Freesurfer March 2013

freesurfer@nmr.mgh.harvard.edu

155 participants
331 discussions

Job: Research Associate in Cognitive Neuroscience
by Peter J. Molfese 21 Mar '13

21 Mar '13

Job Announcement – March 2013 Research Associate Haskins Laboratories, 300 George Street, Suite 900, New Haven CT 06511 Project Directors: Dr. Kenneth Pugh, Dr. Jay Rueckl Haskins Laboratories is seeking a Research Associate for projects related to Cognitive Neuroscience and Language/Reading Development as part of several recently funded NIH R01 and P01 grants. Responsibilities will include: - Assisting with MRI data acquisition, analysis, and data management - Assisting with recruitment of both child and adult participants - Performing data analysis for ongoing and completed projects - Administering behavioral assessments and assisting with MRI scans Requirements: - BA in Psychology, Cognitive Science, Computer Science or related field - Previous research experience with human populations Additional Desired Skills: - Previous research experience with neuroimaging techniques and data analysis (EEG/ERP, structural and functional MRI, DTI) - Experience with AFNI, FSL, or SPM - Experience with E-PRIME, Presentation, and/or PsychoPy - Strong analytical skills and basic undergraduate statistics - Strong computer skills using Mac OS X and UNIX/Linux - Programming skills (e.g. Python, R, MATLAB, C/C++, JAVA) are highly desirable Interested applicants should contact Dr. Steve Frost (frosts(a)haskins.yale.edu) with cover letter, resume, and three letters of recommendation. This position will remain open until filled; desired start date is on or before June 1, 2013. Compensation is commensurate with skills and experience. Haskins provides a vibrant research and learning environment, and actively supports skill development for all employees. Haskins Laboratories is a private, non-profit research institute with a primary focus on speech, language, reading, and their biological basis. Haskins has long-standing, formal affiliations with the University of Connecticut and Yale University. Haskins Laboratories is an Equal Opportunity Employer.

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3T MPRage flags
by Joshua Lee 21 Mar '13

21 Mar '13

The new Freesurfer has an optional flag to adjust NU intensity correction parameters for images acquired on 3T scanners. There exists also a flag for MPRage sequences. I use 3T MPRages. What is the recommended use in this case? Thanks Josh

4 3

Brainsuite --> FreeSurfer
by Valtina Pouegue 21 Mar '13

21 Mar '13

Hi, I've done a segmentation with Brainsuite ( and FreeSurfer) and I would like to get measurements with FreeSurfer. SO, I convert my rile ( readdfs --> write_surf ) from BRainsuite in Matlab to be usable with Freesurfer. Then, I tried to get measurements with the command .'mris_anatomical_stats' . with the file created previously in Matlab (I called it 'rh.pial'). But I got this error like the system is not able to read wm.mgz.That's why I thought I could juste replace th 'rh.pial' of the segmentation with Freesurfey by the 'rh.pial' created with Matalb and then run mris_anatomical_Stats. IS this a good approximation. Could you recommand another way. VP

2 6

mri_ca_registration, mri_cvs_registration
by martina.andellini＠fastwebnet.it 21 Mar '13

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

20 Mar '13

File attacked ----Messaggio originale---- Da: stdp82(a)virgilio.it Data: 20-mar-2013 22.34 A: <ayendiki(a)nmr.mgh.harvard.edu> Cc: <freesurfer(a)nmr.mgh.harvard.edu> Ogg: [Freesurfer] R: Re: Problem with tracula: incomplete or lacking tracts Thank you Anastasia. I'm checking gradient table but I would like underline that I'm noting some holes in dti_FA.nii.gz and not in dwi.nii.gz (I have attacked the relative images). Stefano ----Messaggio originale---- Da: ayendiki(a)nmr.mgh.harvard.edu Data: 20-mar-2013 16.40 A: <stdp82(a)virgilio.it> Cc: <freesurfer(a)nmr.mgh.harvard.edu> Ogg: Re: [Freesurfer] Problem with tracula: incomplete or lacking tracts Hi Stefano - Have you checked that your gradient table is correct by looking at the output of the tensor fit? a.y On Wed, 20 Mar 2013, stdp82(a)virgilio.it wrote: > 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_mask > 2-rerun data with new version 5.2 > 3-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. > > > > > >_______________________________________________ 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.

