Freesurfer

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Re: [Freesurfer] mri_watershed and other errors.
by Darren Gitelman 05 Sep '12

05 Sep '12

Nick I ran: recon-all -skullstrip -no-wsgcaatlas -clean-bm -s 3157 and got the exact same problem with brainmask.mgz Darren On Wed, Sep 5, 2012 at 3:37 PM, Nick Schmansky <nicks(a)nmr.mgh.harvard.edu>wrote: > Darren, > > I forgot to mention that you'll need to add > > -clean-bm > > after the -no-wsgcaatlas flag, otherwise the prior brainmask.mgz will be > retained and the new one will be saved as brainmask.auto.mgz. > > Nick > > > On Wed, 2012-09-05 at 09:54 -0500, Darren Gitelman wrote: > > Nick, List: > > > > > > > > Still no luck with this data. See attached as an example. > > > > > > > > To get to this point I had run: > > > > > > > > recon-all -all > > > > > > > > This ran to the error: mri_watershed Error: GLOBAL region of the > > brain empty ! > > > > > > > > Then I followed your recommendation below > > > > > > > > recon-all -s <subjid> -skullstrip -no-wsgcaatlas, which had no errors > > and then > > > > recon-all -s <subjid> -autorecon2 -autorecon3 > > > > > > > > This produced the result attached. > > > > > > > > I then deleted this directory and re-imported all the dicom data for > > this subject. Looked at the images, which look fine. > > > > Then I ran recon-all -s <subjid> -autorecon1 > > > > > > > > This fails with the mri_watershed error. > > > > > > > > Then I ran recon-all -s <subjid> -skullstrip -no-wsgcaatlas. > > > > > > > > This runs without error but when I look at the brainmask.mgz it looks > > just like the attached image. > > > > > > > > Is there some way to set the thresholds differently? The T1 image > > looks fine to me although perhaps the intensity is slightly less than > > usual, but it doesn't seem particularly noisy. > > > > > > > > Darren > > > > > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer(a)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. > -- Darren Gitelman, MD Northwestern University 710 N. Lake Shore Dr. Abbott 11th Floor Chicago, IL 60611 Ph: (312) 908-8614 Fax: (312) 908-5073

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Re: [Freesurfer] mri_watershed and other errors.
by Darren Gitelman 05 Sep '12

05 Sep '12

Nick, List: Still no luck with this data. See attached as an example. To get to this point I had run: recon-all -all This ran to the error: mri_watershed Error: GLOBAL region of the brain empty ! Then I followed your recommendation below recon-all -s <subjid> -skullstrip -no-wsgcaatlas, which had no errors and then recon-all -s <subjid> -autorecon2 -autorecon3 This produced the result attached. I then deleted this directory and re-imported all the dicom data for this subject. Looked at the images, which look fine. Then I ran recon-all -s <subjid> -autorecon1 This fails with the mri_watershed error. Then I ran recon-all -s <subjid> -skullstrip -no-wsgcaatlas. This runs without error but when I look at the brainmask.mgz it looks just like the attached image. Is there some way to set the thresholds differently? The T1 image looks fine to me although perhaps the intensity is slightly less than usual, but it doesn't seem particularly noisy. Darren

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Re: [Freesurfer] Covary for categorical variable in QDEC
by Jeff Sadino 05 Sep '12

