Freesurfer January 2013

freesurfer@nmr.mgh.harvard.edu

111 participants
203 discussions

Re: [Freesurfer] beta
by Bruce Fischl 22 Jan '13

22 Jan '13

Hi Colin yes, but we simply don't have the person power to do it at the moment. Our FS support grant ends in a month and is not going to get renewed, so it's going to be hard to do anytime soon. sorry Bruce On Mon, 21 Jan 2013, Colin Reveley wrote: > do you plan to support data that is more that 256^3, ever? > > just, do you plan to support that > > On 21 January 2013 22:17, Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> wrote: > no, it won't change anything on the subcortical side yet > On Mon, 21 Jan 2013, Joshua Lee wrote: > > > Thanks Bruce. That sounds great. Will subcortical segmentations also benefit yet. I remember that you once > told me that there were > some problems with it. > - > Josh > > > On Mon, Jan 21, 2013 at 12:39 PM, Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> wrote: > Hi Josh > > the way we are handling sub-mm data is to run it through the standard recon-all, then run a > postprocessing surface > deformation on the higher res data. Our preliminary results are pretty encouraging on T1s, T2s and > FLAIRs. > > cheers > Bruce > > > On Mon, 21 Jan 2013, Joshua Lee wrote: > > Does this mean that using Freesurfer at sub-1mm isotropic resolutions will not be possible next > version? > Josh > > > On Sun, Jan 20, 2013 at 8:07 AM, Nick Schmansky <nicks(a)nmr.mgh.harvard.edu> wrote: > Colin, > > It will still error if any dimension is greater than 256, which then means > the flag -cw256 must be added to recon-all. This flag chops dimensions > greater than 256 down to 256. The reason it doesnt do it automatically is > that with this chopping, its not certain that it isnt removing into the > head, so the user needs to be aware of this, so that they can inspect > orig.mgz with freeview to make sure the head is fully visible. > > Nick > > > Does the beta permit volumes bigger than 256^3 voxels? just asking....and > > just asking about raw dimensions in unit-voxels at the start of pipeline > > > > cheers > > > > Colin > > > > On 18 January 2013 17:00, <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. v5.2.0 beta, round two (Nick Schmansky) > >> 2. Re: pial not computing (Borzello, Mia) > >> 3. Re: pial not computing (Bruce Fischl) > >> 4. Re: FW: longitudinal analysis (Alex Hanganu) > >> > >> > >> ---------- Forwarded message ---------- > >> From: Nick Schmansky <nicks(a)nmr.mgh.harvard.edu> > >> To: <freesurfer(a)nmr.mgh.harvard.edu> > >> Cc: > >> Date: Fri, 18 Jan 2013 11:20:43 -0500 > >> Subject: [Freesurfer] v5.2.0 beta, round two > >> For those willing and brave enough, another beta of v5.2.0 has been > >> posted > >> here for you to download and test: > >> > >> ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/5.2.0-BETA/ > >> > >> The Mac builds should work (note: the lion build is 64b, snow-leopard is > >> 32b). > >> > >> The final release still awaits some critical improvements to the Tracula > >> stream, but the main recon-all stream with this beta is final. The > >> final > >> release is expected the first week of February. > >> > >> Freesurfer team > >> > >> > >> > >> > >> > >> ---------- Forwarded message ---------- > >> From: "Borzello, Mia" <MBORZELLO(a)partners.org> > >> To: "freesurfer(a)nmr.mgh.harvard.edu" <freesurfer(a)nmr.mgh.harvard.edu> > >> Cc: > >> Date: Fri, 18 Jan 2013 16:25:40 +0000 > >> Subject: Re: [Freesurfer] pial not computing > >> great. is there a freesurfer page on mris_topo_fixer? I'm not sure > >> how/where to run this and I don't see a page on the freesurfer site. > >> > >> Thanks so much, > >> m > >> ________________________________________ > >> From: Bruce Fischl [fischl(a)nmr.mgh.harvard.edu] > >> Sent: