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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.

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[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

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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

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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. >> >> >> >> >>

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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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Over estimation of pial surface
by Charles Malpas 25 Mar '13

25 Mar '13

Dear Freesurfer experts, I am having a strange problem with a single brain. Freesurfer is over estimating the pial surface by a great deal. Two things are weird: (a) it occurs to the same brain scanned 6 months apart, and (b) it doesn't occur is 5.1 (I am using 5.2 now). I have attached some screen shots. Any help would be greatly appreciated! Kind regards, - Charles -- *Charles Malpas * Master of Psychology (Clinical Neuropsychology) / PhD Candidate Melbourne School of Psychological Sciences & Department of Medicine (RMH) The University of Melbourne 3010 *Melbourne Brain Centre @ RMH* Neuropsychiatry Research Group* * Level 4, Main Building, Royal Melbourne Hospital Phone: 0451 116 434 Email: c.malpas(a)student.unimelb.edu.au Skype: charles.malpas

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R: Re: R: Re: hippo subfield
by stdp82＠virgilio.it 24 Mar '13

24 Mar '13

Hi Zeke, process finished without error in 2h. Thanks, Stefano ----Messaggio originale---- Da: zkaufman(a)nmr.mgh.harvard.edu Data: 23-mar-2013 20.13 A: "freesurfer(a)nmr.mgh.harvard.edu"<freesurfer(a)nmr.mgh.harvard.edu> Ogg: Re: [Freesurfer] R: Re: hippo subfield It's not enough to simply put the zip file in the /Applications/freesurfer/bin directory,,, you must extract its contents to that directory. Just extract the zip file (anywhere on your machine will do). Then copy and paste the extracted files to /Application/freesurfer/bin -Zeke On Mar 22, 2013, at 7:00 PM, <stdp82(a)virgilio.it> wrote: > Hi Zeke, > > as you explain I have download the kvl.zip and put it in /Application/freesurfer/bin. > > After rerunning I have: > > [iMac-di-Stefano:freesurfer/subjects/subject_prova] Stefano% recon-all -s Diff01 -hippo-subfields > Subject Stamp: freesurfer-Darwin-lion-stable-pub-v5.2.0 > Current Stamp: freesurfer-Darwin-lion-stable-pub-v5.2.0 > INFO: SUBJECTS_DIR is /Applications/freesurfer/subjects/subject_prova > Actual FREESURFER_HOME /Applications/freesurfer > -rw-rw-r-- 1 Stefano wheel 697785 Mar 22 23:56 /Applications/freesurfer/subjects/subject_prova/Diff01/scripts/recon-all.log > Darwin iMac-di-Stefano.local 12.3.0 Darwin Kernel Version 12.3.0: Sun Jan 6 22:37:10 PST 2013; root:xnu-2050.22.13~1/RELEASE_X86_64 x86_64 > #-------------------------------------------- > #@# Hippocampal Subfields processing Fri Mar 22 23:56:49 CET 2013 > \n mkdir -p /Applications/freesurfer/subjects/subject_prova/Diff01/tmp/subfieldResults > \n kvlSegmentHippocampalSubfields.sh Diff01 left /Applications/freesurfer/subjects/subject_prova /Applications/freesurfer/subjects/subject_prova/Diff01/tmp/subfieldResults \n > Doing