Freesurfer March 2013

freesurfer@nmr.mgh.harvard.edu

155 participants
331 discussions

(no subject)
by martina.andellini＠fastwebnet.it 20 Mar '13

20 Mar '13

Hi FreeSurfer experts, I would need to use the registration tools in freesurfer because the fsl ones ga ve me some problem. Just to try I have run mri_ca_registration and mri_cvs_registration and so I hav e three questions: 1) mri_ca_registration generates a talairach tansform file in .m3z format and I would need to apply it to my high res image. Any hint? 2) Converting RB_all_2008-03-26.gca to nii and opening it to mricron it seems to superimposable to the mni atlas. does it mean that what it comes out from mri_c a_registration coincides to an mni atlas image? 3) Running mri_cvs_registration (on bert data...just to try) I do not know where to find the registered volume file (I have tried few volume .mgz but with no su ccess...). Should i look for a transform file too? Thanks so much! Martina

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non-parallel version of LME models MATLAB scripts
by Lalonde, Francois (NIH/NIMH) [E] 20 Mar '13

20 Mar '13

In running a mass-univariate LME models analysis I keep running into calls to the parallel computing toolbox (parfor, matlabpool, etc…). I was able to comment out these lines in some of the scripts but I've run up to one that is particularly difficult to modify (I am not an expert in MATLAB). The script called lme_mass_fit_Rgw has proven to be too difficult. Would it be possible to get a version of the of the LME models analysis that runs on the base MATLAB program only? It will admittedly take longer but will make the analysis more accessible. Also, I was unable to find the function "for_progress" which is called along with "parfor_progress". Thanks, Francois

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Problem with tracula: incomplete or lacking tracts
by stdp82＠virgilio.it 20 Mar '13

20 Mar '13

Hi list and Anastasia, if you remember the last week I had same problems with tracula output: the final tract are lacking or incomplete for same subjects. Some of these are less wrong (only forceps major), other have more evident error (you can see this in picture that I have attacked). To resolve this issue I have: 1-checked the correct overlap of dwi and dwi_mask2-rerun data with new version 5.23-rerun new registration using bbregister (fsl/spm option): for example, in the subject of the picture attacked, the .mincost file now contains as first value 0.87 (previous it was 1.1) Please, give me an advise Thanks Stefano ----Messaggio originale----Da: stdp82(a)virgilio.itData: 12-mar-2013 17.47A: <ayendiki(a)nmr.mgh.harvard.edu>Cc: <freesurfer(a)nmr.mgh.harvard.edu>Ogg: [Freesurfer] R: Re: R: Re: Question on tracula and dwi-T1 overlapI got it from mri directory but I'm understanding that this directory isn't ok.I'm attacking the image from dlabel/diff/aparc+aseg.bbr.nii Stefano ----Messaggio originale---- Da: ayendiki(a)nmr.mgh.harvard.edu Data: 12-mar-2013 17.19 A: <stdp82(a)virgilio.it> Cc: <freesurfer(a)nmr.mgh.harvard.edu> Ogg: Re: [Freesurfer] R: Re: Question on tracula and dwi-T1 overlap Can you please answer my question? I can't really tell if the issue is due poor dwi-aseg overlap unless you tell me where you got that aseg volume from. On Tue, 12 Mar 2013, stdp82(a)virgilio.it wrote: > Thank you Anastasia. What do you think about the issue in the file attacked > (I'm noting that same subjects are lacking of same > tracts or same tracts are incomplete) > > > Stefano > > > ----Messaggio originale---- > Da: ayendiki(a)nmr.mgh.harvard.edu > Data: 12-mar-2013 17.02 > A: <stdp82(a)virgilio.it> > Cc: <freesurfer(a)nmr.mgh.harvard.edu> > Ogg: Re: [Freesurfer] Question on tracula and dwi-T1 overlap > > > Hi Stefano - Where did you get the aseg.nii.gz from? Anything that's in > the dlabel/diff/ directory has been mapped to the same space as the DWI, > so those are the volumes that can be compared directly to dwi.nii.gz. > > a.y > > On Tue, 12 Mar 2013, stdp82(a)virgilio.it wrote: > > > Hi list, > > > > I have two questions, please. > > > > I'm using version 5.1 to complete my analysis. > > > > 1- I have attacked two images from aseg.nii.gz and dwi.nii.gz of the same > > subject (figure 1 and 3). You can note the dwi do not overlap to the aseg. > > How can I resolve this issue? > > > > 2-After TRACULA analysis, I'm noting that same subjects are lacking of > same > > tracts or same tracts are incomplete (figure 3). > > > > Could it depends from the issue in question 1? I'm thinking to rerun all > > using version 5.2 but before starting new analyses, I'd like to ask you > > which is the possible error. > > > > > > Stefano > > > >_______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > The information in this e-mail is intended only for the person to whom it is > addressed. If you believe this e-mail was sent to you in error and the > e-mail > contains patient information, please contact the Partners Compliance > HelpLine at > http://www.partners.org/complianceline . If the e-mail was sent to you in > error > but does not contain patient information, please contact the sender and > properly > dispose of the e-mail. > > > >_______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.