05 Sep '12

Hi Doug, What I mean by "covary for a categorical variable", what I want to do is covary for gender. Sorry for my confusion terminology. Thank you for your help! Jeff On Wed, Sep 5, 2012 at 6:00 AM, <freesurfer-request(a)nmr.mgh.harvard.edu>wrote: > Send Freesurfer mailing list submissions to > freesurfer(a)nmr.mgh.harvard.edu > > To subscribe or unsubscribe via the World Wide Web, visit > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > or, via email, send a message with subject or body 'help' to > freesurfer-request(a)nmr.mgh.harvard.edu > > You can reach the person managing the list at > freesurfer-owner(a)nmr.mgh.harvard.edu > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of Freesurfer digest..." > > Today's Topics: > > 1. Re: Repost: Converting BV ROIs to FS (Bruce Fischl) > 2. Re: Repost: Converting BV ROIs to FS (Katie Bettencourt) > 3. Re: freesurfer tutorial data (Help Desk -- Paul Raines) > 4. Re: creating a skull (Borzello, Mia) > 5. Re: error in long_mris_slopes command (Martin Reuter) > 6. mris_anatomical_stats on multiple subjects (Alexandra Tanner) > 7. Re: freesurfer tutorial data (Dix Meiberth) > 8. Re: creating a skull (Bruce Fischl) > 9. Cortical parcellations and probtrackx2 in diffusion space > (Alistair Perry) > 10. Covary for categorical variable in QDEC (Jeff Sadino) > 11. Re: Repost: Converting BV ROIs to FS (Bruce Fischl) > 12. Re: repeated measures ANOVA with two groups (Douglas N Greve) > 13. Re: freesurfer tutorial data (Help Desk -- Paul Raines) > 14. Re: missing ROI when using mri_label2vol to transfer ic2.tri > (Douglas N Greve) > 15. Re: Freesurfer-Error message (Varghese Chikku) > 16. Re: Freesurfer-Error message (Bruce Fischl) > 17. Re: FDR Correction of NHP Surface Data (Douglas N Greve) > 18. Re: mri_watershed and other errors. (Darren Gitelman) > 19. Re: resending question about 3rd level analysis (Douglas N Greve) > 20. Re: mris_anatomical_stats on multiple subjects (Alexandra Tanner) > > > ---------- Forwarded message ---------- > From: Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> > To: Katie Bettencourt <kcb(a)wjh.harvard.edu> > Cc: freesurfer maillist <freesurfer(a)nmr.mgh.harvard.edu> > Date: Tue, 4 Sep 2012 12:24:09 -0400 (EDT) > Subject: Re: [Freesurfer] Repost: Converting BV ROIs to FS > Hi Katie > > I don't think anyone here knows how to do this as we don't use it. Perhaps > the Brain Voyager people do? > > sorry, > Bruce > On Tue, 4 Sep 2012, Katie Bettencourt wrote: > > >> So our lab is running a couple analyses and we are getting >> different results based on whether we use Brain Voyager or >> Freesurfer that we think is due to different ROI selection across >> the two platforms. Is there anyway to load a >> BrainVoyager ROI into freesurfer? The BV data has been talairach >> transformed, does that matter? Less optimal would >> be loading a freesurfer ROI into BV, but if that's easier, we could >> try that way too. >> Any help would be appreciated. >> >> Katie >> >> >> >> > > ---------- Forwarded message ---------- > From: Katie Bettencourt <kcb(a)wjh.harvard.edu> > To: Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> > Cc: freesurfer maillist <freesurfer(a)nmr.mgh.harvard.edu> > Date: Tue, 4 Sep 2012 13:18:42 -0400 > Subject: Re: [Freesurfer] Repost: Converting BV ROIs to FS > Hrm. Ok, is there any way to view data for a subject in Freesurfer on a > talairach transformed brain? What I would be hoping to do is bring up the > data in native subject space, make any ROI label, then also bring the data > up on a talairach transformed brain, make a ROI label, then put both labels > on the same brain (either native or talairach transformed) and see if they > are any different. > > Also, is there a way to input a particular talairach vertex and jump to > that in freesurfer, instead of just moving the mouse around and hoping to > find the right spot? > > Katie > > On Tue, Sep 4, 2012 at 12:24 PM, Bruce Fischl <fischl(a)nmr.mgh.harvard.edu > > wrote: > >> Hi Katie >> >> I don't think anyone here knows how to do this as we don't use it. >> Perhaps the Brain Voyager people do? >> >> sorry, >> Bruce >> >> On Tue, 4 Sep 2012, Katie Bettencourt wrote: >> >> >>> So our lab is running a couple analyses and we are getting >>> different results based on whether we use Brain Voyager or >>> Freesurfer that we think is due to different ROI selection across >>> the two platforms. Is there anyway to load a >>> BrainVoyager ROI into freesurfer? The BV data has been talairach >>> transformed, does that matter? Less optimal would >>> be loading a freesurfer ROI into BV, but if that's easier, we >>> could try that way too. >>> Any help would be appreciated. >>> >>> Katie >>> >>> >>> >>> >>> >> >> 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<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. >> > > > > ---------- Forwarded message ---------- > From: Help Desk -- Paul Raines <help(a)nmr.mgh.harvard.edu> > To: Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> > Cc: freesurfer(a)nmr.mgh.harvard.edu, Dix.Meiberth(a)ukb.uni-bonn.de > Date: Tue, 4 Sep 2012 14:56:22 -0400 (EDT) > Subject: Re: [Freesurfer] freesurfer tutorial data > 2GB sounds like you reaching maybe a file size limit of your operating > system if it is really old. Or if you have are trying to download to a > FAT formated external USB drive or such. > > -- Paul Raines (http://help.nmr.mgh.harvard.**edu<http://help.nmr.mgh.harvard.edu> > ) > > > > On Mon, 3 Sep 2012 11:32am, Bruce Fischl wrote: > > Hi Dix, >> >> not sure what's going on. Have you tried multiple times? >> >> Bruce >> >> On Mon, 3 Sep 2012, Dix.Meiberth(a)ukb.uni-bonn.de wrote: >> >> >>> Dear sirs and madames, >>> >>> unfortunately I wasn't able to download the tutorial data for freesurfer. >>> The download interrupted at 2 GB within the >>> "bruckner_data_tutorial_subjs.**tar.gz" >>> I already did the recon_all process for 90 brains and wanted to improve >>> my >>> skills for the corrections. >>> Is there any advise you can give to get the tutorial data? >>> >>> Best regards, >>> >>> Dix Meiberth >>> (B.Sc. Neurowissenschaften) >>> >>> Funktionelle Bildgebung >>> Klinik und Poliklinik für Psychiatrie und Psychotherapie >>> Universitätsklinikum Bonn >>> Sigmund-Freud-Strasse 25 >>> 53105 Bonn >>> >>> Tel. 0228-287-16366 >>> Dix.Meiberth(a)ukb.uni-bonn.de >>> >> > > ---------- Forwarded message ---------- > From: "Borzello, Mia" <MBORZELLO(a)partners.org> > To: Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> > Cc: freesurfer <freesurfer(a)nmr.mgh.harvard.edu> > Date: Tue, 4 Sep 2012 19:15:08 +0000 > Subject: Re: [Freesurfer] creating a skull > I'm using Unix. Should I try something else? > > Thanks, > m > ________________________________________ > From: Bruce Fischl [fischl(a)nmr.mgh.harvard.edu] > Sent: Monday, September 03, 2012 2:45 PM > To: Borzello, Mia > Cc: freesurfer > Subject: Re: [Freesurfer] creating a skull > > Hi Mia > > what platform are you running on? > > Bruce > On Fri, 31 Aug 2012, Borzello, Mia wrote: > > > I've been referred to the following link on the freesurfer site to > handle this, but is this still current (i.e. is linux still needed to do > this?): > http://mailman.science.ru.nl/pipermail/fieldtrip/2012-January/004679.html > > > > thanks, > > m > > ________________________________________ > > From: Louis Nicholas Vinke [vinke(a)nmr.mgh.harvard.edu] > > Sent: Friday, August 31, 2012 10:29 AM > > To: Borzello, Mia > > Cc: freesurfer > > Subject: Re: [Freesurfer] creating a skull > > > > Hi, > > You need to add an extension onto the file name, something like brain.mgz > > or brain.nii. The extension will tell it what format to save the output > > in. > > -Louis > > > > On Fri, 31 Aug 2012, Borzello, Mia wrote: > > > >> Hi freesurfer family, > >> > >> I am trying to create the inner skull boundary and ran: mri_watershed > -atlas - surf -useSRAS mri.nii brain > >> > >> However, after it finished running it said it was saving "brain", but > "brain" was an unknown file type. Am i supposed to specify that somewhere? > >> > >> Thanks in advance, > >> m > >> > >> _______________________________________________ > >> Freesurfer mailing list > >> Freesurfer(a)nmr.mgh.harvard.edu > >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > >> > >> > >> > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer(a)nmr.mgh.harvard.edu > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > > > > > > > ---------- Forwarded message ---------- > From: Martin Reuter <mreuter(a)nmr.mgh.harvard.edu> > To: Shannon Kogachi <skogachi(a)gmail.com> > Cc: freesurfer(a)nmr.mgh.harvard.edu > Date: Tue, 04 Sep 2012 15:57:21 -0400 > Subject: Re: [Freesurfer] error in long_mris_slopes command > Hi Shannon, > > I have no idea why it would run and then when re-running it fails. Are > you calling it exactly the same way? Do you have write permissions in > those directories. > If it prints the command (mris_label_calc) that it is trying to run, can > you try to run only that command? > > Also you can try the new version from here: > http://martinos.org/~mreuter/long > (parameters are a little different, e.g. you need to specify the > subjects dir with --sd I think and some other flags have changed from > out_??? to name_???, as they can also be inputs ) > > Best, Martin > > On Fri, 2012-08-31 at 09:54 -1000, Shannon Kogachi wrote: > > Hi Freesurfers, > > I've just tried to use the long_mris_slopes command on some > > longitudinal data. I've created my long.qdec.table.dat file. I've run > > this command before without any problems but I need to re-run it > > again. This time when I try to re-run it this error pops up: > > > > ERROR 1 : mris_label_calc intersect did not work? > > > > Is there any way to fix this? it also tells me the following: > > > > cp: target 'path/subjectID/lh.long.cortex.label' is not a directory > > > > Please let me know if there is any way to fix this. thank you!! > > > > -Shannon K. > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer(a)nmr.mgh.harvard.edu > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > > ---------- Forwarded message ---------- > From: "Alexandra Tanner" <atanner(a)nmr.mgh.harvard.edu> > To: "Douglas N Greve" <greve(a)nmr.mgh.harvard.edu> > Cc: freesurfer(a)nmr.mgh.harvard.edu > Date: Tue, 4 Sep 2012 17:44:25 -0400 (EDT) > Subject: [Freesurfer] mris_anatomical_stats on multiple subjects > Hi Doug and Freesurfers, > > I'm currently working on extracting thickness measurements from an ROI I > manually created. I created my ROI label in tksurfer and applied the label > to each subject I'd like to extract thickness data from using > mri_label2label. I then used the following command to generate a stats > file, with the thickness measurement, from my label: > mris_anatomical_stats -f something.stats -l something.label subjid ?h > (http://surfer.nmr.mgh.harvard.edu/fswiki/tksurfer_labeledit) > > This generated a stats file that gave me the average thickness for my ROI > in my subject. I was wondering if there is a way to run the same command, > but on multiple subjects at once, so as not to have to run this command on > each individual subject. Any suggestions would be greatly appreciated! > > Best, > Alex > > > > ---------- Forwarded message ---------- > From: Dix Meiberth <dix.meiberth(a)ukb.uni-bonn.de> > To: Help Desk -- Paul Raines <help(a)nmr.mgh.harvard.edu> > Cc: "freesurfer(a)nmr.mgh.harvard.edu" <freesurfer(a)nmr.mgh.harvard.edu> > Date: Wed, 5 Sep 2012 00:19:50 +0200 > Subject: Re: [Freesurfer] freesurfer tutorial