Freesurfer

freesurfer@nmr.mgh.harvard.edu

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30091 discussions

Surfaces to *native* space
by Oscar Esteban 11 Apr '13

11 Apr '13

Dear all, I think my issue is quite related to this one (if not duplicated, sorry in that case): https://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/2013-February/027622.… As Shani, I used bbregister to coregister diffusion images to anatomical: > bbregister --s OE0_T1 --mov DTI_b0_brain.nii.gz --reg dti2anat.dat --dti --init-fsl Then, I visually checked the outcome and resampled the T1 to DTI space: > tkregister2 --mov DTI_b0.nii.gz --reg dti2anat.dat --surf > mri_vol2vol --mov DTI_b0.nii.gz --targ OE0_T1/mri/T1.mgz --reg dti2anat.dat --o T1-to-DTI.nii.gz --inv > tkregister2 --mov T1-to-DTI.nii.gz --targ DTI_b0.nii.gz --reg T1-to-DTI.nii.gz.reg Everything looks fine, but I cannot get the pial and white surfaces into dti space (please note the --reg-inv param and the ref volume DTI_b0.nii.gz, that should be important IMHO): > mri_surf2surf --s OE0_T1 --sval-xyz white --reg-inv dti2anat.dat DTI_b0.nii.gz --tval lh.white.dti --tval-xyz --hemi lh There seems to exist an orientation problem when trying to visualize the surface > tkmedit -f DTI_b0.nii.gz -surface lh.white.dti I also applied the solution that Douglas recommended Shani, without good results :(. Any light on this would be of the highest interest for me :D Thanks, Oscar -- Oscar Esteban PhD Student / Researcher Biomedical Image Technologies (BIT), UPM ETSI Telecomunicación Lab. C203, Av. Complutense s/n - E-28040 Madrid (Spain) +34 915 495 700 ext.4234 Signal Processing Laboratory (LTS5), EPFL-STI-IEL-LTS5 ELD 224 (Bâtiment ELD), Station 11, CH-1015 Lausanne, Switzerland

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Finding adjacent vertices/labels
by Chris McNorgan 10 Apr '13

10 Apr '13

Hello Freesurfers, I was wondering if there is information embedded in the annotation/label files that could be used to determine whether two labels represent anatomically adjacent regions? For example, I have parcellated a bunch of participants using connectomemapper into 1000 ROIs. I was just now reading Power et al. (2011), who looked at functional connectivity, but specifically excluded connections between spheroid ROIs that were less than 20mm apart. Analogously, I might wish to exclude connections between adjacent labels, but it seemed that manually creating an adjacency matrix for 1000 regions would be impractical, and a good candidate for an automated approach. I'm just not clear what information such an approach might have to work with. Can the adjacency between two vertices be determined based on their values? If so, one approach might be: for each pair of labels (A,B): get set of vertices within A get set of vertices within B for each vertex pair (Ai, Bj) if Ai and Bj are adjacent, stop, and mark A and B as adjacent Cheers, Chris

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Re: [Freesurfer] Comparing HRF undershoots between conditions
by Douglas N Greve 10 Apr '13

10 Apr '13

If you run tkmedit-sess, then open the overlay configuration window, then advance the time point to the delay you want. Otherwise, you can create a contrast where you just look at the delay you want. To do this, run mkcontrast-sess with -setwdelays and specify 0 for all delays and 1 for the delay you want to see. doug On 04/10/2013 04:15 PM, SHAHIN NASR wrote: > That's the problem Doug. I have already generated the FIR model but > how can I show the sig MAP for one "particulat time point". What are > the other ways? > > > On Wed, Apr 10, 2013 at 4:05 PM, Douglas N Greve > <greve(a)nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> wrote: > > Hi Shahin, there are several ways that you could do it. The one > that immediately comes to mind is to use an FIR and then test for > a difference at a particular post stimulus time point. > doug > > > > > On 04/10/2013 03:54 PM, SHAHIN NASR wrote: > > Hi, > I want to generate a map to show the significant > difference between HRF undershoot (negative peak of activity) > between two conditions independent from the positive peak. Is > there anyway, to generate this map? > > P.S.: Please note that I need a map and not a time course graph. > > > -- > Shahin Nasr > > PhD in Cognitive Neuroscience > Martinos Imaging Center, MGH > Harvard Medical School > > > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > greve(a)nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> > Phone Number: 617-724-2358 <tel:617-724-2358> > Fax: 617-726-7422 <tel:617-726-7422> > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > FileDrop: 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/ > > > > > > -- > Shahin Nasr > > PhD in Cognitive Neuroscience > Martinos Imaging Center, MGH > Harvard Medical School -- 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/