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TRACULA missings tracts
by Roschinski, Benjamin 20 Mar '13

20 Mar '13

Dear Freesurfer users and experts, we have some problems using TRACULA. This means that tracks are missing or that they are too short. I hope you can advise me how to fix these problems. Thanks and kind regards Benjamin

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Reposting: interpreting clusters from 2 and 3 way interactions
by Laura M. Tully 20 Mar '13

20 Mar '13

Hi, I wanted to re-post my questions from a couple of days ago below, but with some more specific questions following a search through the archives. I want to be able to extract the beta values from a cluster identified using mc-z in a group by behavioral variable interaction so that I can 1) plot the relationship of thickness to behavioral variable data by group in that cluster, 2) conduct post hoc tests to examine the interaction, and 3) calculate the Rsquare and partial correlations for each variable in the glm (i.e. how much variation in thickness is explained by my behavioral variable). To extract the beta values from a cluster identified by mc-z would I treat the cluster like a label and use mri_segstats to extract the beta weights from the cluster? Would I need to make a label of all the clusters that I want to do this for first? Is there a way to calculate the basic statistics for the glm and extract in table form? i.e. Fs and ps for peaks of each cluster? What about Rsquare, or the correlation between thickness and my behavioral variable in the clusters? or would I need to compute these outside of freesurfer using the extracted betas? Thank you! Laura. On Mon, Mar 18, 2013 at 5:05 PM, Laura M. Tully <tully.laura(a)googlemail.com>wrote: > Hi Freesurfer experts, > > I'm hoping you can help me understand how to interpret interactions in > clusters identified in whole brain analysis using glmfit and glmfit-sim. > Below I describe what I've done and what I'd like to be able to do. Any > suggestions would be most appreciated! > > > - I have two groups (patients, controls) and a behavioral variable of > interest (social functioning). I am interested in cortical thickness > differences between groups (main effect of group), whether cortical > thickness relate to social functioning across the group (main effect of > social functioning), and whether this relationship differs by group (group > x social functioning interaction). > - I ran whole brain analysis using mri_glmfit with group and > functioning as variables of interest whilst controlling for/regressing out > gender, age, and mean thickness. i.e. 4 classes (conmale,confemale, ptmale, > ptfemale) and 3 continuous variables (age, AvgThickness, Functioning) = 16 > regressors. > - I tested the group x functioning interaction with the following > contrast - is it correct? > > 0 0 0 0 0 0 0 0 0 0 0 0 0.5 0.5 -0.5 -0.5 > > - I then ran mri_glmfit-sim to identify clusters that survive multiple > comparisons. This revealed 4 clusters (3 in LH; 1 in RH) that represent > regions showing significant group x functioning interaction. > - I visualized the clusters in tksurfer, and by loading the y.fsgd > file was able to visualize the plotted data to get a sense of the > interaction, but this is as much as I know in terms of how to examine > interactions in the cluster data...... > > My specifc questions include: > > - I understand that the values in xxx.sig.cluster.mgh overlay reflect > log10 p values, the signs of which indicate the direction of the > relationship (i.e. -3 = negative correlation between thickness & variable) > but I'm not sure how to interpret this in the context of an interaction > with group? > - I understand that the values in xxx.y.ocn.dat contain the average > thickness value for each subject in that cluster and that in a simple > between groups test this data could be used to conduct post hoc t-tests to > show the direction of the difference, but again I'm not sure how to use > this data in the context of the interaction. What do the values represent > in a group x variable interaction? > > Ideally, I'd like to extract the contrast estimates for each subject in > the group x functioning contrast and plot it in another program and > conduct pairwise comparisons (t-tests) in order to get a better > understanding of the interaction). I'm not sure how to do this - is it > possible? My thinking is that I do something similar in fMRI analysis in > spm where I can plot the contrasts in a significant cluster and then > extract both the average contrast estimates for each group and the contrast > estimates for each individual subject. > > Thanks in advance! > > Laura. > > > -- > -- > Laura M. Tully, MA > Social Neuroscience & Psychopathology, Harvard University > Center for the Assessment and Prevention of Prodromal States, UCLA Semel > Institute of Neuroscience > ltully(a)mednet.ucla.edu > ltully(a)fas.harvard.edu > 310-267-0170 > -- > My musings as a young clinical scientist: > http://theclinicalbrain.blogspot.com/ > Follow me on Twitter: @tully_laura > -- -- Laura M. Tully, MA Social Neuroscience & Psychopathology, Harvard University Center for the Assessment and Prevention of Prodromal States, UCLA Semel Institute of Neuroscience ltully(a)mednet.ucla.edu ltully(a)fas.harvard.edu 310-267-0170 -- My musings as a young clinical scientist: http://theclinicalbrain.blogspot.com/ Follow me on Twitter: @tully_laura