Thursday, January 17, 2013 1:30 PM > >> To: Borzello, Mia > >> Cc: freesurfer(a)nmr.mgh.harvard.edu > >> Subject: Re: [Freesurfer] pial not computing > >> > >> Hi Mia > >> > >> this is fixed in the newest version. You can grab a new mris_topo_fixer > >> and you rerun and it should be all set. You probably should take a look > >> at the ?h.orig.nofix to make sure it's reasonable (meaning no cerebellum > >> or skull attached, and the hemispherees successfully separated) > >> > >> cheers > >> Bruce > >> On Thu, 17 > >> Jan 2013, Borzello, Mia wrote: > >> > >> > Okay, so it didn't complete without error. I've attached the > >> recon-all.log. Also, I was using another post op patient's MRI scans. > >> > > >> > thanks so much, > >> > m > >> > ________________________________________ > >> > From: freesurfer-bounces(a)nmr.mgh.harvard.edu [ > >> freesurfer-bounces(a)nmr.mgh.harvard.edu] on behalf of Bruce Fischl [ > >> fischl(a)nmr.mgh.harvard.edu] > >> > Sent: Thursday, January 17, 2013 11:22 AM > >> > To: Borzello, Mia > >> > Cc: freesurfer(a)nmr.mgh.harvard.edu > >> > Subject: Re: [Freesurfer] pial not computing > >> > > >> > Hi Mia > >> > > >> > we need to see the recon-all.log. Did it end with an error? > >> > Bruce > >> > On Thu, 17 Jan > >> > 2013, Borzello, Mia wrote: > >> > > >> >> Hi Freesurfers, > >> >> > >> >> I just ran a recon, and it seems that only the lh.pial computed, but > >> not the rh.pial. What would be the cause of this? > >> >> Thanks, > >> >> 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: Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> > >> To: "Borzello, Mia" <MBORZELLO(a)partners.org> > >> Cc: "freesurfer(a)nmr.mgh.harvard.edu" <freesurfer(a)nmr.mgh.harvard.edu> > >> Date: Fri, 18 Jan 2013 11:28:00 -0500 > >> Subject: Re: [Freesurfer] pial not computing > >> it's run as part of recon-all. If you grab a new one and run > >> > >> recon-all -make all ... > >> > >> you should be all set > >> Bruce > >> > >> > >> On Fri, 18 Jan 2013, Borzello, Mia wrote: > >> > >> great. is there a freesurfer page on mris_topo_fixer? I'm not sure > >>> how/where to run this and I don't see a page on the freesurfer site. > >>> > >>> Thanks so much, > >>> m > >>> ______________________________**__________ > >>> From: Bruce Fischl [fischl(a)nmr.mgh.harvard.edu] > >>> Sent: Thursday, January 17, 2013 1:30 PM > >>> To: Borzello, Mia > >>> Cc: freesurfer(a)nmr.mgh.harvard.edu > >>> Subject: Re: [Freesurfer] pial not computing > >>> > >>> Hi Mia > >>> > >>> this is fixed in the newest version. You can grab a new mris_topo_fixer > >>> and you rerun and it should be all set. You probably should take a look > >>> at the ?h.orig.nofix to make sure it's reasonable (meaning no > >>> cerebellum > >>> or skull attached, and the hemispherees successfully separated) > >>> > >>> cheers > >>> Bruce > >>> On Thu, 17 > >>> Jan 2013, Borzello, Mia wrote: > >>> > >>> Okay, so it didn't complete without error. I've attached the > >>>> recon-all.log. Also, I was using another post op patient's MRI scans. > >>>> > >>>> thanks so much, > >>>> m > >>>> ______________________________**__________ > >>>> From: > >>>> freesurfer-bounces(a)nmr.mgh.**harvard.edu<freesurfer-bounces(a)nmr.mgh.harvard.edu>[ > >>>> freesurfer-bounces(a)nmr.mgh.