Freesurfer

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30088 discussions

asegstats2table error
by sabin khadka 04 Mar '14

04 Mar '14

Hi all, While using asegstats2table, I got following error for few subjects, WARN SUBID: nmeasure 66, expecting 55 It let me extract cortical thickness and surface area using aparcstats2table though. Any suggestions? -SABIN

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Re: [Freesurfer] Problematic dilated ventricles
by Douglas N Greve 04 Mar '14

04 Mar '14

The wmparc is off because the surfaces are incorrect. The aseg does not have to follow the surfaces, but wmparc does doug On 03/03/2014 03:10 PM, Victor Kovac wrote: > Hi Bruce and Doug, > > "cp aseg.auto.mgz aseg.mgz" was my last step before running > -autorecon2-cp -autorecon3, as suggested by Bruce before, so I am not > sure what the problem could be. Since there seem to be problems > re-creating the pial/wm surfaces this way, would it be possible for > you to send the entire subject folder to me via GoogleDrive or some > other method? > > I also have another question: I have loaded a subject with tkmedit, > but the segmentation looks drastically improved when the -segmentation > is aseg.auto_noCCseg.mgz instead of -wmparc.mgz (images attached), > though the pial surface does not reflect this. > > Could you tell me why this is? And is it possible to get the pial/wm > surfaces to follow along the lines of the aseg.auto_noCCseg.mgz > segmentation? I am sorry if this is a naive question. > > Also: the images are from the original aseg.auto_noCCseg.mgz of this > subject (MPS2002-3), not the updated one you sent me, Bruce. > > Thank you! > Victor > > > On Mon, Mar 3, 2014 at 10:53 AM, Douglas N Greve > <greve(a)nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> wrote: > > > I think that it should. To be safe, I would "cp aseg.auto.mgz > aseg.mgz" > otherwise aseg.mgz will not change (any differences will be > interpreted > as manual changes) > doug > > > On 03/02/2014 10:07 AM, Bruce Fischl wrote: > > Hi Victor > > > > hmmm, I'm not sure why that didn't work. Perhaps someone else can > > comment? Doug or Nick: if the aseg.mgz is recreated and you > start with > > -autorecon2-cp shouldn't it propagate the effects of the new aseg > > forward? > > > > cheers > > Bruce > > > > > > On Thu, 27 Feb 2014, Victor Kovac wrote: > > > >> Dear Bruce, > >> Have you had any time to try to analyze our subject MPS2002-3? I > >> believe you > >> mentioned you would give it a shot in your free time a couple of > >> months ago. > >> > >> Also, you were kind enough to analyze a subject for me, MPS1036-1, > >> and sent > >> me aseg.auto_noCCseg.new.mgz. I replaced the original file and > >> removed thee > >> "new" within the title, and then, to re-create the pial and wm > >> surfaces, I > >> ran: > >> > >> set mdir=$SUBJECTS_DIR/MPS1036-1/mri > >> mri_cc -aseg aseg.auto_noCCseg.mgz -o aseg.auto.mgz \ > >> -lta $mdir/transforms/cc_up.lta MPS1036-1 > >> cp aseg.auto.mgz aseg.mgz > >> > >> and then: recon-all -autorecon2-cp -autorecon3, which I believe > >> starts the > >> recon-all pipeline at normalization2, as you suggested. > However, this > >> has > >> yielded no effect that I can see when I visualize the subject with > >> > >> tkmedit $proc brainmask.mgz lh.white -aux T1.mgz -aux-surface > rh.white > >> -segmentation wmparc.mgz $FREESURFER_HOME/FreeSurferColorLUT.txt > >> > >> Any advice would be greatly appreciated! Attached is the > >> recon-all.log for > >> this subject. Let me know if I should cc the group. > >> > >> Thank you. > >> Victor > >> > >> > >> On Tue, Jan 7, 2014 at 11:19 AM, Bruce Fischl > >> <fischl(a)nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu>> > >> wrote: > >> Hi Victor > >> > >> for each subject I think you want to run: > >> > >> > >> set mdir=$SUBJECTS_DIR/$subject/mri > >> mri_cc -aseg aseg.auto_noCCseg.mgz -o aseg.auto.mgz \ > >> -lta $mdir/transforms/cc_up.lta $subject > >> cp aseg.auto.mgz aseg.mgz > >> > >> > >> then run recon-all from normalization2 forward (check the > >> recon-all -help for these steps) > >> > >> cheers > >> Bruce > >> > >> On Tue, 7 Jan 2014, Victor Kovac wrote: > >> > >> Hi Bruce, > >> > >> I ran recon-all -autorecon2-cp -autorecon3 -s > >> MPS1036-1 but, again, this did > >> not affect the pial or wm surfaces. I have attached > >> the recon-all.log in > >> case that would be helpful in diagnosing the issue. > >> > >> Any advise would be greatly appreciated. > >> > >> Thanks! > >> Victor > >> > >> > >> On Thu, Jan 2, 2014 at 12:12 PM, Bruce Fischl > >> <fischl(a)nmr.mgh.harvard.edu > <mailto:fischl@nmr.mgh.harvard.edu>> > >> wrote: > >> Hi Victor > >> > >> you