Freesurfer

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Re: [Freesurfer] how to generate aparc.annotion files?
by Douglas N Greve 08 Nov '10

08 Nov '10

You'll probably have to do it by hand with tkregister2. Someone on the list may have solved this problem before. doug Shahin wrote: > Ok now I faced another problem saying that I dont have talairach.xfm > for monkeys. Would you tell me how can I generate it for monkeys? > > Shahin Nasr > > PhD in Cognitive Neuroscience > Martinos Imaging Center, MGH > Harvard Medical School > > > ------------------------------------------------------------------------ > *From:* Douglas N Greve <greve(a)nmr.mgh.harvard.edu> > *To:* Shahin <shahin(a)nmr.mgh.harvard.edu> > *Cc:* Freesurfer <freesurfer(a)nmr.mgh.harvard.edu> > *Sent:* Mon, November 8, 2010 12:55:37 PM > *Subject:* Re: [Freesurfer] how to generate aparc.annotion files? > > It is needed in make_average_surface. I've created a new version that > does not use the aparc (thought I have not tested it). You can get it > from here: > > ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/make_average_… > > Make a backup of your current version of make_average_surface and then > copy this one over it > > douig > > > > Shahin wrote: > > Yes, I have made a template on the basis of many monkeys > > (mris_make_template) and then I have done spherical registeration for > > each individual monkey (to this template) by using mris_register. Now > > it is the final step and I have to run the make_average_subject but it > > generates an error saying that I don't have a lh and rh.aparc.annot > files. > > > > Apparently very old versions of freesurfer (version 3) didnt need > > these files. Am I right? Do you suggest to use old versions? > > > > Shahin Nasr > > > > PhD in Cognitive Neuroscience > > Martinos Imaging Center, MGH > > Harvard Medical School > > > > > > ------------------------------------------------------------------------ > > *From:* Bruce Fischl <fischl(a)nmr.mgh.harvard.edu > <mailto:fischl@nmr.mgh.harvard.edu>> > > *To:* Shahin <shahin(a)nmr.mgh.harvard.edu > <mailto:shahin@nmr.mgh.harvard.edu>> > > *Cc:* Freesurfer <freesurfer(a)nmr.mgh.harvard.edu > <mailto:freesurfer@nmr.mgh.harvard.edu>> > > *Sent:* Mon, November 8, 2010 12:33:03 PM > > *Subject:* Re: [Freesurfer] how to generate aparc.annotion files? > > > > Hi Shahin > > > > have you run spherical registration? If so, to what target? I don't > think > > the monkey-to-human atlas aligment is that robust, so you would need a > > monkey geometry atlas (which is a lot easier to build as you don't > > need to > > do manual labeling for it). Probably someone on list has one? > > > > Bruce > > > > On Mon, 8 Nov 2010, Shahin wrote: > > > > > Thanks Bruce, > > > > > > To avoid this problem, is there anyway to run > > make_average_subject without > > > having lh and rh.aparc.annot files? > > > Shahin Nasr > > > > > > > > > PhD in Cognitive Neuroscience > > > Martinos Imaging Center, MGH > > > Harvard Medical School > > > > > > > > > > > > > > > ________________________________ > > > From: Bruce Fischl <fischl(a)nmr.mgh.harvard.edu > <mailto:fischl@nmr.mgh.harvard.edu> > > <mailto:fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu>>> > > > To: Shahin <shahin(a)nmr.mgh.harvard.edu > <mailto:shahin@nmr.mgh.harvard.edu> > > <mailto:shahin@nmr.mgh.harvard.edu <mailto:shahin@nmr.mgh.harvard.edu>>> > > > Cc: Freesurfer <freesurfer(a)nmr.mgh.harvard.edu > <mailto:freesurfer@nmr.mgh.harvard.edu> > > <mailto:freesurfer@nmr.mgh.harvard.edu > <mailto:freesurfer@nmr.mgh.harvard.edu>>> > > > Sent: Mon, November 8, 2010 12:10:38 PM > > > Subject: Re: [Freesurfer] how to generate aparc.annotion files? > > > > > > Hi Shahin > > > > > > you'll need a monkey atlas based on manually labeled monkey folding > > > patterns. we don't have one, but it's possible that someone else > on the > > > list does (it would be a lot easier to do for monkey than it was for > > human > > > as the folds are so much simpler) > > > > > > cheers > > > Bruce > > > > > > On Mon, 8 Nov 2010, Shahin wrote: > > > > > >> Hi Freesurfers, > > >> > > >> Anybody knows how can I make lh and rh.annotation.aparc files > > for a monkey? > > >> I > > >> need them initiate an brain averaging process. > > >> Shahin Nasr > > >> > > >> > > >> PhD in Cognitive Neuroscience > > >> Martinos Imaging Center, MGH > > >> Harvard Medical School > > >> > > >> > > >> > > > > > > > > > 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 > Fax: 617-726-7422 > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > > _______________________________________________ > 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: www.nmr.mgh.harvard.edu/facility/filedrop/index.html

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how to generate aparc.annotion files?
by Shahin 08 Nov '10

