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workflow of trouble shooting?
by chenchunhuichina 27 Sep '14

27 Sep '14

Dear Freesurfer experts, Sorry I am posting this again, I do not know I missed you reply or nobody replied yet. Can anybody help? I am learning to do trouble shooting on recon-all results. But after read materials on the wiki, I am confused about the workflow. According to the tutorial slices, the work flow should be 1,recon-all �Cautorecon1 (Stages 1-5) 2,Check talairach transform, skull strip, normalization (?) 3,recon-all �Cautorecon2 (Stages 6-23) 4,Check surfaces (1)Add control points: recon-all �Cautorecon2 (Stages 10-23) (2)Edit wm.mgz: recon-all �Cautorecon2-wm (Stages 13-23) (3)Edit brainmask.mgz: recon-all �Cautorecon-pial (Stage 23) 5,recon-all �Cautorecon3 (Stages 24-30) Note: all stages can be run individually (this note was also from the slice) But on the trouble shooting wiki page http://freesurfer.net/fswiki/FsTutorial/TroubleshootingData , the order is 1, edit brain mask 2, edit wm volume 3, correcting topological defects 4, skull strip 5, control point 6, talairach transformation 7, edit aseg My quesion is, shouldn't I stick to the stages 1-30 order? I mean, I think results from earlier stages will influence later stages, so once an earlier stage output was edited, all the following steps should re-run, right? why talairach transformation can be checked later, which I think one should redo nearly every thing, right? Or, are the 7 trouble shooting steps independ from each other, and I can edit in any order i want then re-run all necessary steps? For example, should I edit wm and brian mask together, then run recon-all �Cautorecon2, or should I edit wm and run recon-all �Cautorecon2 then edit brainmask and run recon-all �Cautorecon-pial? Thanks for any help! Best~ 2014-09-26 Chunhui Chen _________________ State Key Laboratory of Cognitive Neuroscience and Learning Beijing Normal University Beijing, China 100875 ��ˣ� Thomas Yeo ��ʱ�䣺 2014-09-26 12:52:20 �ռ��ˣ� freesurfer ��ͣ� ��⣺ [Freesurfer] Brainmap Ontology Dear FreeSurfer List, I like to introduce you to a new set of reference brain networks (cognitive components) estimated from 10,449 experiments and 83 behavioral tasks from the BrainMap database, which can be downloaded here: https://surfer.nmr.mgh.harvard.edu/fswiki/BrainmapOntology_Yeo2015. The networks will be incorporated in some future version of FreeSurfer. Since these networks are estimated from (meta-analytic) task data, they are meant to complement (not replace) the current resting-state networks in FreeSurfer (https://surfer.nmr.mgh.harvard.edu/fswiki/CorticalParcellation_Yeo2011) Cheers, Thomas _______________________________________________ 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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mri_glmfit and volume visuals
by Taylor North 27 Sep '14

27 Sep '14

Hello Freesurfer community, I am using the mri_glmfit model to analyze my group data at two time points. First I ran the following commanded swapping pc1 with spc to get an image of the symmetrized percent change across my group. ------------------------------------------------------------------------------------------------------------------------- long_mris_slopes --qdec long.testretest.qdec \ --meas thickness \ --hemi lh \ --sd $SUBJECTS_DIR \ --do-pc1 --do-label \ --generic-time \ --fwhm 15 \ --qcache fsaverage \ --stack-pc1 lh.testretest.thickness-pc1.stack.mgh \ --isec-labels lh.testretest.fsaverage.cortex.label mri_glmfit --osgm \ --glmdir lh.testretest.thickness-pc1.fwhm15 \ --y lh.testretest.thickness-pc1.stack.fwhm15.mgh \ --label lh.testretest.fsaverage.cortex.label \ --surf fsaverage lh tksurfer fsaverage lh pial -overlay lh.testretest.thickness-pc1.fwhm15/osgm/sig.mgh --------------------------------------------------------------------------------------------------------------------------------------- Next I ran the following command to get volume change results: ---------------------------------------------------------------------------------------------------------------------------------------- long_stats_slopes --qdec long.testretest.qdec \ --stats aseg.stats \ --meas volume \ --sd $SUBJECTS_DIR \ --do-pc1 \ --generic-time \ --stack-pc1 testretest.aseg-pc1.stack.txt mri_glmfit --osgm \ --glmdir testretest.aseg-pc1 \ --table testretest.aseg-pc1.stack.txt cat testretest.aseg-pc1/sig.table.dat ---------------------------------------------------------------------------------------------------------------------------------------------- The results from the volume command are all in a table which is useful however I was wondering if there also is anyway to get a visual picture of the percent volume changes like the first spc command provided? Also is there any command that can give you the percent change in global brain volume? Thanks for the help! Cheers, Taylor North