can look in the recon-all -help and run > >> the stages that are > >> after mri_ca_label. Not sure why -make all > >> didn't work, perhaps > >> Zeke and/or Nick can comment? > >> Bruce > >> > >> > >> On Thu, 2 Jan 2014, Victor Kovac wrote: > >> > >> Dear Bruce, > >> > >> A few weeks ago you made code mods to > >> mri_em_register and got recon-all to > >> process a subject of mine, MPS1036-1. > >> You sent me > >> the new > >> aseg.auto_noCCseg.mgz and told me to run > >> recon-all > >> -make all -s MPS1036-1. > >> > >> I did this but I get the message > >> make: Nothing to be done for 'all' > >> and when I visualize the segmentation > >> with tkmedit, > >> there appears to be no > >> change to the pial or wm surfaces. > >> > >> Could you please advise? > >> > >> Thank you. > >> Victor > >> > >> > >> On Mon, Dec 9, 2013 at 2:11 PM, Bruce > >> Fischl > >> <fischl(a)nmr.mgh.harvard.edu > <mailto:fischl@nmr.mgh.harvard.edu>> > >> wrote: > >> if you rename > >> aseg.auto_noCCseg.new.mgz to be > >> aseg.auto_noCCseg.mgz > >> > >> then run: > >> > >> recon-all -make all -s MPS1036-1 > >> > >> you should be all set > >> > >> Bruce > >> > >> > >> On Mon, 9 Dec 2013, Victor Kovac > >> wrote: > >> > >> I was hoping to MPS1036-1. I > >> only got > >> aseg.auto_noCCseg.new.mgz. > >> Thank you > >> for looking into MPS2002-3 > >> -- it is > >> quite the brain. > >> And somehow, with all > >> those morphological > >> abnormalities, this > >> subject has > >> an IQ of 130. Very > >> strange. > >> Thanks, > >> Victor > >> > >> > >> On Mon, Dec 9, 2013 at 2:03 > >> PM, Bruce > >> Fischl > >> <fischl(a)nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu>> > >> wrote: > >> which one? I'm still > >> messing with > >> MPS2002-3 in > >> my spare time > >> On Mon, 9 Dec 2013, > >> Victor Kovac > >> wrote: > >> > >> Hi Bruce, > >> Is there a way > >> for you to > >> send the > >> subject(s) you > >> analyzed to me? > >> I know > >> it's too big for > >> email, but > >> could you > >> possibly > >> upload it to > >> GoogleDrive? > >> > >> Thanks! > >> Victor > >> > >> > >> On Wed, Dec 4, > >> 2013 at 3:40 > >> PM, Bruce > >> Fischl > >> > >> <fischl(a)nmr.mgh.harvard.edu > <mailto:fischl@nmr.mgh.harvard.edu>> > >> wrote: > >> p.s. the > >> other thing I > >> did was run > >> the graph > >> cut skull > >> stripping, > >> which > >> removed a bunch > >> of extraneous > >> stuff > >> On Wed, 4 > >> Dec 2013, > >> kovac081(a)umn.edu <mailto:kovac081@umn.edu> wrote: > >> > >> Hey! > >> > >> Victor > >> Kovac > >> (kovac081(a)umn.edu > <mailto:kovac081@umn.edu>) > >> has uploaded > >> some files > >> for you at > >> the > >> Martinos Center > >> FileDrop: > >> > >> -> MPS2002-3.zip > >> (292.12 > >> MiB) > >> > >> > >> > >> > <http://gate.nmr.mgh.harvard.edu/filedrop2/?u=8mo9zg0isep&f=55xjt9pflsi> > >> -> MPS2017-1.zip > >> (264.15 > >> MiB) > >> > >> > >> > >> > <http://gate.nmr.mgh.harvard.edu/filedrop2/?u=8mo9zg0isep&f=ak4v31bzu4p> > >> > >> Also, they left > >> this message > >> for you: > >> Hi Bruce, > >> > >> Here are the two > >> subjects > >> with > >> ventriculomegaly that > >> are causing > >> the worst > >> issues. The worst > >> segmentation > >> in > >> MPS2002-3 is in > >> the > >> superior frontal > >> (slices > >> 150-180) and > >> parietal > >> (slices 50-95) > >> cortical areas; > >> this may be > >> due to the > >> numerous > >> dilated > >> Virchow-Robin > >> spaces in his > >> brain, which > >> is another > >> > >> neuropathological feature of > >> this > >> disease. > >> > >> Thanks! > >> Victor > >> > >> Please be aware, > >> your upload > >> will expire > >> on December > >> 31st. If > >> you'd like to > >> download these > >> files, feel > >> free to use > >> the link > >> below: > >> > >> > >> > >> > >> http://gate.nmr.mgh.harvard.edu/filedrop2/?u=8mo9zg0isep > >> > >> Cheers, > >> The NMR Team > >> > >> > >> > >> > >> > >> 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 > <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. > >> > >> > >> > >> > > > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer(a)nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu> > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > greve(a)nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> > Phone Number: 617-724-2358 <tel:617-724-2358> > Fax: 617-726-7422 <tel:617-726-7422> > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 > www.nmr.mgh.harvard.edu/facility/filedrop/index.html > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > Outgoing: > ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > -- Douglas N. Greve, Ph.D. MGH-NMR Center greve(a)nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

