Freesurfer March 2013

freesurfer@nmr.mgh.harvard.edu

155 participants
331 discussions

How to get transform matrix from Vertex Index to Vertex RAS
by ZhiLiangLong 25 Mar '13

25 Mar '13

Hi all: I am studying the coordinate system transforms within subject across imaging modalities on web page: http://surfer.nmr.mgh.harvard.edu/fswiki/CoordinateSystems. I met a problem. First, i run tksurfer : tksurfer subjectname lh inflated -reg register.dat -ov mov.nii , then i chose a point on the surface and save it. There would be Vertex Index value and Vertex RAS value on the panel of TKSurfer Tool. For example: Vertex Index 96063 Vertex RAS (-56.05 0.42 62.6) Now, i want to know how the values between Vertex Index and Vertex RAS transformed each other. I need help. Best wishes!

2 1

ERROR: Help with asegstats2table segmentation error
by Rodrigo Perea 25 Mar '13

25 Mar '13

Could anybody help me with the --segno option during a asegstats2table process. I've run my subjects under recon-all and I am pretty sure the data exists under the stats folder but when I ran: asegstats2table --subjects <MysubjectFolderName> --tablefile aseg.txt --skip --segno 41 (I've tried it with different segnos a s wellŠ) I got the following error: SUBJECTS_DIR : <THE_CORRECT_FOLDER_LOCATION> Parsing the .stats files Building the table.. ERROR: cannot find the corresponding segmentation for the id:41 you provided in any of the .stats files parsed ???? Rodrigo Dennis Perea Graduate Research Assistant rperea(a)kumc.edu Bioengineering Program Alzheimer's Research Center The University of Kansas On 3/25/13 11:34 AM, "freesurfer-request(a)nmr.mgh.harvard.edu" <freesurfer-request(a)nmr.mgh.harvard.edu> wrote: > freesurfer(a)nmr.mgh.harvard.edu

2 1

Re: [Freesurfer] Xhemi stat questions
by Gabriel Gonzalez Escamilla 25 Mar '13

25 Mar '13

2 4

Problem with tracula: incomplete or lacking tracts
by stdp82＠virgilio.it 25 Mar '13