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Rejoindre mon réseau sur LinkedIn
by Sima Chalavi 10 Apr '13

10 Apr '13

LinkedIn ------------ Sima Chalavi souhaite se connecter à vous sur LinkedIn : ------------------------------------------ Je vous invite à faire partie de mon réseau professionnel en ligne sur le site LinkedIn. Accepter l'invitation de Sima Chalavi http://www.linkedin.com/e/-qq80um-hfd0ug20-5o/qaAr-Z_86TRZ5lXG-dA9kZQ49qSe5… Voir le profil de Sima Chalavi http://www.linkedin.com/e/-qq80um-hfd0ug20-5o/rso/245935493/G7CW/name/66471… ------------------------------------------ Vous recevez des invitations par e-mail. Cet e-mail est destiné à Freesurfer List. Découvrez pourquoi nous avons inclus ceci : http://www.linkedin.com/e/-qq80um-hfd0ug20-5o/plh/http%3A%2F%2Fhelp%2Elinke… (c) 2012, LinkedIn Corporation. 2029 Stierlin Ct, Mountain View, CA 94043, USA.

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Comparing HRF undershoots between conditions
by SHAHIN NASR 10 Apr '13

10 Apr '13

Hi, I want to generate a map to show the significant difference between HRF undershoot (negative peak of activity) between two conditions independent from the positive peak. Is there anyway, to generate this map? P.S.: Please note that I need a map and not a time course graph. -- Shahin Nasr PhD in Cognitive Neuroscience Martinos Imaging Center, MGH Harvard Medical School

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Tracula 5.2.0 -path step segmentation fault
by Gerit Pfuhl 10 Apr '13

10 Apr '13

see previous mail, additionally now attached the trac-all -prep and -bedp logfiles Hope that gives clues Sincerely Gerit Pfuhl <http://team-arzgebirg.blogspot.com>

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FS-FAST motion correction / register
by preciado＠nmr.mgh.harvard.edu 10 Apr '13

10 Apr '13

One of my subjects exhibited motion during the middle time point of one the functional scans. FS-FAST then reads all other time points as having a significant amount of motion because the subject was out of place during the point that is marked as the origin. Is there some way that I can set a different time point? I am worried that there will be some over-correction for motion that isn't really there because my middle time point it out of an anomaly. -Ronny

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freesurfer 5.1 vs 5.2
by Gonzalo Rojas Costa 10 Apr '13

10 Apr '13

Hi: How can install version 5.2 in a computer without uninstalling version 5.1 ?... Sincerely, -- Gonzalo Rojas Costa Laboratory for Advanced Medical Image Processing Department of Radiology Clínica las Condes Lo Fontecilla 441, Las Condes, Santiago, Chile. Tel: 56-2-2105170 Cel: 56-9-97771785 www.clc.cl

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question on GLM subgroup
by stdp82＠virgilio.it 10 Apr '13

10 Apr '13

Hi list, I'm performing cortical thickness among 3 groups by using GLM. I created a group descriptor file with 3 groups and 2 covariates (age and mean thickness). I performed 3 comparisons A-B, A-C, B-C. Now, for one of 3 groups (group C) I have: groups C=30 subjects; I'd like to divide it in some pairs. First pair: X (n=15) vs Y (n=15). Second pair: Z (n=15) vs W (n=15). Between first and second pair there isn't interactions. X or Y subgroup can contain also subjects included in Z or W. Z or W subgroup can contain also subjects included in X or Y. Design: group A group B subgroup X vs subgroup Ygroup C ------< subgroup Z vs subgroup W I'm thinking to perform qdec for X-Y and Z-W. Is it correct? What do you advise me? Thanks, Stefano

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R: Re: R: Re: incomplete tracts
by stdp82＠virgilio.it 10 Apr '13

10 Apr '13

No I did not try it. Now I'm trying to perform it. Thanks, 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.

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