hi FS community, I am using FS 5.3 to do a longitudinal analysis on some data of mine. I have manually edited some of the reconstructed scans (i.e. addition of control points and white voxels) where the reconstruction was not as precise: 1) Is the base template created from the recon-all -base command in the wiki preserving those edits or do I need to reapply them in the base template? I know that this has been answered for previous versions of FS but I was wondering whether anything has changed in more recent versions. 2) Is it ok to run the longitudinal analysis described in the wiki when my subjects have an unequal number of timepoints (i.e. one person has 3 different timepoints, whereas another one has five) or should they all have the same number of timepoints? Thanks in advance! Best, Panos ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>> -- >>> Martin Reuter, Ph.D. >>> >>> Instructor in Neurology >>> Harvard Medical School >>> Assistant in Neuroscience >>> Dept. of Radiology, Massachusetts General Hospital >>> Dept. of Neurology, Massachusetts General Hospital >>> Research Affiliate >>> Computer Science and Artificial Intelligence Lab, >>> Dept. of Electrical Engineering and Computer Science, >>> Massachusetts Institute of Technology >>> >>> A.A.Martinos Center for Biomedical Imaging >>> 149 Thirteenth Street, Suite 2301 >>> Charlestown, MA 02129 >>> >>> Phone: +1-617-724-5652 >>> Email: >>> mreu...@nmr.mgh.harvard.edu >>> reu...@mit.edu >>> Web : http://reuter.mit.edu >>> >>> ___ >>> 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 >> >> > > -- > Martin Reuter, Ph.D. > > Instructor in Neurology >Harvard Medical School > Assistant in Neuroscience >Dept. of Radiology, Massachusetts General Hospital >Dept. of Neurology, Massachusetts General Hospital > Research Affiliate >Computer Science and Artificial Intelligence Lab, >Dept. of Electrical Engineering and Computer Science, >Massachusetts Institute of Technology > > A.A.Martinos Center for Biomedical Imaging > 149 Thirteenth Street, Suite 2301 > Charlestown, MA 02129 > > Phone: +1-617-724-5652 > Email: > mreu...@nmr.mgh.harvard.edu > reu...@mit.edu > Web : http://reuter.mit.edu > > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > ___ Freesurfer
[Freesurfer] mri_segstats question
Hi FS community, I had some questions regarding the mri_segstats command: 1) In the excludeid flag, are the ids the ones shown in the FreeSurferColorLUT.txt? 2) In case I would like to measure the mean intensity of the orig file as outlined in the second example in https://surfer.nmr.mgh.harvard.edu/fswiki/mri_segstats: mri_segstats --seg $SUBJECTS_DIR/bert/mri/aseg --ctab $FREESURFER_HOME/FreeSurferColorLUT.txt --nonempty --excludeid 0 --sum bert.aseg.sum --in $SUBJECTS_DIR/bert/mri/orig is the --seg flag necessary in order to calculate only the mean intensity within the skull, or does it serve another purpose? Thanks in advance, Panos ___ 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_segstats question
Hi Doug, Thanks for the quick reply! In addition: 1) The average intensity measure in the above example does not include the intensity of the skull, just everything inside, right? 2) Just to be clear on the purpose of including the segmentations in the command line: The segmentations only specify the areas of the brain that you would like to measure the intensity on, but besides that they don't provide any intensity info by themselves, would that be correct? That is the purpose of the --i flag, right? Thanks again for your help, Panos > > On 4/18/14 3:32 PM, pfot...@nmr.mgh.harvard.edu wrote: >> Hi FS community, >> >> I had some questions regarding the mri_segstats command: >> >> 1) In the excludeid flag, are the ids the ones shown in the >> FreeSurferColorLUT.txt? > Yes >> 2) In case I would like to measure the mean intensity of the orig file >> as >> outlined in the second example in >> https://surfer.nmr.mgh.harvard.edu/fswiki/mri_segstats: >> >> mri_segstats --seg $SUBJECTS_DIR/bert/mri/aseg >> --ctab $FREESURFER_HOME/FreeSurferColorLUT.txt >> --nonempty --excludeid 0 --sum bert.aseg.sum >> --in $SUBJECTS_DIR/bert/mri/orig >> >> is the --seg flag necessary in order to calculate only the mean >> intensity >> within the skull, or does it serve another purpose? > The seg defines the segmentations (eg, 17 is hippocampus) > >> >> Thanks in advance, >> Panos >> ___ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> > > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] mri_segstats question
Hi Doug, Thanks again for your reply. One last question: The aseg.mgz file includes the cortex as well. If I want to extract the cortex from the aseg.mgz file, should I binarize both the aseg.mgz and aparc_aseg.mgz files and subtract them, and then use the result in the mri_segstats command, or is there a different way? Thanks, Panos > > On 4/18/14 4:25 PM, pfot...@nmr.mgh.harvard.edu wrote: >> Hi Doug, >> >> Thanks for the quick reply! In addition: >> >> 1) The average intensity measure in the above example does not include >> the >> intensity of the skull, just everything inside, right? > It includes all the structures that are segmented in seg. If there is > not a skull segmentation, then it will not be in the output list. >> 2) Just to be clear on the purpose of including the segmentations in the >> command line: The segmentations only specify the areas of the brain that >> you would like to measure the intensity on, but besides that they don't >> provide any intensity info by themselves, would that be correct? That is >> the purpose of the --i flag, right? > Correct > doug >> >> Thanks again for your help, >> Panos >> >>> On 4/18/14 3:32 PM, pfot...@nmr.mgh.harvard.edu wrote: Hi FS community, I had some questions regarding the mri_segstats command: 1) In the excludeid flag, are the ids the ones shown in the FreeSurferColorLUT.txt? >>> Yes 2) In case I would like to measure the mean intensity of the orig file as outlined in the second example in https://surfer.nmr.mgh.harvard.edu/fswiki/mri_segstats: mri_segstats --seg $SUBJECTS_DIR/bert/mri/aseg --ctab $FREESURFER_HOME/FreeSurferColorLUT.txt --nonempty --excludeid 0 --sum bert.aseg.sum --in $SUBJECTS_DIR/bert/mri/orig is the --seg flag necessary in order to calculate only the mean intensity within the skull, or does it serve another purpose? >>> The seg defines the segmentations (eg, 17 is hippocampus) >>> Thanks in advance, Panos ___ 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 mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] mri_segstats question
Hi Doug, I'm sorry, what I meant to ask in the previous question is whether there is a way to come up with a segmentation volume for the mri_segstats command that is exactly like aseg.mgz but that does not include the cortex. The reason I'm asking is because by using the aseg.mgz volume in the --seg flag, you're also incorporating the intensity of the cortex when measuring the mean intensity of orig.mgz, but I wanted to see if there was a way to calculate the mean intensity of orig.mgz but without incorporating the intensity of the cortex. Thanks again, Panos > > If you want the volume of cortex, you should definitely not use > aseg.mgz. aparc+aseg is better, but the best is to use the surface-based > measure found in aseg.stats > > doug > > On 04/22/2014 10:55 AM, pfot...@nmr.mgh.harvard.edu wrote: >> Hi Doug, >> >> Thanks again for your reply. One last question: The aseg.mgz file >> includes >> the cortex as well. If I want to extract the cortex from the aseg.mgz >> file, should I binarize both the aseg.mgz and aparc_aseg.mgz files and >> subtract them, and then use the result in the mri_segstats command, or >> is >> there a different way? >> >> Thanks, >> Panos >> >>> On 4/18/14 4:25 PM, pfot...@nmr.mgh.harvard.edu wrote: Hi Doug, Thanks for the quick reply! In addition: 1) The average intensity measure in the above example does not include the intensity of the skull, just everything inside, right? >>> It includes all the structures that are segmented in seg. If there is >>> not a skull segmentation, then it will not be in the output list. 2) Just to be clear on the purpose of including the segmentations in the command line: The segmentations only specify the areas of the brain that you would like to measure the intensity on, but besides that they don't provide any intensity info by themselves, would that be correct? That is the purpose of the --i flag, right? >>> Correct >>> doug Thanks again for your help, Panos > On 4/18/14 3:32 PM, pfot...@nmr.mgh.harvard.edu wrote: >> Hi FS community, >> >> I had some questions regarding the mri_segstats command: >> >> 1) In the excludeid flag, are the ids the ones shown in the >> FreeSurferColorLUT.txt? > Yes >> 2) In case I would like to measure the mean intensity of the orig >> file >> as >> outlined in the second example in >> https://surfer.nmr.mgh.harvard.edu/fswiki/mri_segstats: >> >> mri_segstats --seg $SUBJECTS_DIR/bert/mri/aseg >>--ctab $FREESURFER_HOME/FreeSurferColorLUT.txt >>--nonempty --excludeid 0 --sum bert.aseg.sum >>--in $SUBJECTS_DIR/bert/mri/orig >> >> is the --seg flag necessary in order to calculate only the mean >> intensity >> within the skull, or does it serve another purpose? > The seg defines the segmentations (eg, 17 is hippocampus) > >> Thanks in advance, >> Panos >> ___ >> 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 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 >> >> > > -- > 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 > > > ___ 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 wa
Re: [Freesurfer] mri_segstats question
That is great,
Thanks a lot, Doug!
