Freesurfer

freesurfer@nmr.mgh.harvard.edu

6 participants
30091 discussions

What is "CSF" label is aseg.stats
by Sophie Maingault 22 Jan '13

22 Jan '13

Dear all, I read the others posts about CSF but I didn't find the information that I need. I would like to calculate total CSF and in the aseg.stats file there are : Lateral-Ventricle, Inf-Lat-Vent, 3rd Ventricle, 4th Ventricle, 5th Ventricle but what is CSF ? Because I read that freesurfer can't measure sulcus CSF so I don't understand what is the meaning of "CSF" alone. Thank you for your answer ! Sophie

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Re: [Freesurfer] Trouble with Initial Processing - Very Dark Images
by Dan LaFreniere 22 Jan '13

22 Jan '13

Hey Falk, Much appreciated for your reply on this! Fortunately I was able to correct the issue by contacting our MRI tech - he suggested we use his nifti files instead and the results turned out a lot better. I emailed Bruce but forgot to include the freesurfer mailing list in the CC. Here is an attached screenshot of my final results with the nifti files for the record. Thanks again for the replies! I'm sure I'll be contacting the experts down the road. Cheers, Dan On Tue, Jan 22, 2013 at 4:06 AM, "Falk Lüsebrink" <falk.luese(a)gmx.net>wrote: > Hey Dan, > > Bruce might be right about the SNR, but you could try to adjust the > parameters of the inhomogeneity correction in the N3 algorithm. > > You could either use the following command line: > recon-all -autorecon1 -mprage -nuintensitycor-3t -i <data> -s <subject> > > Or if this still isn't good enough, try changing the parameters of the N3 > manually (e.g. distance and fwhm): > SUBJ=ab11 > > recon-all -motioncor -talairach -tal-check -i <data> -s $SUBJ > > mri_nu_correct.mni --i $SUBJECTS_DIR/$SUBJ/mri/orig.mgz --o > $SUBJECTS_DIR/$SUBJ/mri/nu.mgz --proto-iters 1000 --distance 15 --fwhm 0.5 > --n 1 --uchar $SUBJECTS_DIR/$SUBJ/mri/transforms/talairach.xfm > > recon-all -mprage -normalization -skulstrip -s $SUBJ > > If the skullstrip looks fine continue by using this: > recon-all -mprage -autorecon2 -autorecon3 -s $SUBJ > > Best, > Falk > > > -------- Original-Nachricht -------- > > Datum: Mon, 21 Jan 2013 22:39:29 -0500 > > Von: Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> > > An: Dan LaFreniere <lafreniere.dj(a)gmail.com> > > CC: "freesurfer(a)nmr.mgh.harvard.edu" <freesurfer(a)nmr.mgh.harvard.edu> > > Betreff: Re: [Freesurfer] Trouble with Initial Processing - Very Dark > Images > > > Wow, that's a huge bias field! Control points will help uniformity, but > > the snr may not be good enough for good results > > Bruce > > > > > > > > On Jan 18, 2013, at 11:09 AM, Dan LaFreniere <lafreniere.dj(a)gmail.com> > > wrote: > > > > > 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 > > > > _______________________________________________ > > > 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 > > > > > > The information in this e-mail is intended only for the person to whom it > > is > > 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] (no subject)
by Douglas N Greve 22 Jan '13

22 Jan '13

That should not happen. Concentrating on the Mac for a moment, please send the recon-all.log files for both runs. doug On 01/22/2013 10:36 AM, Varghese Chikku wrote: > Many thanks Doug, > I forgot to mention,I ran same patient,same time point,twice on > Mac and VM and the results varied each time.So why is it happening > though I am using the same machine and same set of images. > Cheers, > Chikku -- 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 FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

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qdec
by Catherine Bois 22 Jan '13

22 Jan '13

Hi, I am considering using qdec, however due to our large dataset (and different individuals having been in charge at different times) I just realized that the folders fsaverage etc are "missing". As these are necessary for the qdec use, is there anything else I can do? Eg a command line to just generate the fsaverage for all my subjects? Thank you for your help -- The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336.

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22 Jan '13

Dear FS-experts, I'm trying to follow the instructions on http://surfer.nmr.mgh.harvard.edu/fswiki/VolumeRoiCorticalThickness to get volumetric stats etc on a functional ROI derived from marsbar. The tutorial looks all clear to me, however, I have already problems at the first step. If I want to view the ROI I see a big orange square instead of the specific region. This almost fills the whole brain. command: tkmedit -f avg152T1.nii -overlay DLPFC.nii -fthresh 0.5 I created the DLPFC.nii in MarsBar (v. 0.42): "ROI definition" > "Export" > "Export ROI to image" (select: DLPFC_roi.mat) > from image (select: avg152T1.nii) > save as DLPFC.nii If I view the ROI on marsbar it looks good. Did I miss some prior step, or is something else wrong? Thanks in advance! Best wishes, Cédric ------------------------------------------------------------ P.C.M.P. Koolschijn (Cédric), PhD Brain and Cognition Weesperplein 4; Room 3.07 1018 XA Amsterdam The Netherlands E P.C.M.P.Koolschijn(a)uva.nl W http://home.medewerker.uva.nl/p.c.m.p.koolschijn/ ------------------------------------------------------------

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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

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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

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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

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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. > >

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