25 Mar '13

Hi Anastasia, I ran again trac-all, after checking all bvecs. Some tract are incomplete. Is possible that it depends from an error in my configuration file? I'm using to create bvecs file DTI TABLE CREATOR. Do you advice mi another one? Thanks, Stefano On Fri, 22 Mar 2013, stdp82(a)virgilio.it wrote: > Thank you Anastasia. > I'm checking bvecs/bvals. I obtain it by DTI table creator > (http://godzilla.kennedykrieger.org/~jfarrell/OTHERphilips/GUI.html) > > bvecs/bvals should be done. > > Gradients can be the unique responsable? > > > Stefano > > > > > ----Messaggio originale---- > Da: ayendiki(a)nmr.mgh.harvard.edu > Data: 22-mar-2013 17.07 > A: <stdp82(a)virgilio.it> > Cc: <freesurfer(a)nmr.mgh.harvard.edu> > Ogg: Re: [Freesurfer] R: Re: R: Re: R: Re: R: R: Re: Problem with tracula: incomplete or lacking tracts > > > Your gradient table is wrong. See where I've marked the corpus callosum in > your screenshot. The eigenvectors are not pointing along the corpus > callosum, but perpendicular to it. So they're off by 90 degrees, which > means the same is true about the vectors in your gradient table. > > On Fri, 22 Mar 2013, stdp82(a)virgilio.it wrote: > > > Hi Anastasia - I attacked the screenshots. > > Thanks, > > > > > > Stefano > > > > > > > > ----Messaggio originale---- > > Da: ayendiki(a)nmr.mgh.harvard.edu > > Data: 22-mar-2013 1.39 > > A: <stdp82(a)virgilio.it> > > Cc: <freesurfer(a)nmr.mgh.harvard.edu> > > Ogg: Re: [Freesurfer] R: Re: R: Re: R: R: Re: Problem with tracula: incomplete or lacking tracts > > > > > > Hi Stefano - There's nothing in these screenshots that tells you that the > > eigenvectors are correct. These are vectors, so the way to check them is > > to display them as lines. You display dtifit_V1 as lines, overlaid on > > dtifit_FA. Then you see if the lines point in the right direction. > > > > a.y > > > > On Fri, 22 Mar 2013, stdp82(a)virgilio.it wrote: > > > > > Here they are attacked. > > > Thanks, > > > > > > > > > Stefano > > > > > > > > > > > > > > > ----Messaggio originale---- > > > Da: ayendiki(a)nmr.mgh.harvard.edu > > > Data: 21-mar-2013 21.50 > > > A: <stdp82(a)virgilio.it> > > > Cc: <freesurfer(a)nmr.mgh.harvard.edu> > > > Ogg: Re: R: Re: [Freesurfer] R: R: Re: Problem with tracula: incomplete or > > > lacking tracts > > > > > > > > > Can you send a screenshot that shows dtifit_V1 and dtifit_FA? > > > > > > On Thu, 21 Mar 2013, stdp82(a)virgilio.it wrote: > > > > > > > I have checked the gradient directions. How can I resolve the brain mask > > > > problem. > > > > Can I send you my files of this subject? > > > > Stefano > > > > > > > > > > > > > > > > ----Messaggio originale---- > > > > Da: ayendiki(a)nmr.mgh.harvard.edu > > > > Data: 20-mar-2013 22.46 > > > > A: <stdp82(a)virgilio.it> > > > > Cc: <freesurfer(a)nmr.mgh.harvard.edu> > > > > Ogg: Re: [Freesurfer] R: R: Re: Problem with tracula: incomplete or > > > lacking > > > > tracts > > > > > > > > > > > > There are chunks of the brain missing from the brain mask. This may cause > > > > some tracts to be incomplete or missing. > > > > > > > > But you should still check that the gradient directions are correct, so > > > > you know if you have multiple problems or just one. The FA map can't tell > > > > you if the gradient table was correct, you have to check the eigenvectors > > > > in dtifit_V1 for that. > > > > > > > > > > > > On Wed, 20 Mar 2013, stdp82(a)virgilio.it wrote: > > > > > > > > > File attacked > > > > > > > > > > ----Messaggio originale---- > > > > > Da: stdp82(a)virgilio.it > > > > > Data: 20-mar-2013 22.34 > > > > > A: <ayendiki(a)nmr.mgh.harvard.edu> > > > > > Cc: <freesurfer(a)nmr.mgh.harvard.edu> > > > > > Ogg: [Freesurfer] R: Re: Problem with tracula: incomplete or lacking > > > > tracts > > > > > > > > > > Thank you Anastasia. I'm checking gradient table but I would like > > > > underline that I'm noting some holes in > > > > > dti_FA.nii.gz and not in dwi.nii.gz (I have attacked the relative > > > > images). > > > > > > > > > > Stefano > > > > > > > > > > ----Messaggio originale---- > > > > > Da: ayendiki(a)nmr.mgh.harvard.edu > > > > > Data: 20-mar-2013 16.40 > > > > > A: <stdp82(a)virgilio.it> > > > > > Cc: <freesurfer(a)nmr.mgh.harvard.edu> > > > > > Ogg: Re: [Freesurfer] Problem with tracula: incomplete or lacking tracts > > > > > > > > > > > > > > > Hi Stefano - Have you checked that your gradient table is correct by > > > > > looking at the output of the tensor fit? > > > > > > > > > > a.y > > > > > > > > > > On Wed, 20 Mar 2013, stdp82(a)virgilio.it wrote: > > > > > > > > > > > Hi list and Anastasia, > > > > > > if