Freesurfer April 2013

freesurfer@nmr.mgh.harvard.edu

131 participants
220 discussions

Re: [Freesurfer] Longitudinal analysis of one timepoint
by Sarah Whittle 03 May '13

03 May '13

Hi, RE the below post, we have longitudinal data from three time points, but a number of participants have scans for only one or two time points. We've done all of the cross-sectional analysis (including a lot of manual editing) and are ready to run everything through the longitudinal stream. Our plan was to run sets of analyses for all of the possible combinations of longitudinal scans. e.g., Time 1, Time 2, Time 3; Time 1, Time 2; Time 1, Time 3; Time 2, Time 3 Obviously the new feature in version 5.2 (i.e., being able to run all images together, regardless of whether some time points are missing for some people) would be MUCH better. Is this possible to do using our 5.1 cross-sectionally processed images? Given the time we've put into manual editing, we really wouldn't want to have to run everything again through 5.2. Thanks, Sarah .... Hi Henk-Jan, to avoid bias between subjects with single time points and others, we run them through the same steps. This way it is possible to include them into the statistical analysis. (For this an artificial base is created with the head in an upright and straight position). This feature will be available in 5.2. Nothing with respect to processing commands changes, you will simply pass only a single time point to the -base and then run it with -long. Nice and transparent :-). Anyway, you probably should wait till 5.2. There is several programs that changed for this to work. Also the current recon-all contains many changes not related to this. If you absolutely cannot wait, let me know and I'll take a look at how difficult it is to go back and adjust 5.1. Best, Martin On Tue, 2012-12-04 at 17:06 +0000, Westeneng, H.J. wrote: > Hi Freesurfer experts, > > > > This week a read the article of Bernal-Rusiel et al. titled > “Statistical analysis of longitudinal neuroimage data with Linear > Mixed Effects models”. In this article you described the submission of > single time-point scans to the longitudinal pipeline of Freesurfer. > I’m very interested in how to do this. Your help will be appreciated. > > > > Thanks in advance, > > > > Henk-Jan > > > > ______________________________________________________________________ > > De informatie opgenomen in dit bericht kan vertrouwelijk zijn en is > uitsluitend bestemd voor de geadresseerde. Indien u dit bericht > onterecht ontvangt, wordt u verzocht de inhoud niet te gebruiken en de > afzender direct te informeren door het bericht te retourneren. Het > Universitair Medisch Centrum Utrecht is een publiekrechtelijke > rechtspersoon in de zin van de W.H.W. (Wet Hoger Onderwijs en > Wetenschappelijk Onderzoek) en staat geregistreerd bij de Kamer van > Koophandel voor Midden-Nederland onder nr. 30244197. > > Denk s.v.p aan het milieu voor u deze e-mail afdrukt. > > > ______________________________________________________________________ > > This message may contain confidential information and is intended > exclusively for the addressee. If you receive this message > unintentionally, please do not use the contents but notify the sender > immediately by return e-mail. University Medical Center Utrecht is a > legal person by public law and is registered at the Chamber of > Commerce for Midden-Nederland under no. 30244197. > > Please consider the environment before printing this e-mail. > > _______________________________________________ > Freesurfer mailing list > Freesurfer at nmr.mgh.harvard.edu<https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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tracula FS 5.2
by Antonenko, Daria 03 May '13

03 May '13

Hi FS experts, I tried to run Tracula with the new FS 5.2 release and came across memory allocation problems in the preprocessing step and would appreciate some advice on solving them: MRIalloc(218, 182, 182): could not allocate 158704 bytes for 98th slice Cannot allocate memory Linux daria-Think 3.5.0-17-generic #28-Ubuntu SMP Tue Oct 9 19:32:08 UTC 2012 i686 i686 i686 GNU/Linux trac-preproc exited with ERRORS at Tue Apr 9 22:21:43 CEST 2013 I attached the log-file. Let me know if you need further information about my system. Thank you in advance, Daria

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ROI analyses
by Tudor Popescu 02 May '13

02 May '13

Dear Freesurfers, I am doing an ROI analysis (group comparison) of cortical thickness, and I have some questions that I could use some help with. Many thanks in advance! Tudor 1) I used aparcstats2table to extract CT values for structures from the Destrieux atlas, but I cannot identify some important cortical structures among the names in that list. For example, I don't see anything corresponding to the Superior Parietal Lobule, or the Intraparietal Sulcus (the latter actually does appear but is coupled with another structure, under the name "lh_S_intrapariet_and_P_trans_thickness") 2) Can the same table (of the average CT of each cortical parcellation) be extracted using parcellations based on an atlas other than the Destrieux (e.g. the Harvard-Oxford, or the Julich)? 3) (I can't see whether there's a tutorial for this, as the main FS site seems to be down at the moment) How can a group comparison of CT be done inside a given ROI, and in what ways can the ROI be specified? I guess the command line version of QDEC would produce, in this case, the same contrasts as QDEC, but within the ROI as opposed to the whole brain 4) How do the results of these two different types of ROI group analyses differ, and is one of them more "correct" than the other: A) running the command prompt version of QDEC within the confines of a certain atlas-defined ROI, and looking at the resulting statistical map (clusters), as per question 3; B) extracting the CT values for that ROI for all subjects using aparcstats2table, and doing t-tests to look for a group difference.