**harvard.edu<freesurfer-bounces(a)nmr.mgh.harvard.edu>] > >>>> on behalf of Bruce Fischl [fischl(a)nmr.mgh.harvard.edu] > >>>> Sent: Thursday, January 17, 2013 11:22 AM > >>>> To: Borzello, Mia > >>>> Cc: freesurfer(a)nmr.mgh.harvard.edu > >>>> Subject: Re: [Freesurfer] pial not computing > >>>> > >>>> Hi Mia > >>>> > >>>> we need to see the recon-all.log. Did it end with an error? > >>>> Bruce > >>>> On Thu, 17 Jan > >>>> 2013, Borzello, Mia wrote: > >>>> > >>>> Hi Freesurfers, > >>>>> > >>>>> I just ran a recon, and it seems that only the lh.pial computed, but > >>>>> not the rh.pial. What would be the cause of this? > >>>>> Thanks, > >>>>> 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> > >>>> > >>> > >>> ______________________________**_________________ > >>> 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: Alex Hanganu <al.hanganu(a)yahoo.ca> > >> To: FS Mailing List <Freesurfer(a)nmr.mgh.harvard.edu> > >> Cc: > >> Date: Fri, 18 Jan 2013 11:39:31 -0500 > >> Subject: Re: [Freesurfer] FW: longitudinal analysis > >> Hi Paul, > >> > >> I also had such problems previously. My initial analyses were performed > >> on > >> mac. Though it might seem strange, some analyses resolved after I just > >> restarted the computer. Other ones I analysed on centos. Now I am doing > >> all > >> the recons on linux. > >> > >> best wishes, > >> > >> Alex. > >> > >> > >> > >> Le 1/18 9:22, paul horton a écrit : > >> > >> > >> > >> > Date: Fri, 18 Jan 2013 08:54:48 -0500 > >> > From: fischl(a)nmr.mgh.harvard.edu > >> > To: horton_paul(a)hotmail.com > >> > Subject: RE: [Freesurfer] longitudinal analysis > >> > > >> > Hi Paul > >> > > >> > can you cc the list so that others can answer? > >> > > >> > thanks > >> > Bruce > >> > On Fri, 18 Jan 2013, paul > >> > horton wrote: > >> > > >> > > Hi Brian, > >> > > > >> > > Thanks for your reply. > >> > > > >> > > I am running freesurfer 4.5.0. We are using the older version so > >> that > >> the > >> > > analyses performed are the same across subjects. > >> > > > >> > > Best wishes > >> > > > >> > > Paul > >> > > > >> > > Date: Fri, 18 Jan 2013 08:21:05 -0500 > >> > > From: fischl(a)nmr.mgh.harvard.edu > >> > > To: horton_paul(a)hotmail.com > >> > > CC: freesurfer(a)nmr.mgh.harvard.edu > >> > > Subject: Re: [Freesurfer] longitudinal analysis > >> > > > >> > > Hi Paul > >> > > > >> > > what is the actual binary being run? > >> > > > >> > > Bruce > >> > > On Fri, 18 Jan 2013, paul horton wrote: > >> > > > >> > > > Hi guys, > >> > > > > >> > > > I am currently running a longitudinal analysis on a set of scan. > >> It > >> is > >> > > > currently running and so far it has taken 5 days. It seems to be > >> taking a > >> > > > large amount of time on a process called labelling slice. I have > >> run > >> the > >> > > > same analysis on other subjects which took about 6 hours to > >> complete. So > >> > > I > >> > > > was wondering if you know of any reason why a set of scans would > >> take long > >> > > er > >> > > > to process than others. I have checked the inital scans and > >> nothing > >> seems > >> > > > obviously wrong with them. > >> > > > > >> > > > Best Wishes > >> > > > > >> > > > Paul > >> > > > > >> > > > > >> > > > >> > > _______________________________________________ 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. > >> > > > >> > > > >> > >> > >> _______________________________________________ > >> Freesurfer mailing > >> listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > >> > >> > >> The information in this e-mail is intended only for the person to whom > >> it is > >> addressed. If you believe this e-mail was sent to you in error and the > >> e-mail > >> contains patient information, please contact the Partners Compliance > >> HelpLine athttp://www.partners.org/complianceline . If the e-mail was > >> sent to you in error > >> but does not contain patient information, please contact the sender and > >> properly > >> dispose of the e-mail. > >> > >> > >> > >> _______________________________________________ > >> Freesurfer mailing list > >> Freesurfer(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. > >> > >> > > _______________________________________________ > > 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 > > > > > > > >