2 1

Re: [Freesurfer] make a volume template from the surface-based template for non-human primates
by Bruce Fischl 20 Mar '13

20 Mar '13

can you send your mris_fill command line? And maybe the lh.white surface you are trying to fill? Bruce On Tue, 19 Mar 2013, Longchuan Li wrote: > Hi, Bruce > > This is the lh.white that gives me the empty volume when I use mris_fill to > sample it to the volume space. Could you help diagnose what is causing it? > Thank you very much in advance! > > Lognchuan > > > ____________________________________________________________________________ > From: Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> > To: Longchuan Li <leonado78(a)yahoo.com> > Cc: FreeSurfer <freesurfer(a)nmr.mgh.harvard.edu> > Sent: Sunday, March 17, 2013 11:47 AM > Subject: Re: [Freesurfer] make a volume template from the surface-based > template for non-human primates > > Hi Longchuan > > I'm not sure what space the volume average is constructed in - Doug would > know. Probably talairach, in which case it won't match the surfaces well. > Can you send along your mris_fill command line? It shouldn't produce an > empty volume. There's no reason to look at the inflated surfaces in the > volume though - they have no volumetric meaning. > > cheers > Bruce > > > On Fri, 15 Mar 2013, Longchuan Li wrote: > > > Hi, Bruce > > > > Sorry for the late reply as I was trying to figure it out by myself. > > I mean the average of the subjects in the volume space that were used for > > generating the surface template. Actually I kind of found a volume average > > in the mri folder named as T1.mgz that seems to correspond to the surface > > template for the non-human primates. Perhaps because my ?h.white and > ?.pial > > surface files do not have the identical origins as that of the volume > > template, when I used the function "mri_surf2vol" to project the mgh > surface > > file to the volume average, I always got the outputs telling me there is 0 > > hits. I tried to diagnose it by projecting the ?h.white and ?h.pial to the > > volume using "mri_fill" and I got an empty volume. I then tried to project > > ?h.inflated to the volume space using the "mri_fill" and this time, I got > a > > mask in the output volume space. Therefore, i suspect that there is a > > mismatch of the origins between the ?h.white and the volume template in > the > > mri folder. > > > > Could you please show me what are the best strategies to correctly project > > the mgh file to the volume template in the 'mri' folder? > > > > Many thanks > > > > Longchuan > > > >___________________________________________________________________________ > _ > > From: Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> > > To: Longchuan Li <leonado78(a)yahoo.com> > > Cc: FreeSurfer <freesurfer(a)nmr.mgh.harvard.edu> > > Sent: Friday, March 15, 2013 4:56 PM > > Subject: Re: [Freesurfer] make a volume template from the surface-based > > template for non-human primates > > > > Hi Longchuan > > > > what kind of volume template do you mean? > > Bruce > > On Fri, 15 Mar 2013, Longchuan Li > > wrote: > > > > > Hi, FreeSurfer experts > > > > > > I have a question regarding making a volume template based on the > surface > > > template for non-human primates. I have made a surface template using a > > > group of monkeys and now, we want to see the result, which is a mgh > > surface > > > file, on the coronal slices of the template. So I am planning to > generate > > a > > > volume template corresponding to the surface template and then project > the > > > mgh file to the volume for viewing. Could someone tell me what is the > best > > > way to generate such a volume template? > > > > > > Many thanks in advance! > > > > > > Longchuan > > > > > > > > > > > > > > > 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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ELF class
by Varghese Chikku 20 Mar '13

