Freesurfer

freesurfer@nmr.mgh.harvard.edu

14 participants
30096 discussions

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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Fw: Making cuts using tksurfer
by Anupa AV 09 Apr '13

09 Apr '13

----- Forwarded Message ----- From: Anupa AV <av.anupa(a)yahoo.com> To: Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> Sent: Friday, April 5, 2013 11:24 AM Subject: Re: [Freesurfer] Fw: Making cuts using tksurfer Dear Sir, Kindly see the attachment. I tried to make it more clearer. Sorry for the previous incomplete attachment. Please give me some inputs to make coronal cut at y=26 (talairach coordinate). I'm also attaching a paper which I'm referring to. ________________________________ From: Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> To: Anupa AV <av.anupa(a)yahoo.com> Cc: Freesurfer <freesurfer(a)nmr.mgh.harvard.edu> Sent: Thursday, April 4, 2013 5:40 PM Subject: Re: [Freesurfer] Fw: Making cuts using tksurfer Hi Anupa it's pretty hard to figure anything out from your images. What is wrong with using the cutting plane tool? You specify 3 points to define the plane, then a 4th to specify which side you want to keep cheers Bruce On Wed, 3 Apr 2013, Anupa AV wrote: > > ----- Forwarded Message ----- > From: Anupa AV <av.anupa(a)yahoo.com> > To: Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> > Sent: Wednesday, April 3, 2013 11:57 AM > Subject: Re: [Freesurfer] Making cuts using tksurfer > > Dear Sir, > > As you recommended, I have made a cut using plane option. Kindly see the > attachment. > My research interst is to make a coronal cut. > I've done it by merging the standard FreeSurfer parcellation labels of the > superior frontal gyrus, the rostral middle frontal gyrus and caudal > middle frontal gyrus (after loading DKatlas). > Then I cut the merged merged region using cut plane option. > Now I want to make a coronal cut at Talairach coordinate y=26(say), so as to > seperate dorsolateral prefrontal cortex from premotor cortex. > > > Can you please tell me how to make a coronal cut at y=26? > > Thanks in advance for your response. > > ____________________________________________________________________________ > From: Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> > To: Anupa AV <av.anupa(a)yahoo.com> > Cc: "freesurfer(a)nmr.mgh.harvard.edu" <freesurfer(a)nmr.mgh.harvard.edu> > Sent: Monday, April 1, 2013 6:15 PM > Subject: Re: [Freesurfer] MAking cuts using tksurfer > > you might try using a cutting plane instead of having to draw the entire > cut. > > cheers > Bruce > On Mon, 1 Apr 2013, Anupa AV wrote: > > > Dear All, > > > > How to explore the "cut" tools in freesurfer using tksurfer? > > I'd like to make a cut along the vertex on the cortical surface (say, > inflated) to divide medial and lateral components. > > How to do it after loading DKatlas labels and I want to cut along the > vertex to divde medial and lateral components.? > > > > Thanks in advance for your response. > > > > > > > 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. > > > > > >

3 2

tksurfer partial overlays?
by raij＠nmr.mgh.harvard.edu 09 Apr '13

09 Apr '13

Hi, We need to display surface data (.w file). However, our algorithm failed to assign values for some vertices (and were therefore given the value of exactly zero), and to clearly differentiate those from vertices where we successfully computed values, we would like the vertices where we could not compute a value to be blank (=only the underlying anatomical surface shows). Normally I would just threshold the values to get rid of the "blank" vertices. However, we want to use tksurfer "offset 0.5" to shift the distribution such that all values smaller than 0.5 are shown as blue and all values larger than 0.5 in red/yellow. The offset also has the effect that the vertices where we were unable to compute a value will now have a value of exactly -0.5. Then, the question becomes how to make tksurfer paint only the vertices where we have a successfully computed value. After the shift, thresholding will no longer work because it only operates on values around zero. We have tried editing the .w file by both (i) removing the values from the vertices that we do not want painted, and (ii) removing the vertices (the entire line, vertex index plus value) from the file, but the tksurfer brain surface window still shows an overlay with a value of 0 in these vertices. Thanks! Tommi --- Tommi Raij, M.D., Ph.D. MGH/MIT/HMS Athinoula A. Martinos Center for Biomedical Imaging Bldg 149, 13th St Charlestown, MA 02129 U.S.A.

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Tracula in freesurfer 5.2.0
by Gerit Pfuhl 09 Apr '13

09 Apr '13

Dear freesurfer experts, I was wondering whether we also need to upgrade the tutorial files when we upgraded from freesurer 5.1.0 to 5.2.0 and use Tracula I got as error that an ROI file of the Tutorial subject Diff001 does not exist. niiRead(): error opening file ../diffusion_tutorial/Diff001/ dlabel/mni/lh.cst_AS_roi1.bbr.nii.gz ERROR: Could not read ./diffusion_tutorial/Diff001/dlabel/mni/lh.cst_AS_roi1.bbr.nii.gz everything before is fine and the path is sound Attached the logfile output (error message right at the end) Thanks for helping Gerit Pfuhl <http://team-arzgebirg.blogspot.com>

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GIFTI file
by Valtina Pouegue 09 Apr '13

09 Apr '13

Hi, I saw in the documentation that since the version 5.2.0 of Freesurferw ecan open and write .gii file. I have a surface in .gii and I would like open it on FS. The fact is that, I didn't find a way to do that in the documentation. Does anyone know a way? Thanks.

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Re: [Freesurfer] incomplete tracts
by Anastasia Yendiki 09 Apr '13

09 Apr '13

Are you running this on your own subject or the tutorial subject? Please include the freesurfer list on all emails with tracula questions. Thanks, a.y On Tue, 9 Apr 2013, Gerit Pfuhl wrote: > Dear Anastasia, > > I got some improvement by setting nctps to 7 (as I had done last week with version 5.1.0). > Now, we installed freesurfer 5.2.0 and I rerun one subject (changed drmirc file) > but I got the following message: > niiRead(): error opening file /fastfs/igis/MRI_fs_rec_dti/diffusion_tutorial/Diff001/dlabel/mni/lh.cst_AS_roi1.bbr.nii.gz > ERROR: Could not read /fastfs/igis/MRI_fs_rec_dti/diffusion_tutorial/Diff001/dlabel/mni/lh.cst_AS_roi1.bbr.nii.gz > > diffusion_tutorial/Diff001/dlabel/mni/lh.cst_AS_roi1.bbr.nii.gz does not exist, so that must be a new data set.??? Though I saw that the > diffusion_tutorial page is from Sep 2012. > > Regards > Gerit > > > On 5 April 2013 18:23, Gerit Pfuhl <gerit.pfuhl(a)gmail.com> wrote: > Hi Anastasia, > > I will know more on monday, Then should also be able to upload files. > > Bests > Gerit > > > On 5 April 2013 17:37, Anastasia Yendiki <ayendiki(a)nmr.mgh.harvard.edu> wrote: > > 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 > > > > > > -- > http://gerit-orientation.blogspot.com > http://team-arzgebirg.blogspot.com > > > > > -- > http://gerit-orientation.blogspot.com > http://team-arzgebirg.blogspot.com > >

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