data > Thx for your responses. But no, I try to copy to my harddrive on my 1 year > old Mac. I think for the fith time right now. There should be no limit but > I will doublecheck. > > Best regards. > > Dix > > Von meinem iPhone gesendet > > Am 04.09.2012 um 20:56 schrieb Help Desk -- Paul Raines < > help(a)nmr.mgh.harvard.edu>: > > > 2GB sounds like you reaching maybe a file size limit of your operating > > system if it is really old. Or if you have are trying to download to a > > FAT formated external USB drive or such. > > > > -- Paul Raines (http://help.nmr.mgh.harvard.edu) > > > > > > > > On Mon, 3 Sep 2012 11:32am, Bruce Fischl wrote: > > > >> Hi Dix, > >> > >> not sure what's going on. Have you tried multiple times? > >> > >> Bruce > >> > >> On Mon, 3 Sep 2012, Dix.Meiberth(a)ukb.uni-bonn.de wrote: > >> > >>> Dear sirs and madames, > >>> unfortunately I wasn't able to download the tutorial data for > freesurfer. > >>> The download interrupted at 2 GB within the > >>> "bruckner_data_tutorial_subjs.tar.gz" > >>> I already did the recon_all process for 90 brains and wanted to > improve my > >>> skills for the corrections. > >>> Is there any advise you can give to get the tutorial data? > >>> Best regards, > >>> Dix Meiberth > >>> (B.Sc. Neurowissenschaften) > >>> Funktionelle Bildgebung > >>> Klinik und Poliklinik für Psychiatrie und Psychotherapie > >>> Universitätsklinikum Bonn > >>> Sigmund-Freud-Strasse 25 > >>> 53105 Bonn > >>> Tel. 0228-287-16366 > >>> Dix.Meiberth(a)ukb.uni-bonn.de > >> > > > > > > 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. > > > > > ---------- Forwarded message ---------- > From: Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> > To: "Borzello, Mia" <MBORZELLO(a)partners.org> > Cc: freesurfer <freesurfer(a)nmr.mgh.harvard.edu> > Date: Tue, 4 Sep 2012 19:35:57 -0400 (EDT) > Subject: Re: [Freesurfer] creating a skull > no, that should be fine > On Tue, 4 Sep 2012, Borzello, Mia wrote: > > I'm using Unix. Should I try something else? >> >> Thanks, >> m >> ______________________________**__________ >> From: Bruce Fischl [fischl(a)nmr.mgh.harvard.edu] >> Sent: Monday, September 03, 2012 2:45 PM >> To: Borzello, Mia >> Cc: freesurfer >> Subject: Re: [Freesurfer] creating a skull >> >> Hi Mia >> >> what platform are you running on? >> >> Bruce >> On Fri, 31 Aug 2012, Borzello, Mia wrote: >> >> I've been referred to the following link on the freesurfer site to >>> handle this, but is this still current (i.e. is linux still needed to do >>> this?): http://mailman.science.ru.nl/**pipermail/fieldtrip/2012-** >>> January/004679.html<http://mailman.science.ru.nl/pipermail/fieldtrip/2012-January/004679.html> >>> >>> thanks, >>> m >>> ______________________________**__________ >>> From: Louis Nicholas Vinke [vinke(a)nmr.mgh.harvard.edu] >>> Sent: Friday, August 31, 2012 10:29 AM >>> To: Borzello, Mia >>> Cc: freesurfer >>> Subject: Re: [Freesurfer] creating a skull >>> >>> Hi, >>> You need to add an extension onto the file name, something like brain.mgz >>> or brain.nii. The extension will tell it what format to save the output >>> in. >>> -Louis >>> >>> On Fri, 31 Aug 2012, Borzello, Mia wrote: >>> >>> Hi freesurfer family, >>>> >>>> I am trying to create the inner skull boundary and ran: mri_watershed >>>> -atlas - surf -useSRAS mri.nii brain >>>> >>>> However, after it finished running it said it was saving "brain", but >>>> "brain" was an unknown file type. Am i supposed to specify that somewhere? >>>> >>>> Thanks in advance, >>>> m >>>> >>>> ______________________________**_________________ >>>> Freesurfer mailing list >>>> Freesurfer(a)nmr.mgh.harvard.edu >>>> https://mail.nmr.mgh.harvard.**edu/mailman/listinfo/**freesurfer<https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> >>>> >>>> >>>> >>>> >>> ______________________________**_________________ >>> Freesurfer mailing list >>> Freesurfer(a)nmr.mgh.harvard.edu >>> https://mail.nmr.mgh.harvard.**edu/mailman/listinfo/**freesurfer<https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> >>> >>> >>> >>> >> >> >> > > > ---------- Forwarded message ---------- > From: Alistair Perry <alistairperry123(a)gmail.com> > To: freesurfer(a)nmr.mgh.harvard.edu > Cc: > Date: Wed, 5 Sep 2012 13:34:36 +1000 > Subject: [Freesurfer] Cortical parcellations and probtrackx2 in diffusion > space > Hello freesurfer experts, > > I know this has been posted elsewhere with the original probtrackx. > > I am basically trying to create a surface file from the aseg+aparc.mgz > cortical parcellation created when running recon-all. I wish to use > this surface file as the seed reference file when performing > probtrackx2. > > I have succeeded sucessfully in transforming the cortical parcellation > into diffusion space, and have created a label file for it. > > However, I am having difficulty understanding converting the label > file into ascii format, as required for probtrackx2. I am aware that > you can convert a label file into ascii format using mri_convert, but > you have to specify the lh.white surface file created when performing > recon-all. This does not make sense to me for one this label file is > not in diffusion space. Plus, why would I only specify one surface > hemisphere when I have a label file that lists vertices across both > hemispheres? > > In the end I am asking whether it is possible/and the best method in > creating an ascii surface file of the whole cortical parcellation in > diffusion space? > > Regards, > > Alistair > > > > ---------- Forwarded message ---------- > From: Jeff Sadino <jsadino.queens(a)gmail.com> > To: freesurfer(a)nmr.mgh.harvard.edu > Cc: Xin Zhang <zhangx(a)hawaii.edu>, Shannon Kogachi <skogachi(a)gmail.com>, > Eric Cunningham <erictcunningham(a)gmail.com> > Date: Tue, 4 Sep 2012 18:43:46 -1000 > Subject: [Freesurfer] Covary for categorical variable in QDEC > Hello, > > Is it possible to covary for a categorical variable in QDEC? I see other > posters have said it is not possible, but I did not see > any official documentation or response regarding the issue. > > Thank You, > Jeff Sadino > > > > ---------- Forwarded message ---------- > From: Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> > To: Katie Bettencourt <kcb(a)wjh.harvard.edu> > Cc: freesurfer maillist <freesurfer(a)nmr.mgh.harvard.edu> > Date: Wed, 5 Sep 2012 09:19:06 -0400 (EDT) > Subject: Re: [Freesurfer] Repost: Converting BV ROIs to FS > Hi Katie > > you can view data on a tal brain by mapping the data using the > talairach.xfm transform. Since you can also use the inverse of the > transform you can map both ways. I think there is a tcl command in tksurfer > for finding the vertex that is closest to a given tal coord. Try: > > select_talairach_point <xtal> <ytal> <ztal> > > cheers > Bruce > > > On Tue, 4 Sep 2012, Katie Bettencourt wrote: > > Hrm. Ok, is there any way to view data for a subject in Freesurfer on a >> talairach transformed brain? What I would be hoping to do is bring up the >> data in native subject space, make any ROI label, then also bring the data >> up on a talairach transformed brain, make a ROI label, then put both >> labels >> on the same brain (either native or talairach transformed) and see if they >> are any different. >> Also, is there a way to input a particular talairach vertex and jump to >> that >> in freesurfer, instead of just moving the mouse around and hoping to find >> the right spot? >> >> Katie >> >> On Tue, Sep 4, 2012 at 12:24 PM, Bruce Fischl <fischl(a)nmr.mgh.harvard.edu >> > >> wrote: >> Hi Katie >> >> I don't think anyone here knows how to do this as we don't use >> it. Perhaps the Brain Voyager people do? >> >> sorry, >> Bruce >> On Tue, 4 Sep 2012, Katie Bettencourt wrote: >> >> >> So our lab is running a couple analyses and we >> are getting different results based on whether we >> use Brain Voyager or >> Freesurfer that we think is due to different >> ROI selection across the two platforms. Is there >> anyway to load a >> BrainVoyager ROI into freesurfer? The BV data >> has been talairach transformed, does that matter? >> Less optimal would >> be loading a freesurfer ROI into BV, but if >> that's easier, we could try that way too. >> Any help would be appreciated. >> >> Katie >> >> >> >> >> >> >> 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<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. >> >> >> >> > > ---------- Forwarded message ---------- > From: Douglas N Greve <greve(a)nmr.mgh.harvard.edu> > To: freesurfer(a)nmr.mgh.harvard.edu > Cc: > Date: Wed, 05 Sep 2012 09:38:36 -0400 > Subject: Re: [Freesurfer] repeated measures ANOVA with two groups > Hi Shannon, sorry for the delay. There are several ways you can do this. > If you already have a slope for each subject, then just use that as input > and use the simple two group FSGD file. If you really want to do the RM > ANOVA, then there are two ways. The simpler way is to create a "stack" of > all subjects for each visit (eg, v1, v2, and v3) using mris_preproc. Next > compute paired differences d12 = v1-v2 and d13 = v1-v3 using fscalc (note > that you do not need v2-v3). Next, create a new stack from d12 and d13 with > mri_concat (eg, mri_concat d12.mgh d13.mgh --o d12+d13.mgh). Then create an > FSGD file with a class for each group and two variables (d12 and d13)). The > structure will look something like this: > > Input subject1 G1 1 0 > Input subject2 G1 1 0 > ... rest of subjects for group 1 ... > Input subject1 G1 0 1 > Input subject2 G1 0 1 > ... rest of subjects for group 1 ... > Input subject1 G2 1 0 > Input subject2 G2 1 0 > ... rest of subjects for group 2 ... > Input subject1 G2 0 1 > Input subject2 G2 0 1 > ... rest of subjects for group 2 ... > > Run the analysis with DOSS. You can use the following contrast matrix to > test for an interaction: > [1 -1 -1 1] > > Let me know if that makes sense or not > doug > > > > On 08/23/2012 09:39 PM, Shannon Kogachi wrote: > >> Hi, >> Is there a way to set up a repeated measures ANOVA and ANCOVA with two >> different groups (ex: study group v. controls) and each subject has more >> than two timepoints? Would it be possible to assign each Input in the fsgd >> file to two classes (ex: timepoint scan and group) or is there another way >> to set up the fsgd file and contrast matrices? I've already used qdec in >> freesurfer 5.1 to calculate rates of change and symmetrized percent changes >> between the timepoints (using long_mris_slopes) but now would like to >> perform a repeated measures test. Thank you! >> >> -Shannon K. >> >> >> ______________________________**_________________ >> Freesurfer mailing list >> Freesurfer(a)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 > greve(a)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: www.nmr.mgh.harvard.edu/**facility/filedrop/index.html<http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > > > > > ---------- Forwarded message ---------- > From: Help Desk -- Paul Raines <help(a)nmr.mgh.harvard.edu> > To: Dix Meiberth <dix.meiberth(a)ukb.uni-bonn.de> > Cc: "freesurfer(a)nmr.mgh.harvard.edu" <freesurfer(a)nmr.mgh.harvard.edu> > Date: Wed, 5 Sep 2012 09:51:17 -0400 (EDT) > Subject: Re: [Freesurfer] freesurfer tutorial data > Instead of FTP, you could try getting the files via HTTP at > > http://surfer.nmr.mgh.harvard.**edu/ftp/dist/freesurfer/<http://surfer.nmr.mgh.harvard.edu/ftp/dist/freesurfer/> > > -- Paul Raines (http://help.nmr.mgh.harvard.