[Freesurfer] recon-all subject -qcache in a different version of freesurfer?
Dear Freesurfer experts, I have processed my images and done analysis with cortical thickness using FS510. Now that I want to do vertex-wise analysis with surface area and volume, I learned that there is a bug in FS510 with this. ( https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2011-August/019903.html ) Before I go on to use recon-all subject -qcache in FS530 to generate vertex-wise surface area and volume maps, I want to make sure that this would not cause concerns about use of mixed versions of Freesurfer, or concerns about interpreting my cortical thickness and surface area/volume findings together. And if it does, what should I do? Thanks a lot, Cherry ___ 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 subject -qcache in a different version of freesurfer?
Great. Thanks Doug. On Thu, Apr 24, 2014 at 10:39 AM, Douglas N Greve wrote: > > It is ok to run -qcache using 5.3. > > > On 04/23/2014 10:54 PM, Yizhou Ma wrote: > > Dear Freesurfer experts, > > > > I have processed my images and done analysis with cortical thickness > > using FS510. Now that I want to do vertex-wise analysis with surface > > area and volume, I learned that there is a bug in FS510 with this. > > ( > https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2011-August/019903.html > ) > > Before I go on to use recon-all subject -qcache in FS530 to generate > > vertex-wise surface area and volume maps, I want to make sure that > > this would not cause concerns about use of mixed versions of > > Freesurfer, or concerns about interpreting my cortical thickness and > > surface area/volume findings together. And if it does, what should I do? > > > > Thanks a lot, > > Cherry > > > > > > > > ___ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > gr...@nmr.mgh.harvard.edu > Phone Number: 617-724-2358 > Fax: 617-726-7422 > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 > www.nmr.mgh.harvard.edu/facility/filedrop/index.html > Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > The information in this e-mail is intended only for the person to whom it > is > addressed. If you believe this e-mail was sent to you in error and the > e-mail > contains patient information, please contact the Partners Compliance > HelpLine at > http://www.partners.org/complianceline . If the e-mail was sent to you in > error > but does not contain patient information, please contact the sender and > properly > dispose of the e-mail. > > ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 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 subject -qcache in a different version of freesurfer?
Hi Doug, To follow-up: I have been running recon-all subject -qcache but for some of my subjects it "exited with ERRORS" due to unmatched number of vertices. I read from previous threads that the general fix is to run -autorecon2 and -autorecon3 again. However, I hesitate to do that in my case due to the difference in Freesurfer versions. What do you think I can do? Thanks, Cherry On Thu, Apr 24, 2014 at 12:06 PM, Yizhou Ma wrote: > Great. Thanks Doug. > > > On Thu, Apr 24, 2014 at 10:39 AM, Douglas N Greve < > gr...@nmr.mgh.harvard.edu> wrote: > >> >> It is ok to run -qcache using 5.3. >> >> >> On 04/23/2014 10:54 PM, Yizhou Ma wrote: >> > Dear Freesurfer experts, >> > >> > I have processed my images and done analysis with cortical thickness >> > using FS510. Now that I want to do vertex-wise analysis with surface >> > area and volume, I learned that there is a bug in FS510 with this. >> > ( >> https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2011-August/019903.html >> ) >> > Before I go on to use recon-all subject -qcache in FS530 to generate >> > vertex-wise surface area and volume maps, I want to make sure that >> > this would not cause concerns about use of mixed versions of >> > Freesurfer, or concerns about interpreting my cortical thickness and >> > surface area/volume findings together. And if it does, what should I do? >> > >> > Thanks a lot, >> > Cherry >> > >> > >> > >> > ___ >> > Freesurfer mailing list >> > Freesurfer@nmr.mgh.harvard.edu >> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> -- >> Douglas N. Greve, Ph.D. >> MGH-NMR Center >> gr...@nmr.mgh.harvard.edu >> Phone Number: 617-724-2358 >> Fax: 617-726-7422 >> >> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting >> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 >> www.nmr.mgh.harvard.edu/facility/filedrop/index.html >> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ >> >> ___ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> >> The information in this e-mail is intended only for the person to whom it >> is >> addressed. If you believe this e-mail was sent to you in error and the >> e-mail >> contains patient information, please contact the Partners Compliance >> HelpLine at >> http://www.partners.org/complianceline . If the e-mail was sent to you >> in error >> but does not contain patient information, please contact the sender and >> properly >> dispose of the e-mail. >> >> > ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 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] Xhemi: vertex-wise volume asymmetry analysis?
Dear freesurfer experts, I am working on a project on cortical asymmetry and I have analyzed vertex-wise cortical thickness/surface area asymmetry. However, I noticed that Freesurfer doesn't not seem to facilitate such analysis for gray matter volume, as after running surfreg -xhemi there is no ?h.volume file in subject/xhemi/surf. I searched the literature and found studies on gray matter density asymmetry with VBM and ROI-based volume asymmetry. Is it true that Freesurfer doesn't offer vertex-wise volume asymmetry analysis? And may I know the rationale? Thanks, Cherry ___ 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] Xhemi: vertex-wise volume asymmetry analysis?
Thanks Doug. I have ?h.volume in subject/surf but not in subject/xhemi/surf. I followed this page http://surfer.nmr.mgh.harvard.edu/fswiki/Xhemi and I think it is a problem with surfreg rather than mris_preproc. Can I just copy the ?h.volume from subject/surf to subject/xhemi/surf? Best, Cherry On Mon, Apr 28, 2014 at 4:01 PM, Douglas N Greve wrote: > > > There should be a ?h.volume file. Are you sure there is not? You can > specify -meas volume when you run mris_preproc > doug > > On 04/27/2014 08:35 PM, Yizhou Ma wrote: > > Dear freesurfer experts, > > > > I am working on a project on cortical asymmetry and I have analyzed > > vertex-wise cortical thickness/surface area asymmetry. However, I > > noticed that Freesurfer doesn't not seem to facilitate such analysis > > for gray matter volume, as after running surfreg -xhemi there is no > > ?h.volume file in subject/xhemi/surf. I searched the literature and > > found studies on gray matter density asymmetry with VBM and ROI-based > > volume asymmetry. Is it true that Freesurfer doesn't offer vertex-wise > > volume asymmetry analysis? And may I know the rationale? > > > > Thanks, > > Cherry > > > > > > ___ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > gr...@nmr.mgh.harvard.edu > Phone Number: 617-724-2358 > Fax: 617-726-7422 > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 > www.nmr.mgh.harvard.edu/facility/filedrop/index.html > Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > The information in this e-mail is intended only for the person to whom it > is > addressed. If you believe this e-mail was sent to you in error and the > e-mail > contains patient information, please contact the Partners Compliance > HelpLine at > http://www.partners.org/complianceline . If the e-mail was sent to you in > error > but does not contain patient information, please contact the sender and > properly > dispose of the e-mail. > > ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 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] Xhemi: vertex-wise volume asymmetry analysis?