>
> You can just do it in matlab, somethhing like
>
> a = MRIread('aparc+aseg.mgz');
> ind = find(a.vol > 999);
> a.vol(ind) = 0;
> MRIwrite(a,'nocortex.mgz')
>
>
>
> On 04/22/2014 11:38 AM, pfot...@nmr.mgh.harvard.edu wrote:
>> Hi Doug,
>>
>> I'm sorry, what I meant to ask in the previous question is whether there
>> is a way to come up with a segmentation volume for the mri_segstats
>> command that is exactly like aseg.mgz but that does not include the
>> cortex. The reason I'm asking is because by using the aseg.mgz volume in
>> the --seg flag, you're also incorporating the intensity of the cortex
>> when
>> measuring the mean intensity of orig.mgz, but I wanted to see if there
>> was
>> a way to calculate the mean intensity of orig.mgz but without
>> incorporating the intensity of the cortex.
>>
>> Thanks again,
>> Panos
>>
>>> If you want the volume of cortex, you should definitely not use
>>> aseg.mgz. aparc+aseg is better, but the best is to use the
>>> surface-based
>>> measure found in aseg.stats
>>>
>>> doug
>>>
>>> On 04/22/2014 10:55 AM, pfot...@nmr.mgh.harvard.edu wrote:
Hi Doug,
Thanks again for your reply. One last question: The aseg.mgz file
includes
the cortex as well. If I want to extract the cortex from the aseg.mgz
file, should I binarize both the aseg.mgz and aparc_aseg.mgz files and
subtract them, and then use the result in the mri_segstats command, or
is
there a different way?
Thanks,
Panos
> On 4/18/14 4:25 PM, pfot...@nmr.mgh.harvard.edu wrote:
>> Hi Doug,
>>
>> Thanks for the quick reply! In addition:
>>
>> 1) The average intensity measure in the above example does not
>> include
>> the
>> intensity of the skull, just everything inside, right?
> It includes all the structures that are segmented in seg. If there is
> not a skull segmentation, then it will not be in the output list.
>> 2) Just to be clear on the purpose of including the segmentations in
>> the
>> command line: The segmentations only specify the areas of the brain
>> that
>> you would like to measure the intensity on, but besides that they
>> don't
>> provide any intensity info by themselves, would that be correct?
>> That
>> is
>> the purpose of the --i flag, right?
> Correct
> doug
>> Thanks again for your help,
>> Panos
>>
>>> On 4/18/14 3:32 PM, pfot...@nmr.mgh.harvard.edu wrote:
Hi FS community,
I had some questions regarding the mri_segstats command:
1) In the excludeid flag, are the ids the ones shown in the
FreeSurferColorLUT.txt?
>>> Yes
2) In case I would like to measure the mean intensity of the orig
file
as
outlined in the second example in
https://surfer.nmr.mgh.harvard.edu/fswiki/mri_segstats:
mri_segstats --seg $SUBJECTS_DIR/bert/mri/aseg
--ctab $FREESURFER_HOME/FreeSurferColorLUT.txt
--nonempty --excludeid 0 --sum bert.aseg.sum
--in $SUBJECTS_DIR/bert/mri/orig
is the --seg flag necessary in order to calculate only the mean
intensity
within the skull, or does it serve another purpose?
>>> The seg defines the segmentations (eg, 17 is hippocampus)
>>>
Thanks in advance,
Panos
___
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 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
>>> --
>>> 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
>>
Re: [Freesurfer] mri_segstats question
Hi Doug,
Thanks again for your help. I had two questions that came up from doing
some preliminary analysis with the mri_segstats:
1) When running the mri_segstats command with --seg
aparc+aseg_nocortex.mgz (which is the result of the matlab code you
provided below) and with --seg wmparc.mgz, even though the average
intensity is very close to each other, the individual intensities of same
structures are different. For instance
Left-Cerebral-White-Matter has an intensity of 145.3869 +/- 21.6883 with
--seg aparc+aseg_nocortex.mgz and an intensity of 149.6910 +/- 15.6547
with --aseg wmparc.mgz. Also the number of voxels of the same structure is
different in each case. Is there a reason why this is happening?
2) If I want to include the wm parcellation map to calculate the mean
intensity, I am assuming that wmparc.mgz would be the correct segmentation
volume to use, right?
3) If the answer to (2) is yes, and if I wanted to measure the average
intensity with --seg wmparc.mgz but after excluding the cortex, should I
run with --seg wmparc.mgz and just not take into consideration all the
*-ctx-* parcellations that come up in the stats file, or is there a way to
remove the cortex from wmparc.mgz and then run mri_segstats with the
wmparc_nocortex.mgz file as the --seg (I tried to subtract a binary map of
the cortex from wmparc.mgz, but had no luck: maybe I was doing something
wrong.)
Thanks in advance for your help!
Best,
Panos
>
> You can just do it in matlab, somethhing like
>
> a = MRIread('aparc+aseg.mgz');
> ind = find(a.vol > 999);
> a.vol(ind) = 0;
> MRIwrite(a,'nocortex.mgz')
>
>
>
> On 04/22/2014 11:38 AM, pfot...@nmr.mgh.harvard.edu wrote:
>> Hi Doug,
>>
>> I'm sorry, what I meant to ask in the previous question is whether there
>> is a way to come up with a segmentation volume for the mri_segstats
>> command that is exactly like aseg.mgz but that does not include the
>> cortex. The reason I'm asking is because by using the aseg.mgz volume in
>> the --seg flag, you're also incorporating the intensity of the cortex
>> when
>> measuring the mean intensity of orig.mgz, but I wanted to see if there
>> was
>> a way to calculate the mean intensity of orig.mgz but without
>> incorporating the intensity of the cortex.
>>
>> Thanks again,
>> Panos
>>
>>> If you want the volume of cortex, you should definitely not use
>>> aseg.mgz. aparc+aseg is better, but the best is to use the
>>> surface-based
>>> measure found in aseg.stats
>>>
>>> doug
>>>
>>> On 04/22/2014 10:55 AM, pfot...@nmr.mgh.harvard.edu wrote:
Hi Doug,
Thanks again for your reply. One last question: The aseg.mgz file
includes
the cortex as well. If I want to extract the cortex from the aseg.mgz
file, should I binarize both the aseg.mgz and aparc_aseg.mgz files and
subtract them, and then use the result in the mri_segstats command, or
is
there a different way?
Thanks,
Panos
> On 4/18/14 4:25 PM, pfot...@nmr.mgh.harvard.edu wrote:
>> Hi Doug,
>>
>> Thanks for the quick reply! In addition:
>>
>> 1) The average intensity measure in the above example does not
>> include
>> the
>> intensity of the skull, just everything inside, right?
> It includes all the structures that are segmented in seg. If there is
> not a skull segmentation, then it will not be in the output list.
>> 2) Just to be clear on the purpose of including the segmentations in
>> the
>> command line: The segmentations only specify the areas of the brain
>> that
>> you would like to measure the intensity on, but besides that they
>> don't
>> provide any intensity info by themselves, would that be correct?
>> That
>> is
>> the purpose of the --i flag, right?
> Correct
> doug
>> Thanks again for your help,
>> Panos
>>
>>> On 4/18/14 3:32 PM, pfot...@nmr.mgh.harvard.edu wrote:
Hi FS community,
I had some questions regarding the mri_segstats command:
1) In the excludeid flag, are the ids the ones shown in the
FreeSurferColorLUT.txt?
>>> Yes
2) In case I would like to measure the mean intensity of the orig
file
as
outlined in the second example in
https://surfer.nmr.mgh.harvard.edu/fswiki/mri_segstats:
mri_segstats --seg $SUBJECTS_DIR/bert/mri/aseg
--ctab $FREESURFER_HOME/FreeSurferColorLUT.txt
--nonempty --excludeid 0 --sum bert.aseg.sum
--in $SUBJECTS_DIR/bert/mri/orig
is the --seg flag necessary in order to calculate only the mean
intensity
within the skull, or does it serve another purpose?