**edu<http://help.nmr.mgh.harvard.edu> > ) > > > > On Tue, 4 Sep 2012 6:19pm, Dix Meiberth wrote: > > Thx for your responses. But no, I try to copy to my harddrive on my 1 >> year old Mac. I think for the fith time right now. There should be no limit >> but I will doublecheck. >> >> Best regards. >> >> Dix >> >> Von meinem iPhone gesendet >> >> Am 04.09.2012 um 20:56 schrieb Help Desk -- Paul Raines < >> help(a)nmr.mgh.harvard.edu>: >> >> 2GB sounds like you reaching maybe a file size limit of your operating >>> system if it is really old. Or if you have are trying to download to a >>> FAT formated external USB drive or such. >>> >>> -- Paul Raines (http://help.nmr.mgh.harvard.**edu<http://help.nmr.mgh.harvard.edu> >>> ) >>> >>> >>> >>> On Mon, 3 Sep 2012 11:32am, Bruce Fischl wrote: >>> >>> Hi Dix, >>>> >>>> not sure what's going on. Have you tried multiple times? >>>> >>>> Bruce >>>> >>>> On Mon, 3 Sep 2012, Dix.Meiberth(a)ukb.uni-bonn.de wrote: >>>> >>>> Dear sirs and madames, >>>>> unfortunately I wasn't able to download the tutorial data for >>>>> freesurfer. >>>>> The download interrupted at 2 GB within the >>>>> "bruckner_data_tutorial_subjs.**tar.gz" >>>>> I already did the recon_all process for 90 brains and wanted to >>>>> improve my >>>>> skills for the corrections. >>>>> Is there any advise you can give to get the tutorial data? >>>>> Best regards, >>>>> Dix Meiberth >>>>> (B.Sc. Neurowissenschaften) >>>>> Funktionelle Bildgebung >>>>> Klinik und Poliklinik für Psychiatrie und Psychotherapie >>>>> Universitätsklinikum Bonn >>>>> Sigmund-Freud-Strasse 25 >>>>> 53105 Bonn >>>>> Tel. 0228-287-16366 >>>>> Dix.Meiberth(a)ukb.uni-bonn.de >>>>> >>>> >>>> >>> >>> 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<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. >>> >> >> >> > > ---------- Forwarded message ---------- > From: Douglas N Greve <greve(a)nmr.mgh.harvard.edu> > To: Longchuan Li <leonado78(a)yahoo.com> > Cc: FreeSurfer <freesurfer(a)nmr.mgh.harvard.edu> > Date: Wed, 05 Sep 2012 09:58:20 -0400 > Subject: Re: [Freesurfer] missing ROI when using mri_label2vol to transfer > ic2.tri > Hi Longchuan, when I asked for the terminal output, I meant the stuff that > gets printed to the screen when the command runs. Try running it outside of > your script to capture the output. Also, does the old program require 20G ? > doug > > On 08/27/2012 04:20 PM, Longchuan Li wrote: > >> Hi, Doug >> Here is the output from my log file and my command. I have been running >> this command many times and sometimes the job got killed, but sometimes >> they finished without error. >> >> /usr/local/sge/bitc/spool/**node13/job_scripts/77912: line 7: 30345 >> Killed /home/lli/freesurferv51/bin/**mri_label2vol.linux >> --offset 1 --annot /home/lli/freesurferv51/** >> subjects/RVJ8_Preuss_20111115/**label/rh.randomroi300_** >> WithoutMedialWall.**MacaqueYerkes6_to_RVJ8_Preuss_**20111115.annot >> --temp /home/lli/freesurferv51/**subjects/RVJ8_Preuss_20111115/**mri/brain.mgz >> --subject RVJ8_Preuss_20111115 --hemi rh --fillthresh 0 --proj frac 0 0.5 >> 0.05 --o /home/lli/freesurferv51/**subjects/RVJ8_Preuss_20111115/** >> mri/rh.randomroi300_**WithoutMedialWall_Ribbon.** >> MacaqueYerkes6_to_RVJ8_Preuss_**20111115_fill0_projs0_proje0.**5_projin0.05.nii.gz >> --identity >> >> Many thanks in advance! >> >> Longchuan >> >> >> ------------------------------**------------------------------** >> ------------ >> *From:* Douglas Greve <greve(a)nmr.mgh.harvard.edu> >> *To:* Longchuan Li <leonado78(a)yahoo.com> >> *Cc:* FreeSurfer <freesurfer(a)nmr.mgh.harvard.**edu<freesurfer(a)nmr.mgh.harvard.edu> >> > >> *Sent:* Monday, August 27, 2012 3:47 PM >> *Subject:* Re: [Freesurfer] missing ROI when using mri_label2vol to >> transfer ic2.tri >> >> What is your command line and what is the terminal output? >> doug >> >> >> On 8/27/12 7:57 PM, Longchuan Li wrote: >> >>> Hi, Doug >>> >>> This is a follow-up question regarding an updated code you sent to me >>> earlier (mri_label2vol.linux). I noticed that this program frequently takes >>> around ~20G RAM to run and easily get killed by Linux (I supposed) when I >>> ran multiple subjects, because of the large amount of RAM used. Has anyone >>> else proposed the issue? and if so, do you have any suggestions on solving >>> the issue? >>> >>> Thank you! >>> >>> Longchuan >>> >>> ------------------------------**------------------------------** >>> ------------ >>> *From:* Leon <leonado78(a)yahoo.com> <mailto:leonado78@yahoo.com> >>> *To:* Douglas N Greve <greve(a)nmr.mgh.harvard.edu> <mailto: >>> greve(a)nmr.mgh.harvard.**edu <greve(a)nmr.mgh.harvard.edu>> >>> *Cc:* FreeSurfer <freesurfer(a)nmr.mgh.harvard.**edu<freesurfer(a)nmr.mgh.harvard.edu>> >>> <mailto:freesurfer@nmr.mgh.**harvard.edu<freesurfer(a)nmr.mgh.harvard.edu> >>> > >>> *Sent:* Friday, June 8, 2012 3:48 PM >>> *Subject:* Re: [Freesurfer] missing ROI when using mri_label2vol to >>> transfer ic2.tri >>> >>> Hi, Doug >>> I have run and checked the data and the problem has been perfectly >>> solved. Thank you for the help! >>> >>> Leon >>> >>> ------------------------------**------------------------------** >>> ------------ >>> *From:* Douglas N Greve <greve(a)nmr.mgh.harvard.edu> <mailto: >>> greve(a)nmr.mgh.harvard.**edu <greve(a)nmr.mgh.harvard.edu>> >>> *To:* Leon <leonado78(a)yahoo.com> <mailto:leonado78@yahoo.com> >>> *Cc:* FreeSurfer <freesurfer(a)nmr.mgh.harvard.**edu<freesurfer(a)nmr.mgh.harvard.edu>> >>> <mailto:freesurfer@nmr.mgh.**harvard.edu<freesurfer(a)nmr.mgh.harvard.edu> >>> > >>> *Sent:* Friday, June 8, 2012 1:32 PM >>> *Subject:* Re: [Freesurfer] missing ROI when using mri_label2vol to >>> transfer ic2.tri >>> >>> I've put a new version of mri_label2vol at that ftp site. When you run >>> it, add "--offset 1". This will change the segmentations IDs to go from >>> 1-162 instead of 0-161. >>> doug >>> >>> On 06/08/2012 11:30 AM, Leon wrote: >>> > Hi, Douglas >>> > >>> > I checked the data this morning and confirmed that the missing ROI in >>> > the volume space is vertex_0 (see attached). Totally there are 162 >>> > entries in the annotation file, but only 161 left in the volume file >>> > after transferring the annotation file to the volume using >>> > mri_label2vol and the intensity value ranges from 1 to 161. >>> > >>> > Thanks >>> > >>> > Leon >>> > >>> > PS: I am sending the message again because I was told that the image >>> > for the previous mail is too big. >>> > >>> > *From:* Leon <leonado78(a)yahoo.com <mailto:leonado78@yahoo.com>> >>> > *To:* Douglas N Greve <greve(a)nmr.mgh.harvard.edu <mailto: >>> greve(a)nmr.mgh.harvard.**edu <greve(a)nmr.mgh.harvard.edu>>> >>> > *Cc:* FreeSurfer <freesurfer(a)nmr.mgh.harvard.**edu<freesurfer(a)nmr.mgh.harvard.edu><mailto: >>> freesurfer(a)nmr.mgh.**harvard.edu <freesurfer(a)nmr.mgh.harvard.edu>>> >>> > *Sent:* Thursday, June 7, 2012 10:52 PM >>> > *Subject:* Re: [Freesurfer] missing ROI when using mri_label2vol to >>> > transfer ic2.tri >>> > >>> > Hi, Douglas >>> > >>> > Thank you very much for taking care of it. The ROIs ending with 2 and >>> > 5s have been correctly labeled and have volumes now after running the >>> > fixed version of mris_make_face_parcellation. However, there is still >>> > one ROI missing in the volume data that is located at the top of the >>> > postcentral gyrus after the annotation file was transferred from the >>> > subject's surface to the volume using mri_label2vol. I checked the >>> > index of the ROI yesterday (I am at home now and do not have access to >>> > the data) and I remember the index of the missing ROI is vertex_0 and >>> > the location of the ROI is identical as the one in the picture I >>> > attached in the previous email. Do you think it might be because the >>> > mri_label2vol overlooks the index of 0, as the intensity value in the >>> > volumes starts with 1? >>> > >>> > I would appreciate your help on this. >>> > >>> > Leon >>> > >>> > *From:* Douglas N Greve <greve(a)nmr.mgh.harvard.edu <mailto: >>> greve(a)nmr.mgh.harvard.**edu <greve(a)nmr.mgh.harvard.edu>>> >>> > *To:* Leon <leonado78(a)yahoo.com <mailto:leonado78@yahoo.com>> >>> > *Cc:* FreeSurfer <freesurfer(a)nmr.mgh.harvard.**edu<freesurfer(a)nmr.mgh.harvard.edu><mailto: >>> freesurfer(a)nmr.mgh.**harvard.edu <freesurfer(a)nmr.mgh.harvard.edu>>> >>> > *Sent:* Thursday, June 7, 2012 2:03 PM >>> > *Subject:* Re: [Freesurfer] missing ROI when using mri_label2vol to >>> > transfer ic2.tri >>> > >>> > Hi Leon, I found the problem. mris_make_face_parcellation was actually >>> > merging several units together. You can get a fixed version from here: >>> > ftp://surfer.nmr.mgh.harvard.**edu/transfer/outgoing/flat/** >>> greve/mris_make_face_**parcellation.linux<ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mris_make_fac…> >>> > Let me know how it goes >>> > doug >>> > >>> > On 06/04/2012 02:44 PM, Leon wrote: >>> > > Hi, Douglas >>> > > I have uploaded the file to the system. >>> > > Also, my new results showed that when ic3.tri (instead of ic2.tri) >>> > > is used as the input, one ROI at the similar location is also >>> missing. >>> > > Hope it will help you diagnose. >>> > > >>> > > Thanks >>> > > Leon >>> > > >>> > > *From:* Douglas N Greve <greve(a)nmr.mgh.harvard.edu <mailto: >>> greve(a)nmr.mgh.harvard.**edu <greve(a)nmr.mgh.harvard.edu>> >>> > <mailto:greve@nmr.mgh.harvard.**edu <greve(a)nmr.mgh.harvard.edu><mailto: >>> greve(a)nmr.mgh.harvard.**edu <greve(a)nmr.mgh.harvard.edu>>>> >>> > > *To:* Leon <leonado78(a)yahoo.com <mailto:leonado78@yahoo.com> >>> <mailto:leonado78@yahoo.com <mailto:leonado78@yahoo.com>>> >>> > > *Cc:* FreeSurfer <freesurfer(a)nmr.mgh.harvard.**edu<freesurfer(a)nmr.mgh.harvard.edu><mailto: >>> freesurfer(a)nmr.mgh.**harvard.edu <freesurfer(a)nmr.mgh.harvard.edu>> >>> > <mailto:freesurfer@nmr.mgh.**harvard.edu<freesurfer(a)nmr.mgh.harvard.edu><mailto: >>> freesurfer(a)nmr.mgh.**harvard.edu <freesurfer(a)nmr.mgh.harvard.edu>>>> >>> > > *Sent:* Monday, June 4, 2012 1:00 PM >>> > > *Subject:* Re: [Freesurfer] missing ROI when using mri_label2vol to >>> > > transfer ic2.tri >>> > > >>> > > Can you upload the subject to our file drop system? >>> > > >>> > > 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> >>> > >>> > <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<http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> >>> > >>> > > >>> > > >>> > > >>> > > >>> > > On 06/04/2012 12:24 PM, Leon wrote: >>> > > > Hi, Douglas >>> > > > >>> > > > Thank you very much for the updated one. I tested the new codes and >>> > > > the problem is still there. The ID for the original version that >>> > > > generates a mask with one missing ROI is: >>> > > > >>> > > > $Id: mri_label2vol.c,v 1.38 2011/09/30 15:17:59 greve Exp $ >>> > > > >>> > > > I remember this is a version I downloaded from a link in FS >>> archive. >>> > > > >>> > > > The ID for the one you sent to me is: >>> > > > >>> > > > $Id: mri_label2vol.c,v 1.34.2.4 2011/09/30 15:19:36 greve Exp $ >>> > > > >>> > > > They look almost identical. Do you have any ideas what else may >>> cause >>> > > > this issue and possible workaround? >>> > > > >>> > > > Thank you >>> > > > >>> > > > Leon >>> > > > >>> > > > >>> > > > *From:* Douglas Greve <greve(a)nmr.mgh.harvard.edu <mailto: >>> greve(a)nmr.mgh.harvard.**edu <greve(a)nmr.mgh.harvard.edu>> >>> > <mailto:greve@nmr.mgh.harvard.**edu <greve(a)nmr.mgh.harvard.edu><mailto: >>> greve(a)nmr.mgh.harvard.**edu <greve(a)nmr.mgh.harvard.edu>>> >>> > > <mailto:greve@nmr.mgh.harvard.**edu <greve(a)nmr.mgh.harvard.edu><mailto: >>> greve(a)nmr.mgh.harvard.**edu <greve(a)nmr.mgh.harvard.edu>> <mailto: >>> greve(a)nmr.mgh.harvard.