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FLASH params for mri_em_register
by Fred Dick 02 May '13

02 May '13

Dear all I'm having difficulties getting correct Talairach.lta's from synthetic flash volumes (Bruce, you are probably sorry you ever told me about this!). Basically the brain is over-scaled (bigger than it should be), which I think is happening because the contrast is so good (gm much darker than wm). Is there an example of how to use the -flash_parms flag, and what mri_em_register is expecting in the parameter file? Thanks, Fred

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Re: [Freesurfer] Freesurfer Digest, Vol 109, Issue 21
by Rotem Saar 30 Apr '13

30 Apr '13

Hi Doug, Thanks for your answer. I changed the last step as u suggested, but I think I need to clarify my question: Indeed values of the CC looks OK, but don't u think other values, like the ventricles are too high ? When I first run the script, I got all values and looked the the CC - it looked fine. Then, I wanted to validate with some other regions, just to show that I got the appropriate (low) FA values for regions I don't expect to see high values in - and things looked odd (too high). I remember Bruce also writing me that the values seems a little high, but we didn't further discuss. I read the following this link: http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/MultiModalDtiIndividual "The CC has an average FA of about 0.75, gyral parcellations are about 0.4, the left putamen is 0.27, and the ventricle is 0.2. This is as expected because the CC is highly directional with no crossing fibers so we would expect the CC to have the highest FA. The gyral white matter is also directional but has fibers crossing in them, so one expects the FA to be lower than CC. The gray matter (putamen) is still lower. The ventricle has no fibers, so we expect it to have the lowest FA". All my values are above 0.4.... Additionally, if in the last step I'm writing --seg /usr/local/freesurfer/subjects/Rotem_try/mri/wmparc.mgz why do I get 182 regions ? in my wmparc.stats I have only 70... I'm probably doing something wrong, but I can't really point to the problem, thus asking for your help. Attached is the table again, Thanks Rotem > The values look about right in the table. Your pipeline looks ok, > thought the last step uses fa_FOLDER-NAME.mask.nii instead of the output > of mri_vol2vol (fa_FOLDER-NAME.nii). > doug > > > > On 03/17/2013 02:16 AM, Rotem Saar wrote: > > > > Hi all, > > I run into somthing that seems odd to me and wanted to consult - > > I run the following script for getting the FA values from my DTI > > scans: > > > > 1) dt_recon --i > > /usr/local/freesurfer/subjects/FOLDER-NAME/DTI/I00001.dcm --s > > FOLDER-NAME --o /usr/local/freesurfer/subjects/FOLDER-NAME/DTI --b > > /usr/local/freesurfer/subjects/FOLDER-NAME/DTI/bvals.bval > > /usr/local/freesurfer/subjects/FOLDER-NAME/DTI/bvecs.bvec > > 2) tkregister2 --s fsaverage --surf white --reg > > /usr/local/freesurfer/subjects/FOLDER-NAME/DTI/fa-tal.nii.reg > > --mov /usr/local/freesurfer/subjects/FOLDER-NAME/DTI/fa-tal.nii > > 3) tkmedit FOLDER-NAME orig.mgz -aux brain.mgz -seg wmparc.mgz > > -reg /usr/local/freesurfer/subjects/FOLDER-NAME/DTI/register.dat > > -overlay /usr/local/freesurfer/subjects/FOLDER-NAME/DTI/fa.nii > > -fthresh 0.2 -fmax 1 > > 4) mri_vol2vol --mov > > /usr/local/freesurfer/subjects/FOLDER-NAME/DTI/fa.nii --targ > > /usr/local/freesurfer/subjects/FOLDER-NAME/mri/orig.mgz --s > > FOLDER-NAME --interp nearest --o > > /usr/local/freesurfer/subjects/FOLDER-NAME/DTI/fa_FOLDER-NAME.nii > > --reg /usr/local/freesurfer/subjects/FOLDER-NAME/DTI/register.dat > > 5) tkregister2 --mov > > /usr/local/freesurfer/subjects/FOLDER-NAME/DTI/fa_FOLDER-NAME.nii > > --targ /usr/local/freesurfer/subjects/FOLDER-NAME/mri/orig.mgz > > --reg > > /usr/local/freesurfer/subjects/FOLDER-NAME/DTI/fa_FOLDER-NAME.nii.reg > > 6) mri_segstats --seg > > /usr/local/freesurfer/subjects/FOLDER-NAME/mri/wmparc.mgz --ctab > > $FREESURFER_HOME/FreeSurferColorLUT.txt --i > > > /usr/local/freesurfer/subjects/FOLDER-NAME/DTI/fa_FOLDER-NAME.mask.nii > > --sum > > > /usr/local/freesurfer/subjects/FOLDER-NAME/stats/all_stats_fa_FOLDER-NAME > > > > > > I got a table with all the FA values (see attached), for each > > segment, but I suspect a problem: I think that the values are too > > high (I set the threshold to 0.2-1), am I right ? > > Can u guide me regarding what I can do to solve the problem ? in > > addition I attached a figure of the corpus-callosum, in which I'm > > interested - i't seems that the green area in not big enough, is > > this fixable ? > > > > Thanks ! > > > > Rotem >