>>> The seg defines the segmentations (eg, 17 is hippocampus)
>>>
Thanks in advance,
Panos
___
Freesurfer mailing list
Freesurfe
Re: [Freesurfer] mri_segstats question
>
> On 04/24/2014 09:40 AM, pfot...@nmr.mgh.harvard.edu wrote:
>> Hi Doug,
>>
>> Thanks again for your help. I had two questions that came up from doing
>> some preliminary analysis with the mri_segstats:
>>
>> 1) When running the mri_segstats command with --seg
>> aparc+aseg_nocortex.mgz (which is the result of the matlab code you
>> provided below) and with --seg wmparc.mgz, even though the average
>> intensity is very close to each other, the individual intensities of
>> same
>> structures are different. For instance
>> Left-Cerebral-White-Matter has an intensity of 145.3869 +/- 21.6883 with
>> --seg aparc+aseg_nocortex.mgz and an intensity of 149.6910 +/- 15.6547
>> with --aseg wmparc.mgz. Also the number of voxels of the same structure
>> is
>> different in each case. Is there a reason why this is happening?
> what are your command lines?
>>
The commands are:
mri_segstats --seg /mri/aparc+aseg_nocortex.mgz --ctab
$FREESURFER_HOME/FreeSurferColorLUT.txt --nonempty --excludeid 0 --sum
/stats/int.aparc+aseg_nocortex.sum --in
/mri/orig.mgz
and
mri_segstats --seg /mri/wmparc.mgz --ctab
$FREESURFER_HOME/FreeSurferColorLUT.txt --nonempty --excludeid 0 --sum
/stats/int.wmparc.sum --in /mri/orig.mgz
>> 2) If I want to include the wm parcellation map to calculate the mean
>> intensity, I am assuming that wmparc.mgz would be the correct
>> segmentation
>> volume to use, right?
> mean intensity of what?
>>
The mean intensity of orig.mgz.
>> 3) If the answer to (2) is yes, and if I wanted to measure the average
>> intensity with --seg wmparc.mgz but after excluding the cortex, should I
>> run with --seg wmparc.mgz and just not take into consideration all the
>> *-ctx-* parcellations that come up in the stats file, or is there a way
>> to
>> remove the cortex from wmparc.mgz and then run mri_segstats with the
>> wmparc_nocortex.mgz file as the --seg (I tried to subtract a binary map
>> of
>> the cortex from wmparc.mgz, but had no luck: maybe I was doing something
>> wrong.)
>>
>> Thanks in advance for your help!
>>
>> Best,
>> Panos
>>
>>
>>
>>
>>> You can just do it in matlab, somethhing like
>>>
>>> a = MRIread('aparc+aseg.mgz');
>>> ind = find(a.vol > 999);
>>> a.vol(ind) = 0;
>>> MRIwrite(a,'nocortex.mgz')
>>>
>>>
>>>
>>> On 04/22/2014 11:38 AM, pfot...@nmr.mgh.harvard.edu wrote:
Hi Doug,
I'm sorry, what I meant to ask in the previous question is whether
there
is a way to come up with a segmentation volume for the mri_segstats
command that is exactly like aseg.mgz but that does not include the
cortex. The reason I'm asking is because by using the aseg.mgz volume
in
the --seg flag, you're also incorporating the intensity of the cortex
when
measuring the mean intensity of orig.mgz, but I wanted to see if there
was
a way to calculate the mean intensity of orig.mgz but without
incorporating the intensity of the cortex.
Thanks again,
Panos
> If you want the volume of cortex, you should definitely not use
> aseg.mgz. aparc+aseg is better, but the best is to use the
> surface-based
> measure found in aseg.stats
>
> doug
>
> On 04/22/2014 10:55 AM, pfot...@nmr.mgh.harvard.edu wrote:
>> Hi Doug,
>>
>> Thanks again for your reply. One last question: The aseg.mgz file
>> includes
>> the cortex as well. If I want to extract the cortex from the
>> aseg.mgz
>> file, should I binarize both the aseg.mgz and aparc_aseg.mgz files
>> and
>> subtract them, and then use the result in the mri_segstats command,
>> or
>> is
>> there a different way?
>>
>> Thanks,
>> Panos
>>
>>> On 4/18/14 4:25 PM, pfot...@nmr.mgh.harvard.edu wrote:
Hi Doug,
Thanks for the quick reply! In addition:
1) The average intensity measure in the above example does not
include
the
intensity of the skull, just everything inside, right?
>>> It includes all the structures that are segmented in seg. If there
>>> is
>>> not a skull segmentation, then it will not be in the output list.
2) Just to be clear on the purpose of including the segmentations
in
the
command line: The segmentations only specify the areas of the
brain
that
you would like to measure the intensity on, but besides that they
don't
provide any intensity info by themselves, would that be correct?
That
is
the purpose of the --i flag, right?
>>> Correct
>>> doug
Thanks again for your help,
Panos
> On 4/18/14 3:32 PM, pfot...@nmr.mgh.harvard.edu wrote:
>> Hi FS community,
>>
>> I had some questions regarding the mri_segstats command:
>>
>> 1) In the excludeid flag, are the ids the ones shown in the
>> FreeSurferColorLUT.txt?
>
[Freesurfer] Extract ROI from anatomical volume
Hi FS experts, I was wondering what the best way to extract an ROI from an anatomical volume would be. For instance, I would like to create a volume of only the wm-lh-precentral based on the orig.mgz volume and on the segmentation map wmparc.mgz. I know that something similar can be done with the mri_extract_label command, but if I'm not mistaken that command can only be applied to a segmentation volume, and not on an anatomical volume like orig.mgz. Thanks in advance, Panos ___ 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 ROI from anatomical volume
Hi Bruce, Yes, that's exactly what I needed, thanks a lot! Best, Panos > Hi Panos > > so you want an intensity volume that is zero everywhere except in a > label? If so, try mri_mask > > cheers > Bruce > > On Mon, 28 Apr 2014, pfot...@nmr.mgh.harvard.edu wrote: > >> Hi FS experts, >> >> I was wondering what the best way to extract an ROI from an anatomical >> volume would be. For instance, I would like to create a volume of only >> the >> wm-lh-precentral based on the orig.mgz volume and on the segmentation >> map >> wmparc.mgz. I know that something similar can be done with the >> mri_extract_label command, but if I'm not mistaken that command can only >> be applied to a segmentation volume, and not on an anatomical volume >> like >> orig.mgz. >> >> Thanks in advance, >> Panos >> ___ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> >> > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] aparc.stats info
Hi FS Comminity, I was wondering whether there is a reference that gives the exact definition of the measures reported in the *h.aparc.stats file (i.e. for the measures Integrated Rectified Mean Curvature, Integrated Rectified Gaussian Curvature, Folding Index and Intrinsic Curvature Index). Thank you for your time, Panos ___ 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] aparc.stats info
Hi Bruce, That's actually great, thanks for your help! Best, Panos > Hi Panos > > the first two are basic differential geometric measures (H and K are the > typical symbols for them). The second two come from a David Van Essen > paper > I think in the late 90s. Sorry, I don't remember the exact reference > > cheers > Bruce > > On Mon, 5 May 2014, pfot...@nmr.mgh.harvard.edu wrote: > >> Hi FS Comminity, >> >> I was wondering whether there is a reference that gives the exact >> definition of the measures reported in the *h.aparc.stats file (i.e. for >> the measures Integrated Rectified Mean Curvature, Integrated Rectified >> Gaussian Curvature, Folding Index and Intrinsic Curvature Index). >> >> Thank you for your time, >> Panos >> ___ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> >> > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] Quesion about lobar volumes
Hi FS Community, I created a lobes annotation file with the --lobesStrict flag of the mri_annotation2label and then converted it to a volume with the mri_label2vol command and the --annot flag. However, the resulting volume is just overlapping on top of the white surface, and not on the whole cortex. Is there a way to create a volume for the lobes that covers the whole cerebral cortex? That is a volume that shows you which part of the cerebral cortex belongs to each of the 6 lobes individually? Thank you in advance, Panos ___ 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] Quesion about lobar volumes
Hi Doug, Thanks for your help, the mri_aparc2aseg command worked fine. In addition, is there a way to get a binary volume for each of the lobes based on the result of the mri_aparc2aseg command? In other parcellation volumes, I would use mri_binarize and the FreeSurferColorLUT.txt table but here I coudn't think how this could be applicable. Thanks again, Panos > > Try using mri_aparc2aseg instead of label2vol. See the --help and/or > look in the recon-all.log file to get the command line used to create > the aparc+aseg.mgz file > doug > > On 05/07/2014 11:12 AM, pfot...@nmr.mgh.harvard.edu wrote: >> Hi FS Community, >> >> I created a lobes annotation file with the --lobesStrict flag of the >> mri_annotation2label and then converted it to a volume with the >> mri_label2vol command and the --annot flag. However, the resulting >> volume >> is just overlapping on top of the white surface, and not on the whole >> cortex. Is there a way to create a volume for the lobes that covers the >> whole cerebral cortex? That is a volume that shows you which part of the >> cerebral cortex belongs to each of the 6 lobes individually? >> >> Thank you in advance, >> Panos >> ___ >> 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 > > > ___ 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] Quesion about lobar volumes