Thanks Doug. I don't see an error message in xhemireg.?h.log files. Please see attached for the files. On Mon, Apr 28, 2014 at 4:22 PM, Douglas N Greve wrote: > > Then something went wrong along the way. Check the xhemi/xhemireg.?h.log > to see if there is an error. If not, send the log file to me > > On 04/28/2014 04:14 PM, Yizhou Ma wrote: > > Thanks Doug. I have ?h.volume in subject/surf but not in > > subject/xhemi/surf. I followed this page > > http://surfer.nmr.mgh.harvard.edu/fswiki/Xhemi and I think it is a > > problem with surfreg rather than mris_preproc. Can I just copy the > > ?h.volume from subject/surf to subject/xhemi/surf? > > > > Best, > > Cherry > > > > > > On Mon, Apr 28, 2014 at 4:01 PM, Douglas N Greve > > mailto:gr...@nmr.mgh.harvard.edu>> wrote: > > > > > > > > There should be a ?h.volume file. Are you sure there is not? You can > > specify -meas volume when you run mris_preproc > > doug > > > > On 04/27/2014 08:35 PM, Yizhou Ma wrote: > > > Dear freesurfer experts, > > > > > > I am working on a project on cortical asymmetry and I have analyzed > > > vertex-wise cortical thickness/surface area asymmetry. However, I > > > noticed that Freesurfer doesn't not seem to facilitate such > analysis > > > for gray matter volume, as after running surfreg -xhemi there is no > > > ?h.volume file in subject/xhemi/surf. I searched the literature and > > > found studies on gray matter density asymmetry with VBM and > > ROI-based > > > volume asymmetry. Is it true that Freesurfer doesn't offer > > vertex-wise > > > volume asymmetry analysis? And may I know the rationale? > > > > > > Thanks, > > > Cherry > > > > > > > > > ___ > > > Freesurfer mailing list > > > Freesurfer@nmr.mgh.harvard.edu > > <mailto:Freesurfer@nmr.mgh.harvard.edu> > > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > -- > > Douglas N. Greve, Ph.D. > > MGH-NMR Center > > gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu> > > Phone Number: 617-724-2358 > > Fax: 617-726-7422 > > > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > > FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 > > www.nmr.mgh.harvard.edu/facility/filedrop/index.html > > <http://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 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 > > -- > 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 > xhemireg.rh.log Description: Binary data xhemireg.lh.log Description: Binary data ___ 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] Xhemi: vertex-wise volume asymmetry analysis?
Hi Doug, I just read from the .log files that the lh.thickness/area/pial/... files in subject/xhemi/surf are copied from subject/surf at the end of the command. Thus it seems that I can just copy lh.volume, too? Thanks, Cherry On Mon, Apr 28, 2014 at 6:25 PM, Yizhou Ma wrote: > Thanks Doug. I don't see an error message in xhemireg.?h.log files. Please > see attached for the files. > > > On Mon, Apr 28, 2014 at 4:22 PM, Douglas N Greve < > gr...@nmr.mgh.harvard.edu> wrote: > >> >> Then something went wrong along the way. Check the xhemi/xhemireg.?h.log >> to see if there is an error. If not, send the log file to me >> >> On 04/28/2014 04:14 PM, Yizhou Ma wrote: >> > Thanks Doug. I have ?h.volume in subject/surf but not in >> > subject/xhemi/surf. I followed this page >> > http://surfer.nmr.mgh.harvard.edu/fswiki/Xhemi and I think it is a >> > problem with surfreg rather than mris_preproc. Can I just copy the >> > ?h.volume from subject/surf to subject/xhemi/surf? >> > >> > Best, >> > Cherry >> > >> > >> > On Mon, Apr 28, 2014 at 4:01 PM, Douglas N Greve >> > mailto:gr...@nmr.mgh.harvard.edu>> wrote: >> > >> > >> > >> > There should be a ?h.volume file. Are you sure there is not? You can >> > specify -meas volume when you run mris_preproc >> > doug >> > >> > On 04/27/2014 08:35 PM, Yizhou Ma wrote: >> > > Dear freesurfer experts, >> > > >> > > I am working on a project on cortical asymmetry and I have >> analyzed >> > > vertex-wise cortical thickness/surface area asymmetry. However, I >> > > noticed that Freesurfer doesn't not seem to facilitate such >> analysis >> > > for gray matter volume, as after running surfreg -xhemi there is >> no >> > > ?h.volume file in subject/xhemi/surf. I searched the literature >> and >> > > found studies on gray matter density asymmetry with VBM and >> > ROI-based >> > > volume asymmetry. Is it true that Freesurfer doesn't offer >> > vertex-wise >> > > volume asymmetry analysis? And may I know the rationale? >> > > >> > > Thanks, >> > > Cherry >> > > >> > > >> > > ___ >> > > Freesurfer mailing list >> > > Freesurfer@nmr.mgh.harvard.edu >> > <mailto:Freesurfer@nmr.mgh.harvard.edu> >> > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> > >> > -- >> > Douglas N. Greve, Ph.D. >> > MGH-NMR Center >> > gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu> >> > Phone Number: 617-724-2358 >> > Fax: 617-726-7422 >> > >> > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting >> > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> >> > FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 >> > www.nmr.mgh.harvard.edu/facility/filedrop/index.html >> > <http://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 > 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 >> >> -- >> Douglas N. Greve, Ph.D. >> MGH-NMR Center >> gr..