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Renaming subject directories
by Anders Hougaard 22 Jan '13

22 Jan '13

Dear Freesurfers, Is it ok to rename a subject directory, then run tkmedit and recon-all procedures and then rename the directory back again or will this cause problems? All the best, Anders

2 1

Citation for mri_glmfit-sim
by Shantanu Ghosh 22 Jan '13

22 Jan '13

Hi Freesurfers, Can you point out the correct paper that I can cite for the clusterwise correction for multiple comparisons computed by mri_glmfit-sim in v5.0 ? Thanks, Shantanu -- Shantanu Ghosh, Ph.D. Harvard Medical School & Massachusetts General Hospital Martinos Center for Biomedical Imaging

2 1

Trouble with Initial Processing - Very Dark Images
by Dan LaFreniere 21 Jan '13

21 Jan '13

Hey all, I'm very new to Freesurfer and am having some issues with the initial processing of our MPRAGE dicom files. So far, I'm able to get initial -autorecon1 steps to work but once this has finished and I open my brainmask.mgz files and the brain is incredibly dark in inferior regions. So much so that the skull strip appears to be removing large chunks of anterior temporal lobes. What remains of the temporal lobes is incredibly dark with grey matter almost indistinguishable from CSF. I would really like to look into freesurfer for cortical thickness analysis of subcortical regions since it seems like such an awesome program but I have really been struggling to get a decent looking brain. It's probably noteworthy that these brains have always been quite dark but I'm usually able to correct them to a point where they're pretty good in other programs. I have read about a few solutions to the problem but am having trouble implementing them. One suggestion was to use the -mprage flag; unfortunately, I'm not sure how to run this or when. Another suggestion was to use control points but I don't yet have the red and blue segmentation boundary lines - I'm using tkmedit FoM04_KA brainmask.mgz -aux T1.mgz to view the files. For reference, this is the line I use to run autorecon1: Recon-all -autorecon1 -subjid FoM04_KA Does anyone have any suggestions as to what I could do? It would be greatly appreciated. I've attached a screenshot to illustrate. Also, we used a 4.7T Varian scanner with 0.375/0.375/1mm voxels. I believe we used a gradient echo multislice sequence. In addition, all subjects' data have been obtained so there is no chance of changing sequences… Best wishes, Dan