Hi Doug, That sounds great! I'll go ahead and do that. I would just be interested in coming up with the binary maps of the lobes, not their associated stats. Should I still go ahead and use mri_segstats or should I use mri_binarize with the --match flag and the new color map instead? Thanks for all your help, Panos > > you'll need to get the code associated with each lobe. You can do this > by running > tkmedit subject nu.mgz -seg lobeseg.mgz -aux lobeseg.mgz > > This will show colors for the seg, but the names will be wrong. Click on > a seg and see what number it gets in the aux. Then create a new color > table to match, then run mri_segstats > > doug > > On 05/07/2014 04:51 PM, pfot...@nmr.mgh.harvard.edu wrote: >> Hi Doug, >> >> Thanks for your help, the mri_aparc2aseg command worked fine. In >> addition, >> is there a way to get a binary volume for each of the lobes based on the >> result of the mri_aparc2aseg command? >> In other parcellation volumes, I would use mri_binarize and the >> FreeSurferColorLUT.txt table but here I coudn't think how this could be >> applicable. >> >> Thanks again, >> Panos >> >> >>> Try using mri_aparc2aseg instead of label2vol. See the --help and/or >>> look in the recon-all.log file to get the command line used to create >>> the aparc+aseg.mgz file >>> doug >>> >>> On 05/07/2014 11:12 AM, pfot...@nmr.mgh.harvard.edu wrote: Hi FS Community, I created a lobes annotation file with the --lobesStrict flag of the mri_annotation2label and then converted it to a volume with the mri_label2vol command and the --annot flag. However, the resulting volume is just overlapping on top of the white surface, and not on the whole cortex. Is there a way to create a volume for the lobes that covers the whole cerebral cortex? That is a volume that shows you which part of the cerebral cortex belongs to each of the 6 lobes individually? Thank you in advance, Panos ___ 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 >>> >>> >>> >> ___ >> 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 > > > ___ 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] Centroid of a binary volume question
Dear FS Community, I was wondering whether there is a way to create a binary volumetric file of just the centroid of a binary volume (represented maybe as a dot of 1x1x1 mm^3 voxel size). I know how to find the coordinates of the centroid (through either the fslstats command or MATLAB), but I didn't know whether there was a way to create a new binary volume of just the centroid through the terminal. (I would do it manually, but I have ~500 binary volumes that I would like to apply the same method to). Thank you in advance for your help! Best, Panos ___ 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] Centroid of a binary volume question
Dear FS Community, I was wondering whether there is a way to create a binary volumetric file of just the centroid of a binary volume (represented maybe as a dot of 1x1x1 mm^3 voxel size). I know how to find the coordinates of the centroid (through either the fslstats command or MATLAB), but I didn't know whether there was a way to create a new binary volume of just the centroid through the terminal. (I would do it manually, but I have ~500 binary volumes that I would like to apply the same method to). Thank you in advance for your help! Best, Panos ___ 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] Centroid of a binary volume question
Hi Bruce and Doug, Both methods sound great. Thank you both for your help! Best, Panos > I don't think there is a single command line to do it, but if you can > get the centroid voxel from somewhere else (eg, fsl), then you can run > mri_volsynth --template template.nii.gz --pdf delta -delta-crsf col row > slice 0 > where col row and slice are the voxel coordinates > > > On 01/25/2016 03:49 PM, pfot...@nmr.mgh.harvard.edu wrote: >> Dear FS Community, >> >> I was wondering whether there is a way to create a binary volumetric >> file >> of just the centroid of a binary volume (represented maybe as a dot of >> 1x1x1 mm^3 voxel size). >> I know how to find the coordinates of the centroid (through either the >> fslstats command or MATLAB), but I didn't know whether there was a way >> to >> create a new binary volume of just the centroid through the terminal. (I >> would do it manually, but I have ~500 binary volumes that I would like >> to >> apply the same method to). >> Thank you in advance for your help! >> >> Best, >> Panos >> ___ >> 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 > > > ___ 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] AAL atlas question
Hi FS community, I have recon-ed a set of subjects and I was interested in also obtaining structural info (cortical thickness, gray matter volume, surface area etc.) based on a different atlas than the ones FS is using, and in particular the AAL atlas. I was wondering whether my approach would be the correct one or whether there is another (better and more accurate) approach: 1) Convert the AAL atlas into a surface (with mri_vol2surf) from the MNI space into the native subjects' space, 2) Use mris_anatomical_stats to calculate the structural stats Sorry for the potentially trivial question, and thank you for your time! Best, Panos ___ 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] AAL atlas question
Hi Doug, Thanks for your response! Panos > I would recon the mni152 (or whatever space the AAL atlas is in), map > the AAL ROIs onto the surface (vol2surf), then use mri_surf2surf to > transfer them to the individual. > > On 02/29/2016 06:37 PM, pfot...@nmr.mgh.harvard.edu wrote: >> Hi FS community, >> >> I have recon-ed a set of subjects and I was interested in also obtaining >> structural info (cortical thickness, gray matter volume, surface area >> etc.) based on a different atlas than the ones FS is using, and in >> particular the AAL atlas. >> >> I was wondering whether my approach would be the correct one or whether >> there is another (better and more accurate) approach: >> >> 1) Convert the AAL atlas into a surface (with mri_vol2surf) from the MNI >> space into the native subjects' space, >> 2) Use mris_anatomical_stats to calculate the structural stats >> >> Sorry for the potentially trivial question, and thank you for your time! >> >> Best, >> Panos >> >> ___ >> 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 > > > ___ 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_vol2vol question
Dear FS community, I used mri_robust_register to register a volume to the fsaverage space, and then tried to use the resulting .lta file to register another vol on the same space as the original volume, to fsaverage, using mri_vol2vol. The structure of the command I used is: mri_vol2vol --mov --targ --lta ./.lta --o However, I keep getting the error: MatrixAsciiReadFrom: could not scanf parms Do you happen to know what is the cause of that error? Thanks in advance. Best, Panos ___ 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_vol2vol question
Sorry for the follow up email, but I realized my mistake. When running the mri_robust_register command even though I used the lta flag for the output register file, I gave the extension .dat to the file. It seems like this is what caused the problem. Panos > Dear FS community, > > I used mri_robust_register to register a volume to the fsaverage space, > and then tried to use the resulting .lta file to register another vol on > the same space as the original volume, to fsaverage, using mri_vol2vol. > The structure of the command I used is: > mri_vol2vol --mov --targ --lta > ./.lta --o > > However, I keep getting the error: > MatrixAsciiReadFrom: could not scanf parms > > Do you happen to know what is the cause of that error? > > Thanks in advance. > > Best, > Panos > ___ > 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] Deformed tksurfer results
Hi, I ran tksurfer (with the inflated surface option) on a couple of my subjects that had a major deformation in their orig.mgz file and the inflated surface of tksurfer looked as if a chunk was missing off of it at the position where the deformation is located. Is that normal? I have attached two images to illustrate what I mean: One of an axial slab of the orig.mgz file where the deformation is shown, and one of the inflated surface of the same subject in tksurfer. Thank you for your time, Panos ___ 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] Deformed tksurfer results