[Freesurfer] mri_glmfit-sim doesn't recognize --label flag
Dear freesurfer experts, I'm doing small volume correction for multiple comparison. However, when I run "mri_glmfit-sim" with "--label mylabelfile", I got the error that "--label unrecognizable". I use "mri_glmfit-sim --help" to see the help information but there is no information regarding "--label" or "--mask". May I know why this? P.S. I use FS510. I have run mri_glmfit-sim successfully without a mask. Thanks, Cherry ___ 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 with --xhemi
> If I do use the LI maps to perform my stats, which would be the > difference in interpretation between the results of using the > --paired-diff maps, and the standarized LI maps? The p-value will not change since the LI is just a scaled version of the paired-diff doug In my opinion, the interpretation will be different, and the difference just depends on the difference between (lh-rh) and LI themselves. The former tells you if the lh is bigger than the rh in absolute values, while the latter tells you to what extent it is asymmetrical. The latter is not a scaled, but a standarized version of the former. Which you use in your study really depends on which you are interested in conceptually. On Tue, Apr 2, 2013 at 12:30 PM, Douglas N Greve wrote: > I think it is best to do it before the smoothing, though my results did > not really change when I did it after. > doug > > > On 04/02/2013 12:07 PM, Gabriel Gonzalez Escamilla wrote: > > sorry I meant to do the division, to standarize the LI after the > > smoothing. > > > > El 02/04/13, *Gabriel Gonzalez Escamilla * escribió: > >> Dear Doug, > >> > >> Interesting but, if I'm understanding this well, to get a normal LI, > >> the --paired-diff-norm should be divided by 2 not multiplied, isn't it? > >> > >> standardLI = (lh-rh)/(lh+rh) > >> FS_LI = (lh-rh)/((lh+rh)/2) <-- as you are dividing the denominator, > >> your LI will be twice an standard one. > >> > >> Further, this division should be done before the smoothing, right? > >> > >> If I do use the LI maps to perform my stats, which would be the > >> difference in interpretation between the results of using the > >> --paired-diff maps, and the standarized LI maps? > >> > >> Regards, > >> Gabriel. > >> > >> > >> El 29/03/13, *Douglas N Greve * escribió: > >>> The --xhemi flag causes both the left and right hemispheres of each > >>> subject to be stacked into the output file. So the output file will > >>> have > >>> number of subjects x2 frames. The order is subject1.lh, subject1.rh, > >>> subject2.lh, subject2.rh, ... > >>> > >>> If you add the --paired-diff, then you will get number of frames = > >>> number of subjects, and each frame will be subject1.lh-rh, > >>> subject2.lh-rh, etc > >>> > >>> If you use the --paired-diff-norm instead, then you will get what you > >>> want subject1.(lh-rh)/((lh+rh)/2), subject2.(lh-rh)/((lh+rh)/2), etc. > >>> > >>> Note that most laterality indices (LI) are (lh-rh)/(lh+rh), so you > >>> would > >>> need to multiply the paired-diff-norm by 2. > >>> > >>> Finally, I want to point out that it may be better to smooth before > >>> computing the LI because the LI computation is non-linear and it has > >>> the > >>> potential to divide by a noisy number. To do this, run without the > >>> --paired-diff flags, then smooth, then run > >>> > >>> mri_concat yourfile.smoothed.mgh --paired-diff-norm --o > >>> yourfile.smoothed.LI.mgh > >>> > >>> In my study, I ran it both ways and it did not make a difference, but I > >>> think smoothing before LI is the safer bet. > >>> > >>> doug > >>> > >>> > >>> On 03/29/2013 12:33 PM, Ejoe Yizhou Ma wrote: > >>> > Hi freesurfer experts, > >>> > > >>> > I'm investigating lh-to-rh asymmetry and am following instructions on > >>> > this page :http://surfer.nmr.mgh.harvard.edu/fswiki/Xhemi. > >>> > My question is, what does the "--xhemi" flag do in the "mris_preproc" > >>> > command? It seems to me that it calculates (lh-rh) value at each > >>> > vertex for every subject. (I tried to use the same subject for each > >>> > pair of input for "--paired-diff", and the result is not a all-zero > >>> > output.) > >>> > > >>> > It would also be nice if someone can tell me how to realize my final > >>> > goal, which is to get the (lh-rh)/[(lh+rh)/2] value at each vertex > >>> for > >>> > each subject in a .mgh file. > >>> > > >>> > Thanks, > >>> > Cherry > >>> > > >>> > > >>> > ___ > >>> > Freesurfer mailing list > >>> > Freesu
Re: [Freesurfer] temporal lobe left out in pial surface - edits on brainmask.mgz or brain.finalsurfs.mgz?
Hi Chris, Thanks a lot. I agree that control points should actually only be put in white matter. I'm just not sure if I can expand the pial surface to a satisfactory extend if I only do edits in the white matter. It seems to me that the problem here is that the signal weakened in the lower part of the brain so that the gray matter doesn't have adequate intensity to be included in the pial surface (the values are around 30). Thanks, Cherry On Wed, May 22, 2013 at 3:14 PM, Chris Watson < christopher.wat...@childrens.harvard.edu> wrote: > You need to place the control points in the white matter, not around it. > > On 05/22/2013 03:04 PM, Yizhou Ma wrote: > > Dear FS experts, > > I have a subject where large portions of temporal lobe is not included > in the pial surface. A member in my lab has suggested edits on > brain.finalsurfs.mgz. However, in the following page it is indicated that > edits on brain.finalsurfs.mgz is only intended for cases regarding > inclusion of cerebellum. Can anyone please let me know which volume I > should be working on in this case? > > http://ftp.nmr.mgh.harvard.edu/fswiki/FsTutorial/PialEdits > > Thanks, > Cherry > > > ___ > Freesurfer mailing > listfreesur...@nmr.mgh.harvard.eduhttps://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 > athttp://www.partners.org/complianceline . If the e-mail was sent to you in > error > but does not contain patient information, please contact the sender and > properly > dispose of the e-mail. > > > ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] temporal lobe left out in pial surface - edits on brainmask.mgz or brain.finalsurfs.mgz?
Ok. I'll give it a try. Thanks, Chris & Bruce! On Wed, May 22, 2013 at 3:29 PM, Bruce Fischl wrote: > Hi Cherry > > Chris is right. Putting control points in the WM will help the pial > surface as well. > > cheers > Bruce > > On Wed, 22 May 2013, Yizhou Ma wrote: > > Hi Chris, >> Thanks a lot. I agree that control points should actually only be put in >> white matter. I'm just not sure if I can expand the pial surface to a >> satisfactory extend if I only do edits in the white matter. It seems to me >> that the problem here is that the signal weakened in the lower part of the >> brain so that the gray matter doesn't have adequate intensity to be >> included >> in the pial surface (the values are around 30). >> >> Thanks, >> Cherry >> >> >> On Wed, May 22, 2013 at 3:14 PM, Chris Watson >> > >> wrote: >> You need to place the control points in the white matter, not >> around it. >> >> On 05/22/2013 03:04 PM, Yizhou Ma wrote: >> Dear FS experts, >> I have a subject where large portions of temporal lobe is not >> included in the pial surface. A member in my lab has suggested >> edits on brain.finalsurfs.mgz. However, in the following page it >> is indicated that edits on brain.finalsurfs.mgz is only intended >> for cases regarding inclusion of cerebellum. Can anyone please >> let me know which volume I should be working on in this case? >> >> http://ftp.nmr.mgh.harvard.**edu/fswiki/FsTutorial/**PialEdits<http://ftp.nmr.mgh.harvard.edu/fswiki/FsTutorial/PialEdits> >> >> Thanks, >> Cherry >> >> >> __**_ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.**edu/mailman/listinfo/**freesurfer<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-mai >> l >> contains patient information, please contact the Partners Compliance >> HelpLin >> e at >> http://www.partners.org/**complianceline<http://www.partners.org/complianceline>. >> If the e-mail was sent to you in er >> ror >> but does not contain patient information, please contact the sender and >> prop >> erly >> dispose of the e-mail. >> >> >> >> >> >> ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] temporal lobe left out in pial surface - edits on brainmask.mgz or brain.finalsurfs.mgz?