2 1

Re: [Freesurfer] beta
by Colin Reveley 21 Jan '13

21 Jan '13

Does the beta permit volumes bigger than 256^3 voxels? just asking....and just asking about raw dimensions in unit-voxels at the start of pipeline cheers Colin On 18 January 2013 17:00, <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. v5.2.0 beta, round two (Nick Schmansky) > 2. Re: pial not computing (Borzello, Mia) > 3. Re: pial not computing (Bruce Fischl) > 4. Re: FW: longitudinal analysis (Alex Hanganu) > > > ---------- Forwarded message ---------- > From: Nick Schmansky <nicks(a)nmr.mgh.harvard.edu> > To: <freesurfer(a)nmr.mgh.harvard.edu> > Cc: > Date: Fri, 18 Jan 2013 11:20:43 -0500 > Subject: [Freesurfer] v5.2.0 beta, round two > For those willing and brave enough, another beta of v5.2.0 has been posted > here for you to download and test: > > ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/5.2.0-BETA/ > > The Mac builds should work (note: the lion build is 64b, snow-leopard is > 32b). > > The final release still awaits some critical improvements to the Tracula > stream, but the main recon-all stream with this beta is final. The final > release is expected the first week of February. > > Freesurfer team > > > > > > ---------- Forwarded message ---------- > From: "Borzello, Mia" <MBORZELLO(a)partners.org> > To: "freesurfer(a)nmr.mgh.harvard.edu" <freesurfer(a)nmr.mgh.harvard.edu> > Cc: > Date: Fri, 18 Jan 2013 16:25:40 +0000 > Subject: Re: [Freesurfer] pial not computing > great. is there a freesurfer page on mris_topo_fixer? I'm not sure > how/where to run this and I don't see a page on the freesurfer site. > > Thanks so much, > m > ________________________________________ > From: Bruce Fischl [fischl(a)nmr.mgh.harvard.edu] > Sent: Thursday, January 17, 2013 1:30 PM > To: Borzello, Mia > Cc: freesurfer(a)nmr.mgh.harvard.edu > Subject: Re: [Freesurfer] pial not computing > > Hi Mia > > this is fixed in the newest version. You can grab a new mris_topo_fixer > and you rerun and it should be all set. You probably should take a look > at the ?h.orig.nofix to make sure it's reasonable (meaning no cerebellum > or skull attached, and the hemispherees successfully separated) > > cheers > Bruce > On Thu, 17 > Jan 2013, Borzello, Mia wrote: > > > Okay, so it didn't complete without error. I've attached the > recon-all.log. Also, I was using another post op patient's MRI scans. > > > > thanks so much, > > m > > ________________________________________ > > From: freesurfer-bounces(a)nmr.mgh.harvard.edu [ > freesurfer-bounces(a)nmr.mgh.harvard.edu] on behalf of Bruce Fischl [ > fischl(a)nmr.mgh.harvard.edu] > > Sent: Thursday, January 17, 2013 11:22 AM > > To: Borzello, Mia > > Cc: freesurfer(a)nmr.mgh.harvard.edu > > Subject: Re: [Freesurfer] pial not computing > > > > Hi Mia > > > > we need to see the recon-all.log. Did it end with an error? > > Bruce > > On Thu, 17 Jan > > 2013, Borzello, Mia wrote: > > > >> Hi Freesurfers, > >> > >> I just ran a recon, and it seems that only the lh.pial computed, but > not the rh.pial. What would be the cause of this? > >> Thanks, > >> 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: Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> > To: "Borzello, Mia" <MBORZELLO(a)partners.org> > Cc: "freesurfer(a)nmr.mgh.harvard.edu" <freesurfer(a)nmr.mgh.harvard.edu> > Date: Fri, 18 Jan 2013 11:28:00 -0500 > Subject: Re: [Freesurfer] pial not computing > it's run as part of recon-all. If you grab a new one and run > > recon-all -make all ... > > you should be all set > Bruce > > > On Fri, 18 Jan 2013, Borzello, Mia wrote: > > great. is there a freesurfer page on mris_topo_fixer? I'm not sure >> how/where to run this and I don't see a page on the freesurfer site. >> >> Thanks so much, >> m >> ______________________________**__________ >> From: Bruce Fischl [fischl(a)nmr.mgh.harvard.edu] >> Sent: Thursday, January 17, 2013 1:30 PM >> To: Borzello, Mia >> Cc: freesurfer(a)nmr.mgh.harvard.edu >> Subject: Re: [Freesurfer] pial not computing >> >> Hi Mia >> >> this is fixed in the newest version. You can grab a new mris_topo_fixer >> and you rerun and it should be all set. You probably should take a look >> at the ?h.orig.nofix to make sure it's reasonable (meaning no cerebellum >> or skull attached, and the hemispherees successfully separated) >> >> cheers >> Bruce >> On Thu, 17 >> Jan 2013, Borzello, Mia wrote: >> >> Okay, so it didn't complete without error. I've attached the >>> recon-all.log. Also, I was using another post op patient's MRI scans. >>> >>> thanks so much, >>> m >>> ______________________________**__________ >>> From: freesurfer-bounces(a)nmr.mgh.