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workflow of trouble shooting?
by chenchunhuichina 26 Sep '14

26 Sep '14

Dear Freesurfer experts, I am learning to do trouble shooting on recon-all results. But after read materials on the wiki, I am confused about the workflow. According to the tutorial slices, the work flow should be 1,recon-all �Cautorecon1 (Stages 1-5) 2,Check talairach transform, skull strip, normalization (?) 3,recon-all �Cautorecon2 (Stages 6-23) 4,Check surfaces (1)Add control points: recon-all �Cautorecon2 (Stages 10-23) (2)Edit wm.mgz: recon-all �Cautorecon2-wm (Stages 13-23) (3)Edit brainmask.mgz: recon-all �Cautorecon-pial (Stage 23) 5,recon-all �Cautorecon3 (Stages 24-30) Note: all stages can be run individually (this note was also from the slice) But on the trouble shooting wiki page http://freesurfer.net/fswiki/FsTutorial/TroubleshootingData , the order is 1, edit brain mask 2, edit wm volume 3, correcting topological defects 4, skull strip 5, control point 6, talairach transformation 7, edit aseg My quesion is, shouldn't I stick to the stages 1-30 order? I mean, I think results from earlier stages will influence later stages, so once an earlier stage output was edited, all the following steps should re-run, right? why talairach transformation can be checked later, which I think one should redo nearly every thing, right? Or, are the 7 trouble shooting steps independ from each other, and I can edit in any order i want then re-run all necessary steps? For example, should I edit wm and brian mask together, then run recon-all �Cautorecon2, or should I edit wm and run recon-all �Cautorecon2 then edit brainmask and run recon-all �Cautorecon-pial? Thanks for any help! Best~ 2014-09-26 Chunhui Chen _________________ State Key Laboratory of Cognitive Neuroscience and Learning Beijing Normal University Beijing, China 100875 ��ˣ� Thomas Yeo ��ʱ�䣺 2014-09-26 12:52:20 �ռ��ˣ� freesurfer ��ͣ� ��⣺ [Freesurfer] Brainmap Ontology Dear FreeSurfer List, I like to introduce you to a new set of reference brain networks (cognitive components) estimated from 10,449 experiments and 83 behavioral tasks from the BrainMap database, which can be downloaded here: https://surfer.nmr.mgh.harvard.edu/fswiki/BrainmapOntology_Yeo2015. The networks will be incorporated in some future version of FreeSurfer. Since these networks are estimated from (meta-analytic) task data, they are meant to complement (not replace) the current resting-state networks in FreeSurfer (https://surfer.nmr.mgh.harvard.edu/fswiki/CorticalParcellation_Yeo2011) Cheers, Thomas _______________________________________________ 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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Re: [Freesurfer] Postdoctoral Position in Neuroimaging in the Alzheimer’s disease and other cognitive disorders Unit of the Hospital Clinic, Barcelona, Spain
by Juan Domingo Gispert López 26 Sep '14