**edu <greve(a)nmr.mgh.harvard.edu> <mailto: >>> greve(a)nmr.mgh.harvard.**edu <greve(a)nmr.mgh.harvard.edu>>>>> >>> > > > *To:* freesurfer(a)nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.** >>> harvard.edu <freesurfer(a)nmr.mgh.harvard.edu>> >>> > <mailto:freesurfer@nmr.mgh.**harvard.edu<freesurfer(a)nmr.mgh.harvard.edu><mailto: >>> freesurfer(a)nmr.mgh.**harvard.edu <freesurfer(a)nmr.mgh.harvard.edu>>> >>> > > <mailto:freesurfer@nmr.mgh.**harvard.edu<freesurfer(a)nmr.mgh.harvard.edu><mailto: >>> freesurfer(a)nmr.mgh.**harvard.edu <freesurfer(a)nmr.mgh.harvard.edu>> >>> > <mailto:freesurfer@nmr.mgh.**harvard.edu<freesurfer(a)nmr.mgh.harvard.edu><mailto: >>> freesurfer(a)nmr.mgh.**harvard.edu <freesurfer(a)nmr.mgh.harvard.edu>>>> >>> > > > *Sent:* Friday, June 1, 2012 11:29 PM >>> > > > *Subject:* Re: [Freesurfer] missing ROI when using mri_label2vol to >>> > > > transfer ic2.tri >>> > > > >>> > > > >>> > > > What version are you using? I fix a problem last Sept that might be >>> > > > like this. I've put a new version of mri_label2vol here: >>> > > > >>> > > >>> > ftp://surfer.nmr.mgh.harvard.**edu/transfer/outgoing/flat/** >>> greve/mri_label2vol.linux<ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_label2vol…> >>> > > > Try this and let me know if it works. >>> > > > doug >>> > > > >>> > > > >>> > > > On 6/1/12 10:46 PM, Leon wrote: >>> > > >> Hi, Bruce >>> > > >> Here are my two command lines >>> > > >> For transferring the annot from the source template to the target >>> > > >> subject: >>> > > >> >>> > > >> /home/freesurfer/bin/mri_**surf2surf --srcsubject ${srcsubject} >>> > > >> --sval-annot rh.ic2.annot --trgsubject ${trgsubject} --trgsurfval >>> > > >> src_2_trg.annot --hemi rh --surfreg sphere.reg0 >>> > > >> >>> > > >> Where sphere.reg0 is the registration from the target subject to >>> the >>> > > >> source subject. >>> > > >> >>> > > >> For transfer them to the volume file: >>> > > >> >>> > > >> /home/freesurfer/bin/mri_**label2vol --annot src_2_trg.annot >>> --temp >>> > > >> ${fs_dir}/${trgsubject}/mri/**brain.mgz --subject ${trgsubject} >>> --hemi >>> > > >> rh --fillthresh 0 --proj frac 0.3 0.8 0.05 --o src_2_trg_annot.mgz >>> > > >> --identity >>> > > >> >>> > > >> >>> > > >> Here is output for one of my transformations: >>> > > >> >>> > > >> Setting mapmethod to nnf >>> > > >> Source registration surface changed to sphere.reg0 >>> > > >> Target registration surface changed to sphere.reg0 >>> > > >> srcsubject = MacaqueA >>> > > >> srcval = (null) >>> > > >> srctype = >>> > > >> trgsubject = MacaqueB >>> > > >> trgval = >>> > > >> >>> > > >>> > /home/freesurfer/freesurfer/**subjects/MacaqueB/label/rh.** >>> MacaqueA_to_MacaqueB.annot >>> > > >> trgtype = >>> > > >> srcsurfreg = sphere.reg0 >>> > > >> trgsurfreg = sphere.reg0 >>> > > >> srchemi = rh >>> > > >> trghemi = rh >>> > > >> frame = 0 >>> > > >> fwhm-in = 0 >>> > > >> fwhm-out = 0 >>> > > >> label-src = (null) >>> > > >> label-trg = (null) >>> > > >> OKToRevFaceOrder = 1 >>> > > >> Reading source surface reg >>> > > >> /home/freesurfer/freesurfer/**subjects/MacaqueA/surf/rh.** >>> sphere.reg0 >>> > > >> Loading source data >>> > > >> Reading surface file >>> > > >> /home/freesurfer/freesurfer/**subjects/MacaqueA/surf/rh.orig >>> > > >> reading colortable from annotation file... >>> > > >> colortable with 162 entries read (originally >>> > > >> /usr/local/freesurfer/lib/bem/**ic2.tri) >>> > > >> Reading target surface reg >>> > > >> /home/freesurfer/freesurfer/**subjects/MacaqueB/surf/rh.** >>> sphere.reg0 >>> > > >> Done >>> > > >> Mapping Source Volume onto Source Subject Surface >>> > > >> surf2surf_nnfr: building source hash (res=16). >>> > > >> Surf2Surf: Forward Loop (61916) >>> > > >> >>> > > >> Surf2Surf: Dividing by number of hits (61916) >>> > > >> INFO: nSrcLost = 17467 >>> > > >> nTrg121 = 61916, nTrgMulti = 0, MnTrgMultiHits = 0 >>> > > >> nSrc121 = 35292, nSrcLost = 17467, nSrcMulti = 28910, >>> MnSrcMultiHits >>> > > >> = 0.920927 >>> > > >> Saving target data >>> > > >> Converting to target annot >>> > > >> Saving to target annot >>> > > >> >>> > > >>> > /home/freesurfer/freesurfer/**subjects/MacaqueB/label/rh.** >>> MacaqueA_to_MacaqueB.annot >>> > > >> step2: writing the surface label to volume... >>> > > >> Number of labels: 0 >>> > > >> Annot File: >>> > > >> >>> > > >>> > /home/freesurfer/freesurfer/**subjects/MacaqueB/label/rh.** >>> MacaqueA_to_MacaqueB.annot >>> > > >> Template Volume: >>> > > >> /home/freesurfer/freesurfer/**subjects/MacaqueB/mri/brain.**mgz >>> > > >> Outut Volume: >>> > > >> >>> > > >>> > /home/freesurfer/freesurfer/**subjects/MacaqueB/mri/rh_** >>> MacaqueA_to_MacaqueB_fill0_**porjs0.3_proje0.8_projin0.05.**mgz >>> > > >> Registration File: (null) >>> > > >> Fill Threshold: 0 >>> > > >> Label Vox Vol: 1 >>> > > >> ProjType: frac >>> > > >> ProjTypeId: 2 >>> > > >> ProjStart: 0.3 >>> > > >> ProjStop: 0.8 >>> > > >> ProjDelta: 0.05 >>> > > >> Subject: MacaqueB >>> > > >> Hemi: rh >>> > > >> UseNewASeg2Vol: 1 >>> > > >> DoLabelStatVol 0 >>> > > >> $Id: mri_label2vol.c,v 1.38 2011/09/30 15:17:59 greve Exp $ >>> > > >> Template RAS-to-Vox: -------- >>> > > >> -1.000 -0.000 -0.000 160.000; >>> > > >> -0.000 -0.000 -1.000 160.000; >>> > > >> -0.000 1.000 -0.000 160.000; >>> > > >> -0.000 -0.000 -0.000 1.000; >>> > > >> Template Voxel Volume: 1 >>> > > >> nHits Thresh: 0 >>> > > >> Using Identity Matrix >>> > > >> RegMat: -------- >>> > > >> 1.000 0.000 0.000 0.000; >>> > > >> 0.000 1.000 0.000 0.000; >>> > > >> 0.000 0.000 1.000 0.000; >>> > > >> 0.000 0.000 0.000 1.000; >>> > > >> Label RAS-to-Vox: -------- >>> > > >> -1.000 0.000 0.000 160.000; >>> > > >> 0.000 0.000 -1.000 160.000; >>> > > >> 0.000 1.000 0.000 160.000; >>> > > >> 0.000 0.000 0.000 1.000; >>> > > >> INFO: loading surface >>> > > >> /home/freesurfer/freesurfer/**subjects/MacaqueB/surf/rh.**white >>> > > >> nvertices = 61916 >>> > > >> Reading thickness >>> > > >> /home/freesurfer/freesurfer/**subjects/MacaqueB/surf/rh.** >>> thickness >>> > > >> Loading annotations from >>> > > >> >>> > > >>> > /home/freesurfer/freesurfer/**subjects/MacaqueB/label/rh.** >>> MacaqueA_to_MacaqueB.annot >>> > > >> reading colortable from annotation file... >>> > > >> colortable with 162 entries read (originally >>> > > >> /usr/local/freesurfer/lib/bem/**ic2.tri) >>> > > >> annotidmax = 162 >>> > > >> Allocating Hit Volume (1013448704) voxels >>> > > >> nlabels = 162 >>> > > >> >>> > > >> PVF (null) >>> > > >> Thesholding hit volume. >>> > > >> mri_label2vol done >>> > > >> >>> > > >> *From:* Bruce Fischl <fischl(a)nmr.mgh.harvard.edu <mailto: >>> fischl(a)nmr.mgh.**harvard.edu <fischl(a)nmr.mgh.harvard.edu>> >>> > <mailto:fischl@nmr.mgh.**harvard.edu <fischl(a)nmr.mgh.harvard.edu><mailto: >>> fischl(a)nmr.mgh.**harvard.edu <fischl(a)nmr.mgh.harvard.edu>>> >>> > > <mailto:fischl@nmr.mgh.**harvard.edu <fischl(a)nmr.mgh.harvard.edu><mailto: >>> fischl(a)nmr.mgh.**harvard.edu <fischl(a)nmr.mgh.harvard.edu>> <mailto: >>> fischl(a)nmr.mgh.**harvard.edu <fischl(a)nmr.mgh.harvard.edu> <mailto: >>> fischl(a)nmr.mgh.**harvard.edu <fischl(a)nmr.mgh.harvard.edu>>>>> >>> > > >> <mailto:fischl@nmr.mgh.**harvard.edu <fischl(a)nmr.mgh.harvard.edu><mailto: >>> fischl(a)nmr.mgh.**harvard.edu <fischl(a)nmr.mgh.harvard.edu>> >>> > <mailto:fischl@nmr.mgh.**harvard.edu <fischl(a)nmr.mgh.harvard.edu><mailto: >>> fischl(a)nmr.mgh.**harvard.edu <fischl(a)nmr.mgh.harvard.edu>>> <mailto: >>> fischl(a)nmr.mgh.**harvard.edu <fischl(a)nmr.mgh.harvard.edu> <mailto: >>> fischl(a)nmr.mgh.**harvard.edu <fischl(a)nmr.mgh.harvard.edu>> >>> > <mailto:fischl@nmr.mgh.**harvard.edu <fischl(a)nmr.mgh.harvard.edu><mailto: >>> fischl(a)nmr.mgh.**harvard.edu <fischl(a)nmr.mgh.harvard.edu>>>>> >>> > > >> *To:* Leon <leonado78(a)yahoo.com <mailto:leonado78@yahoo.com> >>> <mailto:leonado78@yahoo.com <mailto:leonado78@yahoo.com>> >>> > <mailto:leonado78@yahoo.com <mailto:leonado78@yahoo.com> <mailto: >>> leonado78(a)yahoo.com <mailto:leonado78@yahoo.com>>>**> >>> > > <mailto:leonado78@yahoo.com <mailto:leonado78@yahoo.com> <mailto: >>> leonado78(a)yahoo.com <mailto:leonado78@yahoo.com>> >>> > <mailto:leonado78@yahoo.com <mailto:leonado78@yahoo.com> <mailto: >>> leonado78(a)yahoo.com <mailto:leonado78@yahoo.com>>>**> >>> > > >> *Cc:* FreeSurfer <freesurfer(a)nmr.mgh.harvard.**edu<freesurfer(a)nmr.mgh.harvard.edu><mailto: >>> freesurfer(a)nmr.mgh.**harvard.edu <freesurfer(a)nmr.mgh.harvard.edu>> >>> > <mailto:freesurfer@nmr.mgh.**harvard.edu<freesurfer(a)nmr.mgh.harvard.edu><mailto: >>> freesurfer(a)nmr.mgh.**harvard.edu <freesurfer(a)nmr.mgh.harvard.edu>>> >>> > > <mailto:freesurfer@nmr.mgh.**harvard.edu<freesurfer(a)nmr.mgh.harvard.edu><mailto: >>> freesurfer(a)nmr.mgh.**harvard.edu <freesurfer(a)nmr.mgh.harvard.edu>> >>> > <mailto:freesurfer@nmr.mgh.**harvard.edu<freesurfer(a)nmr.mgh.harvard.edu><mailto: >>> freesurfer(a)nmr.mgh.**harvard.edu <freesurfer(a)nmr.mgh.harvard.edu>>>>> >>> > > >> <mailto:freesurfer@nmr.mgh.**harvard.edu<freesurfer(a)nmr.mgh.harvard.edu><mailto: >>> freesurfer(a)nmr.mgh.**harvard.edu <freesurfer(a)nmr.mgh.harvard.edu>> >>> > <mailto:freesurfer@nmr.mgh.**harvard.edu<freesurfer(a)nmr.mgh.harvard.edu><mailto: >>> freesurfer(a)nmr.mgh.**harvard.edu <freesurfer(a)nmr.mgh.harvard.edu>>> >>> > > <mailto:freesurfer@nmr.mgh.**harvard.edu<freesurfer(a)nmr.mgh.harvard.edu><mailto: >>> freesurfer(a)nmr.mgh.**harvard.edu <freesurfer(a)nmr.mgh.harvard.edu>> >>> > <mailto:freesurfer@nmr.mgh.**harvard.edu<freesurfer(a)nmr.mgh.harvard.edu><mailto: >>> freesurfer(a)nmr.mgh.**harvard.edu <freesurfer(a)nmr.mgh.harvard.edu>>>>> >>> > > >> *Sent:* Friday, June 1, 2012 8:02 PM >>> > > >> *Subject:* Re: [Freesurfer] missing ROI when using mri_label2vol >>> to >>> > > >> transfer ic2.tri >>> > > >> >>> > > >> Can you send us your command lines and screen output? >>> > > >> >>> > > >> >>> > > >> >>> > > >> On Jun 1, 2012, at 7:44 PM, Leon <leonado78(a)yahoo.com <mailto: >>> leonado78(a)yahoo.com> >>> > <mailto:leonado78@yahoo.com <mailto:leonado78@yahoo.com>> >>> > > <mailto:leonado78@yahoo.com <mailto:leonado78@yahoo.com> <mailto: >>> leonado78(a)yahoo.com <mailto:leonado78@yahoo.com>>> >>> > > >> <mailto:leonado78@yahoo.com <mailto:leonado78@yahoo.com> <mailto: >>> leonado78(a)yahoo.com <mailto:leonado78@yahoo.com>> >>> > <mailto:leonado78@yahoo.com <mailto:leonado78@yahoo.com> <mailto: >>> leonado78(a)yahoo.com <mailto:leonado78@yahoo.com>>>**>> wrote: >>> > > >> >>> > > >>> Hi, folks >>> > > >>> >>> > > >>> when I transferred the annotation file obtained using >>> > > >>> mri_make_face_parcellation based on ic2 (162 labels) to a volume >>> > > >>> file using mri_label2vol, I found that one ROI patch was missing >>> in >>> > > >>> the volume file (see attached). I searched archives and the >>> closest >>> > > >>> thread I could found is that somebody reported an ROI with the >>> last >>> > > >>> index was missing in the mgz file after they were transferred >>> from >>> > > >>> the annotation file to the volume file. >>> > > >>> >>> > > >>> Could someone help on this? If this happens to be a bug, is there >>> > > >>> any other strategy that will allow me to get a GM/WM ribbon >>> without >>> > > >>> a hole on it? >>> > > >>> >>> > > >>> Many thanks in advance >>> > > >>> Leon >>> > > >>> <MissingROI.jpg> >>> > > >>> ______________________________**_________________ >>> > > >>> Freesurfer mailing list >>> > > >>> Freesurfer(a)nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.