**harvard.edu<freesurfer-bounces(a)nmr.mgh.harvard.edu>[ >>> freesurfer-bounces(a)nmr.mgh.**harvard.edu<freesurfer-bounces(a)nmr.mgh.harvard.edu>] >>> on behalf of Bruce Fischl [fischl(a)nmr.mgh.harvard.edu] >>> Sent: Thursday, January 17, 2013 11:22 AM >>> To: Borzello, Mia >>> Cc: freesurfer(a)nmr.mgh.harvard.edu >>> Subject: Re: [Freesurfer] pial not computing >>> >>> Hi Mia >>> >>> we need to see the recon-all.log. Did it end with an error? >>> Bruce >>> On Thu, 17 Jan >>> 2013, Borzello, Mia wrote: >>> >>> Hi Freesurfers, >>>> >>>> I just ran a recon, and it seems that only the lh.pial computed, but >>>> not the rh.pial. What would be the cause of this? >>>> Thanks, >>>> 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> >>> >> >> ______________________________**_________________ >> 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: Alex Hanganu <al.hanganu(a)yahoo.ca> > To: FS Mailing List <Freesurfer(a)nmr.mgh.harvard.edu> > Cc: > Date: Fri, 18 Jan 2013 11:39:31 -0500 > Subject: Re: [Freesurfer] FW: longitudinal analysis > Hi Paul, > > I also had such problems previously. My initial analyses were performed on > mac. Though it might seem strange, some analyses resolved after I just > restarted the computer. Other ones I analysed on centos. Now I am doing all > the recons on linux. > > best wishes, > > Alex. > > > > Le 1/18 9:22, paul horton a écrit : > > > > > Date: Fri, 18 Jan 2013 08:54:48 -0500 > > From: fischl(a)nmr.mgh.harvard.edu > > To: horton_paul(a)hotmail.com > > Subject: RE: [Freesurfer] longitudinal analysis > > > > Hi Paul > > > > can you cc the list so that others can answer? > > > > thanks > > Bruce > > On Fri, 18 Jan 2013, paul > > horton wrote: > > > > > Hi Brian, > > > > > > Thanks for your reply. > > > > > > I am running freesurfer 4.5.0. We are using the older version so that > the > > > analyses performed are the same across subjects. > > > > > > Best wishes > > > > > > Paul > > > > > > Date: Fri, 18 Jan 2013 08:21:05 -0500 > > > From: fischl(a)nmr.mgh.harvard.edu > > > To: horton_paul(a)hotmail.com > > > CC: freesurfer(a)nmr.mgh.harvard.edu > > > Subject: Re: [Freesurfer] longitudinal analysis > > > > > > Hi Paul > > > > > > what is the actual binary being run? > > > > > > Bruce > > > On Fri, 18 Jan 2013, paul horton wrote: > > > > > > > Hi guys, > > > > > > > > I am currently running a longitudinal analysis on a set of scan. It > is > > > > currently running and so far it has taken 5 days. It seems to be > taking a > > > > large amount of time on a process called labelling slice. I have run > the > > > > same analysis on other subjects which took about 6 hours to > complete. So > > > I > > > > was wondering if you know of any reason why a set of scans would > take long > > > er > > > > to process than others. I have checked the inital scans and nothing > seems > > > > obviously wrong with them. > > > > > > > > Best Wishes > > > > > > > > Paul > > > > > > > > > > > > > > _______________________________________________ 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. > > > > > > > > > _______________________________________________ > Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > The information in this e-mail is intended only for the person to whom it is > addressed. If you believe this e-mail was sent to you in error and the e-mail > contains patient information, please contact the Partners Compliance HelpLine athttp://www.partners.org/complianceline . If the e-mail was sent to you in error > but does not contain patient information, please contact the sender and properly > dispose of the e-mail. > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer(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. > >