26 Sep '14

Dear all, I would like to draw your attention to the following job opportunity: Job Summary: IDIBAPS invites applications for a full-time postdoctoral position to conduct post-processing and analyzing of MRI neuroimaging data (e.g. structural, fMRI, DWI), as part of a clinical research program in the Alzheimer’s disease and other cognitive disorders Unit of the Hospital Clinic (Barcelona, Spain). Principal Responsibilities: The primary responsibility of this position includes post-processing and analyzing brain MRI data within the project entitled “Organising Knowledge about Neurodegenerative Disease Mechanisms for the improvement of Drug Development and Therapy” code number:115568, funded by the “FRAUNHOFERGESELLSCHAFT ZUR FOERDERUNG DER ANGEWANDTEN FORSCHUNG E.V”. This study will enhance our knowledge of the AD pathological processes in order to prevent or delay the disease. Within this study we are collecting a comprehensive amount of data, including blood samples, mental health, quality of life and risk factors, as well as, neuroimaging procedures to assess brain function. Required Qualifications: · PhD in Biomedical Engineering, Medical Physics, Neuroscience or related disciplines. · Strong background in MRI analysis and related statistical methods for research (SPM, Freesurfer, FSL or similar). · Experience with image processing and data analysis. · Ability to think independently and work collaboratively. Benefits · Starting date: November 2014. · The postdoctoral position is scheduled initially for two years (open to renewal). · Salary will depend on experience. Additional Information: To apply, please submit a single PDF file containing the following: 1) Cover letter describing research interests and relevant background; 2) CV with list of publications; 3) The names of three individuals who could provide reference letters to rrhh.fundacio(a)clinic.ub.es<mailto:rrhh.fundacio@clinic.ub.es> Juan D. Gispert Head Neuroimaging Research Pasqual Maragall Foundation T. +34 93 316 09 90 Dr. Aiguader, 88 (Edifici PRBB) - 08003 Barcelona. Spain. http://www.fpmaragall.org/en_index.html ________________________________ Aquest missatge i els seus annexos poden contenir informació confidencial i exclusiva per al destinatari. El seu contingut no constitueix un compromís per part de l'emissor. Si rep aquest missatge per error, si us plau elimini’l sense revisar-lo ni reenviar-lo i notifiqui-ho al remitent. Gràcies per la seva col·laboració. Este mensaje y sus anexos pueden contener información confidencial y exclusiva para el destinatario. Su contenido no constituye un compromiso por parte del emisor. Si recibe este mensaje por error, por favor elimínelo sin revisarlo ni reenviarlo y notifíquelo al remitente. Gracias por su colaboración. This message and attachments may contain confidential and exclusive information intended only for the individual named. The content of this message does not imply any commitment by the sender. If you have received this e-mail by mistake, please delete it before reading or distributing and notify the sender. Thank you for your cooperation. [cid:image006.jpg@01CD0B4C.79CA6620] Gràcies per estalviar paper. Gracias por ahorrar papel.Thanks for saving paper.

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Brainmap Ontology
by Thomas Yeo 26 Sep '14

26 Sep '14

Dear FreeSurfer List, I like to introduce you to a new set of reference brain networks (cognitive components) estimated from 10,449 experiments and 83 behavioral tasks from the BrainMap database, which can be downloaded here: https://surfer.nmr.mgh.harvard.edu/fswiki/BrainmapOntology_Yeo2015. The networks will be incorporated in some future version of FreeSurfer. Since these networks are estimated from (meta-analytic) task data, they are meant to complement (not replace) the current resting-state networks in FreeSurfer (https://surfer.nmr.mgh.harvard.edu/fswiki/CorticalParcellation_Yeo2011) Cheers, Thomas

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Re: [Freesurfer] possible to use freesurfer segmentations to get mean values for anatomic structures from other sequences
by Douglas Greve 25 Sep '14

25 Sep '14

Hi Sal, yes you can. Use bbregister to register the lowb image to the anatomical. This creates a registration matrix. Use mri_vol2vol and the registration to map the ADC map to the anatomical, then use mri_segstats to extract the values doug ps. Please post questions to the FS list instead of us directly so that others can benefit and it gets archived. thanks! On 5/25/13 1:03 PM, Salil Soman wrote: > Dear Dr. Greve, > > Is it possible to register a nonstructural MR sequences (e.g. an ADC > map) with the aseg.mgz file (or aparc+aseg.mgz file, etc) and then, > using the segmentation from the aseg (or aparc+aseg) file to output a > mean ADC value for each anatomic area segmented? > > Thank you for your time and consideration. > > Best wishes, > > Sal > > Salil Soman, MD, MS

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Re: [Freesurfer] A question about spherical registration
by Reza Rajimehr 25 Sep '14