** >>> harvard.edu <Freesurfer(a)nmr.mgh.harvard.edu>> >>> > <mailto:Freesurfer@nmr.mgh.**harvard.edu<Freesurfer(a)nmr.mgh.harvard.edu><mailto: >>> Freesurfer(a)nmr.mgh.**harvard.edu <Freesurfer(a)nmr.mgh.harvard.edu>>> >>> > > <mailto:Freesurfer@nmr.mgh.**harvard.edu<Freesurfer(a)nmr.mgh.harvard.edu><mailto: >>> Freesurfer(a)nmr.mgh.**harvard.edu <Freesurfer(a)nmr.mgh.harvard.edu>> >>> > <mailto:Freesurfer@nmr.mgh.**harvard.edu<Freesurfer(a)nmr.mgh.harvard.edu><mailto: >>> Freesurfer(a)nmr.mgh.**harvard.edu <Freesurfer(a)nmr.mgh.harvard.edu>>>> >>> > > <mailto:Freesurfer@nmr.mgh.**harvard.edu<Freesurfer(a)nmr.mgh.harvard.edu><mailto: >>> Freesurfer(a)nmr.mgh.**harvard.edu <Freesurfer(a)nmr.mgh.harvard.edu>> >>> > <mailto:Freesurfer@nmr.mgh.**harvard.edu<Freesurfer(a)nmr.mgh.harvard.edu><mailto: >>> Freesurfer(a)nmr.mgh.**harvard.edu <Freesurfer(a)nmr.mgh.harvard.edu>>> >>> > > <mailto:Freesurfer@nmr.mgh.**harvard.edu<Freesurfer(a)nmr.mgh.harvard.edu><mailto: >>> Freesurfer(a)nmr.mgh.**harvard.edu <Freesurfer(a)nmr.mgh.harvard.edu>> >>> > <mailto:Freesurfer@nmr.mgh.**harvard.edu<Freesurfer(a)nmr.mgh.harvard.edu><mailto: >>> Freesurfer(a)nmr.mgh.**harvard.edu <Freesurfer(a)nmr.mgh.harvard.edu>>>>> >>> > > >>> https://mail.nmr.mgh.harvard.**edu/mailman/listinfo/**freesurfer<https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> >>> > > >> >>> > > >> ______________________________**_________________ >>> > > >> Freesurfer mailing list >>> > > >> Freesurfer(a)nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.** >>> harvard.edu <Freesurfer(a)nmr.mgh.harvard.edu>> >>> > <mailto:Freesurfer@nmr.mgh.**harvard.edu<Freesurfer(a)nmr.mgh.harvard.edu><mailto: >>> Freesurfer(a)nmr.mgh.**harvard.edu <Freesurfer(a)nmr.mgh.harvard.edu>>> >>> > > <mailto:Freesurfer@nmr.mgh.**harvard.edu<Freesurfer(a)nmr.mgh.harvard.edu><mailto: >>> Freesurfer(a)nmr.mgh.**harvard.edu <Freesurfer(a)nmr.mgh.harvard.edu>> >>> > <mailto:Freesurfer@nmr.mgh.**harvard.edu<Freesurfer(a)nmr.mgh.harvard.edu><mailto: >>> Freesurfer(a)nmr.mgh.**harvard.edu <Freesurfer(a)nmr.mgh.harvard.edu>>>> >>> > > <mailto:Freesurfer@nmr.mgh.**harvard.edu<Freesurfer(a)nmr.mgh.harvard.edu><mailto: >>> Freesurfer(a)nmr.mgh.**harvard.edu <Freesurfer(a)nmr.mgh.harvard.edu>> >>> > <mailto:Freesurfer@nmr.mgh.**harvard.edu<Freesurfer(a)nmr.mgh.harvard.edu><mailto: >>> Freesurfer(a)nmr.mgh.**harvard.edu <Freesurfer(a)nmr.mgh.harvard.edu>>> >>> > > <mailto:Freesurfer@nmr.mgh.**harvard.edu<Freesurfer(a)nmr.mgh.harvard.edu><mailto: >>> Freesurfer(a)nmr.mgh.**harvard.edu <Freesurfer(a)nmr.mgh.harvard.edu>> >>> > <mailto:Freesurfer@nmr.mgh.**harvard.edu<Freesurfer(a)nmr.mgh.harvard.edu><mailto: >>> Freesurfer(a)nmr.mgh.**harvard.edu <Freesurfer(a)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-mail >>> > > >> contains patient information, please contact the Partners >>> Compliance >>> > > >> HelpLine at >>> > > >> http://www.partners.org/**complianceline<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(a)nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.** >>> harvard.edu <Freesurfer(a)nmr.mgh.harvard.edu>> >>> > <mailto:Freesurfer@nmr.mgh.**harvard.edu<Freesurfer(a)nmr.mgh.harvard.edu><mailto: >>> Freesurfer(a)nmr.mgh.**harvard.edu <Freesurfer(a)nmr.mgh.harvard.edu>>> >>> > > <mailto:Freesurfer@nmr.mgh.**harvard.edu<Freesurfer(a)nmr.mgh.harvard.edu><mailto: >>> Freesurfer(a)nmr.mgh.**harvard.edu <Freesurfer(a)nmr.mgh.harvard.edu>> >>> > <mailto:Freesurfer@nmr.mgh.**harvard.edu<Freesurfer(a)nmr.mgh.harvard.edu><mailto: >>> Freesurfer(a)nmr.mgh.**harvard.edu <Freesurfer(a)nmr.mgh.harvard.edu>>>> >>> > > <mailto:Freesurfer@nmr.mgh.**harvard.edu<Freesurfer(a)nmr.mgh.harvard.edu><mailto: >>> Freesurfer(a)nmr.mgh.**harvard.edu <Freesurfer(a)nmr.mgh.harvard.edu>> >>> > <mailto:Freesurfer@nmr.mgh.**harvard.edu<Freesurfer(a)nmr.mgh.harvard.edu><mailto: >>> Freesurfer(a)nmr.mgh.**harvard.edu <Freesurfer(a)nmr.mgh.harvard.edu>>> >>> > > <mailto:Freesurfer@nmr.mgh.**harvard.edu<Freesurfer(a)nmr.mgh.harvard.edu><mailto: >>> Freesurfer(a)nmr.mgh.**harvard.edu <Freesurfer(a)nmr.mgh.harvard.edu>> >>> > <mailto:Freesurfer@nmr.mgh.**harvard.edu<Freesurfer(a)nmr.mgh.harvard.edu><mailto: >>> Freesurfer(a)nmr.mgh.**harvard.edu <Freesurfer(a)nmr.mgh.harvard.edu>>>>> >>> > > >> https://mail.nmr.mgh.harvard.**edu/mailman/listinfo/**freesurfer<https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> >>> > > > >>> > > > ______________________________**_________________ >>> > > > Freesurfer mailing list >>> > > > Freesurfer(a)nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.** >>> harvard.edu <Freesurfer(a)nmr.mgh.harvard.edu>> >>> > <mailto:Freesurfer@nmr.mgh.**harvard.edu<Freesurfer(a)nmr.mgh.harvard.edu><mailto: >>> Freesurfer(a)nmr.mgh.**harvard.edu <Freesurfer(a)nmr.mgh.harvard.edu>>> >>> > > <mailto:Freesurfer@nmr.mgh.**harvard.edu<Freesurfer(a)nmr.mgh.harvard.edu><mailto: >>> Freesurfer(a)nmr.mgh.**harvard.edu <Freesurfer(a)nmr.mgh.harvard.edu>> >>> > <mailto:Freesurfer@nmr.mgh.**harvard.edu<Freesurfer(a)nmr.mgh.harvard.edu><mailto: >>> Freesurfer(a)nmr.mgh.**harvard.edu <Freesurfer(a)nmr.mgh.harvard.edu>>>> >>> > > <mailto:Freesurfer@nmr.mgh.**harvard.edu<Freesurfer(a)nmr.mgh.harvard.edu><mailto: >>> Freesurfer(a)nmr.mgh.**harvard.edu <Freesurfer(a)nmr.mgh.harvard.edu>> >>> > <mailto:Freesurfer@nmr.mgh.**harvard.edu<Freesurfer(a)nmr.mgh.harvard.edu><mailto: >>> Freesurfer(a)nmr.mgh.**harvard.edu <Freesurfer(a)nmr.mgh.harvard.edu>>> >>> > > <mailto:Freesurfer@nmr.mgh.**harvard.edu<Freesurfer(a)nmr.mgh.harvard.edu><mailto: >>> Freesurfer(a)nmr.mgh.**harvard.edu <Freesurfer(a)nmr.mgh.harvard.edu>> >>> > <mailto:Freesurfer@nmr.mgh.**harvard.edu<Freesurfer(a)nmr.mgh.harvard.edu><mailto: >>> Freesurfer(a)nmr.mgh.**harvard.edu <Freesurfer(a)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-mail >>> > > > contains patient information, please contact the Partners >>> Compliance >>> > > > HelpLine at >>> > > > http://www.partners.org/**complianceline<http://www.partners.org/complianceline>. If the e-mail was sent to you >>> > > > in error >>> > > > but does not contain patient information, please contact the sender >>> > > > and properly >>> > > > dispose of the e-mail. >>> > > > >>> > > > >>> > > >>> > > -- >>> > > Douglas N. Greve, Ph.D. >>> > > MGH-NMR Center >>> > > greve(a)nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.**edu<greve(a)nmr.mgh.harvard.edu>> >>> <mailto:greve@nmr.mgh.harvard.**edu <greve(a)nmr.mgh.harvard.edu> <mailto: >>> greve(a)nmr.mgh.harvard.**edu <greve(a)nmr.mgh.harvard.edu>>> >>> > <mailto:greve@nmr.mgh.harvard.**edu <greve(a)nmr.mgh.harvard.edu><mailto: >>> greve(a)nmr.mgh.harvard.**edu <greve(a)nmr.mgh.harvard.edu>> <mailto: >>> greve(a)nmr.mgh.harvard.**edu <greve(a)nmr.mgh.harvard.edu> <mailto: >>> greve(a)nmr.mgh.harvard.**edu <greve(a)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: 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> >>> > >>> > > >>> > > ______________________________**_________________ >>> > > Freesurfer mailing list >>> > > Freesurfer(a)nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.** >>> harvard.edu <Freesurfer(a)nmr.mgh.harvard.edu>> >>> > <mailto:Freesurfer@nmr.mgh.**harvard.edu<Freesurfer(a)nmr.mgh.harvard.edu><mailto: >>> Freesurfer(a)nmr.mgh.**harvard.edu <Freesurfer(a)nmr.mgh.harvard.edu>>> >>> > <mailto:Freesurfer@nmr.mgh.**harvard.edu<Freesurfer(a)nmr.mgh.harvard.edu><mailto: >>> Freesurfer(a)nmr.mgh.**harvard.edu <Freesurfer(a)nmr.mgh.harvard.edu>> >>> > <mailto:Freesurfer@nmr.mgh.**harvard.edu<Freesurfer(a)nmr.mgh.harvard.edu><mailto: >>> Freesurfer(a)nmr.mgh.**harvard.edu <Freesurfer(a)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 >>> > greve(a)nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.**edu<greve(a)nmr.mgh.harvard.edu>> >>> <mailto:greve@nmr.mgh.harvard.**edu <greve(a)nmr.mgh.harvard.edu> <mailto: >>> greve(a)nmr.mgh.harvard.**edu <greve(a)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: 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> >>> > >>> > >>> > ______________________________**_________________ >>> > Freesurfer mailing list >>> > Freesurfer(a)nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.** >>> harvard.edu <Freesurfer(a)nmr.mgh.harvard.edu>> <mailto: >>> Freesurfer(a)nmr.mgh.**harvard.edu <Freesurfer(a)nmr.mgh.harvard.edu><mailto: >>> Freesurfer(a)nmr.mgh.**harvard.edu <Freesurfer(a)nmr.mgh.harvard.edu>>> >>> > https://mail.nmr.mgh.harvard.**edu/mailman/listinfo/**freesurfer<https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> >>> > >>> > >>> > >>> > ______________________________**_________________ >>> > Freesurfer mailing list >>> > Freesurfer(a)nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.** >>> harvard.edu <Freesurfer(a)nmr.mgh.harvard.edu>> <mailto: >>> Freesurfer(a)nmr.mgh.**harvard.edu <Freesurfer(a)nmr.mgh.harvard.edu><mailto: >>> Freesurfer(a)nmr.mgh.**harvard.edu <Freesurfer(a)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-mail >>> > contains patient information, please contact the Partners Compliance >>> > HelpLine at >>> > http://www.partners.org/**complianceline<http://www.partners.org/complianceline>. If the e-mail was sent to you >>> > in error >>> > but does not contain patient information, please contact the sender >>> > and properly >>> > dispose of the e-mail. >>> > >>> > >>> > >>> > >>> >>> -- >>> Douglas N. Greve, Ph.D. >>> MGH-NMR Center >>> greve(a)nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.**edu<greve(a)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: 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> >>> > >>> >>> ______________________________**_________________ >>> Freesurfer mailing list >>> Freesurfer(a)nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.**harvard.edu<Freesurfer(a)nmr.mgh.harvard.edu> >>> > >>> https://mail.nmr.mgh.harvard.**edu/mailman/listinfo/**freesurfer<https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> >>> >>> >>> >>> ______________________________**_________________ >>> Freesurfer mailing list >>> Freesurfer(a)nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.**harvard.edu<Freesurfer(a)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-mail >>> contains patient information, please contact the Partners Compliance >>> HelpLine at >>> http://www.partners.org/**complianceline<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(a)nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.