Hi Bruce, I'm sorry, I didn't phrase the question correctly. I do know why the orig.mgz comes out like that, however, I don't now why does the inflated surface in tksurfer look as if a chunk is missing out of it. Thanks again, Panos > Hi Panos, > > you probably want to get a neuroradiologist to look at that scan. > > cheers > Bruce > On Tue, 30 > Jul 2013, pfot...@nmr.mgh.harvard.edu wrote: > >> Hi, >> >> I ran tksurfer (with the inflated surface option) on a couple of my >> subjects that had a major deformation in their orig.mgz file and the >> inflated surface of tksurfer looked as if a chunk was missing off of it >> at >> the position where the deformation is located. Is that normal? >> >> I have attached two images to illustrate what I mean: One of an axial >> slab >> of the orig.mgz file where the deformation is shown, and one of the >> inflated surface of the same subject in tksurfer. >> >> Thank you for your time, >> Panos >> ___ >> 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] Controlling for shape (and size) of a ROI in co-registration
Hi FS Community, Is there a way to control for the size and shape of a ROI when applying co-registration? For instance, I drew a ROI in a scan through freesurfer, and then when I coregistered that ROI to another scan, the resulting ROI had a different shape and number of voxels compared to the original ROI. IS there a way to control for that? Thank you for your time. Best, Panos ___ 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] Controlling for shape (and size) of a ROI in co-registration
I see, thanks Bruce! > Hi Panos, > > not unless you want to restrict the registration to be rigid (6 dofs) > > cheers > Bruce > On > Mon, > 5 Aug 2013, pfot...@nmr.mgh.harvard.edu wrote: > >> Hi FS Community, >> >> Is there a way to control for the size and shape of a ROI when applying >> co-registration? For instance, I drew a ROI in a scan through >> freesurfer, >> and then when I coregistered that ROI to another scan, the resulting ROI >> had a different shape and number of voxels compared to the original ROI. >> IS there a way to control for that? >> >> Thank you for your time. >> >> Best, >> Panos >> ___ >> 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] Binary mask
Hi FS Community, Is there a way to create a binary mask of everything that is inside the cortical ribbon of a subject (including the cortical ribbon)? I ran: mri_binarize --i aseg.mgz --match 3 --match 42 --o test.mgz which gave me a binary mask of the cerebral cortex, but I was wondering whether there is a way to create a binary mask of the cerebral cortex as well as everything inside of it. Thank you for your time. Best, Panos ___ 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] Recon-all error
Hi FS Commuity, I am using the stable version 5.3 of FS to recon-all a subject of mine, but the job is aborted and gives the following message: The command that I ran is: recon-all -all -subjid /cluster/ichresearch/Petechial/MEG/CAA_022_struc Subject Stamp: freesurfer-Linux-centos6_x86_64-stable-v5.3.0-20130514 Current Stamp: freesurfer-Linux-centos6_x86_64-stable-v5.3.0-20130514 INFO: SUBJECTS_DIR is /autofs/cluster/ichresearch/Petechial/MEG Actual FREESURFER_HOME /autofs/cluster/freesurfer/centos6_x86_64/stable5_3_0 Linux eesmith 2.6.32-279.22.1.el6.x86_64 #1 SMP Wed Feb 6 03:10:46 UTC 2013 x86_64 x86_64 x86_64 GNU/Linux # #@# MotionCor Tue Aug 27 11:09:19 EDT 2013 Found 2 runs /autofs/cluster/ichresearch/Petechial/MEG/CAA_022_struc/mri/orig/001.mgz /autofs/cluster/ichresearch/Petechial/MEG/CAA_022_struc/mri/orig/002.mgz Checking for (invalid) multi-frame inputs... if: Expression Syntax. Exit 1 Also, I tried doing the same recon-all with the stable 5.0 version and it runs fine. Therefore, I was wondering whether you could tell me why is this happening. By the way I have also attached the recon-all.log. Thank you for your time. Best, PanosTue Aug 27 11:08:47 EDT 2013 /autofs/cluster/ichresearch/Petechial/MEG/CAA_022_struc /usr/local/freesurfer/stable5_3_0/bin/recon-all -all -subjid /cluster/ichresearch/Petechial/MEG/CAA_022_struc subjid CAA_022_struc setenv SUBJECTS_DIR /autofs/cluster/ichresearch/Petechial/MEG FREESURFER_HOME /usr/local/freesurfer/stable5_3_0 Actual FREESURFER_HOME /autofs/cluster/freesurfer/centos6_x86_64/stable5_3_0 build-stamp.txt: freesurfer-Linux-centos6_x86_64-stable-v5.3.0-20130514 Linux eesmith 2.6.32-279.22.1.el6.x86_64 #1 SMP Wed Feb 6 03:10:46 UTC 2013 x86_64 x86_64 x86_64 GNU/Linux cputime unlimited filesize unlimited datasize unlimited stacksize10240 kbytes coredumpsize 0 kbytes memoryuseunlimited vmemoryuse unlimited descriptors 4096 memorylocked 64 kbytes maxproc 4096 total used free sharedbuffers cached Mem: 80599447591652 468292 01453972 236756 -/+ buffers/cache:59009242159020 Swap:0 0 0 program versions used $Id: recon-all,v 1.379.2.73 2013/05/12 23:15:37 nicks Exp $ $Id: mri_motion_correct.fsl,v 1.14 2011/03/02 20:16:39 nicks Exp $ mri_convert -all-info ProgramName: mri_convert ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/27-15:08:48-GMT BuildTimeStamp: May 14 2013 15:52:47 CVS: $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ User: pfotiad Machine: eesmith Platform: Linux PlatformVersion: 2.6.32-279.22.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 FLIRT version 5.5 $Id: talairach_avi,v 1.9 2011/03/02 18:38:06 nicks Exp $ mri_convert --version stable5 ProgramName: tkregister2_cmdl ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/27-15:08:49-GMT BuildTimeStamp: May 14 2013 15:52:47 CVS: $Id: tkregister2.c,v 1.121.2.1 2011/03/28 20:25:16 greve Exp $ User: pfotiad Machine: eesmith Platform: Linux PlatformVersion: 2.6.32-279.22.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 Program nu_correct, built from: Package MNI N3, version 1.10, compiled by nicks@minerva (x86_64-unknown-linux-gnu) on 2010-02-20 at 17:32:37 ProgramName: mri_make_uchar ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/27-15:08:51-GMT BuildTimeStamp: May 14 2013 15:52:47 CVS: $Id: mri_make_uchar.c,v 1.4 2011/03/02 00:04:14 nicks Exp $ User: pfotiad Machine: eesmith Platform: Linux PlatformVersion: 2.6.32-279.22.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_normalize ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/27-15:08:51-GMT BuildTimeStamp: May 14 2013 15:52:47 CVS: $Id: mri_normalize.c,v 1.73.2.1 2012/10/17 19:11:32 nicks Exp $ User: pfotiad Machine: eesmith Platform: Linux PlatformVersion: 2.6.32-279.22.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_watershed ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/27-15:08:52-GMT BuildTimeStamp: May 14 2013 15:52:47 CVS: $Id: mri_watershed.cpp,v 1.96.2.1 2011/11/08 22:18:44 nicks Exp $ User: pfotiad Machine: eesmith Platform: Linux PlatformVersion: 2.6.32-279.22.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_gcut ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/27-15:08:53-GMT BuildTimeStamp: May 14 2013 15:52:47 CVS: $Id: mri_gcut.cpp,v 1.14 2011/03/02 00:04:16 nicks Exp $ User: pfotiad Machine: eesmith Platform: Linux PlatformVersion: 2.6.32-279.22.1.el6.x86_64 CompilerName: GCC CompilerVersion
Re: [Freesurfer] Recon-all error
Hi Doug, The same error message comes up. Panos > try this instead > > recon-all -all -subjid CAA_022_struc > > On 08/27/2013 11:23 AM, pfot...@nmr.mgh.harvard.edu wrote: >> Hi FS Commuity, >> >> I am using the stable version 5.3 of FS to recon-all a subject of mine, >> but the job is aborted and gives the following message: >> >> The command that I ran is: recon-all -all -subjid >> /cluster/ichresearch/Petechial/MEG/CAA_022_struc >> >> >> Subject Stamp: >> freesurfer-Linux-centos6_x86_64-stable-v5.3.0-20130514 >> Current Stamp: >> freesurfer-Linux-centos6_x86_64-stable-v5.3.0-20130514 >> INFO: SUBJECTS_DIR is /autofs/cluster/ichresearch/Petechial/MEG >> Actual FREESURFER_HOME >> /autofs/cluster/freesurfer/centos6_x86_64/stable5_3_0 >> Linux eesmith 2.6.32-279.22.1.el6.x86_64 #1 SMP Wed Feb 6 03:10:46 >> UTC >> 2013 x86_64 x86_64 x86_64 GNU/Linux >> # >> #@# MotionCor Tue Aug 27 11:09:19 EDT 2013 >> Found 2 runs >> /autofs/cluster/ichresearch/Petechial/MEG/CAA_022_struc/mri/orig/001.mgz >> /autofs/cluster/ichresearch/Petechial/MEG/CAA_022_struc/mri/orig/002.mgz >> Checking for (invalid) multi-frame inputs... >> if: Expression Syntax. >> Exit 1 >> >> Also, I tried doing the same recon-all with the stable 5.0 version and >> it >> runs fine. Therefore, I was wondering whether you could tell me why is >> this happening. By the way I have also attached the recon-all.log. >> >> Thank you for your time. >> >> Best, >> Panos >> >> >> ___ >> 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 > > > ___ 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] Recon-all error
echo $inputargs >> $ENVF echo -debug -all -subjid CAA_022_struc uname -a >> $ENVF uname -a echo "" >> $ENVF echo limit >> $ENVF limit echo "" >> $ENVF echo printenv >> $ENVF printenv endif endif if ( $DoVersionsOnly ) then if ( 0 ) then if ( $#LF == 0 ) then if ( 0 == 0 ) then set LF = ( $subjdir/scripts/$LF_DEFAULT_NAME ) set LF = ( /autofs/cluster/ichresearch/Petechial/MEG/CAA_022_struc/scripts/recon-all.log ) if ( -e $LF ) then if ( -e /autofs/cluster/ichresearch/Petechial/MEG/CAA_022_struc/scripts/recon-all.log ) then ls -l $LF ls -l /autofs/cluster/ichresearch/Petechial/MEG/CAA_022_struc/scripts/recon-all.log -rw-rw-r-- 1 pfotiad smithich 16476 Aug 27 12:35 /autofs/cluster/ichresearch/Petechial/MEG/CAA_022_struc/scripts/recon-all.log if ( ! $AppendLog ) then if ( ! 1 ) then if ( $?RECONALL_MAKE_SUBJECT ) goto skip_new_invo if ( 0 ) goto skip_new_invo echo "\n\n" >> $LF echo \n\n echo "New invocation of recon-all " >> $LF echo New invocation of recon-all echo "\n\n" >> $LF echo \n\n endif endif