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R: Re: R: Re: R: Re: incomplete tracts
by stdp82＠virgilio.it 30 Apr '13

30 Apr '13

Hi Anastasia, when I run the configuration file (which I'm attaching)ERROR: Could not find CVS template I apologize but which is the correct directory of CVS template? Thanks, Stefano ----Messaggio originale---- Da: ayendiki(a)nmr.mgh.harvard.edu Data: 26-apr-2013 20.08 A: <stdp82(a)virgilio.it> Cc: <freesurfer(a)nmr.mgh.harvard.edu> Ogg: Re: [Freesurfer] R: Re: R: Re: incomplete tracts Hi Stefano - Just use the default for that, you don't need to specify the location. a.y On Sun, 21 Apr 2013, stdp82(a)virgilio.it wrote: > Hi Anastasia, > I apologize but I do not find CVS template? Where it should be located? > > Thank you very much, > > > Stefano > > > > ----Messaggio originale---- > Da: ayendiki(a)nmr.mgh.harvard.edu > Data: 9-apr-2013 17.50 > A: <stdp82(a)virgilio.it> > Cc: <freesurfer(a)nmr.mgh.harvard.edu> > Ogg: Re: [Freesurfer] R: Re: incomplete tracts > > > Hi Stefano - Did you try CVS for the inter-subject registration? It > doesn't look like it from the configuration file. > > a.y > > On Tue, 9 Apr 2013, stdp82(a)virgilio.it wrote: > > > Hi Anastasia, > > yes, I tried.I'm attacking the last configuration file that I used. > > > > Thanks, > > > > > > Stefano > > > > ----Messaggio originale---- > > Da: ayendiki(a)nmr.mgh.harvard.edu > > Data: 9-apr-2013 1.42 > > A: <stdp82(a)virgilio.it> > > Cc: <freesurfer(a)nmr.mgh.harvard.edu> > > Ogg: Re: [Freesurfer] incomplete tracts > > > > > > What registration methods are you using for the intra-subject and > > inter-subject registration? Have you tried the different options? > > > > On Fri, 5 Apr 2013, stdp82(a)virgilio.it wrote: > > > > > Yes, 5.2. Incomplete tracts are usually fmajor or cab. Rarely fminor. > > > > > > ----Messaggio originale---- > > > Da: ayendiki(a)nmr.mgh.harvard.edu > > > Data: 5-apr-2013 18.57 > > > A: <stdp82(a)virgilio.it> > > > Cc: "freesurfer(a)nmr.mgh.harvard.edu"<freesurfer(a)nmr.mgh.harvard.edu> > > > Ogg: Re: [Freesurfer] R: Re: R: Re: incomplete tracts > > > > > > > > > What you say "again" you mean with 5.2? > > > > > > On Fri, 5 Apr 2013, stdp82(a)virgilio.it wrote: > > > > > > > Hi Anastasia, > > > > yes, for some subject the low-b volume is in the end. > > > > Some subjects have again incomplete tracts. > > > > I'm attacking an example of configuration file that I'm using. > > > > I hope that you can check it please. > > > > > > > > Thanks, > > > > > > > > > > > > Stefano > > > > > > > > ----Messaggio originale---- > > > > Da: ayendiki(a)nmr.mgh.harvard.edu > > > > Data: 5-apr-2013 18.45 > > > > A: <stdp82(a)virgilio.it> > > > > Cc: "freesurfer(a)nmr.mgh.harvard.edu"<freesurfer(a)nmr.mgh.harvard.edu> > > > > Ogg: Re: R: Re: [Freesurfer] incomplete tracts > > > > > > > > > > > > Hi Stefano - In your case we determined that the ones that had the low-b > > > > volume in the end didn't run correctly, right? In that case, I didn't > > need > > > > to see anything, you were going to try running 5.2. > > > > > > > > a.y > > > > > > > > On Fri, 5 Apr 2013, stdp82(a)virgilio.it wrote: > > > > > > > > > Hi Anastasia, > > > > > could I send you the data of a subject that I don't run correctly? > > > > > > > > > > I still have some subjects with tracts incomplete and I do not know if > > > it depends > > > > from > > > > > my analysis or whether the images are not good. > > > > > > > > > > Thanks, > > > > > > > > > > > > > > > Stefano > > > > > > > > > > > > > > > ----Messaggio originale---- > > > > > Da: ayendiki(a)nmr.mgh.harvard.edu > > > > > Data: 5-apr-2013 17.37 > > > > > A: "Gerit Pfuhl"<gerit.pfuhl(a)gmail.com> > > > > > Cc: "freesurfer(a)nmr.mgh.harvard.edu"<freesurfer(a)nmr.mgh.harvard.edu> > > > > > Ogg: Re: [Freesurfer] incomplete tracts > > > > > > > > > > > > > > > Hi Gerit - If it's