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tkregister2 problem with MR
by Borzello, Mia 04 Mar '14

04 Mar '14

Hi Freesurfers, I'm wondering if there is a way to set the contrast when in tkregister. When I compare the MR with the CT, I get the following image (attached)- is this a problem with the MR I initially chose to run the reconstruction on? Thanks, m

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Help with Temporal horn
by Rashmi Singh 04 Mar '14

04 Mar '14

Hello, How can I generate volume for temporal horn, temporal white matter and temporal gray matter. Thanks Rashmi Sent from my iPhone

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Matlab help
by Saurabh Thakur 04 Mar '14

04 Mar '14

Hello Freesurfer, I am trying to runs MRIread.m file in matlab. But it is not reading the brain.mgz or any other format. Can u help in this regards. Thanks in advance, cheers Saurabh Thakur,

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Hippocampus segmented file in tkmedit.
by Saurabh Thakur 04 Mar '14

04 Mar '14

How to create only Hippocampus segmented file in tkmedit. aseg.mgz. for Hippocampus file. Please cheers Saurabh Thakur,

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shrink the white matter surface
by charujing123 04 Mar '14

04 Mar '14

Hi all, I got a thin pial thickness when I got a default recon-all -all, which can be got in the attachment. Now I want to get a appropriate result by shrinking the whiter susface. Would you please tell me what option I should add when I run "recon-all -s subject -all -??" Thanks. All the best. Rujing Zha 2014-03-04 charujing123

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How to create a figure for a scientific article
by charles laidi 03 Mar '14

03 Mar '14

Dear Freesurfers, I have just performed cerebellar segmentation with freesurfer. I checked the segmentation was correct using freeview : freeview -v t1_xxx/mri/aseg.mgz:colormap=lut:opacity=0.2 I would like to create a figure for my article. However, I'm not able to find a way to highlight only cerebellar cortex / white matter with freeview, instead of having every label of other subcortical structures in different colors. I would like to have only the cerebellum colored. Could this be done with freeview ? Thanks a lot, Charles

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Re: [Freesurfer] hippocampal subfields
by Gregory Kirk 03 Mar '14

03 Mar '14

Hi, just wondering if you have a guesstimate on the ETA of the new atlas ? thanks On 03/03/14, Juan Eugenio Iglesias wrote: > Dear Gabor, > the segmentation benefits to some extent from higher resolution data, > but produces decent estimates of the subfields at 1x1x1. We are working > on a new atlas that will incorporate much more detail, and will more > effectively take advantage of high-resolution images. > Kind regards, > Juan Eugenio Iglesias > > On Mon, 2014-03-03 at 13:49 +0100, Gabor Perlaki wrote: > > Dear all, > > > > > > 1. Which is the suggested resolution for hippocampal subfields > > segmentation with freesurfer? I've seen articles with 0.5*0.5*0.5mm^3 > > and with 1.0*1.0*1.0mm^3 as well. Does the hippocampal subfields > > segmentation really work with 1.0*1.0*1.0 resolution? > > 2. The article "Automated Segmentation of Hippocampal Subfields from > > Ultra-High Resolution In Vivo MRI." suggested on Freesurfer's page > > uses FOV=448. We are unable to set up the matrix to achieve 0.38mm > > resolution using this FOV. Is there any other suggested article to set > > up our measurements? > > > > Thanks, > > > > -- > > Gabor Perlaki > > > > _______________________________________________ > > 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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hippocampal subfields
by Gabor Perlaki 03 Mar '14

03 Mar '14

Dear all, 1. Which is the suggested resolution for hippocampal subfields segmentation with freesurfer? I've seen articles with 0.5*0.5*0.5mm^3 and with 1.0*1.0*1.0mm^3 as well. Does the hippocampal subfields segmentation really work with 1.0*1.0*1.0 resolution? 2. The article "Automated Segmentation of Hippocampal Subfields from Ultra-High Resolution In Vivo MRI<https://surfer.nmr.mgh.harvard.edu/pub/articles/VanLeemputHippocampus2009.p…>." suggested on Freesurfer's page uses FOV=448. We are unable to set up the matrix to achieve 0.38mm resolution using this FOV. Is there any other suggested article to set up our measurements? Thanks, -- Gabor Perlaki

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