[Freesurfer] Measuring cortical thickness at a specific location
Hi FS experts, I was wondering whether it would be possible to measure the average cortical thickness at a specific slice (either axial, coronal, or sagittal). I read in Bruce's paper: "Measuring the thickness of the human cerebral cortex from magnetic resonance images" that "Measuring the thickness from the coronal slice at the point indicated by the green cross would result in an estimate in excess of 1 cm." Is that always the case, or has there been a way to bypass that issue? Thank you for your time, Panos ___ 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] Measuring cortical thickness at a specific location
Hi Bruce, Thank you for your reply. I was interested in looking how the thickness changes from the posterior to the anterior side of the brain and vice versa (the thickness gradient). Thank you again for your time! Panos > Hi Panos > > it would certainly be possible to make that measurement, but it wouldn't > tell you anything biologically interesting. Why would you want to do such > a > thing? It will reflect the (arbitrary) image slice orientation and not the > brain. > > cheers > Bruce > > > On Mon, 12 May 2014, pfot...@nmr.mgh.harvard.edu wrote: > >> Hi FS experts, >> >> I was wondering whether it would be possible to measure the average >> cortical thickness at a specific slice (either axial, coronal, or >> sagittal). I read in Bruce's paper: "Measuring the thickness of the >> human >> cerebral cortex from magnetic resonance images" that "Measuring the >> thickness from the coronal slice at the point indicated by the green >> cross >> would result in an estimate in excess of 1 cm." Is that always the case, >> or has there been a way to bypass that issue? >> >> Thank you for your time, >> Panos >> ___ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> >> > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] Measuring cortical thickness at a specific location
Hi Bruce, Just to clarify, when you say "average the thickness along each A/P coordinate" do you mean by looking up at the average cortical thickness of each parcellation and then calculating their average from P->A, or is there another way to find the average thickness of each slice and then see how that average changes from P->A? Thanks again for your time, Panos > I see. Then measure the thickness normally, then see how it changes in > those directions. You could average the thickness along each A/P > coordinate > - that wouldn't be a problem. You just don't want to measure it that way > > cheers > Bruce > > > On Mon, 12 May 2014, > pfot...@nmr.mgh.harvard.edu wrote: > >> Hi Bruce, >> >> Thank you for your reply. I was interested in looking how the thickness >> changes from the posterior to the anterior side of the brain and vice >> versa (the thickness gradient). >> >> Thank you again for your time! >> Panos >> >> >>> Hi Panos >>> >>> it would certainly be possible to make that measurement, but it >>> wouldn't >>> tell you anything biologically interesting. Why would you want to do >>> such >>> a >>> thing? It will reflect the (arbitrary) image slice orientation and not >>> the >>> brain. >>> >>> cheers >>> Bruce >>> >>> >>> On Mon, 12 May 2014, pfot...@nmr.mgh.harvard.edu wrote: >>> Hi FS experts, I was wondering whether it would be possible to measure the average cortical thickness at a specific slice (either axial, coronal, or sagittal). I read in Bruce's paper: "Measuring the thickness of the human cerebral cortex from magnetic resonance images" that "Measuring the thickness from the coronal slice at the point indicated by the green cross would result in an estimate in excess of 1 cm." Is that always the case, or has there been a way to bypass that issue? Thank you for your time, Panos ___ 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 mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] Measuring cortical thickness at a specific location
Hi Bruce, I see, that's really helpful, thank you! Best, Panos > Hi Panos > > I would make an average thickness map in fsaverage space, then in matlab > divvy up the a-p direction into bins (say 100 of them) and compute the > average in each bin based on the a/p coordinate > > cheers > Bruce > On Tue, 13 May 2014, > pfot...@nmr.mgh.harvard.edu wrote: > >> Hi Bruce, >> >> Just to clarify, when you say "average the thickness along each A/P >> coordinate" do you mean by looking up at the average cortical thickness >> of >> each parcellation and then calculating their average from P->A, or is >> there another way to find the average thickness of each slice and then >> see >> how that average changes from P->A? >> Thanks again for your time, >> Panos >> >>> I see. Then measure the thickness normally, then see how it changes in >>> those directions. You could average the thickness along each A/P >>> coordinate >>> - that wouldn't be a problem. You just don't want to measure it that >>> way >>> >>> cheers >>> Bruce >>> >>> >>> On Mon, 12 May 2014, >>> pfot...@nmr.mgh.harvard.edu wrote: >>> Hi Bruce, Thank you for your reply. I was interested in looking how the thickness changes from the posterior to the anterior side of the brain and vice versa (the thickness gradient). Thank you again for your time! Panos > Hi Panos > > it would certainly be possible to make that measurement, but it > wouldn't > tell you anything biologically interesting. Why would you want to do > such > a > thing? It will reflect the (arbitrary) image slice orientation and > not > the > brain. > > cheers > Bruce > > > On Mon, 12 May 2014, pfot...@nmr.mgh.harvard.edu wrote: > >> Hi FS experts, >> >> I was wondering whether it would be possible to measure the average >> cortical thickness at a specific slice (either axial, coronal, or >> sagittal). I read in Bruce's paper: "Measuring the thickness of the >> human >> cerebral cortex from magnetic resonance images" that "Measuring the >> thickness from the coronal slice at the point indicated by the green >> cross >> would result in an estimate in excess of 1 cm." Is that always the >> case, >> or has there been a way to bypass that issue? >> >> Thank you for your time, >> Panos >> ___ >> 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 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 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] Measuring cortical thickness at a specific location
Hi Bruce, Sorry, I had a last follow up question. I just realized that the resulting bins will be in the fsaverage space, and hence I wouldn't be able to use mris_anatomical_stats to calculate the average thickness of the bins, since the fsaverage "subject" does not have a wm.mgz file. Did you have another way in mind to calculate the thickness of each bin, or do you believe that mris_anatomical stats should do the trick with a specific flag? Thanks a ton, Panos > Hi Bruce, > > I see, that's really helpful, thank you! > > Best, > Panos > > >> Hi Panos >> >> I would make an average thickness map in fsaverage space, then in matlab >> divvy up the a-p direction into bins (say 100 of them) and compute the >> average in each bin based on the a/p coordinate >> >> cheers >> Bruce >> On Tue, 13 May 2014, >> pfot...@nmr.mgh.harvard.edu wrote: >> >>> Hi Bruce, >>> >>> Just to clarify, when you say "average the thickness along each A/P >>> coordinate" do you mean by looking up at the average cortical thickness >>> of >>> each parcellation and then calculating their average from P->A, or is >>> there another way to find the average thickness of each slice and then >>> see >>> how that average changes from P->A? >>> Thanks again for your time, >>> Panos >>> I see. Then measure the thickness normally, then see how it changes in those directions. You could average the thickness along each A/P coordinate - that wouldn't be a problem. You just don't want to measure it that way cheers Bruce On Mon, 12 May 2014, pfot...@nmr.mgh.harvard.edu wrote: > Hi Bruce, > > Thank you for your reply. I was interested in looking how the > thickness > changes from the posterior to the anterior side of the brain and vice > versa (the thickness gradient). > > Thank you again for your time! > Panos > > >> Hi Panos >> >> it would certainly be possible to make that measurement, but it >> wouldn't >> tell you anything biologically interesting. Why would you want to do >> such >> a >> thing? It will reflect the (arbitrary) image slice orientation and >> not >> the >> brain. >> >> cheers >> Bruce >> >> >> On Mon, 12 May 2014, pfot...@nmr.mgh.harvard.edu wrote: >> >>> Hi FS experts, >>> >>> I was wondering whether it would be possible to measure the average >>> cortical thickness at a specific slice (either axial, coronal, or >>> sagittal). I read in Bruce's paper: "Measuring the thickness of the >>> human >>> cerebral cortex from magnetic resonance images" that "Measuring the >>> thickness from the coronal slice at the point indicated by the >>> green >>> cross >>> would result in an estimate in excess of 1 cm." Is that always the >>> case, >>> or has there been a way to bypass that issue? >>> >>> Thank you for your time, >>> Panos >>> ___ >>> 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 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 mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] Measuring cortical thickness at a specific location
