Freesurfer September 2014

freesurfer@nmr.mgh.harvard.edu

120 participants
164 discussions

Overclocking CPU for Freesurfer
by Chiu, Bryan (PHTH) 29 Sep '14

29 Sep '14

Hi, Is anyone aware of any issues that arise from overclocking and using Freesurfer? I was looking to see how much it would speed up recon-all with OpenMP using a stable overclock. _______________________________________ Bryan Chiu Undergraduate Research Assistant Aging, Mobility, and Cognitive Neuroscience Lab Djavad Mowafaghian Centre for Brain Health Department of Physical Therapy Faculty of Medicine University of British Columbia

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Pial Surface Incorrect For Native T1
by Zachary Greenberg 29 Sep '14

29 Sep '14

Hello Freesurfer experts, I am having a tough time getting my pial surfaces into the correct anatomical space. I work with ECoG Patients, so we have pre-implant high resolution T1s (GE SPGR), and post-implant high resolution CTs that show the location of ECoG electrodes within the patient's skull. Our goal: display ECoG electrodes in their correct positions on the patient's native pial surface. Right now, my pipeline works like this: -ACPC align the T1, leave it in LAS orientation. -recon-all the acpc T1, using -3T -all -openmp 8 -use-gpu -corregister the CT to the acpc T1 (SPM), get electrode coords in T1 space -plot the electrodes on the resultant .pial surface from freesurfer The problem is, I can definitely tell that the position of the pial mesh is off (probably by 10 millimeters or so), as the electrodes (which have the correct coordinates from the T1 correg, confirmed visually by overlaying the CT on T1) are not in their correct positions on the mesh. Likewise, DTI fibers reconstructed from EPIs correctly corregistered to the T1 also appear off position within the .pial mesh. Here is what I have tried: compute the transform from .pial to .pial.native as suggested on https://surfer.nmr.mgh.harvard.edu/fswiki/FsAnat-to-NativeAnat tkregister2 --mov rawavg.mgz --targ orig.mgz --reg register.native.dat --noedit --regheader mri_surf2surf --sval-xyz pial --reg register.native.dat rawavg.mgz --tval lh.pial.native --tval-xyz --hemi lh --s subjectname This results in a mesh that is flipped (left is right) and rotated such that anterior is inferior (frontal cortex is pointing downward). The mesh appears this way when plotted in any viewer besides freesurfer (MATLAB mesh, Pyqt) but appears in the correct orientation in freeview. Replacing orig.mgz with the original T1.nii in the command above produces the opposite effect, freeview plots the orientation wrong, and any other viewer plots the Mesh oriented correctly, and the mesh appears to be identical to the originally output .pial mesh (electrodes are still wrong). Any help in pin pointing what is going wrong here would be greatly appreciated. I have a feeling it has something to do with the mesh being in surface RAS and the original T1 being in LAS. Thanks a bunch, -Zack

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mri_watershed problems
by Sam Zorowitz 29 Sep '14

29 Sep '14

Dear Freesurfer community, I am running into issues with mri_watershed, which I am using the create the BEM surfaces. In testing different preflooding height threshold (recommended for accurate skull-stripping), I am running into the issues that an -h 56 produces results where the cerebellum is stripped away, but -h 57 leaves far too much non-brain material in the image. As a result, my BEM surfaces are unrepresentative of the brain (either shrunken in or enlarged). I do, however, already have a satisfying brain-mask. Is there a way to pass the brain mask to mri_watershed to create new BEM surfaces without it creating a new brain mask? Sam Zorowitz Clinical Research Coordinator Division of Neurotherapeutics Department of Psychiatry: Neurosciences Massachusetts General Hospital 149 13th Street, Rm 2620e Charlestown, MA 02129

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how to deal with a big brain lesion?
by Abel Lei 29 Sep '14

29 Sep '14

Hi FreeSurfer experts, I happen to have a participant whose brain lesion from stroke (hemorrhage) distributed over a wide area. Therefore, the recon-all result is showing a big whole, about half a size of the cortex, on the anterior part of the left hemisphere corresponding to the lesion site. When I checked the previous mails, it is recommended to edit the WM volume for the whole caused by lesions: https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/WhiteMatterEdits_freev… But because the size of the lesion is so big, involving more than 100 slides coronally, the process to fill the lesion area by Voxel Edit will be as long as tracing the lesion manually slide by slide. I wonder if you would have other suggestions to correct such a big geometric accuracy. Please let me know if you need other info. Thank you so much for your help! -Abel

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Out of memory error on mri_cvs_register
by Ali-Reza Mohammadi-Nejad 29 Sep '14

29 Sep '14

Hi I am trying to do an mri_cvs_register for two subjects analyzed with FS-5.1.0 on a 64-bit CentOS linux vmware on a 64 bit windows 7 with 16GB memory. I am running a signle mri_cvs_register and after certain time the process terminates with out of memory error. I have done this work a lot of times with different preprocessed subjects. Could you please let me to know that, How can I solve this problem? Best regards, Mohammadi-Nejad

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Functional Overlay onto Structural
by Chiu, Bryan (PHTH) 28 Sep '14

28 Sep '14

Hi, I need to overlay some functional imaging data onto a structural scan to create some figures. How would I do this? I tried an older tutorial but it seems the files don't exist anymore in the tutorial dataset (https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Visualization) However the image provided is what I would like to create as a figure. It is not necessary to overlay onto the participants brain and could easily get away with overlaying it on a standard brain. I was given analysis files from FSL. Namely the one I was told to overlay was *.nii.gz file following the FEAT analysis from FSL. Regards in advance. _______________________________________ Bryan Chiu Undergraduate Research Assistant Aging, Mobility, and Cognitive Neuroscience Lab Djavad Mowafaghian Centre for Brain Health Department of Physical Therapy Faculty of Medicine University of British Columbia

2 1

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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Freesurfer September 2014