Hi Michael, This method seems cool. I'll try to implement it. Thank you so much. Best, Cherry On Wed, May 22, 2013 at 4:17 PM, Harms, Michael wrote: > > I've also posted in the past on a set of "expert options" that helped > our surfaces in the temporal lobe considerably. You should be able to > locate that post in the archives. > > -- > Michael Harms, Ph.D. > --- > Conte Center for the Neuroscience of Mental Disorders > Washington University School of Medicine > Department of Psychiatry, Box 8134 > 660 South Euclid Ave. Tel: 314-747-6173 > St. Louis, MO 63110 Email: mha...@wustl.edu > > From: Yizhou Ma > Date: Wednesday, May 22, 2013 2:30 PM > To: Bruce Fischl > Cc: freesurfer , Chris Watson < > christopher.wat...@childrens.harvard.edu> > > Subject: Re: [Freesurfer] temporal lobe left out in pial surface - edits > on brainmask.mgz or brain.finalsurfs.mgz? > > Ok. I'll give it a try. Thanks, Chris & Bruce! > > > On Wed, May 22, 2013 at 3:29 PM, Bruce Fischl > wrote: > >> Hi Cherry >> >> Chris is right. Putting control points in the WM will help the pial >> surface as well. >> >> cheers >> Bruce >> >> On Wed, 22 May 2013, Yizhou Ma wrote: >> >> Hi Chris, >>> Thanks a lot. I agree that control points should actually only be put in >>> white matter. I'm just not sure if I can expand the pial surface to a >>> satisfactory extend if I only do edits in the white matter. It seems to >>> me >>> that the problem here is that the signal weakened in the lower part of >>> the >>> brain so that the gray matter doesn't have adequate intensity to be >>> included >>> in the pial surface (the values are around 30). >>> >>> Thanks, >>> Cherry >>> >>> >>> On Wed, May 22, 2013 at 3:14 PM, Chris Watson >>> > >>> wrote: >>> You need to place the control points in the white matter, not >>> around it. >>> >>> On 05/22/2013 03:04 PM, Yizhou Ma wrote: >>> Dear FS experts, >>> I have a subject where large portions of temporal lobe is not >>> included in the pial surface. A member in my lab has suggested >>> edits on brain.finalsurfs.mgz. However, in the following page it >>> is indicated that edits on brain.finalsurfs.mgz is only intended >>> for cases regarding inclusion of cerebellum. Can anyone please >>> let me know which volume I should be working on in this case? >>> >>> http://ftp.nmr.mgh.harvard.**edu/fswiki/FsTutorial/**PialEdits<http://ftp.nmr.mgh.harvard.edu/fswiki/FsTutorial/PialEdits> >>> >>> Thanks, >>> Cherry >>> >>> >>> __**_ >>> Freesurfer mailing list >>> Freesurfer@nmr.mgh.harvard.edu >>> https://mail.nmr.mgh.harvard.**edu/mailman/listinfo/**freesurfer<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-mai >>> l >>> contains patient information, please contact the Partners Compliance >>> HelpLin >>> e at >>> http://www.partners.org/**complianceline<http://www.partners.org/complianceline>. >>> If the e-mail was sent to you in er >>> ror >>> but does not contain patient information, please contact the sender and >>> prop >>> erly >>> dispose of the e-mail. >>> >>> >>> >>> >>> >>> > > -- > > The materials in this message are private and may contain Protected > Healthcare Information or other information of a sensitive nature. If you > are not the intended recipient, be advised that any unauthorized use, > disclosure, copying or the taking of any action in reliance on the contents > of this information is strictly prohibited. If you have received this email > in error, please immediately notify the sender via telephone or return mail. > ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] temporal lobe left out in pial surface - edits on brainmask.mgz or brain.finalsurfs.mgz?
Hi all, This is a follow-up on my question so that people can know what I've tried and how it works. I added control points in the white matter and the delineation of the temporal lobe has improved to a satisfying level. We also find what Michael has suggested very interesting. But it seems that if we change the parameters for certain subjects, we would have to rerun all of the other subjects with the same set of parameters, which may not be desirable at the moment. Thanks for all the help, Cherry On Wed, May 22, 2013 at 4:46 PM, Yizhou Ma wrote: > Hi Michael, > > This method seems cool. I'll try to implement it. Thank you so much. > > Best, > Cherry > > > On Wed, May 22, 2013 at 4:17 PM, Harms, Michael wrote: > >> >> I've also posted in the past on a set of "expert options" that helped >> our surfaces in the temporal lobe considerably. You should be able to >> locate that post in the archives. >> >> -- >> Michael Harms, Ph.D. >> --- >> Conte Center for the Neuroscience of Mental Disorders >> Washington University School of Medicine >> Department of Psychiatry, Box 8134 >> 660 South Euclid Ave. Tel: 314-747-6173 >> St. Louis, MO 63110 Email: mha...@wustl.edu >> >> From: Yizhou Ma >> Date: Wednesday, May 22, 2013 2:30 PM >> To: Bruce Fischl >> Cc: freesurfer , Chris Watson < >> christopher.wat...@childrens.harvard.edu> >> >> Subject: Re: [Freesurfer] temporal lobe left out in pial surface - edits >> on brainmask.mgz or brain.finalsurfs.mgz? >> >> Ok. I'll give it a try. Thanks, Chris & Bruce! >> >> >> On Wed, May 22, 2013 at 3:29 PM, Bruce Fischl > > wrote: >> >>> Hi Cherry >>> >>> Chris is right. Putting control points in the WM will help the pial >>> surface as well. >>> >>> cheers >>> Bruce >>> >>> On Wed, 22 May 2013, Yizhou Ma wrote: >>> >>> Hi Chris, >>>> Thanks a lot. I agree that control points should actually only be put in >>>> white matter. I'm just not sure if I can expand the pial surface to a >>>> satisfactory extend if I only do edits in the white matter. It seems to >>>> me >>>> that the problem here is that the signal weakened in the lower part of >>>> the >>>> brain so that the gray matter doesn't have adequate intensity to be >>>> included >>>> in the pial surface (the values are around 30). >>>> >>>> Thanks, >>>> Cherry >>>> >>>> >>>> On Wed, May 22, 2013 at 3:14 PM, Chris Watson >>>> > >>>> wrote: >>>> You need to place the control points in the white matter, not >>>> around it. >>>> >>>> On 05/22/2013 03:04 PM, Yizhou Ma wrote: >>>> Dear FS experts, >>>> I have a subject where large portions of temporal lobe is not >>>> included in the pial surface. A member in my lab has suggested >>>> edits on brain.finalsurfs.mgz. However, in the following page it >>>> is indicated that edits on brain.finalsurfs.mgz is only intended >>>> for cases regarding inclusion of cerebellum. Can anyone please >>>> let me know which volume I should be working on in this case? >>>> >>>> http://ftp.nmr.mgh.harvard.**edu/fswiki/FsTutorial/**PialEdits<http://ftp.nmr.mgh.harvard.edu/fswiki/FsTutorial/PialEdits> >>>> >>>> Thanks, >>>> Cherry >>>> >>>> >>>> __**_ >>>> Freesurfer mailing list >>>> Freesurfer@nmr.mgh.harvard.edu >>>> https://mail.nmr.mgh.harvard.**edu/mailman/listinfo/**freesurfer<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-mai >>>> l >>>> contains patient information, please contact the Partners Compliance >>>> HelpLin >>>> e at >>>> http://www.partners.org/**complianceline<http://www.partners.org/complianceline>. >>>> If the e-mail was sent to you in er >>>> ror >>>> but does not contain patient information, please contact the sender and >>>> prop >>>&
[Freesurfer] Total gray matter volume for aparc.2009?