left side > meshFileName: /Applications/freesurfer/data/GEMS/CurrentMeshCollection30.gz > compressionLookupTableFileName: /Applications/freesurfer/data/GEMS/compressionLookupTable_left.txt > boundingBoxFileName: /Applications/freesurfer/data/GEMS/imageDump.mgz > subjectName: Diff01 > side: left > inputDirectory: /Applications/freesurfer/subjects/subject_prova > outputDirectory: /Applications/freesurfer/subjects/subject_prova/Diff01/tmp/subfieldResults > directory /Applications/freesurfer/subjects/subject_prova/Diff01/tmp/subfieldResults/Diff01 already exists > directory /Applications/freesurfer/subjects/subject_prova/Diff01/tmp/subfieldResults/Diff01/left already exists > cd /Applications/freesurfer/subjects/subject_prova/Diff01/tmp/subfieldResults/Diff01/left > cp -f /Applications/freesurfer/subjects/subject_prova/Diff01/mri/nu.mgz . > cp -f /Applications/freesurfer/subjects/subject_prova/Diff01/mri/aseg.mgz . > cp -f /Applications/freesurfer/subjects/subject_prova/Diff01/mri/transforms/talairach.xfm . > cp /Applications/freesurfer/data/GEMS/imageDump.mgz . > kvlApplyTransform imageDump.mgz -0.9991 -0.0328 0.0258 144.0010 -0.0330 0.9994 -0.0086 2.6560 0.0255 0.0094 0.9996 -3.1939 > dyld: Library not loaded: libITKCommon.3.16.dylib > Referenced from: /Applications/freesurfer/bin/kvlApplyTransform > Reason: image not found > /Applications/freesurfer/bin/kvlSegmentHippocampalSubfields.sh: line 18: 5481 Trace/BPT trap: 5 kvlApplyTransform imageDump.mgz -0.9991 -0.0328 0.0258 144.0010 -0.0330 0.9994 -0.0086 2.6560 0.0255 0.0094 0.9996 -3.1939 > failed to do kvlApplyTransform imageDump.mgz -0.9991 -0.0328 0.0258 144.0010 -0.0330 0.9994 -0.0086 2.6560 0.0255 0.0094 0.9996 -3.1939 > Darwin iMac-di-Stefano.local 12.3.0 Darwin Kernel Version 12.3.0: Sun Jan 6 22:37:10 PST 2013; root:xnu-2050.22.13~1/RELEASE_X86_64 x86_64 > > recon-all -s Diff01 exited with ERRORS at Fri Mar 22 23:56:49 CET 2013 > > For more details, see the log file /Applications/freesurfer/subjects/subject_prova/Diff01/scripts/recon-all.log > To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > > > > ----Messaggio originale---- > Da: zkaufman(a)nmr.mgh.harvard.edu > Data: 22-mar-2013 20.53 > A: <stdp82(a)virgilio.it>, <freesurfer(a)nmr.mgh.harvard.edu> > Ogg: Re: [Freesurfer] hippo subfield > > Stefano, > > In order to fix this issue please follow these instruction exactly: > > 1) Download the file "kvl.zip" from this link: > ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/fsdev/zkaufman/ > > 2) Overwrite the existing kvl files in /Application/freesurfer/bin with > the files in kvl.zip > > I was able to replicate your issue and solve it using the steps above. > If these steps do not solve the issue for you, please respond with a the > exact error you receive. > > Hope this helps. > > -Zeke > > > > > > On 03/22/2013 12:00 PM, stdp82(a)virgilio.it wrote: > > I'm running: > > > > recon-all -s Diff02 -hippo-subfields > > > > with the following error. > > > > Thanks. > > > > > > Stefano > > > > Subject Stamp: freesurfer-Darwin-lion-stable-pub-v5.2.0 > > Current Stamp: freesurfer-Darwin-lion-stable-pub-v5.2.0 > > INFO: SUBJECTS_DIR is /Applications/freesurfer/subjects/subject_prova/Diff02 > > Actual FREESURFER_HOME /Applications/freesurfer > > -rw-rw-r-- 1 Stefano wheel 499999 