Hi Bruce, I was having issues with the part after that, that is how to calculate the average thickness of those bins, after I create them. Thanks again Best, Panos > Hi Panos > > no, mris_anatomical_stats won't do it. I would map the average thickness > to fsaverage coords, then load that into matlab and go from there using > the [xyz] coords of fsaverage for the binning, which is pretty much > MNI305 > > cheers > Bruce > On Tue, 13 May 2014, pfot...@nmr.mgh.harvard.edu wrote: > >> Hi Bruce, >> >> Sorry, I had a last follow up question. I just realized that the >> resulting >> bins will be in the fsaverage space, and hence I wouldn't be able to use >> mris_anatomical_stats to calculate the average thickness of the bins, >> since the fsaverage "subject" does not have a wm.mgz file. Did you have >> another way in mind to calculate the thickness of each bin, or do you >> believe that mris_anatomical stats should do the trick with a specific >> flag? >> >> Thanks a ton, >> Panos >> >>> Hi Bruce, >>> >>> I see, that's really helpful, thank you! >>> >>> Best, >>> Panos >>> >>> Hi Panos I would make an average thickness map in fsaverage space, then in matlab divvy up the a-p direction into bins (say 100 of them) and compute the average in each bin based on the a/p coordinate cheers Bruce On Tue, 13 May 2014, pfot...@nmr.mgh.harvard.edu wrote: > Hi Bruce, > > Just to clarify, when you say "average the thickness along each A/P > coordinate" do you mean by looking up at the average cortical > thickness > of > each parcellation and then calculating their average from P->A, or is > there another way to find the average thickness of each slice and > then > see > how that average changes from P->A? > Thanks again for your time, > Panos > >> I see. Then measure the thickness normally, then see how it changes >> in >> those directions. You could average the thickness along each A/P >> coordinate >> - that wouldn't be a problem. You just don't want to measure it that >> way >> >> cheers >> Bruce >> >> >> On Mon, 12 May 2014, >> pfot...@nmr.mgh.harvard.edu wrote: >> >>> Hi Bruce, >>> >>> Thank you for your reply. I was interested in looking how the >>> thickness >>> changes from the posterior to the anterior side of the brain and >>> vice >>> versa (the thickness gradient). >>> >>> Thank you again for your time! >>> Panos >>> >>> Hi Panos it would certainly be possible to make that measurement, but it wouldn't tell you anything biologically interesting. Why would you want to do such a thing? It will reflect the (arbitrary) image slice orientation and not the brain. cheers Bruce On Mon, 12 May 2014, pfot...@nmr.mgh.harvard.edu wrote: > Hi FS experts, > > I was wondering whether it would be possible to measure the > average > cortical thickness at a specific slice (either axial, coronal, or > sagittal). I read in Bruce's paper: "Measuring the thickness of > the > human > cerebral cortex from magnetic resonance images" that "Measuring > the > thickness from the coronal slice at the point indicated by the > green > cross > would result in an estimate in excess of 1 cm." Is that always > the > case, > or has there been a way to bypass that issue? > > Thank you for your time, > Panos > ___ > 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 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 >
Re: [Freesurfer] Measuring cortical thickness at a specific location
Hi Bruce, Thanks again for your help so far. I had a few follow up questions: 1) As far as mapping the average thickness to fsaverage coords, when I was constructing the average thickness map I used mris_preproc with --target fsaverage (and then mri_concat), so it's already in fsaverage coordinates right? Or do I need to apply mri_surf2surf? 2) I used read_curv to load it into matlab which gives a matrix where I'm assuming that n is the number of total vertices of the cortex, right? 3) Concerning the binning in matlab, I know how to do it in the order of increasing vertex number, but I had trouble incorporating the [xyz] fsaverage coordinates. Is there a way to rearrange the matrix (that is the result of read_curv) into another matrix where the thickness values are sorted based on the fsaverage coordinates? Best, Panos > Hi Panos > > no, mris_anatomical_stats won't do it. I would map the average thickness > to fsaverage coords, then load that into matlab and go from there using > the [xyz] coords of fsaverage for the binning, which is pretty much > MNI305 > > cheers > Bruce > On Tue, 13 May 2014, pfot...@nmr.mgh.harvard.edu wrote: > >> Hi Bruce, >> >> Sorry, I had a last follow up question. I just realized that the >> resulting >> bins will be in the fsaverage space, and hence I wouldn't be able to use >> mris_anatomical_stats to calculate the average thickness of the bins, >> since the fsaverage "subject" does not have a wm.mgz file. Did you have >> another way in mind to calculate the thickness of each bin, or do you >> believe that mris_anatomical stats should do the trick with a specific >> flag? >> >> Thanks a ton, >> Panos >> >>> Hi Bruce, >>> >>> I see, that's really helpful, thank you! >>> >>> Best, >>> Panos >>> >>> Hi Panos I would make an average thickness map in fsaverage space, then in matlab divvy up the a-p direction into bins (say 100 of them) and compute the average in each bin based on the a/p coordinate cheers Bruce On Tue, 13 May 2014, pfot...@nmr.mgh.harvard.edu wrote: > Hi Bruce, > > Just to clarify, when you say "average the thickness along each A/P > coordinate" do you mean by looking up at the average cortical > thickness > of > each parcellation and then calculating their average from P->A, or is > there another way to find the average thickness of each slice and > then > see > how that average changes from P->A? > Thanks again for your time, > Panos > >> I see. Then measure the thickness normally, then see how it changes >> in >> those directions. You could average the thickness along each A/P >> coordinate >> - that wouldn't be a problem. You just don't want to measure it that >> way >> >> cheers >> Bruce >> >> >> On Mon, 12 May 2014, >> pfot...@nmr.mgh.harvard.edu wrote: >> >>> Hi Bruce, >>> >>> Thank you for your reply. I was interested in looking how the >>> thickness >>> changes from the posterior to the anterior side of the brain and >>> vice >>> versa (the thickness gradient). >>> >>> Thank you again for your time! >>> Panos >>> >>> Hi Panos it would certainly be possible to make that measurement, but it wouldn't tell you anything biologically interesting. Why would you want to do such a thing? It will reflect the (arbitrary) image slice orientation and not the brain. cheers Bruce On Mon, 12 May 2014, pfot...@nmr.mgh.harvard.edu wrote: > Hi FS experts, > > I was wondering whether it would be possible to measure the > average > cortical thickness at a specific slice (either axial, coronal, or > sagittal). I read in Bruce's paper: "Measuring the thickness of > the > human > cerebral cortex from magnetic resonance images" that "Measuring > the > thickness from the coronal slice at the point indicated by the > green > cross > would result in an estimate in excess of 1 cm." Is that always > the > case, > or has there been a way to bypass that issue? > > Thank you for your time, > Panos > ___ > 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 l
[Freesurfer] Classifying thickness question
Hi Bruce, I had a few questions concerning the mris_classify_thickness algorithm that you wrote: 1) Are there any other options (i.e. other flags) that can be specified in the mris_classify_thickness -o [options] ... : ... commandline? Because in the description of the command there is nothing reported under the "valid options are:" I believe I saw some other options reported in the code of the specific function, but I wasn't sure whether they could be used. 2) Are the two classes defined as two different groups of subjects such as male/female or healthy/disease? 3) I ran the command on 4 subjects (class1: 2 diseased subj, class2: 2 healthy subjs) and the result was 2 data files with 202 pairs of cortical thickness values each. However, I'm not really sure what those values represent. Are they vertex-wise thickness values that correlate somehow between , and , respectively, or are they clustered-wise thickness values? 4) Are there any other outputs besides those two data files that the command can come up with? Thanks in advance for all your help! Panos ___ 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] Classifying thickness question