2 1

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

20 Mar '13

Thank you Anastasia. I'm checking gradient table but I would like underline that I'm noting some holes in dti_FA.nii.gz and not in dwi.nii.gz (I have attacked the relative images). Stefano ----Messaggio originale---- Da: ayendiki(a)nmr.mgh.harvard.edu Data: 20-mar-2013 16.40 A: <stdp82(a)virgilio.it> Cc: <freesurfer(a)nmr.mgh.harvard.edu> Ogg: Re: [Freesurfer] Problem with tracula: incomplete or lacking tracts Hi Stefano - Have you checked that your gradient table is correct by looking at the output of the tensor fit? a.y On Wed, 20 Mar 2013, stdp82(a)virgilio.it wrote: > 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_mask > 2-rerun data with new version 5.2 > 3-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. > > > > > >_______________________________________________ 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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libjpeg.so.62
by Varghese Chikku 20 Mar '13

20 Mar '13

Hi I am getting an error while using qdec. It says error while loading shared libraries ,libjpeg.so.62 cannot open shared object file No such file or directory I ran reconall with out any problem. Any idea, tx chikku

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

20 Mar '13

Sorry - meant to respond to list. Thanks for the response Doug - I have a few follow up questions I hope you can clarify: > > - is the xxx.ocn.annot file created by mri_glmfit-sim considered a > "label" by freesurfer? or does it need to be converted to a label before I > can use mri_segstats to extract the betas from the cluster(s) in the > xxx.ocn.annot? I tried using the following command line to attempt to > extract the betas from the cluster annotation file created by > mri_glmfit-sim, but received an error: > > mri_segstats --i beta.mgh --annot fsaverage hemi contrast/xxx.ocn.annot > --avgwf avgwf.dat > > > - how does one convert an xxx.ocn.annot file to a label? > > > - If I have run 3 different glms looking at the relationship between > thickness and 3 different behavioral variables, and found 1 (or more) > cluster in each glm using mri_glmfit-sim can I create 1 annotation/label > with all the clusters from the separate glms and then extract the betas > from that one annotation using mri_segstats? Or do I need to treat each glm > separately? > > > - I saw on the listserv some references to matlab functions that > can calculate r square and partial correlations for glms with more than one > predictor variable (e.g pcc between thickness and behavioral variable 1; > pcc between thickness and behavioral variable2; Rsq for overall model) but > I could not find the .m scripts for the functions (MRIread > or fast_glm_pcc?) - would these functions be appropriate and if so where > might I find them? > > Thanks in advance for your help! > > Laura. > > > On Wed, Mar 20, 2013 at 8:29 AM, Douglas N Greve < > greve(a)nmr.mgh.harvard.edu> wrote: > >> >> On 03/20/2013 10:17 AM, Laura M. Tully wrote: >> > 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? >> You can do it label by label. Or, if the annotation created by >> mri_glmfit-sim has all the clusters you want, you can use that (also in >> mri_segstats). You can also create an annotation from individual labels >> with mris_label2annot. >> > >> > 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? >> You will need to do it outside of FS. What are Fs and ps? >> doug >> >> > >> > Thank you! >> > >> > Laura. >> > >> > >> > >> > >> > >> > >> > On Mon, Mar 18, 2013 at 5:05 PM, Laura M. Tully >> > <tully.laura(a)googlemail.com <mailto:tully.laura@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? >> > >> > 0000000000000.50.5-0.5-0.5 >> > >> > * 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 <mailto:ltully@mednet.ucla.edu> >> > ltully(a)fas.harvard.edu <mailto:ltully@fas.harvard.edu> >> > 310-267-0170 <tel: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 <mailto:ltully@mednet.ucla.edu> >> > ltully(a)fas.harvard.edu <mailto:ltully@fas.harvard.edu> >> > 310-267-0170 >> > -- >> > My musings as a young clinical scientist: >> > http://theclinicalbrain.blogspot.com/ >> > Follow me on Twitter: @tully_laura >> > >> > >> > _______________________________________________ >> > 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/ >> >> _______________________________________________ >> 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. >> >> > > > -- > -- > 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

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freeview warning: invalid drawable
by Glen Lee 20 Mar '13

20 Mar '13

Dear freesurfer experts, I'm wondering why I get this warning message when I open up any surf template in either fsaverage or fsaverage_sym directory. FYI, I'm using freeview v1.0 if anybody know, please help. -Glen $ freeview -f lh.inflated 2013-03-20 16:03:05.801 freeview.bin[52449:907] invalid drawable 2013-03-20 16:03:05.805 freeview.bin[52449:907] invalid drawable 2013-03-20 16:03:05.823 freeview.bin[52449:907] invalid drawable 2013-03-20 16:03:05.825 freeview.bin[52449:907] invalid drawable 2013-03-20 16:03:05.844 freeview.bin[52449:907] invalid drawable 2013-03-20 16:03:05.846 freeview.bin[52449:907] invalid drawable 2013-03-20 16:03:05.863 freeview.bin[52449:907] invalid drawable 2013-03-20 16:03:05.865 freeview.bin[52449:907] invalid drawable QObject::connect: Connecting from QAbstractButton::toggled(bool) to COMPAT slot (QGroupBox::setShown(bool)) QObject::connect: Connecting from QAbstractButton::toggled(bool) to COMPAT slot (QGroupBox::setShown(bool)) 2013-03-20 16:03:06.211 freeview.bin[52449:907] invalid drawable 2013-03-20 16:03:06.212 freeview.bin[52449:907] invalid drawable 2013-03-20 16:03:06.213 freeview.bin[52449:907] invalid drawable 2013-03-20 16:03:11.634 freeview.bin[52449:907] invalid drawable 2013-03-20 16:03:11.638 freeview.bin[52449:907] invalid drawable 2013-03-20 16:03:11.649 freeview.bin[52449:907] invalid drawable