Dear Freesurfer experts, I'm doing ROI analysis on surface area and gray matter volume using the aparc.2009 parcellation. Now that I wanted to use corresponding whole brain measures as covariates, I could not find whole brain gray matter volume measures in the aparc.a2009s.stats file. However, I find one in the aseg.stats file. Since I believe these two file use different approaches to estimate gray matter volume, I'm stuck with what I choose for the whole brain measure. Do I use the value in aseg.stats or do I add up the volumes of regions in aparc.a2009s.stats? And advice is appreciated. Thanks, Cherry ___ 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] Total gray matter volume for aparc.2009?
This is very helpful, Doug. Then I should the value in aseg.stats. Thank you very much. On Mon, Sep 16, 2013 at 4:20 PM, Douglas Greve wrote: > > Hi Cherry, the total gray matter volume in aseg.stats is a combination of > the two approaches. For cortical structures, it computes the volume using > surface-based methods. The subcortical structures it uses the volume-based > method. To compute total GM, you need both. > doug > > > > On 9/16/13 9:11 PM, Yizhou Ma wrote: > > Dear Freesurfer experts, > > I'm doing ROI analysis on surface area and gray matter volume using the > aparc.2009 parcellation. Now that I wanted to use corresponding whole brain > measures as covariates, I could not find whole brain gray matter volume > measures in the aparc.a2009s.stats file. However, I find one in the > aseg.stats file. Since I believe these two file use different approaches to > estimate gray matter volume, I'm stuck with what I choose for the whole > brain measure. Do I use the value in aseg.stats or do I add up the volumes > of regions in aparc.a2009s.stats? And advice is appreciated. > > Thanks, > Cherry > > > ___ > Freesurfer mailing > listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > The information in this e-mail is intended only for the person to whom it > is > addressed. If you believe this e-mail was sent to you in error and the > e-mail > contains patient information, please contact the Partners Compliance > HelpLine at > http://www.partners.org/complianceline . If the e-mail was sent to you in > error > but does not contain patient information, please contact the sender and > properly > dispose of the e-mail. > > ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] Paired t-test with independent samples
Hi Jurgen, I actually just came across a similar situation in which I tried to convince my PI that a paired t test is more appropriate. In my humble opinion, if you are applying an independent group test, than the matching design is irrelevant in this analysis because you're not taking any advantage that might accompany the matching. On the other hand, a paired t test lends more power if your subjects are sufficiently matched, while being more conservative when the matching is a failure (i.e. if you thick the two groups are actually idependent. In that case you'll get the same t value but a smaller df in a paired t analysis). That being said, I suggest you consult a statistical advisor for the appropriate solution. Cherry On Tue, Jul 24, 2012 at 11:53 AM, Douglas N Greve wrote: > Hi Jurgen, I don't think it is too unusual to do this kind of thing, ie, > a paired test where pairing is based on gender, age, and education, but > you know your data and field better than I do. It is not the case that > one is more conservative than another (they are the same) assuming that > the underlying assumptions are met. The underlying assumptions are more > stringent for the paired than for the unpaired. > doug > > On 07/24/2012 06:22 AM, Jürgen Hänggi wrote: > > Dear statistic experts > > > > We have done statistics between two independent groups using an > independent > > t-test. One group consistent of 13 male patients and the other group > > consistent of 13 male control subjects who were matched to the patients > with > > respect to age and education (in years). > > > > The reviewer proposed that it might be more appropriate to use a paired > > t-test. > > However, we can imaging a design where such an approach is adequate e.g. > > monozygotic twins reared in shared environments who are discordant for a > > particular trait. > > > > In our opinion, the matching of only age and education is not sufficient > in > > order to apply a paired t-test. > > In addition, the paired t-test is more anti-conservative than the > > independent t-test and therefore advantages our hypothesis and this > might be > > identified as a statistical "trick" by other reviewers. > > > > Any comment about whether or not the suggested paired t-test is > appropriate > > in our study is highly appreciated. > > > > Thanks in advance > > Regards > > Jürgen Hänggi > > > > > > > Jürgen Hänggi, Ph.D. > > Division Neuropsychology > > Institute of Psychology > > University of Zurich > > Binzmuehlestrasse 14, PO Box 25 > > 8050 Zurich, Switzerland > > 0041 44 635 73 97 (phone office) > > 0041 76 445 86 84 (phone mobile) > > 0041 44 635 74 09 (fax office) > > BIN 4.D.04 (office room number) > > j.haenggi[at]psychologie.uzh.ch (email) > > http://www.psychologie.uzh.ch/neuropsy/ (website) > > http://www.juergenhaenggi.ch (private website) > > > > This e-mail (and any attachment/s) contains confidential and/or > privileged > > information. If you are not the intended recipient (or have received this > > e-mail in error) please notify the sender immediately and destroy this > > e-mail. Any unauthorised copying, disclosure or distribution of the > > material in this e-mail is strictly forbidden. > > > > > > > > > > > > > ___ > > 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: www.nmr.mgh.harvard.edu/facility/filedrop/index.html > > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > The information in this e-mail is intended only for the person to whom it > is > addressed. If you believe this e-mail was sent to you in error and the > e-mail > contains patient information, please contact the Partners Compliance > HelpLine at > http://www.partners.org/complianceline . If the e-mail was sent to you in > error > but does not contain patient information, please contact the sender and > properly > dispose of the e-mail. > > ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and p
Re: [Freesurfer] contrast matrix