20 Mar '13

Hi Fs Team, I am getting this errow while trying to use freeview. reesurfer@freesurfer-VirtualBox:~$ freeview freeview.bin: error while loading shared libraries: libjpeg.so.62: wrong ELF class: ELFCLASS32 Any Help Tx chikku

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R: R: Re: R: Re: Question on tracula and dwi-T1 overlap
by stdp82＠virgilio.it 20 Mar '13

20 Mar '13

Hi list and Anastasia, if you remember the last week I had same problems with tracula output: the final tract are lacking or incomplete for same subjects. Some of these are less wrong (only forceps major), other have more evident error (you can see this in picture that I have attacked). To resolve this issue I have: 1-checked the correct overlap of dwi and dwi_mask2-rerun data with new version 5.23-rerun new registration using bbregister (fsl/spm option): for example, in the subject of the picture attacked, the .mincost file now contains as first value 0.87 (previous it was 1.1) Please, give me an advise Thanks Stefano ----Messaggio originale---- Da: stdp82(a)virgilio.it Data: 12-mar-2013 17.47 A: <ayendiki(a)nmr.mgh.harvard.edu> Cc: <freesurfer(a)nmr.mgh.harvard.edu> Ogg: [Freesurfer] R: Re: R: Re: Question on tracula and dwi-T1 overlap I got it from mri directory but I'm understanding that this directory isn't ok.I'm attacking the image from dlabel/diff/aparc+aseg.bbr.nii Stefano ----Messaggio originale---- Da: ayendiki(a)nmr.mgh.harvard.edu Data: 12-mar-2013 17.19 A: <stdp82(a)virgilio.it> Cc: <freesurfer(a)nmr.mgh.harvard.edu> Ogg: Re: [Freesurfer] R: Re: Question on tracula and dwi-T1 overlap Can you please answer my question? I can't really tell if the issue is due poor dwi-aseg overlap unless you tell me where you got that aseg volume from. On Tue, 12 Mar 2013, stdp82(a)virgilio.it wrote: > Thank you Anastasia. What do you think about the issue in the file attacked > (I'm noting that same subjects are lacking of same > tracts or same tracts are incomplete) > > > Stefano > > > ----Messaggio originale---- > Da: ayendiki(a)nmr.mgh.harvard.edu > Data: 12-mar-2013 17.02 > A: <stdp82(a)virgilio.it> > Cc: <freesurfer(a)nmr.mgh.harvard.edu> > Ogg: Re: [Freesurfer] Question on tracula and dwi-T1 overlap > > > Hi Stefano - Where did you get the aseg.nii.gz from? Anything that's in > the dlabel/diff/ directory has been mapped to the same space as the DWI, > so those are the volumes that can be compared directly to dwi.nii.gz. > > a.y > > On Tue, 12 Mar 2013, stdp82(a)virgilio.it wrote: > > > Hi list, > > > > I have two questions, please. > > > > I'm using version 5.1 to complete my analysis. > > > > 1- I have attacked two images from aseg.nii.gz and dwi.nii.gz of the same > > subject (figure 1 and 3). You can note the dwi do not overlap to the aseg. > > How can I resolve this issue? > > > > 2-After TRACULA analysis, I'm noting that same subjects are lacking of > same > > tracts or same tracts are incomplete (figure 3). > > > > Could it depends from the issue in question 1? I'm thinking to rerun all > > using version 5.2 but before starting new analyses, I'd like to ask you > > which is the possible error. > > > > > > Stefano > > > >_______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > The information in this e-mail is intended only for the person to whom it is > addressed. If you believe this e-mail was sent to you in error and the > e-mail > contains patient information, please contact the Partners Compliance > HelpLine at > http://www.partners.org/complianceline . If the e-mail was sent to you in > error > but does not contain patient information, please contact the sender and > properly > dispose of the e-mail. > > > >_______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.