**harvard.edu<Freesurfer(a)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-mail >> contains patient information, please contact the Partners Compliance >> HelpLine at >> http://www.partners.org/**complianceline<http://www.partners.org/complianceline>. If the e-mail was sent to you in error >> but does not contain patient information, please contact the sender and >> properly >> dispose of the e-mail. >> >> >> > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > greve(a)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: www.nmr.mgh.harvard.edu/**facility/filedrop/index.html<http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > > > > > ---------- Forwarded message ---------- > From: Varghese Chikku <chikkuv(a)tcd.ie> > To: Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> > Cc: freesurfer(a)nmr.mgh.harvard.edu > Date: Wed, 5 Sep 2012 16:01:08 +0200 > Subject: Re: [Freesurfer] Freesurfer-Error message > > Thanks Bruce, > > Still no luck,this what I am getting > > > > > > /freesurfer/subjects/test1> recon-all -i > /media/sf_freesurferstudys/raw/raw_scr/T1pre/Image00001.dcm -subjid test7 > -all Subject Stamp: freesurfer-Linux-centos4-stable-pub-v5.1.0 > > Current Stamp: freesurfer-Linux-centos4-stable-pub-v5.1.0 > > INFO: SUBJECTS_DIR is /home/virtualuser/freesurfer/subjects > > Actual FREESURFER_HOME /home/virtualuser/freesurfer Linux FreeSurfer > 2.6.28-11-generic #42-Ubuntu SMP Fri Apr 17 01:57:59 UTC 2009 i686 GNU/Linux > > /home/virtualuser/freesurfer/subjects/test7 > > > > mri_convert /media/sf_freesurferstudys/raw/raw_scr/T1pre/Image00001.dcm > /home/virtualuser/freesurfer/subjects/test7/mri/orig/001.mgz > > > > mri_convert /media/sf_freesurferstudys/raw/raw_scr/T1pre/Image00001.dcm > /home/virtualuser/freesurfer/subjects/test7/mri/orig/001.mgz > > file not found or unknown file type for file > /media/sf_freesurferstudys/raw/raw_scr/T1pre/Image00001.dcm > > Linux FreeSurfer 2.6.28-11-generic #42-Ubuntu SMP Fri Apr 17 01:57:59 UTC > 2009 i686 GNU/Linux > > > > recon-all -s test7 exited with ERRORS at Wed Sep 5 09:51:17 EDT 2012 > > > > For more details, see the log file > /home/virtualuser/freesurfer/subjects/test7/scripts/recon-all.log > > To report a problem, see > http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > > > > FreeSurfer:~/freesurfer/subjects/test1> > > > On 4 September 2012 14:37, Bruce Fischl <fischl(a)nmr.mgh.harvard.edu>wrote: > >> if that's the name of the image file. Can you post the list on your >> replies so others can answer? >> >> thanks >> Bruce >> >> On Tue, 4 Sep 2012, Varghese Chikku wrote: >> >> Hi Bruce, >>> Many thanks for you mail. >>> Is this the command you referring to. >>> recon-all -i /media/sf_freesurferstudys/**raw/raw_scr/T1pre/Image00001.* >>> *dcm -subjid test4 >>> Thanks >>> Chikku >>> >>> On 3 September 2012 17:33, Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> >>> wrote: >>> Hi Chikku >>> >>> you need to give it the path to an image file (any one will do) >>> and it will figure out the other slices that makeup >>> the same series. What is the resolution of your data? 50 slices >>> isn't usually enough to cover the brain at high >>> enough resolution to get good thickness results. >>> >>> cheers >>> Bruce >>> >>> >>> On Mon, 3 Sep 2012, Varghese Chikku wrote: >>> >>> >>> Hi, >>> >>> While running the following command: >>> >>> recon-all -i /media/sf_freesurferstudys/**raw/raw_scr/T1pre >>> -subjid test2 >>> >>> I keep seeing the following error: >>> >>> ... >>> >>> corRead(): can't open file >>> /media/sf_freesurferstudys/**raw/raw_scr/T1pre/COR-.info >>> $Id: mri_convert.c,v 1.179.2.1 2011/03/22 16:37:02 nicks Exp >>> $ >>> reading from /media/sf_freesurferstudys/** >>> raw/raw_scr/T1pre... >>> Linux FreeSurfer 2.6.28-11-generic #42-Ubuntu SMP Fri Apr 17 >>> 01:57:59 UTC >>> 2009 i686 GNU/Linux >>> recon-all -s test2 exited with ERRORS at Fri Aug 31 04:20:28 >>> EDT 2012 >>> >>> >>> My image files, in dcm format, are at >>> /media/sf_freesurferstudys/**raw/raw_scr/T1pre : >>> >>> /media/sf_freesurferstudys/**raw/raw_scr/T1pre> ls >>> Image00001 Image00010 Image00019 Image00028 Image00037 >>> Image00046 >>> Image00002 Image00011 Image00020 Image00029 Image00038 >>> Image00047 >>> Image00003 Image00012 Image00021 Image00030 Image00039 >>> Image00048 >>> Image00004 Image00013 Image00022 Image00031 Image00040 >>> Image00049 >>> Image00005 Image00014 Image00023 Image00032 Image00041 >>> Image00050 >>> Image00006 Image00015 Image00024 Image00033 Image00042 >>> Image00007 Image00016 Image00025 Image00034 Image00043 >>> Image00008 Image00017 Image00026 Image00035 Image00044 >>> Image00009 Image00018 Image00027 Image00036 Image00045 >>> >>> Many thanks for your help. >>> chikku >>> >>> >>> >>> >>> 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<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. >>> >>> >>> >>> > > > ---------- Forwarded message ---------- > From: Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> > To: "Varghese, Chikku" <Chikku.Varghese(a)perceptive.com> > Cc: "freesurfer(a)nmr.mgh.harvard.edu" <freesurfer(a)nmr.mgh.harvard.edu> > Date: Wed, 5 Sep 2012 10:07:22 -0400 (EDT) > Subject: Re: [Freesurfer] Freesurfer-Error message > Is that the actual name of the file? Does it have a dcm extension? > On Wed, 5 Sep 2012, Varghese, Chikku wrote: > > Thanks Bruce, >> Still no luck,this what I am getting >> >> >> /freesurfer/subjects/test1> recon-all -i /media/sf_freesurferstudys/** >> raw/raw_scr/T1pre/Image00001.**dcm -subjid test7 -all >> Subject Stamp: freesurfer-Linux-centos4-**stable-pub-v5.1.0 >> Current Stamp: freesurfer-Linux-centos4-**stable-pub-v5.1.0 >> INFO: SUBJECTS_DIR is /home/virtualuser/freesurfer/**subjects >> Actual FREESURFER_HOME /home/virtualuser/freesurfer >> Linux FreeSurfer 2.6.28-11-generic #42-Ubuntu SMP Fri Apr 17 01:57:59 UTC >> 2009 i686 GNU/Linux >> /home/virtualuser/freesurfer/**subjects/test7 >> >> mri_convert /media/sf_freesurferstudys/**raw/raw_scr/T1pre/Image00001.**dcm >> /home/virtualuser/freesurfer/**subjects/test7/mri/orig/001.**mgz >> >> mri_convert /media/sf_freesurferstudys/**raw/raw_scr/T1pre/Image00001.**dcm >> /home/virtualuser/freesurfer/**subjects/test7/mri/orig/001.**mgz >> file not found or unknown file type for file /media/sf_freesurferstudys/* >> *raw/raw_scr/T1pre/Image00001.**dcm >> Linux FreeSurfer 2.6.28-11-generic #42-Ubuntu SMP Fri Apr 17 01:57:59 UTC >> 2009 i686 GNU/Linux >> >> recon-all -s test7 exited with ERRORS at Wed Sep 5 09:51:17 EDT 2012 >> >> For more details, see the log file /home/virtualuser/freesurfer/** >> subjects/test7/scripts/recon-**all.log >> To report a problem, see http://surfer.nmr.mgh.harvard.** >> edu/fswiki/BugReporting<http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> >> >> FreeSurfer:~/freesurfer/**subjects/test1> >> >> -----Original Message----- >> From: Bruce Fischl [mailto:fischl@nmr.mgh.**harvard.edu<fischl(a)nmr.mgh.harvard.edu> >> ] >> Sent: Dienstag, 4. September 2012 18:25 >> To: Varghese, Chikku >> Subject: Re: [Freesurfer] Freesurfer-Error message >> >> you need a -all at the end to tell it what to do. And please cc the list >> so others can answer! >> >> On Tue, 4 Sep 2012, Varghese, Chikku wrote: >> >> >>> recon-all -i >>> /media/sf_freesurferstudys/**raw/raw_scr/T1pre/Image00001.**dcm -subjid >>> test4 >>> >>> Is it this command I should use? >>> >>> >>> >>> >> >> 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<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. >> >> >> >> >> > > > ---------- Forwarded message ---------- > From: Douglas N Greve <greve(a)nmr.mgh.harvard.edu> > To: freesurfer(a)nmr.mgh.harvard.edu > Cc: > Date: Wed, 05 Sep 2012 10:47:59 -0400 > Subject: Re: [Freesurfer] FDR Correction of NHP Surface Data > Hi Clark, I just made a modification to mri_binarize to make it take an > FDR as input. It computes the threshold and binarizes the input based on > the threshold. I've put a copy here: > > ftp://surfer.nmr.mgh.harvard.**edu/transfer/outgoing/flat/** > greve/mri_binarize.linux<ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_binarize.…> > > Run it with --help to get more info. > > doug > > > On 08/29/2012 02:08 PM, Clark Fisher wrote: > >> Hi Sebastian, >> >> I think you are right, both about tksurfer thresholding and the correct >> interpretation of FDR. As you point out though, there is some value in >> having maps that show how relatively well different points on the surface >> fit your model. >> >> At the very least, is there any way to automate the retrieving of the >> threshold that tksurfer provides? I'd still also be interested in some >> adjustment to the whole map, if there's a way to do that as well. >> >> I could probably find a way to do this in Matlab, but I trust the >> bug-squishing abilities of the freesurfer community more than I trust my >> own. >> >> -Clark >> >> >> On Aug 28, 2012, at 2:34 PM, Sebastian Moeller wrote: >> >> Hi Clark, >>> >>> >>> On Aug 28, 2012, at 11:15 AM, Clark Fisher wrote: >>> >>> Hi Bruce, >>>> >>>> Thanks. I actually have used this function of tksurfer, but am looking >>>> for a way to save the corrected maps, so that they could be manipulated by >>>> other tools (for instance, viewed by PySurfer). >>>> >>> Does it really correct the map? I thought all it does is figure >>> out the corrected threshold. By the way, if I understand correctly, FDR >>> maps should be considered to be binary, that is you really do not know >>> which voxels might be false positives, so you should not interpret all >>> voxels to be equally significant. Having said that, almost everybody I know >>> still looks at the p-value spatial distribution when looking at those FDR >>> thresholded maps… (then again, I do not know any statistician...) >>> >>> >>> best >>> Sebastian >>> >>> I recognize that this may not be an officially supported functionality, >>>> but is there some way to save the adjusted overlays from tksurfer, or >>>> create them in some other way? >>>> >>>> Best, >>>> Clark >>>> >>>> >>>> On Aug 28, 2012, at 1:58 PM, Bruce Fischl wrote: >>>> >>>> Hi Clark >>>>> >>>>> you shouldn't need either. Load your overlays then click the button to >>>>> compute the FDR threshold in the tksurfer configure overlay interface. >>>>> >>>>> cheers >>>>> Bruce >>>>> On Tue, 28 Aug 2012, Clark Fisher wrote: >>>>> >>>>> Ok, maybe I'm making this question too intricate. Here's the short >>>>>> version: >>>>>> How can I FDR correct painted surface significance maps when I have >>>>>> no talraich .xfm file and no cortical segmentation? >>>>>> Thanks again, >>>>>> Clark >>>>>> Hi Freesurfers, >>>>>> I have another monkey-specific question. I'd like to output >>>>>> FDR-corrected signficance surface maps for my monkey data, or at least >>>>>> FDR-threshold the maps. It seems like mri_surfcluster might be one way to >>>>>> go about this however: >>>>>> 1) I don't have any .xfm files for my monkeys, as I'm working >>>>>> in native space, and >>>>>> 2) Without segmentation, I don't have a good mask to use for >>>>>> the cortex only. My first attempts at work-arounds would be: >>>>>> 1)Try to create an identity .xfm file >>>>>> 2)Use the cortical ribbons from mris_volmask as a cortex mask >>>>>> Should these work? If so, how should I make an identity .xfm file? >>>>>> If not, is there another way to FDR correct my surface data? >>>>>> Thanks, >>>>>> Clark >>>>>> ______________________________**_________________ >>>>>> Freesurfer mailing list >>>>>> Freesurfer(a)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-mail >>>>>> contains patient information, please contact the Partners Compliance >>>>>> HelpLine at >>>>>> http://www.partners.org/**complianceline<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(a)nmr.mgh.harvard.edu >>>> https://mail.nmr.mgh.harvard.**edu/mailman/listinfo/**freesurfer<https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> >>>> >>> -- >>> Sebastian Moeller >>> >>> telephone: +1-626-325-8598 /+1-626-395-6523 / +1-626-395-6616 >>> fax: 626-395-8826 >>> German GSM: +49 - 15 77 - 1 90 31 41 >>> mobile: +1-626-325-8598 >>> +1-626-807-5242 >>> US CDMA: +1-626-807-5242 >>> moeller(a)caltech.edu >>> >>> Division of Biology >>> MC 114-96 >>> California Institute of Technology >>> 1200 East California Boulevard >>> CA 91125, Pasadena >>> USA >>> >>> >> ______________________________**_________________ >> Freesurfer mailing list >> Freesurfer(a)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 > greve(a)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: www.nmr.mgh.harvard.edu/**facility/filedrop/index.html<http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > > > > ... > > [Message clipped]