Mar 22 16:53 > > /Applications/freesurfer/subjects/subject_prova/Diff02/Diff02/scripts/recon-all.log > > Darwin iMac-di-Stefano.local 12.3.0 Darwin Kernel Version 12.3.0: Sun > > Jan 6 22:37:10 PST 2013; root:xnu-2050.22.13~1/RELEASE_X86_64 x86_64 > > #-------------------------------------------- > > #@# Hippocampal Subfields processing Fri Mar 22 16:56:31 CET 2013 > > \n mkdir -p > > /Applications/freesurfer/subjects/subject_prova/Diff02/Diff02/tmp/subfieldResults > > \n kvlSegmentHippocampalSubfields.sh Diff02 left > > /Applications/freesurfer/subjects/subject_prova/Diff02 > > /Applications/freesurfer/subjects/subject_prova/Diff02/Diff02/tmp/subfieldResults > > \n > > Doing left side > > meshFileName: /Applications/freesurfer/data/GEMS/CurrentMeshCollection30.gz > > compressionLookupTableFileName: > > /Applications/freesurfer/data/GEMS/compressionLookupTable_left.txt > > boundingBoxFileName: /Applications/freesurfer/data/GEMS/imageDump.mgz > > subjectName: Diff02 > > side: left > > inputDirectory: /Applications/freesurfer/subjects/subject_prova/Diff02 > > outputDirectory: > > /Applications/freesurfer/subjects/subject_prova/Diff02/Diff02/tmp/subfieldResults > > directory > > /Applications/freesurfer/subjects/subject_prova/Diff02/Diff02/tmp/subfieldResults/Diff02 > > already exists > > directory > > /Applications/freesurfer/subjects/subject_prova/Diff02/Diff02/tmp/subfieldResults/Diff02/left > > already exists > > cd > > /Applications/freesurfer/subjects/subject_prova/Diff02/Diff02/tmp/subfieldResults/Diff02/left > > cp -f > > /Applications/freesurfer/subjects/subject_prova/Diff02/Diff02/mri/nu.mgz . > > cp -f > > /Applications/freesurfer/subjects/subject_prova/Diff02/Diff02/mri/aseg.mgz . > > cp -f > > /Applications/freesurfer/subjects/subject_prova/Diff02/Diff02/mri/transforms/talairach.xfm > > . > > cp /Applications/freesurfer/data/GEMS/imageDump.mgz . > > kvlApplyTransform imageDump.mgz -0.9991 -0.0328 0.0258 144.0010 -0.0330 > > 0.9994 -0.0086 2.6560 0.0255 0.0094 0.9996 -3.1939 > > dyld: Library not loaded: libITKCommon.3.16.dylib > > Referenced from: /Applications/freesurfer/bin/kvlApplyTransform > > Reason: image not found > > /Applications/freesurfer/bin/kvlSegmentHippocampalSubfields.sh: line 18: > > 77530 Trace/BPT trap: 5 kvlApplyTransform imageDump.mgz -0.9991 > > -0.0328 0.0258 144.0010 -0.0330 0.9994 -0.0086 2.6560 0.0255 0.0094 > > 0.9996 -3.1939 > > *failed to do kvlApplyTransform imageDump.mgz > > -0.9991 -0.0328 0.0258 144.0010 > > -0.0330 0.9994 -0.0086 2.6560 > > 0.0255 0.0094 0.9996 -3.1939* > > *Darwin iMac-di-Stefano.local 12.3.0 Darwin Kernel Version 12.3.0: Sun > > Jan 6 22:37:10 PST 2013; root:xnu-2050.22.13~1/RELEASE_X86_64 x86_64* > > * > > * > > *recon-all -s Diff02 exited with ERRORS at Fri Mar 22 16:56:31 CET 2013* > > > > For more details, see the log file > > /Applications/freesurfer/subjects/subject_prova/Diff02/Diff02/scripts/recon-all.log > > To report a problem, see > > http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > > > > > > _______________________________________________ > > 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. > > > _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Re: [Freesurfer] Brodmann area thickness, surface area and volume
by _andreia_＠sapo.pt 24 Mar '13