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Updated info for freesurfer 5.2 on Fedora 18. update from Bugzilla. Freesurfer used unsupported, nonstandard salt to crypt()
by Knut J Bjuland 20 Mar '13

20 Mar '13

HI I have copied the info from Bugzilla. Product: Fedora https://bugzilla.redhat.com/show_bug.cgi?id=905638 Patsy Franklin <pfrankli(a)redhat.com> changed: What |Removed |Added ---------------------------------------------------------------------------- Flags|needinfo?(pfrankli(a)redhat.c | |om) | Flags|needinfo?(pfrankli(a)redhat.c | |om) | --- Comment #27 from Patsy Franklin <pfrankli(a)redhat.com> --- The most immediate solution is for the application to be changed to use a compliant crypt salt value. After further investigation, we found that the application is passing unsupported, nonstandard salt to crypt(). This will result in crypt() returning NULL and setting errno to EINVAL. It does not appear that the application is checking for a NULL return value from crypt. It also appears that the application is using this NULL return value in a subsequent function call resulting in a segmentation fault. Previously glibc would accept unsupported salt values, but newer versions of the library have become stricter. We are currently reviewing the implementation to see if the accepted salt values can be expanded while still meeting our standards compliance requirements. -- Knut J

1 0

Medial orbitofrontal QA question
by Alice Burnett 19 Mar '13

19 Mar '13

Hi FreeSurfer experts, I have been working with a dataset we have run through FreeSurfer 5.0 and am interested in the medial orbitofrontal region (Desikan atlas). We have an unexpected surface area finding, so we want to rule out any systematic error in the generation of the area measurements. We followed the wiki instructions for processing and checked and edited all images as necessary, so the pial and white surface placement looks OK. I'm wondering, would you have any particular recommendations for QA checking the mOFC or things we should be looking out for? Thanks so much! Alice This e-mail and any attachments to it (the "Communication") are, unless otherwise stated, confidential, may contain copyright material and is for the use only of the intended recipient. If you receive the Communication in error, please notify the sender immediately by return e-mail, delete the Communication and the return e-mail, and do not read, copy, retransmit or otherwise deal with it. Any views expressed in the Communication are those of the individual sender only, unless expressly stated to be those of Murdoch Childrens Research Institute (MCRI) ABN 21 006 566 972 or any of its related entities. MCRI does not accept liability in connection with the integrity of or errors in the Communication, computer virus, data corruption, interference or delay arising from or in respect of the Communication. P Please consider the environment before printing this email ______________________________________________________________________ This email has been scanned by the Symantec Email Security.cloud service. For more information please visit http://www.symanteccloud.com ______________________________________________________________________

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Freesurfer March 2013