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tksurfer not working properly
by Deirdre O Shea 05 Sep '12

05 Sep '12

Hello, I am just getting to get grips with using FreeSurfer to reconstruct images, however, any time I try to load tksurfer it only displays a very small part of the image (see attached for what i mean). I was hoping someone could give me an explanation as to why this may be happening and whether there is a solution to fixing it. Best Deirdre

2 1

Covary for categorical variable in QDEC
by Jeff Sadino 05 Sep '12

05 Sep '12

Hello, Is it possible to covary for a categorical variable in QDEC? I see other posters have said it is not possible, but I did not see any official documentation or response regarding the issue. Thank You, Jeff Sadino

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Re: [Freesurfer] mri_watershed and other errors.
by Darren Gitelman 05 Sep '12

05 Sep '12

Bruce: Thank you for looking. I have uploaded the files: I uploaded them in Dicom Format. This is a T1, MPRAGE, image, acquired with GRAPPA, resolution 1x1x1. Name: 3157.tar.gz Darren On Wed, Sep 5, 2012 at 11:27 AM, Bruce Fischl <fischl(a)nmr.mgh.harvard.edu>wrote: > Hi Darren > > can you describe your input data? What format, resolution, etc... is it? > If you upload it we'll take a look > cheers > Bruce > On Wed, 5 Sep 2012, Darren Gitelman > wrote: > > > > > Nick, List: > > > > > > > > Still no luck with this data. See attached as an example. > > > > > > > > To get to this point I had run: > > > > > > > > recon-all -all > > > > > > > > This ran to the error: mri_watershed Error: GLOBAL region of the brain > empty ! > > > > > > > > Then I followed your recommendation below > > > > > > > > recon-all -s <subjid> -skullstrip -no-wsgcaatlas, which had no errors > and then > > > > recon-all -s <subjid> -autorecon2 -autorecon3 > > > > > > > > This produced the result attached. > > > > > > > > I then deleted this directory and re-imported all the dicom data for > this subject. Looked at the images, which look fine. > > > > Then I ran recon-all -s <subjid> -autorecon1 > > > > > > > > This fails with the mri_watershed error. > > > > > > > > Then I ran recon-all -s <subjid> -skullstrip -no-wsgcaatlas. > > > > > > > > This runs without error but when I look at the brainmask.mgz it looks > just like the attached image. > > > > > > > > Is there some way to set the thresholds differently? The T1 image looks > fine to me although perhaps the intensity is slightly > > less than usual, but it doesn't seem particularly noisy. > > > > > > > > Darren > > > > > > > > > > > > > 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. > -- Darren Gitelman, MD Northwestern University 710 N. Lake Shore Dr. Abbott 11th Floor Chicago, IL 60611 Ph: (312) 908-8614 Fax: (312) 908-5073

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Re: [Freesurfer] Freesurfer Digest, Vol 103, Issue 4
by Istvan Akos Morocz 05 Sep '12

05 Sep '12

a Lichthofi tarsasag --- na jo, eleget hulyeskedtem : szep romantikus szeretkezesbe esunk mi ketten bele, minekunk, magunknak - de csak, ha elkergetjuk ezeket a suket hurrikan felhoket. meggebednenk ebben a nedvesegben! napok ota 85 es 95% kozott mozgunk itt Brooklineban. On Wed, 5 Sep 2012, freesurfer-request(a)nmr.mgh.harvard.edu wrote: > Send Freesurfer mailing list submissions to > freesurfer(a)nmr.mgh.harvard.edu > > To subscribe or unsubscribe via the World Wide Web, visit > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > or, via email, send a message with subject or body 'help' to > freesurfer-request(a)nmr.mgh.harvard.edu > > You can reach the person managing the list at > freesurfer-owner(a)nmr.mgh.harvard.edu > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of Freesurfer digest..." > > > Today's Topics: > > 1. Re: Repost: Converting BV ROIs to FS (Bruce Fischl) > 2. Re: Repost: Converting BV ROIs to FS (Katie Bettencourt) > 3. Re: freesurfer tutorial data (Help Desk -- Paul Raines) > 4. Re: creating a skull (Borzello, Mia) > 5. Re: error in long_mris_slopes command (Martin Reuter) > 6. mris_anatomical_stats on multiple subjects (Alexandra Tanner) > 7. Re: freesurfer tutorial data (Dix Meiberth) > 8. Re: creating a skull (Bruce Fischl) > 9. Cortical parcellations and probtrackx2 in diffusion space > (Alistair Perry) > 10. Covary for categorical variable in QDEC (Jeff Sadino) > 11. Re: Repost: Converting BV ROIs to FS (Bruce Fischl) > 12. Re: repeated measures ANOVA with two groups (Douglas N Greve) > 13. Re: freesurfer tutorial data (Help Desk -- Paul Raines) > 14. Re: missing ROI when using mri_label2vol to transfer ic2.tri > (Douglas N Greve) > 15. Re: Freesurfer-Error message (Varghese Chikku) > 16. Re: Freesurfer-Error message (Bruce Fischl) > 17. Re: FDR Correction of NHP Surface Data (Douglas N Greve) > 18. Re: mri_watershed and other errors. (Darren Gitelman) > 19. Re: resending question about 3rd level analysis (Douglas N Greve) > 20. Re: mris_anatomical_stats on multiple subjects (Alexandra Tanner) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Tue, 4 Sep 2012 12:24:09 -0400 (EDT) > From: Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> > Subject: Re: [Freesurfer] Repost: Converting BV ROIs to FS > To: Katie Bettencourt <kcb(a)wjh.harvard.edu> > Cc: freesurfer maillist <freesurfer(a)nmr.mgh.harvard.edu> > Message-ID: > <alpine.LRH.2.00.1209041223450.1723(a)gate.nmr.mgh.harvard.edu> > Content-Type: text/plain; charset="iso-8859-1" > > Hi Katie > > I don't think anyone here knows how to do this as we don't use it. > Perhaps the Brain Voyager people do? > > sorry, > Bruce > On Tue, 4 Sep 2012, Katie Bettencourt > wrote: > >> >> So our lab is running a couple analyses and we are getting different results based on whether we use Brain Voyager or >> Freesurfer that we think is due to different ROI selection across the two platforms. ?Is there anyway to load a >> BrainVoyager ROI into freesurfer? ?The BV data has been talairach transformed, does that matter? ?Less optimal would >> be loading a freesurfer ROI into BV, but if that's easier, we could try that way too. >> Any help would be appreciated. >> >> Katie >> >> >> >> > > ------------------------------ > > Message: 2 > Date: Tue, 4 Sep 2012 13:18:42 -0400 > From: Katie Bettencourt <kcb(a)wjh.harvard.edu> > Subject: Re: [Freesurfer] Repost: Converting BV ROIs to FS > To: Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> > Cc: freesurfer maillist <freesurfer(a)nmr.mgh.harvard.edu> > Message-ID: > <CA+XrXCYEw2A0Dzt+dQKkOV_86fodwdemKnsdESEjXHKa-n_x+g(a)mail.gmail.com> > Content-Type: text/plain; charset="iso-8859-1" > > Hrm. Ok, is there any way to view data for a subject in Freesurfer on a > talairach transformed brain? What I would be hoping to do is bring up the > data in native subject space, make any ROI label, then also bring the data > up on a talairach transformed brain, make a ROI label, then put both labels > on the same brain (either native or talairach transformed) and see if they > are any different. > > Also, is there a way to input a particular talairach vertex and jump to > that in freesurfer, instead of just moving the mouse around and hoping to > find the right spot? > > Katie > > On Tue, Sep 4, 2012 at 12:24 PM, Bruce Fischl <fischl(a)nmr.mgh.harvard.edu>wrote: > >> Hi Katie >> >> I don't think anyone here knows how to do this as we don't use it. Perhaps >> the Brain Voyager people do? >> >> sorry, >> Bruce >> >> On Tue, 4 Sep 2012, Katie Bettencourt wrote: >> >> >>> So our lab is running a couple analyses and we are getting >>> different results based on whether we use Brain Voyager or >>> Freesurfer that we think is due to different ROI selection across >>> the two platforms. Is there anyway to load a >>> BrainVoyager ROI into freesurfer? The BV data has been talairach >>> transformed, does that matter? Less optimal would >>> be loading a freesurfer ROI into BV, but if that's easier, we could >>> try that way too. >>> Any help would be appreciated. >>> >>> Katie >>> >>> >>> >>> >>> >> >> 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<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. >> >

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resending question about 3rd level analysis
by Susan Alice McLaughlin 05 Sep '12

05 Sep '12

Hi, I'm resending this e-mail, as it didn't seem to go through correctly yesterday: I’m a Freesurfer novice, and I’m confused about how to run a 3rd level cross-subject analysis on the surface using as input cross-run .gfeats from 10 subjects generated from a 2nd level analysis in FSL. Following the directions posted at http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/FslGroupFeat, I have sampled the .gfeat copes and varcopes into standard surface space, using mris_preproc. I would then go on to perform a 3rd level surface based analysis as the instructions suggest, using: mri_glmfit --y xrun/lh.cope1.mgh --yffxvar xrun/lh.varcope1.mgh --ffxdof 163 --osgm --glmdir xrun/lh.osgm.ffx --surf fsaverage lh --label $SUBJECTS_DIR/fsaverage/label/lh.cortex.label However, I want to use a random as opposed to fixed effects analysis. How do I do this? I tried --yrfxvar as opposed to --yffxvar but it didn’t work. And if I’m going to display the map resulting from this analysis, do I need to correct for multiple comparisons? Many thanks in advance, Susan McLaughlin Doctoral Candidate SPACE Lab (Stimulus-Parametric Imaging of Auditory Cortex) Dept. of Speech and Hearing Sciences University of Washington

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Re: [Freesurfer] FDR Correction of NHP Surface Data
by Clark Fisher 05 Sep '12

05 Sep '12

Ok, maybe I'm making this question too intricate. Here's the short version: How can I FDR correct painted surface significance maps when I have no talraich .xfm file and no cortical segmentation? Thanks again, Clark Hi Freesurfers, I have another monkey-specific question. I'd like to output FDR-corrected signficance surface maps for my monkey data, or at least FDR-threshold the maps. It seems like mri_surfcluster might be one way to go about this however: 1) I don't have any .xfm files for my monkeys, as I'm working in native space, and 2) Without segmentation, I don't have a good mask to use for the cortex only. My first attempts at work-arounds would be: 1)Try to create an identity .xfm file 2)Use the cortical ribbons from mris_volmask as a cortex mask Should these work? If so, how should I make an identity .xfm file? If not, is there another way to FDR correct my surface data? Thanks, Clark _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.

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Re: [Freesurfer] Freesurfer-Error message
by Bruce Fischl 05 Sep '12

05 Sep '12

Is that the actual name of the file? Does it have a dcm extension? On Wed, 5 Sep 2012, Varghese, Chikku wrote: > Thanks Bruce, > Still no luck,this what I am getting > > > /freesurfer/subjects/test1> recon-all -i /media/sf_freesurferstudys/raw/raw_scr/T1pre/Image00001.dcm -subjid test7 -all > Subject Stamp: freesurfer-Linux-centos4-stable-pub-v5.1.0 > Current Stamp: freesurfer-Linux-centos4-stable-pub-v5.1.0 > INFO: SUBJECTS_DIR is /home/virtualuser/freesurfer/subjects > Actual FREESURFER_HOME /home/virtualuser/freesurfer > Linux FreeSurfer 2.6.28-11-generic #42-Ubuntu SMP Fri Apr 17 01:57:59 UTC 2009 i686 GNU/Linux > /home/virtualuser/freesurfer/subjects/test7 > > mri_convert /media/sf_freesurferstudys/raw/raw_scr/T1pre/Image00001.dcm /home/virtualuser/freesurfer/subjects/test7/mri/orig/001.mgz > > mri_convert /media/sf_freesurferstudys/raw/raw_scr/T1pre/Image00001.dcm /home/virtualuser/freesurfer/subjects/test7/mri/orig/001.mgz > file not found or unknown file type for file /media/sf_freesurferstudys/raw/raw_scr/T1pre/Image00001.dcm > Linux FreeSurfer 2.6.28-11-generic #42-Ubuntu SMP Fri Apr 17 01:57:59 UTC 2009 i686 GNU/Linux > > recon-all -s test7 exited with ERRORS at Wed Sep 5 09:51:17 EDT 2012 > > For more details, see the log file /home/virtualuser/freesurfer/subjects/test7/scripts/recon-all.log > To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > > FreeSurfer:~/freesurfer/subjects/test1> > > -----Original Message----- > From: Bruce Fischl [mailto:fischl@nmr.mgh.harvard.edu] > Sent: Dienstag, 4. September 2012 18:25 > To: Varghese, Chikku > Subject: Re: [Freesurfer] Freesurfer-Error message > > you need a -all at the end to tell it what to do. And please cc the list so others can answer! > > On Tue, 4 Sep 2012, Varghese, Chikku wrote: > >> >> recon-all -i >> /media/sf_freesurferstudys/raw/raw_scr/T1pre/Image00001.dcm -subjid >> test4 >> >> Is it this command I should use? >> >> >> > > > 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. > > > >

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