4 6

Re: [Freesurfer] None segmentation
by Bruce Fischl 21 Jan '13

21 Jan '13

Hi Knut in the bert aseg I have for coronal slice 114 the none is correct - it's outside the brain I think. Bruce On Mon, 21 Jan 2013, Knut J Bjuland wrote: > Hi Bruce, > > I found a None segmentation between left hippocampus and left ventral DC in > Bert, which is similar to none segmentation in the hippocampus in mine > subjects. Should I been concerned about this type of segmentation error in > hippocampus and thalamus. I found this none segmentation in Bert at coronal > slice 114. Is there any guide line on how much none segmentation that is > allowed? I have used the Bert subject as atlas. > > > Knut J > > > > > > > > On 01/21/2013 03:22 PM, Bruce Fischl wrote: >> Hi Knut, >> >> I'm not positive what you mean, but if you want None voxels that are >> adjacent to hippocampus you could use mri_morphometry to dilate each >> hippocampus, then do the rest in 3-4 lines of matlab. Something like >> >> [vol_lh_dilated,M,mr] = load_mgh('lh.hippo.dilated.mgz') ; >> [vol_lh,M,mr] = load_mgh('aseg.mgz') ; >> >> ind = find(vol_lh_dilated == 17 & vol_lh == 0); >> >> although you may need to binarize, in which case you would replace the 17 >> above with 1. >> >> >> cheers >> Bruce >> >> On Mon, 21 Jan 2013, Knut J Bjuland wrote: >> >>> >>> >>> Hi, >>> >>> How can I calculate the number of None segmentation in right or left >>> hippocampus or another structure in Matlab or in Freesufer? >>> >>> Knut J >>> >>> >> >> >> The information in this e-mail is intended 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. > >

1 0

R: Re: ERROR: nu_correct
by Andrea Tateo 21 Jan '13

21 Jan '13

It could be Let me check Thank you very much Andrea ----Messaggio originale---- Da: fischl(a)nmr.mgh.harvard.edu Data: 20-gen-2013 15.13 A: "Andrea Tateo"<andrea.tateo(a)virgilio.it> Cc: "freesurfer(a)nmr.mgh.harvard.edu"<freesurfer(a)nmr.mgh.harvard.edu> Ogg: Re: [Freesurfer] ERROR: nu_correct Sounds like it ran out of memory. Is that possible?Bruce On Jan 20, 2013, at 4:14 AM, Andrea Tateo <andrea.tateo(a)virgilio.it> wrote: Hi freesurfer experts, my jobs are finished with this output Processing:.................................................................DoneKilledERROR: nu_correct Can you help me? endless thanks Andrea_______________________________________________ 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.

1 0

None segmentation
by Knut J Bjuland 21 Jan '13

21 Jan '13

Hi, How can I calculate the number of None segmentation in right or left hippocampus or another structure in Matlab or in Freesufer? Knut J

2 1

ERROR: nu_correct
by Andrea Tateo 20 Jan '13

20 Jan '13

Hi freesurfer experts, my jobs are finished with this output Processing:.................................................................DoneKilledERROR: nu_correct Can you help me? endless thanks Andrea

2 1

mean cluster surface area in qdec
by xiangbo_2010 20 Jan '13

20 Jan '13

Dear Freesurfer Experts, I would like the mean surface area measures of each cluster i found in qdec. I used qdec for a group comparison in surface area between a patient group and a healthy control group. I found 4 different significant clusters (FDR corrected). I would like to extract the mean surface area of each significant cluster in the patient group and in the healthy control group. Where can i found the file with this information? Many thanks, Bo Xiang

1 0

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Freesurfer January 2013