08 Nov '10

Hi Freesurfers, Anybody knows how can I make lh and rh.annotation.aparc files for a monkey? I need them initiate an brain averaging process. Shahin Nasr PhD in Cognitive Neuroscience Martinos Imaging Center, MGH Harvard Medical School

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DTI question
by Gabriel Go.Es. 08 Nov '10

08 Nov '10

Hello Freesurfers I'm starting to work with DTI data and I have a couple of questions; I have 2 identical DTI sequences for some subjects and I would like to work with them, does anyone knows if it's better to concatenate them or to make an average of them? And I'm wondering when I make an eddy-current or motion correction (alignment to the B0 or T2) if there is any algorithm to change the vectors to the corresponidng alignment? Best Regards Gabriel

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FS 5.1
by Alan Francis 08 Nov '10

08 Nov '10

Hi Bruce, Doug: I am planning to process scans in a longitudinal study on First break SZ. I heard that FS 5.1 will have features that will be better than 5.0. Any idea on when 5.1 will be released? thanks much, Alan BIDMC

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QDEC or SPSS?
by liyari5018 08 Nov '10

08 Nov '10

Hi all, I do group analysis using QDEC to detect the difference between the normal group and the patient group, the result shows some significant difference brain area (normal > patient, red, uncorrected p=0.001). I extract the average cortical thickness in this area(ROI), then export those thickness data into SPSS to do statistic analysis, but I do not find the difference between two groups in this areas, even find some opposite results. （I checked my data carefully!） So I want to know how does this happen? Thanks for your reply! Best, LJ

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Old FS version
by pikase＠tin.it 07 Nov '10

07 Nov '10

Hello Freesurfers! Is it possible to obtain a copy of an old version of FS? More specifically, I need this version to complete some analyses: freesurfer-Darwin-leopard-i686-stable-pub-v4.3.1-full.dmg Thank you in advance (and great job with the 5.0!) Laura

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clarification regarding total GM and WM volume
by Samantha Clark 06 Nov '10

06 Nov '10

Dear Freesurfer team, I was a little confused by the recent e-mails about total GM and WM. If you could help clarify the below mentioned, I would really appreciate it (am using freesurfer: stable 4 version). 1) For cortical thickness analysis, there is no necessity to normalize each parcellation thickness value 2) For each GM and WM parcellation, we can norrnalize them with the total cerebral cortex volume and WM volume listed in the aseg.stats file 3) If the talairach registration is not the best, its best to not normalize the volumes with the ICV value Thanks so much, Samantha

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Loading two cortical thickness maps simultaneously in TkSurfer or Freeview
by Aly Negreira 06 Nov '10

06 Nov '10

Hi All, I'm sure this is ridiculously simple, but cant seem to load two sig.mgh files (both are cortical thinning maps produced from mri_glmfit) in either TkSurfer or Freeview at the same time. This doesn't seem possible in tksurfer unless i merge the files, which im having trouble figuring out how to do (mri_concat doesnt give me what I want and neither does mri_binarize). I am unclear on how to load sig.mgh files in Freeview and the online guide has yet to create this page. Any advice? Thanks! ALy Machine: Tain Env: dev Files: /space/tain/1/freeview_test/*

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Custom color scale for overlays in tksurfer/freeview
by f.leone＠donders.ru.nl 06 Nov '10

06 Nov '10

Hi everyone, I saw there has been posts on this before, and I know more people here at the center have this request, so I wanted to ask it again, now also for freeview: is it possible to have custom coloring on the surfaces? It is not that I need specific colors, it is just that I find the default coloring not high resolution enough to see anything more than general level differences (e.g., if I have values 0 to 100, I can only see differences between below or above 60 (red vs yellow, plus there is osme dark red for below 40), while I would like to be able to see the gradient and in between values. Or isn't this normal behavior? Can it for example be due to using Virtual GL or due to using double precision values? I just tested using integer data (ranging from 0 to 40) and that was a bit better, but still not as good as I would expect. Anyone any ideas on what I might be doing wrong / whether there is an alternative? kind regards, Frank -- Frank T.M. Leoné, MSc Graduate student | Donders Institute for Brain, Cognition and Behaviour f.leone(a)donders.ru.nl | +31 24 36 12542 / +31 24 36 68388 | Room B.1.31 / Room 1.34

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Re: [Freesurfer] Lobe mapping, based on the Desikan-Killiany Atlas
by rahul＠nmr.mgh.harvard.edu 05 Nov '10

05 Nov '10

Hi Ruthger, The temporal lobe list/label should include the banks of the superior temporal sulcus (bankssts). Not sure why it's not in there but we will include it. Thanks for pointing this out! Best, Rahul > Dear Freesurfers, > > I would like to do Lobe mapping, based on the Desikan-Killiany atlas, see > http://surfer.nmr.mgh.harvard.edu/fswiki/CorticalParcellation. > > I was wondering if there is a reason why the banksts is not included in > the list under temporal lobe. My first guess is because this is a sulcus, > but I would like to be sure what is the reason. > > Thank you very much for your suggestions! > > Ruthger Righart (PhD) > > Institute for Stroke and Dementia Research (ISD) > Klinikum der Universität München > Max-Lebsche-Platz 30 > 81377 Munich | Germany > > Ruthger.Righart(a)med.uni-muenchen.de > > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > >

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