not an issue with the gradient table but instead a > > > > > tractography initialization issue, I strongly recommend running 5.2 > > with > > > > > bbregister for the registration (which is the default in 5.2 anyway). > > > > > > > > > > You can also upload an example data set with issues (include: dmri, > > > > > dmri.bedpostX, dlabel, dpath, scripts) here for me to take a look: > > > > > https://gate.nmr.mgh.harvard.edu/filedrop2/ > > > > > > > > > > Hope this helps, > > > > > a.y > > > > > > > > > > On Fri, 5 Apr 2013, Gerit Pfuhl wrote: > > > > > > > > > > > Dear Anastasia, > > > > > > > > > > > > thanks for the help. There is also a line option in freeview. > > However > > > we still > > > > have > > > > > > brains with missing tracks, I rerun them with increasing the ncpts > > and > > > registering > > > > > to > > > > > > bbr (since that is default in Tracula 5.2.). We are reasonable > > > confident that our > > > > > bvel > > > > > > and bvac are correct, since we have roughly 20 cases out of 90 > > > processed brains > > > > > where > > > > > > there are no missing tracts. Further sometimes only one tract is > > > missing, > > > > sometimes > > > > > it > > > > > > is more severe. We could not find any correlation with recon-all > > > problems or DTI > > > > raw > > > > > > data issues (all but one were without moving artefacts). Since we > > are > > > running > > > > > bedpostx > > > > > > outside of trac-all (i.e. trac-prep then bedpostx then trac-path) > > > might it be an > > > > > issue > > > > > > that is solved with installing the 5.2. version? Would that run in > > > freesurfer > > > > 5.1.0? > > > > > > I guess we need to change the dcmrirc files only a bit. > > > > > > > > > > > > Kind regards > > > > > > Gerit Pfuhl > > > > > > > > > > > > > > > > > > On 3 April 2013 16:59, Anastasia Yendiki > > > <ayendiki(a)nmr.mgh.harvard.edu> wrote: > > > > > > > > > > > > Hi Benjamin - I'd look in a coronal view to see if the lines > > in > > > the corpus > > > > > > callosum follow the curvature of the corpus callosum, and in a > > > sagittal > > > > > > view to see if the lines in the cingulum follow the curvature > > of > > > the > > > > > > cingulum. Does this make sense? > > > > > > > > > > > > a.y > > > > > > > > > > > > On Wed, 3 Apr 2013, Roschinski, Benjamin wrote: > > > > > > > > > > > > Dear Anastasia, > > > > > > > > > > > > we dislpayed dtifit_V1 as lines, overlaid on dtifit_FA because > > > our > > > > > > gradient table is wrong but I am not really sure how to > > analyse > > > > > > these informations. You wrote to Stefano the lines have to > > point > > > in > > > > > > the right direction and that the eigenvectors are not pointing > > > along > > > > > > his corpus callosum. Can you give me a more detailed > > description > > > > > > what I have to do when I dislpay dtifit_V1 as lines, overlaid > > on > > > > > > dtifit_FA. > > > > > > > > > > > > Thanks and kind regards > > > > > > Benjamin > > > > > > > > > > > > _______________________________________________ > > > > > > 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. > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > -- > > > > > > http://gerit-orientation.blogspot.com > > > > > > http://team-arzgebirg.blogspot.com > > > > > > > > > > > > > > > > > _______________________________________________ > > > > > 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 > > > > > > 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: recon-all -autorecon2 bug?
by Ioana Coman 30 Apr '13

30 Apr '13

Hi, I am facing the same error like Miklos Argyelan http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg28047.html and Jitesh Joshi http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg28071.html I am using freesurfer-Linux-centos6_x86_64-stable-pub-v5.2.0 with the updated version of the bbregister script. Thank you, Ioana