Hi Bo, I'm definitely not an expert of this, but I see that you really nead some help, so I tried to look at your matrix. From my humble opinion it doesn't look correct. Firstly, the first 9 groups are male groups and the last 9 are female groups. Then why are all female groups assigned 0 in the matrix? Secondly, since the interaction you are interested in have a df of 4, do you think maybe you should have 4 rows rather than 8 in your matrix? Cherry On Sat, Nov 17, 2012 at 9:21 PM, xiangbo_2010 wrote: > Hi Freesurfer experts, > > I'm very sorry to bother you, but I am very confused with the following > questions: > > My experimental design includes three discrete factors: factor > 1 with three levels (A,B,C ); factor 2 with three levels (O,P,Q); gender > (F, M), and one covariate. > > So I can get 18 classes: FAO, FAP,FAQ,FBO,FBP,FBQ,FCO,FCP,FCQ,MAO, > MAP,MAQ,MBO,MBP,MBQ,MCO,MCP,MCQ. I want to perform the interaction > between factor 1 and factor 2 regressing out the effect of gender and one > covariate, but I don't know the rules for setting the contrasts for the > F-test. The contrast matrix I used is: > > 1 1 1 -1 -1 -1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 > > 1 -1 0 1 -1 0 1 -1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 > > 1 1 1 0 0 0 -1 -1 -1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 > > 1 0 -1 1 0 -1 1 0 -1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 > 0 > > 0 0 0 0 0 0 0 0 0 1 1 1 -1 -1 -1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 > 0 > > 0 0 0 0 0 0 0 0 0 1 -1 0 1 -1 0 1 -1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 > 0 > > 0 0 0 0 0 0 0 0 0 1 1 1 0 0 0 -1 -1 -1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 > 0 > > 0 0 0 0 0 0 0 0 0 1 0 -1 1 0 -1 1 0 -1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 > 0 > > is it correct? > > > > Any help will be very appreciated. > > > > Best wishes, > > > > Bo Xiang > > > > > > > > > > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > The information in this e-mail is intended only for the person to whom it > is > addressed. If you believe this e-mail was sent to you in error and the > e-mail > contains patient information, please contact the Partners Compliance > HelpLine at > http://www.partners.org/complianceline . If the e-mail was sent to you in > error > but does not contain patient information, please contact the sender and > properly > dispose of the e-mail. > > ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] contrast matrix
Hi Doug, Thanks for replying. Yet I have a question on this matrix. From what I see, each row corresponds to one contrast, which has one df. Thus why are we having 8 rows while the interaction has a df of 4? Thanks, Cherry On Sun, Nov 18, 2012 at 6:23 PM, Douglas Greve wrote: > > Hi Bo, you can think of the Ftest as a logical 'OR' between the t-test > contrasts indicated in each row. Each row is a difference of differences, so > > 1. (A-B)om - (A-B)pm --> Does the difference between A and B differ > between groups O and P for Males? > 2. (A-B)om - (A-B)qm > 3. (A-C)om - (A-C)pm > 4. (A-C)om - (A-C)qm > 5. (A-B)of - (A-B)pf --> Does the difference between A and B differ > between groups O and P for Females? > 6. (A-B)of - (A-B)qf > 7. (A-C)of - (A-C)pf > 8. (A-C)of - (A-C)pf > > I've put together the first 9 columns of the first 4 rows. The last 9 > columns are all 0s. For the last for rows, the 0s and below matrix are > swapped to give you the same for the females > > doug > > AOM BOM APM BPM AQM BQM COM CPM > CQM > -- > +AOM -BOM -APM -BPM0000 > 0 > +AOM -BOM00 -AQM +BQM00 > 0 > +AOM0 -APM000 -COM +CPM > 0 > +AOM000 -AQM -COM0 > +CQM > > > > On 11/17/12 9:21 PM, xiangbo_2010 wrote: > > Hi Freesurfer experts, > > I'm very sorry to bother you, but I am very confused with the following > questions: > > My experimental design includes three discrete factors: factor > 1 with three levels (A,B,C ); factor 2 with three levels (O,P,Q); gender > (F, M), and one covariate. > > So I can get 18 classes: FAO, FAP,FAQ,FBO,FBP,FBQ,FCO,FCP,FCQ,MAO, > MAP,MAQ,MBO,MBP,MBQ,MCO,MCP,MCQ. I want to perform the interaction > between factor 1 and factor 2 regressing out the effect of gender and one > covariate, but I don't know the rules for setting the contrasts for the > F-test. The contrast matrix I used is: > > 1 1 1 -1 -1 -1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 > > 1 -1 0 1 -1 0 1 -1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 > > 1 1 1 0 0 0 -1 -1 -1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 > > 1 0 -1 1 0 -1 1 0 -1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 > 0 > > 0 0 0 0 0 0 0 0 0 1 1 1 -1 -1 -1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 > 0 > > 0 0 0 0 0 0 0 0 0 1 -1 0 1 -1 0 1 -1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 > 0 > > 0 0 0 0 0 0 0 0 0 1 1 1 0 0 0 -1 -1 -1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 > 0 > > 0 0 0 0 0 0 0 0 0 1 0 -1 1 0 -1 1 0 -1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 > 0 > > is it correct? > > > > Any help will be very appreciated. > > > > Best wishes, > > > > Bo Xiang > > > > > > > > > > > ___ > Freesurfer mailing > listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > The information in this e-mail is intended only for the person to whom it > is > addressed. If you believe this e-mail was sent to you in error and the > e-mail > contains patient information, please contact the Partners Compliance > HelpLine at > http://www.partners.org/complianceline . If the e-mail was sent to you in > error > but does not contain patient information, please contact the sender and > properly > dispose of the e-mail. > > ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] mris_thickness & qcache for xhemi surfaces
Dear Freesurfer experts, I'm trying to investigate lh-to-rh asymmetry, so I register my subjects to the subject of fsaverage_sym following the instructions on this page: http://surfer.nmr.mgh.harvard.edu/fswiki/Xhemi. After all the surfreg commands I've got ?h.thickness files in subjid/xhemi/surf. In my lab we generally process ?h.thickness files with the next two commands before statistically analysis: "mris_thickness -max 10 subjid ?h thickness_max10" "recon-all -qcache -measure thickness_max10 -target fsaverage_510 -fwhm 10 -no-isrunning -s subjid -hemi ?h" To keep with this protocol, my questions are 1) how do I use "mris_thickness" properly so that I don't overwrite the files registered to fsaverage_510? 2) in "recon-all -qcache", will it do the trick by substituting "fsaverage_sym" for "fsaverage_510"? Thank you in advance, Cherry ___ 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_thickness & qcache for xhemi surfaces