24 Mar '13

Hi all, I want to study Brodmann Areas cortical thickness, surface area and volume. I've added the 5.2 BAxxx.threshold.label to my 5.0 fsaverage and run the recon-all BA labels command. Now I run aparcstats2table and get a table with the values but they are the same as before running the BAxxx.threshold.label. So, everything is working but the values haven't changed. Am I missing something? Do I need to run any other command so to the threshold have effect? Andreia Quoting Anastasia Yendiki <ayendiki(a)nmr.mgh.harvard.edu>: > Sounds like centos4 is probably the safest bet for you, although you > should ask the list this question. > > Sorry, I don't know what values you want to get in a table. > > On Sat, 23 Mar 2013, _andreia_(a)sapo.pt wrote: > >> Ah ok! Anyway, I'm thinking of working with 5.2, should I download >> the version for centOS 4 then? >> >> After running the new BAxxx.thresh.label files how can I get the >> values in a table? >> >> >> >> >> Quoting Anastasia Yendiki <ayendiki(a)nmr.mgh.harvard.edu>: >> >>> It doesn't matter. You just need to use those .label files from >>> the fsaverage directory in the 5.2 distritbution. You don't need >>> to run any of the executables from the 5.2 distribution. >>> >>> On Sat, 23 Mar 2013, _andreia_(a)sapo.pt wrote: >>> >>>> I'm using Centos5, which file should I download? The one for >>>> CentOS 6 or > 4? >>>> > > Quoting Anastasia Yendiki <ayendiki(a)nmr.mgh.harvard.edu>: >>>> > > You'll need to go to the section of recon-all.log under the >>>> heading "BA > > labels". You'll need to rerun the commands in >>>> that section, but instead > > of using the BAxxx.label files, us >>>> the BAxxx.thresh.label files, which > > you'll find in the >>>> fsaverage subject dir in the 5.2 distribution. >>>> > > > On Sat, 23 Mar 2013, _andreia_(a)sapo.pt wrote: >>>> > > > > Hello Anastasia, >>>> > > > How should I proceed to get the different BAs measures >>>> output with > > > > FS > 5.0? >>>> > > > Thank you very much! >>>> > > > Andreia >>>> > > > > Quoting Anastasia Yendiki <ayendiki(a)nmr.mgh.harvard.edu>: >>>> > > > > The thresholded labels are in the 5.2 version of >>>> fsaverage > > > > > under: >>>> > > > $FREESURFER_HOME/subjects/fsaverage/label/*.thresh.label >>>> > > > > > On Sat, 23 Mar 2013, Bruce Fischl wrote: >>>> > > > > > > Anastasia? >>>> > > > > On Sat, 23 Mar 2013, _andreia_(a)sapo.pt wrote: >>>> > > > > > > Ok, that was my guess... I am running against a >>>> deadline, > > > > > > > any > > > > > news on >>>> > > > > > automatically computing the correct threshold script? >>>> Will I > > > > > > be > > > > able to >>>> > > > > > use it in 5.0? >>>> > > > > > > > Thanks you! >>>> > > > > > > > Andreia >>>> > > > > > > > > > Quoting Bruce Fischl <fischl(a)nmr.mgh.harvard.edu>: >>>> > > > > > > > > yes. Surface area will be the affected much >>>> more than > > > > > > > > > > > > > > > > thickness (and > > >>>> > > volume of > > > > > > > > > course scales with area) >>>> > > > > > > > On Fri, 22 Mar 2013, _andreia_(a)sapo.pt wrote: >>>> > > > > > > > > Hi Bruce, >>>> > > > > > > > > > Thank you for the quick response! >>>> > > > > > > > > > In the meanwhile, does that also apply to >>>> cortical > > > > > > > > > > > > > > > > > > thickness > > >>>> > > > > and > > > > > > > > > > > > volume? >>>> > > > > > > > > > Thank you! >>>> > > > > > > > > > Andreia >>>> > > > > > > > > > Quoting Bruce Fischl <fischl(a)nmr.mgh.harvard.edu>: >>>> > > > > > > > > > > Hi Andreia >>>> > > > > > > > > > > > the issue is that the BA labels contain >>>> every > > > > > > > > > > > > point > > > > > > > > > > >>>> that > > > > > > > > > > > > > > > > > > > > has any > > > >>>> non-zero >>>> > > > > > > > > probability (no matter how small!) of being >>>> in that > > > > > > > > > label. > > > > > > > So > > > > >>>> > the > > > > > > > > > > > > total >>>> > > > > > > > > label area is almost certainly always bigger >>>> than the > > > > > > > > > > > > > > > > actual > > > > > >>>> BA. > > > > > > > > > > > > Anastasia >>>> > > > > > > > > has some scripts for automatically computing >>>> the > > > > > > > > > correct > > > > > > > > > > > > >>>> threshold, > > > > > > > > > > > > and I >>>> > > > > > > > > believe she and Nick integrated them into 5.2 >>>> so that > > > > > > > > > the > > > > > > > stats > > > > >>>> > are >>>> > > > > > > > > computed both thresholded and unthresholded, >>>> > > > > > > > > > hopefully > > > > > > > they can > > > > >>>> > > > > > > > > > > > > > comment. >>>> > > > > > > > > Bruce >>>> > > > > > > > > > > > > > > > > > On Fri, 22 Mar 2013, > > > >>>> > > > > > > > > > > > > > > > _andreia_(a)sapo.pt >>>> > > > > > > > > wrote: >>>> > > > > > > > > > > > > Hi all, >>>> > > > > > > > > > > > > > I'm using FS 5.0 and some time ago >>>> I was > > > > > > > > > > > > > > told by > > > > > > > > > > >>>> > > > > > > > > > > > > > > > > > > > > > > > > > > >>>> Bruce that I had > > > > > > > > > > > > > > > > > > > > > > >>>> > > > > > > > > to >>>> > > > > > > > > > threshold the BA in order to have an >>>> approximate > > > > > > > > > > area > > > > > > > > when >>>> > > > > > > > > > > > > > > > > > > > > overlaying >>>> > > > > > > > > > in the inflated surface. To get surface >>>> area values > > > > > > > > > > I > > > > > > > > also > > >>>> > > > > need to > > > > > > > > > > > > > > use >>>> > > > > > > > > > the label_area and put a threshold >>>> > > > > > > > > > having the possibility to choose the >>>> surface that I > > > > > > > > > > > > > > > > > > want, > >>>> > > > > > either > > > > > > > > > > > > > > white >>>> > > > > > > > > > or pial. >>>> > > > > > > > > > > > > > But I can also get the BA stats in >>>> a table > > > > > > > > > > > > > > for > > > > > > > > > > > >>>> > all > > > > > > > > > > > > > > > > > > > > > > > > >>>> subjects and > > > > > > > > > > > > > > > > > > > > > > > > >>>> > > > > > > areas >>>> > > > > > > > > > using either mris_anatomical_stats (on each >>>> label) > > > > > > > > > > or > > > > > > > > usinga > > > >>>> > > > > > > > > > > > > > > > > > script by >>>> > > > > > > > > > Jamaan to get the table (since I already >>>> have the > > > > > > > > > > > > > > > > > > ?.BA.stats > >>>> > > > > > > > > > > > > > > > > > > > files), >>>> > > > > > > > > > right? >>>> > > > > > > > > > > > > > My question is, which is the >>>> better/correct > > > > > > > > > > > > > > way > > > > > > > >>>> > > > > > to > > > > > > > > > > > > > > > > > > > > > > > >>>> > get the > > > > > > > > > > > > > > > > > > > > > > > > > > >>>> > > > > thickness >>>> > > > > > > > > > and surface area values of the BA to export >>>> for > > > > > > > > > > > > > > > > > > statistical > > > >>>> > > > > > > > > > > > > > > > > > analysis >>>> > > > > > > > > > since there are the thresolds issue. >>>> > > > > > > > > > > > > > I want to study mainly cortical >>>> thickness > > > > > > > > > > > > > > and > > > > > > > > > > >>>> > > surface > > > > > > > > > > > > > > > > > > > > > > > >>>> > area but > > > > > > > > > > > > > > > > > > > > > > > > >>>> > > > > > > also >>>> > > > > > > > > > look also at the volume (which is >>>> surface-based, > > > > > > > > > > thus >>>> > > > > > > > > > thickness*surface are will not be = volume >>>> since > > > > > > > > > > they > > > > > > > > are an > > >>>> > > > > > > > > > > > > > > > > > > average >>>> > > > > > > > > > from each label, right?). >>>> > > > > > > > > > > > > > I' not sure of which approach to >>>> follow > > > > > > > > > > > > > > now... > > > > > > > > > > >>>> > > Does > > > > > > > > > > > > > > > > > > > > > > > > >>>> it depend on > > > > > > > > > > > > > > > > > > > > > > > > >>>> > > > > > > the >>>> > > > > > > > > > measure I'll be using? >>>> > > > > > > > > > > > > > Thank you! >>>> > > > > > > > > > > > > > Andreia >>>> > > > > > > > > > > > > > > > > > >>>> _______________________________________________ >>>> > > > > > > > > > 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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