25 Sep '14

Thank you Doug for your comprehensive response. This looks clear, and I am going to try it out. Just one question for now: In step 1 (create a template from a single subject), I do not yet have "sphere.reg". Should I write "--surf-reg sphere"? make_average_surface --subjects $subjectlist[1] \ --out iter00 --template-only --surf-reg sphere Reza Hi Reza, I think that this should work. doug set subjectlist = (subject1 subject2 ...) 1. Create a template from a single subject make_average_surface --subjects $subjectlist[1] \ --out iter00 --template-only --surf-reg sphere.reg 2. Register each subject to this template, including first subject. Each of these may take 30 min, so, if you have a lot of subjects, you may want to submit each job to the cluster. foreach subject ($subjectlist) # Create subject/surf/iter00.sphere.reg, --no-annot for monkey surfreg --s $subject --t iter00 --no-annot end 3. Create a new template from all subjects using the new registration make_average_surface --subjects $subjectlist \ --out iter01 --template-only --surf-reg iter00.sphere.reg 4. Register each subject to this new template foreach subject ($subjectlist) # Create subject/surf/iter01.sphere.reg, --no-annot for monkey surfreg --s $subject --t iter01 --no-annot end 5. Return to step 3. Iterate 4 or 5 times to remove the dependence on the first subject. When using mri_surf2surf or mris_preproc, spec --surfreg iterXX.sphere.reg. For mris_preproc also spec --targ iterXX On 09/19/2014 10:24 AM, Reza Rajimehr wrote: > Hi, > > I have a question about spherical registration, and I couldn't find a > relevant answer in the mailing list. > > I have two subjects S1 and S2 with corresponding functionals. I want to > show the functionals of each subject on the surfaces of the third subject > S3. I have .sphere files for S1, S2, and S3, but I don't have .sphere.reg > files yet because these are monkey subjects and I did not want to register > them to the buckner40.tif template. Since my goal is not group averaging, > and it is just to map functionals to the same-subject anatomicals and then > to the target-subject anatomicals, I was thinking of one of the following > solutions: > > 1) Convert sphere of S3 to a template .tif file, then use mris_register to > register spheres of S1, S2, and S3 to that template and generate > sphere.reg for all the subjects. Not sure if mris_make_template works for > one subject though. > > 2) Make a template from "S1 and S2" through the procedure described at > https://surfer.nmr.mgh.harvard.edu/fswiki/SurfaceRegAndTemplates#Creatingar…. > Then register S1, S2, and S3 to that template and generate sphere.reg for > all the subjects. > > Which approach is recommended? > > BTW, I do not know of a monkey template that is based on the surfaces from > a large group of monkeys. > > Thanks for any advice, > Reza

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Question about Longitudinal LME Modeling
by Karishma Smart 25 Sep '14

25 Sep '14

Dear Freesurfers, If I am planning to do a longitudinal analysis, I understand that the LME Model is probably the most appropriate choice. However, it says on the website that it is for univariate and mass-univariate analyses. I would need a longitudinal model that can handle *multivariate* statistics (a longitudinal study using multi-modal imaging + covariates). Can the LME model do this? If not, is there another way to do this in FreeSurfer? Thanks! Karishma -- Karishma Smart B.A. Biological Sciences Cornell University Class of 2013 Boston University School of Graduate Medical Sciences Class of 2015

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A question about spherical registration
by Reza Rajimehr 25 Sep '14

25 Sep '14

Hi, I have a question about spherical registration, and I couldn't find a relevant answer in the mailing list. I have two subjects S1 and S2 with corresponding functionals. I want to show the functionals of each subject on the surfaces of the third subject S3. I have .sphere files for S1, S2, and S3, but I don't have .sphere.reg files yet because these are monkey subjects and I did not want to register them to the buckner40.tif template. Since my goal is not group averaging, and it is just to map functionals to the same-subject anatomicals and then to the target-subject anatomicals, I was thinking of one of the following solutions: 1) Convert sphere of S3 to a template .tif file, then use mris_register to register spheres of S1, S2, and S3 to that template and generate sphere.reg for all the subjects. Not sure if mris_make_template works for one subject though. 2) Make a template from "S1 and S2" through the procedure described at https://surfer.nmr.mgh.harvard.edu/fswiki/SurfaceRegAndTemplates#Creatingar…. Then register S1, S2, and S3 to that template and generate sphere.reg for all the subjects. Which approach is recommended? BTW, I do not know of a monkey template that is based on the surfaces from a large group of monkeys. Thanks for any advice, Reza

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MNI Coordinates
by Venkataraman, Archana 25 Sep '14

25 Sep '14

Hi Freesurfer experts, I have a set of RAS coordinates in the Freesurfer fsaverage space. What is the easiest way to transform them to MNI152 space? Thanks. - Archana

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