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Re: [Freesurfer] Asymmetries of cortical thickness
by Douglas N Greve 20 Mar '13

20 Mar '13

Hi Sophie, you can run the following command: cd $SUBJECTS_DIR/yoursubject mris_apply_reg --src xhemi/surf/lh.thickness --streg xhemi/surf/lh.fsaverage_sym.sphere.reg surf/lh.fsaverage_sym.sphere.reg --tval surf/lh.rh.thickness.mgh lh.rh.thickness.mgh will now have the rh thicknesses on the rh surface mris_apply_reg is only available in 5.2. If you don't have 5.2, I can get you a version of this program if you tell me your OS. Also note that you need to go through the xhemi-reg procedure first. doug On 03/18/2013 10:40 AM, Sophie Maingault wrote: > Yes if it is possible I would like to know how to do it ? > > Thanks ! > > Sophie > > -----Message d'origine----- > De : Douglas N Greve [mailto:greve@nmr.mgh.harvard.edu] > Envoyé : lundi 18 mars 2013 14:39 > À : Sophie Maingault; Freesurfer(a)nmr.mgh.harvard.edu > Objet : Re: [Freesurfer] Asymmetries of cortical thickness > > It is possible, it is just not a good idea because if you map rh to lh > and then compare to lh, the rh will have been interpolated to get it > into the lh. Even if there are no differences between the two, you will > see differences because of the interpolation. Mapping both to > fsaverage_sym means that both will be interpolated. If this > interpolation does not bother you, then I can show you how to get it > from rh to lh. > doug > > > > > On 03/18/2013 09:24 AM, Sophie Maingault wrote: >> So i didn't understand what you mean by "just specify one subject when > your >> mris_preproc" ? Because, in fact I don't want to use the registration on >> fsaverage_sym. I would like just to create a file lh.thickness less >> rh.thickness vertex per vertex, maybe it is not possible ? >> >> -----Message d'origine----- >> De : Douglas N Greve [mailto:greve@nmr.mgh.harvard.edu] >> Envoyé : lundi 18 mars 2013 14:15 >> À : Sophie Maingault; Freesurfer(a)nmr.mgh.harvard.edu >> Objet : Re: [Freesurfer] Asymmetries of cortical thickness >> >> No, it is not, the target needs to be fsaverage_sym >> doug >> >> >> On 03/18/2013 09:13 AM, Sophie Maingault wrote: >>> So I do : mris_preproc --target fsaverage --xhemi --hemi lh --paired-diff >>> --meas thickness --out lh.lh-rh.thickness.sm00.mgh --s t0001 --s t0003 > --s >>> t0009 --s t0027 --s t0031 --s t0033 --s t0126 --s t0148 --s t0171 --s >> t0174 >>> --s t0199 --s t0203 --s t0212 --s t0215 --s t0242 --s t0245 --s t0253 --s >>> t0254 --s t0256 --s t0268 >>> >>> You think it's ok ? >>> >>> Sophie >>> >>> -----Message d'origine----- >>> De : freesurfer-bounces(a)nmr.mgh.harvard.edu >>> [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] De la part de Douglas N >>> Greve >>> Envoyé : lundi 18 mars 2013 13:49 >>> À : freesurfer(a)nmr.mgh.harvard.edu >>> Objet : Re: [Freesurfer] Asymmetries of cortical thickness >>> >>> you will have to use the same stream, just specify one subject when your >>> mris_preproc >>> doug >>> >>> >>> On 03/18/2013 08:06 AM, Sophie Maingault wrote: >>>> Hello, >>>> >>>> Iobtained a map of cortical thickness asymmetries after the >>>> registration on the symmetric atlas. But I would to obtain the same >>>> map with raw data I mean just by subtract lh.thickness and >>>> rh.thickness. How can I modify the part #Create a stack of subjects in >>>> wiki page ? I have to register to fsaverage (and not fsaverage_sym) >>>> and then do the same thing ? >>>> >>>> Thanks you for your help. >>>> >>>> Sophie >>>> >>>> >>>> >>>> _______________________________________________ >>>> 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/

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Freesurfer March 2013