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Re: [Freesurfer] Freesurfer Digest, Vol 110, Issue 20
by Rotem Saar 29 Apr '13

29 Apr '13

Dear Doug, I have uploaded the files to the "filedrop" (file name: Rotem_try.tar.gz) and activated the link (I hope I did it OK). I will appreciate your help as I'm stuck - can't see the problem...:) Thanks for all your help !! Rotem ------------------------------ > > Message: 9 > Date: Thu, 11 Apr 2013 12:51:38 -0400 > From: Douglas N Greve <greve(a)nmr.mgh.harvard.edu> > Subject: Re: [Freesurfer] DTI: problems with (high) FA values > To: freesurfer(a)nmr.mgh.harvard.edu > Message-ID: <5166EA1A.8000701(a)nmr.mgh.harvard.edu> > Content-Type: text/plain; charset=ISO-8859-1; format=flowed > > That is a good value, so the regis not the problem. If you upload your > dt_recon folder as well as your recon-all folder for that subject I'll > take a look. > doug > > On 04/11/2013 10:02 AM, Rotem Saar wrote: > > Hi Douge, > > > > In your last reply to my email (that contained questions regarding > > some really high FA values - see recent emails below), u asked me to > > write u the first value in register.dat.mincost - > > I'm copying the line I have: > > > > 0.280554 140.210312 156.795241 11.152485 > > > > Does this takes us one step further towards understanding the problem > > and its solution ? > > > > Thanks for your time, > > Rotem > > > > > > > > On 04/07/2013 06:48 AM, Rotem Saar wrote: > > > Hi Doug, > > > > > > Thanks for your answer. > > > I changed the last step as u suggested, but I think I need to clarify > > > my question: > > > Indeed values of the CC looks OK, but don't u think other values, like > > > the ventricles are too high ? > > *_yes, the ventricles look too high_* > > > > > > When I first run the script, I got all values and looked the the CC - > > > it looked fine. Then, I wanted to validate with some other regions, > > > just to show that I got the appropriate (low) FA values for regions I > > > don't expect to see high values in - and things looked odd (too high). > > > > > > I remember Bruce also writing me that the values seems a little high, > > > but we didn't further discuss. I read the following this link: > > > > > > http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/MultiModalDtiIndividual > > > > > > "The CC has an average FA of about 0.75, gyral parcellations are about > > > 0.4, the left putamen is 0.27, and the ventricle is 0.2. This is as > > > expected because the CC is highly directional with no crossing fibers > > > so we would expect the CC to have the highest FA. The gyral white > > > matter is also directional but has fibers crossing in them, so one > > > expects the FA to be lower than CC. The gray matter (putamen) is still > > > lower. The ventricle has no fibers, so we expect it to have the lowest > > > FA". > > > > > > All my values are above 0.4.... > > > > > > Additionally, if in the last step I'm writing --seg > > > /usr/local/freesurfer/ > > subjects/Rotem_try/mri/wmparc.mgz > > > > > > why do I get 182 regions ? in my wmparc.stats I have only 70... > > The wmparc includes all the subcortical and cortical regions too, but > > only the WM regions are reported in the wmparc.stats file. *_To only > > report the WM regions, add to mri_segstats --ctab > > $FREESURFER_HOME/_**_WMParcStatsLUT.txt_* > > > > > > I'm probably doing something wrong, but I can't really point to the > > > problem, thus asking for your help. > > _*I don't know either. If I had to guess, I'd say it is a registration > > problem. What is the first value in register.dat.mincost?*_ > > doug > > > > > > Attached is the table again, > > > > > > Thanks > > > Rotem > > > > > > > > > The values look about right in the table. Your pipeline looks ok, > > > thought the last step uses fa_FOLDER-NAME.mask.nii instead of the > > > output > > > of mri_vol2vol (fa_FOLDER-NAME.nii). > > > doug > > > > > > > > > > > > On 03/17/2013 02:16 AM, Rotem Saar wrote: > > > > > > > > Hi all, > > > > I run into somthing that seems odd to me and wanted to > > consult - > > > > I run the following script for getting the FA values from > > my DTI > > > > scans: > > > > > > > > 1) dt_recon --i > > > > /usr/local/freesurfer/subjects/FOLDER-NAME/DTI/I00001.dcm --s > > > > FOLDER-NAME --o > > > /usr/local/freesurfer/subjects/FOLDER-NAME/DTI --b > > > > /usr/local/freesurfer/subjects/FOLDER-NAME/DTI/bvals.bval > > > > /usr/local/freesurfer/subjects/FOLDER-NAME/DTI/bvecs.bvec > > > > 2) tkregister2 --s fsaverage --surf white --reg > > > > /usr/local/freesurfer/subjects/FOLDER-NAME/DTI/fa-tal.nii.reg > > > > --mov > > /usr/local/freesurfer/subjects/FOLDER-NAME/DTI/fa-tal.nii > > > > 3) tkmedit FOLDER-NAME orig.mgz -aux brain.mgz -seg > wmparc.mgz > > > > -reg > > /usr/local/freesurfer/subjects/FOLDER-NAME/DTI/register.dat > > > > -overlay > /usr/local/freesurfer/subjects/FOLDER-NAME/DTI/fa.nii > > > > -fthresh 0.2 -fmax 1 > > > > 4) mri_vol2vol --mov > > > > /usr/local/freesurfer/subjects/FOLDER-NAME/DTI/fa.nii --targ > > > > /usr/local/freesurfer/subjects/FOLDER-NAME/mri/orig.mgz --s > > > > FOLDER-NAME --interp nearest --o > > > > /usr/local/freesurfer/subjects/FOLDER-NAME/DTI/fa_FOLDER-NAME.nii > > > > --reg > > > /usr/local/freesurfer/subjects/FOLDER-NAME/DTI/register.dat > > > > 5) tkregister2 --mov > > > > /usr/local/freesurfer/subjects/FOLDER-NAME/DTI/fa_FOLDER-NAME.nii > > > > --targ > /usr/local/freesurfer/subjects/FOLDER-NAME/mri/orig.mgz > > > > --reg > > > > > > > /usr/local/freesurfer/subjects/FOLDER-NAME/DTI/fa_FOLDER-NAME.nii.reg > > > > 6) mri_segstats --seg > > > > /usr/local/freesurfer/subjects/FOLDER-NAME/mri/wmparc.mgz --ctab > > > > $FREESURFER_HOME/FreeSurferColorLUT.txt --i > > > > > > > /usr/local/freesurfer/subjects/FOLDER-NAME/DTI/fa_FOLDER-NAME.mask.nii > > > > --sum > > > > > > > > > /usr/local/freesurfer/subjects/FOLDER-NAME/stats/all_stats_fa_FOLDER-NAME > > > > > > > > > > > > I got a table with all the FA values (see attached), for each > > > > segment, but I suspect a problem: I think that the values > > > are too > > > > high (I set the threshold to 0.2-1), am I right ? > > > > Can u guide me regarding what I can do to solve the > > problem ? in > > > > addition I attached a figure of the corpus-callosum, in > > > which I'm > > > > interested - i't seems that the green area in not big > > enough, is > > > > this fixable ? > > > > > > > > Thanks ! > > > > > > > > Rotem > > > > > > > > > > > > > > > _______________________________________________ > > > 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> > > Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > > > > > > > > > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer(a)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 > Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > > > > ------------------------------ > > Message: 10 > Date: Thu, 11 Apr 2013 17:47:14 +0000 > From: "Yang, Daniel" <yung-jui.yang(a)yale.edu> > Subject: Re: [Freesurfer] Very different results between 5.1.0 and > 5.2.0 > To: Pedro Paulo de Magalh?es Oliveira Junior <ppj(a)netfilter.com.br> > Cc: "freesurfer(a)nmr.mgh.harvard.edu" <freesurfer(a)nmr.mgh.harvard.edu> > Message-ID: <CD8C6E39.1A7E1%yung-jui.yang(a)yale.edu> > Content-Type: text/plain; charset="windows-1252" > > Hi PPJ and all, > > I found that the 5.2 ? 5.1 difference is primarily seen in the cortical > thickness, and much less so in the aseg.volume. > > Here, I picked right-amygdala volume as an example of aseg.volume and > rh_bankssts_thickness as an example of rh.aparc.thickness. > > While the correlation between the two versions of right-amygdala is r = > .92 (n = 161), that of the rh_bankssts_thickness is r = .45. > > Presumably I believe the correlation should be > .90 for a strong > continuity between the two versions? > > Do you have anything in the cortical thickness? > > Daniel > > -- > Yung-Jui "Daniel" Yang, PhD > Postdoctoral Researcher > Yale Child Study Center > New Haven, CT > (203) 737-5454 > > From: Pedro Paulo de Magalh?es Oliveira Junior <ppj(a)netfilter.com.br > <mailto:ppj@netfilter.com.br>> > Date: Wednesday, April 10, 2013 11:07 AM > To: Daniel Yang <yung-jui.yang(a)yale.edu<mailto:yung-jui.yang@yale.edu>> > Cc: Bruce Fischl <fischl(a)nmr.mgh.harvard.edu<mailto: > fischl(a)nmr.mgh.harvard.edu>>, "freesurfer(a)nmr.mgh.harvard.edu<mailto: > freesurfer(a)nmr.mgh.harvard.edu>" <freesurfer(a)nmr.mgh.harvard.edu<mailto: > freesurfer(a)nmr.mgh.harvard.edu>> > Subject: Re: [Freesurfer] Very different results between 5.1.0 and 5.2.0 > > Ok, I'll try to put together a stat from aparc too. > > --------------------------------------------------------------------- > Pedro Paulo de Magalh?es Oliveira Junior > Netfilter & SpeedComm Telecom > -- www.netfilter.com.br<http://www.netfilter.com.br> > -- For mobile: http://itunes.apple.com/br/artist/netfilter/id365306441 > > > > On Wed, Apr 10, 2013 at 12:04 PM, Yang, Daniel <yung-jui.yang(a)yale.edu > <mailto:yung-jui.yang@yale.edu>> wrote: > Hi PPJ, > > Thanks! It looks interesting. I also found FS 5.2 is faster. Is there any > chance you could also provide the cortical thickness of the 2009 atlas > (e.g., rh)? > > I will take a look into the aseg.volume in my data too. > > Best, > Daniel > > > -- > Yung-Jui "Daniel" Yang, PhD > Postdoctoral Researcher > Yale Child Study Center > New Haven, CT > (203) 737-5454<tel:%28203%29%20737-5454> > > From: Pedro Paulo de Magalh?es Oliveira Junior <ppj(a)netfilter.com.br > <mailto:ppj@netfilter.com.br>> > Date: Wednesday, April 10, 2013 10:49 AM > To: Bruce Fischl <fischl(a)nmr.mgh.harvard.edu<mailto: > fischl(a)nmr.mgh.harvard.edu>> > Cc: Daniel Yang <yung-jui.yang(a)yale.edu<mailto:yung-jui.yang@yale.edu>>, " > freesurfer(a)nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>" < > freesurfer(a)nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>> > Subject: Re: [Freesurfer] Very different results between 5.1.0 and 5.2.0 > > You'll find attached some preliminary data of the comparison we did among > versions. > > --------------------------------------------------------------------- > Pedro Paulo de Magalh?es Oliveira Junior > Netfilter & SpeedComm Telecom > -- www.netfilter.com.br<http://www.netfilter.com.br> > -- For mobile: http://itunes.apple.com/br/artist/netfilter/id365306441 > > > > On Wed, Apr 10, 2013 at 10:42 AM, Bruce Fischl <fischl(a)nmr.mgh.harvard.edu > <mailto:fischl@nmr.mgh.harvard.edu>> wrote: > Hi PPJ > That's exactly what we are doing. Good to hear its stable for you > Bruce > > > > On Apr 10, 2013, at 8:38 AM, Pedro Paulo de Magalh?es Oliveira Junior< > ppj(a)netfilter.com.br<mailto:ppj@netfilter.com.br>> wrote: > > I have processed more that 600 brains with both versions in the last weeks > and the only difference I'm seeing between version 5.2.0 and 5.1, besides > the obvious new features, is processing time. > > Version 5.2 is 10% faster than 5.1 in an Amazon EC2 instance. > > Besides that there's no visible difference in terms of cortical thickness, > volumes, etc. > > If you have access to computer resources to spare you can run recon-all of > both versions in some well known database of images and do a more formal > test. > > > > > > > --------------------------------------------------------------------- > Pedro Paulo de Magalh?es Oliveira Junior > Netfilter & SpeedComm Telecom > -- www.netfilter.com.br<http://www.netfilter.com.br> > -- For mobile: http://itunes.apple.com/br/artist/netfilter/id365306441 > > > > On Wed, Apr 10, 2013 at 8:11 AM, Yang, Daniel <yung-jui.yang(a)yale.edu > <mailto:yung-jui.yang@yale.edu>> wrote: > Dear FreeSurfer Experts and Users, > > Did anyone find similar things using FS 5.2 (please see my previous post > below)? That is, FS 5.2 is including more non-cortical "black spaces" > within pial surfaces, compared to FS 5.1? > > I'm not interested in nitpicking but I feel this is a rather serious > issue, so I would like to raise it again before it's completely forgotten. > > At the meantime I keep receiving Emails from people asking me this issue. > > Thanks! > Daniel > > -- > Yung-Jui "Daniel" Yang, PhD > Postdoctoral Researcher > Yale Child Study Center > New Haven, CT > (203) 737-5454<tel:%28203%29%20737-5454> > > > > > > > On 3/19/13 7:07 AM, "Yang, Daniel" <yung-jui.yang(a)yale.edu<mailto: > yung-jui.yang(a)yale.edu>> wrote: > > > > >Posting one of the brains. > > > >https://yalesurvey.qualtrics.com/SE/?SID=SV_ddwW7I9yMQuCtPn > > > > > >It seems to me that neither version is perfect; however, 5.2.0 is > >capturing more "black spaces" in the region I'm looking at. > > > >It's in the right hemisphere, TAL coordinate about ~ (44, -46, 20). > > > >Given that the correlation between 5.1.0 and 5.2.0 is r = .33 in the > >region I examined with my samples, it's not a systematic "predictable" > >bias. > > > >Any solution? > > > >-- > >Yung-Jui "Daniel" Yang, PhD > >Postdoctoral Researcher > >Yale Child Study Center > >New Haven, CT > >(203) 737-5454<tel:%28203%29%20737-5454> > > > > > > > > > > > > > >On 3/18/13 6:27 PM, "Matt Glasser" <matt(a)ma-tea.com<mailto: > matt(a)ma-tea.com>> wrote: > > > >>Do the surfaces look correct in these regions? You might post some > >>screenshots of subjects who have a big difference between 5.1 and 5.2 > >>with > >>the 5.1 and 5.2 white and pial surfaces on volume slices that highlight > >>the difference. Without this kind of info, its hard to know which was > >>more correct, 5.1 or 5.2. > >> > >>Peace, > >> > >>Matt. > >> > >>On 3/18/13 5:13 PM, "Ritobrato Datta" <ridatta(a)mail.med.upenn.edu > <mailto:ridatta@mail.med.upenn.edu>> wrote: > >> > >>>I concur. I have seen similar results in primary visual cortex from ~40 > >>>subjects. While fs 5.1 estimated mean thickness in the range of 1.5 to > >>>1.9 in V1, fs 5.2 is giving me V1 thickness in the range of 2 to 2.3. > >>> > >>>Ritobrato Datta, Ph.D. > >>>Post Doctoral Researcher > >>>Department of Neurology > >>>University of Pennsylvania School of Medicine > >>>3rd Floor, Room 312 > >>>3710 Hamilton Walk (Goddard Laboratories) > >>>Philadelphia, PA 19104-6241 > >>>email - ridatta(a)mail.med.upenn.edu<mailto:ridatta@mail.med.upenn.edu> > >>> > >>> > >>>----- Original Message ----- > >>>From: Daniel Yang <yung-jui.yang(a)yale.edu<mailto:yung-jui.yang@yale.edu > >> > >>>To: freesurfer(a)nmr.mgh.harvard.edu<mailto: > freesurfer(a)nmr.mgh.harvard.edu> > >>>Sent: Mon, 18 Mar 2013 17:44:44 -0400 (EDT) > >>>Subject: [Freesurfer] Very different results between 5.1.0 and 5.2.0 > >>> > >>>Dear FreeSurfer Experts, > >>> > >>>I ran FreeSurfer 5.1.0 and FreeSurfer 5.2.0 on identical set of 161 > >>>subjects, and I'm interested in rh_superior_temporal_sulcus_thickness in > >>>particular. > >>> > >>>Previously, the mean thickness is 2.24 mm in 5.1.0; now it is 3.28 mm in > >>>5.2.0. They are significantly different, t(160) = 56.71. > >>> > >>>The correlation between the two versions is r = .33 > >>> > >>>Is this something possible?? I can't see what went wrong in my > >>>procedures. > >>> > >>>Thanks! > >>>Daniel > >>> > >>>-- > >>>Yung-Jui "Daniel" Yang, PhD > >>>Postdoctoral Researcher > >>>Yale Child Study Center > >>>New Haven, CT > >>>(203) 737-5454<tel:%28203%29%20737-5454> > >>> > >>>_______________________________________________ > >>>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 > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > >

2 2

convert labels to volumetric masks
by limengsecret 29 Apr '13

29 Apr '13

Dear FreeSurfers, I want to convert cortical labels to volumetric masks, the mask created are used to register with the normalized functional data and to define the roi, so could I run the following command? tkregister2 -mov sub/func.nii -noedit -s fsaverage -regheader -reg ./register.dat/ and the func.nii has been normalized (sub.nii) to the MNI space. And if the command is wrong, which command should I use? Best wishes, Meng

2 1

how to register my surface label to the epi volume
by limeilingcheng 29 Apr '13

29 Apr '13

Hi all, Now I got some results by freesurfer, finally I selected two vertexs which the coordinate values were(Talx=-40.5, Taly= -14.5,Talz=-12.7 and Tal x=55.1, Tal y=-23.9, Tal z=-1.8 ), the corresponding regions reported by freesurfer were left superiortemporal and right superiortemporal. In the following step, I want to make the left and right superiortemporal as ROIs and observe the functional connectivity between the ROIs and the voxels in the whol brain. However, it is difficult for me to understand how to register this surface label to the epi volume. and how to created the masks in FSL using the labels and Harvard-Oxford atlas to ensure the correct anatomical location. 2013-04-29 limeilingcheng

2 1

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Freesurfer April 2013