Thanks, Doug. I'm not planning to use qdec. It's just that I used to generate the ?h.thickness_max10.fwhm10.fsaverage_510.mgh files (which are what we name the files after running the two commands) before I use mris_preproc and mri_glmfit. I also generally skip the "smooth" step in freesurfer tutorial since the files are smoothed in the first place. Any suggestions? Cherry On Thu, Mar 28, 2013 at 12:53 PM, Douglas N Greve wrote: > > > Actually, #2 will not work. I don't think you can use qdec with the > xhemi stuff anyway. You should use the mris_preproc command followed by > mri_glmfit. > doug > > > On 03/28/2013 12:51 PM, Douglas N Greve wrote: > > On 03/28/2013 12:16 PM, Ejoe Yizhou Ma wrote: > >> Dear Freesurfer experts, > >> > >> I'm trying to investigate lh-to-rh asymmetry, so I register my > >> subjects to the subject of fsaverage_sym following the instructions on > >> this page: http://surfer.nmr.mgh.harvard.edu/fswiki/Xhemi. After all > >> the surfreg commands I've got ?h.thickness files in subjid/xhemi/surf. > >> > >> In my lab we generally process ?h.thickness files with the next two > >> commands before statistically analysis: > >> > >> "mris_thickness -max 10 subjid ?h thickness_max10" > >> "recon-all -qcache -measure thickness_max10 -target fsaverage_510 > >> -fwhm 10 -no-isrunning -s subjid -hemi ?h" > >> > >> To keep with this protocol, my questions are > >> 1) how do I use "mris_thickness" properly so that I don't overwrite > >> the files registered to fsaverage_510? > > I think it will recreate the basic ?h.thickness file and will not touch > > registrations. > >> 2) in "recon-all -qcache", will it do the trick by substituting > >> "fsaverage_sym" for "fsaverage_510"? > >> > > Yes, that should work. > >> Thank you in advance, > >> Cherry > >> > >> > >> > >> ___ > >> 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: www.nmr.mgh.harvard.edu/facility/filedrop/index.html > Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > The information in this e-mail is intended only for the person to whom it > is > addressed. If you believe this e-mail was sent to you in error and the > e-mail > contains patient information, please contact the Partners Compliance > HelpLine at > http://www.partners.org/complianceline . If the e-mail was sent to you in > error > but does not contain patient information, please contact the sender and > properly > dispose of the e-mail. > > ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 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_thickness & qcache for xhemi surfaces
I see. Then I think I'd better just follow the instructions on the Xhemi page. Thanks! On Thu, Mar 28, 2013 at 1:06 PM, Douglas N Greve wrote: > Hi Cherry, what I meant was that you cannot use the qcache with xhemi. > You'll need to run the mris_preproc command as listed on the web page. > doug > > > On 03/28/2013 01:00 PM, Ejoe Yizhou Ma wrote: > >> Thanks, Doug. >> >> I'm not planning to use qdec. It's just that I used to generate the >> ?h.thickness_max10.fwhm10.**fsaverage_510.mgh files (which are what we >> name the files after running the two commands) before I use mris_preproc >> and mri_glmfit. I also generally skip the "smooth" step in freesurfer >> tutorial since the files are smoothed in the first place. >> >> Any suggestions? >> >> Cherry >> >> On Thu, Mar 28, 2013 at 12:53 PM, Douglas N Greve < >> gr...@nmr.mgh.harvard.edu >> <mailto:gr...@nmr.mgh.harvard.**edu>> >> wrote: >> >> >> >> Actually, #2 will not work. I don't think you can use qdec with the >> xhemi stuff anyway. You should use the mris_preproc command >> followed by >> mri_glmfit. >> doug >> >> >> On 03/28/2013 12:51 PM, Douglas N Greve wrote: >> > On 03/28/2013 12:16 PM, Ejoe Yizhou Ma wrote: >> >> Dear Freesurfer experts, >> >> >> >> I'm trying to investigate lh-to-rh asymmetry, so I register my >> >> subjects to the subject of fsaverage_sym following the >> instructions on >> >> this page: >> http://surfer.nmr.mgh.harvard.**edu/fswiki/Xhemi<http://surfer.nmr.mgh.harvard.edu/fswiki/Xhemi> >> . >> After all >> >> the surfreg commands I've got ?h.thickness files in >> subjid/xhemi/surf. >> >> >> >> In my lab we generally process ?h.thickness files with the next two >> >> commands before statistically analysis: >> >> >> >> "mris_thickness -max 10 subjid ?h thickness_max10" >> >> "recon-all -qcache -measure thickness_max10 -target fsaverage_510 >> >> -fwhm 10 -no-isrunning -s subjid -hemi ?h" >> >> >> >> To keep with this protocol, my questions are >> >> 1) how do I use "mris_thickness" properly so that I don't overwrite >> >> the files registered to fsaverage_510? >> > I think it will recreate the basic ?h.thickness file and will >> not touch >> > registrations. >> >> 2) in "recon-all -qcache", will it do the trick by substituting >> >> "fsaverage_sym" for "fsaverage_510"? >> >> >> > Yes, that should work. >> >> Thank you in advance, >> >> Cherry >> >> >> >> >> >> >> >> __**_ >> >> Freesurfer mailing list >> >> Freesurfer@nmr.mgh.harvard.edu >> <mailto:freesur...@nmr.mgh.**harvard.edu >> > >> >> >> >> https://mail.nmr.mgh.harvard.**edu/mailman/listinfo/**freesurfer<https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> >> >> -- >> Douglas N. Greve, Ph.D. >> MGH-NMR Center >> gr...@nmr.mgh.harvard.edu >> <mailto:gr...@nmr.mgh.harvard.**edu >> > >> Phone Number: 617-724-2358 >> Fax: 617-726-7422 >> >> Bugs: >> surfer.nmr.mgh.harvard.edu/**fswiki/BugReporting<http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> >> >> <http://surfer.nmr.mgh.**harvard.edu/fswiki/**BugReporting<http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> >> > >> FileDrop: >> www.nmr.mgh.harvard.edu/**facility/filedrop/index.html<http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> >> >> <http://www.nmr.mgh.harvard.**edu/facility/filedrop/index.**html<http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> >> > >> >> Outgoing: >> >> ftp://surfer.nmr.mgh.harvard.**edu/transfer/outgoing/flat/**greve/<ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/> >> >> __**_ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu <mailto:freesur...@nmr.mgh.** >> harvard.edu > >> >> >> https://mail.nmr.