Hi Bruce, I see. Thanks for letting me know, I'll definitely check it out! Best, Panos > Hi Panos > > that binary is as old as the hills and there are way, way newer and > better things to use (you might check out RvoxM) > > cheers > Bruce > On Thu, 22 May 2014, > pfot...@nmr.mgh.harvard.edu wrote: > >> Hi Bruce, >> >> I had a few questions concerning the mris_classify_thickness algorithm >> that you wrote: >> 1) Are there any other options (i.e. other flags) that can be specified >> in >> the >> mris_classify_thickness -o [options] >> >> ... : >> ... >> commandline? Because in the description of the command there is nothing >> reported under the "valid options are:" I believe I saw some other >> options >> reported in the code of the specific function, but I wasn't sure whether >> they could be used. >> >> 2) Are the two classes defined as two different groups of subjects such >> as >> male/female or healthy/disease? >> >> 3) I ran the command on 4 subjects (class1: 2 diseased subj, class2: 2 >> healthy subjs) and the result was 2 data files with 202 pairs of >> cortical >> thickness values each. However, I'm not really sure what those values >> represent. Are they vertex-wise thickness values that correlate somehow >> between , and , >> respectively, or are they clustered-wise thickness values? >> >> 4) Are there any other outputs besides those two data files that the >> command can come up with? >> >> Thanks in advance for all your help! >> Panos >> ___ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> >> > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] CSF volume
Hi FS community, I was wondering whether there is a way to calculate accurately the CSF volume with FreeSurfer (I have both T1 and T2 images). Should I just add the ventricular structures and the CSF volume reported in aseg.stats or is there another way to account for the sulcal CSF based on the T2 and add it to the other volumes? Thanks in advance, Panos ___ 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] CSF volume
Hi Bruce, Thanks for your reply! I had a couple follow up questions: 1) In order to calculate the total ventricular CSF, should I add the CSF volume reported in the aseg.stats file to the other ventricular volumes or no? 2) Would there be a way to segment the sulcal CSF based on the T2 image? Thanks again for your help, Panos > Hi Panos > > sorry, we don't segment sulcal CSF > > Bruce > On Mon, 16 Jun 2014, > pfot...@nmr.mgh.harvard.edu wrote: > >> Hi FS community, >> >> I was wondering whether there is a way to calculate accurately the CSF >> volume with FreeSurfer (I have both T1 and T2 images). Should I just add >> the ventricular structures and the CSF volume reported in aseg.stats or >> is >> there another way to account for the sulcal CSF based on the T2 and add >> it >> to the other volumes? >> >> Thanks in advance, >> Panos >> ___ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> >> > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] CSF volume
I see, thanks! > 1. No, just add up all the ventricle measures. > 2. I think FSL might do this, but you would probably have to mask out the > ventricles as I doubt they label sulcal csf separately > > > On Tue, 17 Jun 2014, > pfot...@nmr.mgh.harvard.edu wrote: > >> Hi Bruce, >> >> Thanks for your reply! I had a couple follow up questions: >> >> 1) In order to calculate the total ventricular CSF, should I add the CSF >> volume reported in the aseg.stats file to the other ventricular volumes >> or >> no? >> >> 2) Would there be a way to segment the sulcal CSF based on the T2 image? >> >> Thanks again for your help, >> Panos >> >>> Hi Panos >>> >>> sorry, we don't segment sulcal CSF >>> >>> Bruce >>> On Mon, 16 Jun 2014, >>> pfot...@nmr.mgh.harvard.edu wrote: >>> Hi FS community, I was wondering whether there is a way to calculate accurately the CSF volume with FreeSurfer (I have both T1 and T2 images). Should I just add the ventricular structures and the CSF volume reported in aseg.stats or is there another way to account for the sulcal CSF based on the T2 and add it to the other volumes? Thanks in advance, Panos ___ 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 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] Question about LGI
Hi FS Community, I was wondering whether LGI and Surface Area need to be corrected for total Intracranial Volume. Thanks in advance, Panos ___ 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] Question about LGI
Hi Marie, Thank you for your reply. I wanted to compare the LGI and Surface Area between two cohorts, from which one has a significantly higher intracranial volume than the other. I was wondering about the correction because the results, especially in the case of SA, are the opposite before and after correcting for total intraranial volume, and for LGI, it just removed the significance of the association. Thanks again, Panos > > Hi Panos, > > It all depends on what your question is: whether the between-group > difference in LGI and surface area is an absolute difference (then don't > correct), or whether you want to see if it holds after correction. In any > case, by geometric definition, the relationship between surface area, and > thus LGI, and volume is governed by a power law, which means that if you > linearly correct for intracranial volume, some of its effect will remain. > > Hope it helps, > > Marie > > On Jul 10, 2014, at 10:57 AM, > wrote: > >> Hi FS Community, >> >> I was wondering whether LGI and Surface Area need to be corrected for >> total Intracranial Volume. >> >> Thanks in advance, >> Panos >> ___ >> 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] White matter comparison
Hi FS Experts, I am interested in doing a group analysis between different cohorts using the white matter volume as the variable of interest. Would the best way to do that be to follow the group analysis pipeline described in the wiki for cortical thickness (but replace the --meas thickness with --meas white), or is there a different approach that I should follow? Thanks in advance for your advice, Panos ___ 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] White matter comparison
Hi Doug, Yes, doing a VBM analysis would be precisely what I had in mind. Thanks, Panos > > I'm not sure what you mean. Do you want to do something like a VBM > analysis on WM? > doug > > On 11/13/2014 04:31 PM, pfot...@nmr.mgh.harvard.edu wrote: >> Hi FS Experts, >> >> I am interested in doing a group analysis between different cohorts >> using >> the white matter volume as the variable of interest. Would the best way >> to >> do that be to follow the group analysis pipeline described in the wiki >> for >> cortical thickness (but replace the --meas thickness with --meas white), >> or is there a different approach that I should follow? >> >> Thanks in advance for your advice, >> Panos >> >> ___ >> 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 > > > ___ 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] White matter comparison
Hi Doug, I see, making wm masks and converting them to mni space sounds like a great idea for what I had in mind. Thanks for your help! Best, Panos > > We are not properly set up for doing VBM. I suppose you could make > binary WM masks and map them into mni305 space or CVS space, but we > don't have a way to do jacobian modulation. If you want a VBM an > analysis, why not use SPM or FSL? > doug > > On 11/17/2014 01:27 PM, pfot...@nmr.mgh.harvard.edu wrote: >> Hi Doug, >> >> Yes, doing a VBM analysis would be precisely what I had in mind. >> >> Thanks, >> Panos >> >>> I'm not sure what you mean. Do you want to do something like a VBM >>> analysis on WM? >>> doug >>> >>> On 11/13/2014 04:31 PM, pfot...@nmr.mgh.harvard.edu wrote: Hi FS Experts, I am interested in doing a group analysis between different cohorts using the white matter volume as the variable of interest. Would the best way to do that be to follow the group analysis pipeline described in the wiki for cortical thickness (but replace the --meas thickness with --meas white), or is there a different approach that I should follow? Thanks in advance for your advice, Panos ___ 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 >>> >>> >>> >> ___ >> 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 > > > ___ 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] Supplementary Motor area
Hello, I am interested in performing some statistical analysis in the Supplementary motor area, but I think that none of the current Freesurfer atlases have it defined as an ROI (for instance in the parcellation of the cortex). Therefore, I was wondering whether there is a way to come up with an ROI map for that region, on the fsaverage brain. (I believe that the Harvard-Oxford atlas has it already defined, so would that mean that I would need to process all the subjects with FSL?) Thanks in advance, Panos ___ 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.