you remember the last week I had same problems with tracula output: > > > > the final tract are lacking or > > > > > > incomplete for same subjects. Some of these are less wrong (only > > > forceps > > > > major), other have more evident > > > > > > error (you can see this in picture that I have attacked). > > > > > > > > > > > > To resolve this issue I have: > > > > > > > > > > > > 1-checked the correct overlap of dwi and dwi_mask > > > > > > 2-rerun data with new version 5.2 > > > > > > 3-rerun new registration using bbregister (fsl/spm option): for > > > example, > > > > in the subject of the picture > > > > > > attacked, the .mincost file now contains as first value 0.87 (previous > > > > it was 1.1) > > > > > > > > > > > > Please, give me an advise > > > > > > > > > > > > Thanks > > > > > > > > > > > > > > > > > > Stefano > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > ----Messaggio originale---- > > > > > > Da: stdp82(a)virgilio.it > > > > > > Data: 12-mar-2013 17.47 > > > > > > A: <ayendiki(a)nmr.mgh.harvard.edu> > > > > > > Cc: <freesurfer(a)nmr.mgh.harvard.edu> > > > > > > Ogg: [Freesurfer] R: Re: R: Re: Question on tracula and dwi-T1 overlap > > > > > > > > > > > > I got it from mri directory but I'm understanding that this directory > > > > isn't ok.I'm attacking the image > > > > > > from dlabel/diff/aparc+aseg.bbr.nii > > > > > > > > > > > > > > > > > > Stefano > > > > > > > > > > > > > > > > > > > > > > > > ----Messaggio originale---- > > > > > > Da: ayendiki(a)nmr.mgh.harvard.edu > > > > > > Data: 12-mar-2013 17.19 > > > > > > A: <stdp82(a)virgilio.it> > > > > > > Cc: <freesurfer(a)nmr.mgh.harvard.edu> > > > > > > Ogg: Re: [Freesurfer] R: Re: Question on tracula and dwi-T1 overlap > > > > > > > > > > > > > > > > > > Can you please answer my question? I can't really tell if the issue is > > > > due > > > > > > poor dwi-aseg overlap unless you tell me where you got that aseg > > > volume > > > > > > from. > > > > > > > > > > > > On Tue, 12 Mar 2013, stdp82(a)virgilio.it wrote: > > > > > > > > > > > > > Thank you Anastasia. What do you think about the issue in the file > > > > attacked > > > > > > > (I'm noting that same subjects are lacking of same > > > > > > > tracts or same tracts are incomplete) > > > > > > > > > > > > > > > > > > > > > Stefano > > > > > > > > > > > > > > > > > > > > > ----Messaggio originale---- > > > > > > > Da: ayendiki(a)nmr.mgh.harvard.edu > > > > > > > Data: 12-mar-2013 17.02 > > > > > > > A: <stdp82(a)virgilio.it> > > > > > > > Cc: <freesurfer(a)nmr.mgh.harvard.edu> > > > > > > > Ogg: Re: [Freesurfer] Question on tracula and dwi-T1 overlap > > > > > > > > > > > > > > > > > > > > > Hi Stefano - Where did you get the aseg.nii.gz from? Anything that's > > > > in > > > > > > > the dlabel/diff/ directory has been mapped to the same space as the > > > > DWI, > > > > > > > so those are the volumes that can be compared directly to > > > dwi.nii.gz. > > > > > > > > > > > > > > a.y > > > > > > > > > > > > > > On Tue, 12 Mar 2013, stdp82(a)virgilio.it wrote: > > > > > > > > > > > > > > > Hi list, > > > > > > > > > > > > > > > > I have two questions, please. > > > > > > > > > > > > > > > > I'm using version 5.1 to complete my analysis. > > > > > > > > > > > > > > > > 1- I have attacked two images from aseg.nii.gz and dwi.nii.gz of > > > the > > > > same > > > > > > > > subject (figure 1 and 3). You can note the dwi do not overlap to > > > the > > > > aseg. > > > > > > > > How can I resolve this issue? > > > > > > > > > > > > > > > > 2-After TRACULA analysis, I'm noting that same subjects are > > > lacking > > > > of > > > > > > > same > > > > > > > > tracts or same tracts are incomplete (figure 3). > > > > > > > > > > > > > > > > Could it depends from the issue in question 1? I'm thinking to > > > rerun > > > > all > > > > > > > > using version 5.2 but before starting new analyses, I'd like to > > > ask > > > > you > > > > > > > > which is the possible error. > > > > > > > > > > > > > > > > > > > > > > > > Stefano > > > > > > > > > > > > > > > >_______________________________________________ > > > > > > > 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 > > > > > > > > > > > > > > > > > > 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 > > > > > > > > > > > > > > > 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 > > > > > > > > > > > > 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 > > > > > > 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 > > > 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 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.