Re: [Freesurfer] mris_thickness & qcache for xhemi surfaces
Hi Doug, As I'm trying to run mris_preproc on this page ( http://surfer.nmr.mgh.harvard.edu/fswiki/Xhemi), I want to know what the --xhemi argument is for. Is it for calculating the difference between lh and rh thickness? I wanted to calculate a asymmetry index for each vertex, which is (lh-rh)/[(lh+rh)/2] rather than (lh-rh). Can I do that using mris_preproc and how? Thanks, Cherry On Thu, Mar 28, 2013 at 1:32 PM, Ejoe Yizhou Ma wrote: > I see. Then I think I'd better just follow the instructions on the Xhemi > page. Thanks! > > > On Thu, Mar 28, 2013 at 1:06 PM, Douglas N Greve < > gr...@nmr.mgh.harvard.edu> wrote: > >> Hi Cherry, what I meant was that you cannot use the qcache with xhemi. >> You'll need to run the mris_preproc command as listed on the web page. >> doug >> >> >> On 03/28/2013 01:00 PM, Ejoe Yizhou Ma wrote: >> >>> Thanks, Doug. >>> >>> I'm not planning to use qdec. It's just that I used to generate the >>> ?h.thickness_max10.fwhm10.**fsaverage_510.mgh files (which are what we >>> name the files after running the two commands) before I use mris_preproc >>> and mri_glmfit. I also generally skip the "smooth" step in freesurfer >>> tutorial since the files are smoothed in the first place. >>> >>> Any suggestions? >>> >>> Cherry >>> >>> On Thu, Mar 28, 2013 at 12:53 PM, Douglas N Greve < >>> gr...@nmr.mgh.harvard.edu >>> <mailto:gr...@nmr.mgh.harvard.**edu>> >>> wrote: >>> >>> >>> >>> Actually, #2 will not work. I don't think you can use qdec with the >>> xhemi stuff anyway. You should use the mris_preproc command >>> followed by >>> mri_glmfit. >>> doug >>> >>> >>> On 03/28/2013 12:51 PM, Douglas N Greve wrote: >>> > On 03/28/2013 12:16 PM, Ejoe Yizhou Ma wrote: >>> >> Dear Freesurfer experts, >>> >> >>> >> I'm trying to investigate lh-to-rh asymmetry, so I register my >>> >> subjects to the subject of fsaverage_sym following the >>> instructions on >>> >> this page: >>> http://surfer.nmr.mgh.harvard.**edu/fswiki/Xhemi<http://surfer.nmr.mgh.harvard.edu/fswiki/Xhemi> >>> . >>> After all >>> >> the surfreg commands I've got ?h.thickness files in >>> subjid/xhemi/surf. >>> >> >>> >> In my lab we generally process ?h.thickness files with the next >>> two >>> >> commands before statistically analysis: >>> >> >>> >> "mris_thickness -max 10 subjid ?h thickness_max10" >>> >> "recon-all -qcache -measure thickness_max10 -target fsaverage_510 >>> >> -fwhm 10 -no-isrunning -s subjid -hemi ?h" >>> >> >>> >> To keep with this protocol, my questions are >>> >> 1) how do I use "mris_thickness" properly so that I don't >>> overwrite >>> >> the files registered to fsaverage_510? >>> > I think it will recreate the basic ?h.thickness file and will >>> not touch >>> > registrations. >>> >> 2) in "recon-all -qcache", will it do the trick by substituting >>> >> "fsaverage_sym" for "fsaverage_510"? >>> >> >>> > Yes, that should work. >>> >> Thank you in advance, >>> >> Cherry >>> >> >>> >> >>> >> >>> >> __**_ >>> >> Freesurfer mailing list >>> >> Freesurfer@nmr.mgh.harvard.edu >>> <mailto:freesur...@nmr.mgh.**harvard.edu >>> > >>> >>> >> >>> https://mail.nmr.mgh.harvard.**edu/mailman/listinfo/**freesurfer<https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> >>> >>> -- >>> Douglas N. Greve, Ph.D. >>> MGH-NMR Center >>> gr...@nmr.mgh.harvard.edu >>> <mailto:gr...@nmr.mgh.harvard.**edu >>> > >>> Phone Number: 617-724-2358 >>> Fax: 617-726-7422 >>> >>> Bugs: >>> surfer.nmr.mgh.harvard.edu/**fswiki/BugReporting<http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> >>> >>>
[Freesurfer] mris_preproc with --xhemi
Hi freesurfer experts, I'm investigating lh-to-rh asymmetry and am following instructions on this page :http://surfer.nmr.mgh.harvard.edu/fswiki/Xhemi. My question is, what does the "--xhemi" flag do in the "mris_preproc" command? It seems to me that it calculates (lh-rh) value at each vertex for every subject. (I tried to use the same subject for each pair of input for "--paired-diff", and the result is not a all-zero output.) It would also be nice if someone can tell me how to realize my final goal, which is to get the (lh-rh)/[(lh+rh)/2] value at each vertex for each subject in a .mgh file. Thanks, Cherry ___ 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 with --xhemi
Thanks, Doug. This is very helpful! On Fri, Mar 29, 2013 at 12:48 PM, Douglas N Greve wrote: > The --xhemi flag causes both the left and right hemispheres of each > subject to be stacked into the output file. So the output file will have > number of subjects x2 frames. The order is subject1.lh, subject1.rh, > subject2.lh, subject2.rh, ... > > If you add the --paired-diff, then you will get number of frames = > number of subjects, and each frame will be subject1.lh-rh, > subject2.lh-rh, etc > > If you use the --paired-diff-norm instead, then you will get what you > want subject1.(lh-rh)/((lh+rh)/2), subject2.(lh-rh)/((lh+rh)/2), etc. > > Note that most laterality indices (LI) are (lh-rh)/(lh+rh), so you would > need to multiply the paired-diff-norm by 2. > > Finally, I want to point out that it may be better to smooth before > computing the LI because the LI computation is non-linear and it has the > potential to divide by a noisy number. To do this, run without the > --paired-diff flags, then smooth, then run > > mri_concat yourfile.smoothed.mgh --paired-diff-norm --o > yourfile.smoothed.LI.mgh > > In my study, I ran it both ways and it did not make a difference, but I > think smoothing before LI is the safer bet. > > doug > > > On 03/29/2013 12:33 PM, Ejoe Yizhou Ma wrote: > > Hi freesurfer experts, > > > > I'm investigating lh-to-rh asymmetry and am following instructions on > > this page :http://surfer.nmr.mgh.harvard.edu/fswiki/Xhemi. > > My question is, what does the "--xhemi" flag do in the "mris_preproc" > > command? It seems to me that it calculates (lh-rh) value at each > > vertex for every subject. (I tried to use the same subject for each > > pair of input for "--paired-diff", and the result is not a all-zero > > output.) > > > > It would also be nice if someone can tell me how to realize my final > > goal, which is to get the (lh-rh)/[(lh+rh)/2] value at each vertex for > > each subject in a .mgh file. > > > > Thanks, > > Cherry > > > > > > ___ > > 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: www.nmr.mgh.harvard.edu/facility/filedrop/index.html > Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > The information in this e-mail is intended only for the person to whom it > is > addressed. If you believe this e-mail was sent to you in error and the > e-mail > contains patient information, please contact the Partners Compliance > HelpLine at > http://www.partners.org/complianceline . If the e-mail was sent to you in > error > but does not contain patient information, please contact the sender and > properly > dispose of the e-mail. > > ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 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.