2 1

[Fwd: Segmentation Brush Info]
by Stefanie Scheuchenstuhl 25 Mar '13

25 Mar '13

------------------------ Ursprüngliche Nachricht ------------------------ Betreff: Segmentation Brush Info Von: "Stefanie Scheuchenstuhl" <scheuchenst1(a)zedat.fu-berlin.de> Datum: Mo, März 25, 2013 16:53 An: freesurfer(a)nmr.mgh.harvard.ed -------------------------------------------------------------------------- Dear Freesurfer experts, i have question regarding the segmentation tools. I am currently checking the Hippocampus-Segmentation by using tkmedit and found out that irrespective of what brain area i choose in the Segmentation Brush Info, the corrected area is always labeled Right-Cerebral-WM-unknown. Which was also the first label used when i started. So i ask my self (and you) is this label important for further analysis or not? And if so, how can this error be corrected? Thanks so much! Best, Stefanie

1 0

Talairach manual correction
by _andreia_＠sapo.pt 25 Mar '13

25 Mar '13

Hello! After completing the talairach correction in tkregister2 (saving the changes with the SAVEREG button), I am running recon-all -all -s subj. But now I'm wondering if by doing it this way the changes will be incorporated or the process will start from the beggining leaving everything as before the manual corrections... Is there any flag needed? Thank you, Andreia

2 1

Re: [Freesurfer] cortical recontruction error
by Claudia Dacquino 25 Mar '13

25 Mar '13

I'm sorry, I did mean the moderator of Freesurfer mailing list. 2013/3/25 Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> > you should be able to use our ftp site or file drop. Which administrator > do you mean? > > On Mon, 25 Mar 2013, Claudia Dacquino wrote: > > I was trying, but the administrator did reject that, because the file is >> too big. >> >> 2013/3/25 Claudia Dacquino <claudia.dacquino(a)gmail.com> >> Hi Bruce, >> I'll try to upload dataset. >> Thanks, >> Claudia >> >> 2013/3/23 Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> >> Hi Claudia >> >> hmmm, someone else mentioned that mri_cc hangs for them but >> we've never seen it. If you upload your dataset >> I'll see if we can replicate the problem >> Bruce >> On Fri, 22 Mar 2013, Claudia Dacquino wrote: >> >> Dear Freesurfers, >> I'm new and I'm starting using Freesurfer. >> I'm having a problem with one subject, during the >> cortical reconstruction >> (recon-all) the process stops at this stage: >> >> mri_cc -aseg aseg.auto_noCCseg.mgz -o aseg.auto.mgz >> <subjid> >> >> at this point: >> >> final transformation (x=128.0, yr=0.978, zr=0.153): >> 1.000 -0.003 0.017 -1.456; >> 0.003 1.000 0.000 8.654; >> -0.017 0.000 1.000 25.201; >> 0.000 0.000 0.000 1.000; >> >> without giving me any error message, it just stops. >> >> Do you have some ideas for why it happens? >> >> thanks to everyone, >> Claudia >> >> >> >> >> >> 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. >> >> >> >> >>

2 3

Re: [Freesurfer] cortical recontruction error
by Claudia Dacquino 25 Mar '13

25 Mar '13

I was trying, but the administrator did reject that, because the file is too big. 2013/3/25 Claudia Dacquino <claudia.dacquino(a)gmail.com> > I was trying, but the administrator did reject that, because the file is > too big. > > > 2013/3/25 Claudia Dacquino <claudia.dacquino(a)gmail.com> > >> Hi Bruce, >> I'll try to upload dataset. >> Thanks, >> Claudia >> >> >> 2013/3/23 Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> >> >>> Hi Claudia >>> >>> hmmm, someone else mentioned that mri_cc hangs for them but we've never >>> seen it. If you upload your dataset I'll see if we can replicate the problem >>> Bruce >>> >>> On Fri, 22 Mar 2013, Claudia Dacquino wrote: >>> >>> Dear Freesurfers, >>>> I'm new and I'm starting using Freesurfer. >>>> I'm having a problem with one subject, during the cortical >>>> reconstruction >>>> (recon-all) the process stops at this stage: >>>> >>>> mri_cc -aseg aseg.auto_noCCseg.mgz -o aseg.auto.mgz <subjid> >>>> >>>> at this point: >>>> >>>> final transformation (x=128.0, yr=0.978, zr=0.153): >>>> 1.000 -0.003 0.017 -1.456; >>>> 0.003 1.000 0.000 8.654; >>>> -0.017 0.000 1.000 25.201; >>>> 0.000 0.000 0.000 1.000; >>>> >>>> without giving me any error message, it just stops. >>>> >>>> Do you have some ideas for why it happens? >>>> >>>> thanks to everyone, >>>> Claudia >>>> >>>> >>>> >>>> >>> >>> 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. >>> >> >> >

1 0

Xhemi stat questions
by Gabriel Gonzalez Escamilla 25 Mar '13

25 Mar '13

2 1

Which T1 data used for segmentations in fsaverage subject?
by Ed Gronenschild 25 Mar '13

25 Mar '13

Hi freesurfites, The mri folder of the fsaverage subject contains the segmenation files, such as aparc+aseg.mgz, etc. and in the surf folder there the corresponding surface files (?h.pial. ?h.white, etc). Question: which T1 data was used for these segmentations? Cheers, Ed

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Freesurfer March 2013