Freesurfer February 2019

freesurfer@nmr.mgh.harvard.edu

114 participants
196 discussions

Alignment to ACPC
by Sadia Sheikh 26 Feb '19

26 Feb '19

External Email - Use Caution Hello Freesurfer experts Freesurfer preprocessed data by(recon-all) are ACPC aligned? If not how can I align my files to ACPC? I read the documents but I am still very confused about the alignment and coordinate system in freesurfer. Thanks in advance Regards Sadia Research Student

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Freesurfer pre-processing on different operating systems
by Tim Schäfer 25 Feb '19

25 Feb '19

External Email - Use Caution Dear Freesurfer experts, we recently got access to a Linux-based cluster computer, and I need to run FreeSurfer pre-processing for several 100 subjects soon. We also have a Mac Pro with many cores that we used in the past and that could take part in the pre-processing. I found an older reference which suggests you should not run the pre-processing for one study on different architectures/operating systems [1] because this may affect the results. Does this still apply to Freesurfer 6? What are your recommendations in this regard? Also, out of curiosity: it is obvious why one should not use different Freesurfer versions, but what are the reasons for the reported differences between architectures/workstations? [1] https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0038234 Tim -- Dr. Tim Schäfer Postdoc Computational Neuroimaging Department of Child and Adolescent Psychiatry, Psychosomatics and Psychotherapy University Hospital Frankfurt, Goethe University Frankfurt am Main, Germany

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Different paradigm files
by Zhi Li 25 Feb '19

25 Feb '19

External Email - Use Caution Hello FreeSurfer experts, It seems that all the subjects adopt a single same paradigm file in FsFast, am I correct? So how to handle it if each subject has different paradigm files, e.g., different onset time and duration? I could do the first-level analysis in each individual data, however, I cannot concatenate data with 'isxconcat-sess' due to that there is not an analysis folder generated from a same paradigm file. Any suggestions? Thanks and best regards, Lizhi

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dt_recon and mri_vol2vol issue
by Daniel Callow 25 Feb '19

25 Feb '19

External Email - Use Caution Hello freesurfer experts, I am running dt_recon with the following script dt_recon --sd /Volumes/DANIEL/dti_freesurf/diffusion_recons --i /Volumes/DANIEL/dti_freesurf/diffusion_recons/${subj}.${cond}/image000001.dcm --s ${subj}.${cond} --b dwi.bvals dwi.voxel_space.bvecs --o /Volumes/DANIEL/dti_freesurf/dtrecon/${subj}.${cond}. and mri_vol2vol to get the wmparc and aseg.mgz files in my lowb space with the script below mri_vol2vol --mov $subj_dir/dtrecon/${subj}.${cond}./lowb.nii.gz --targ $subj_dir/diffusion_recons/${subj}.${cond}/mri/wmparc.mgz --inv --interp nearest --o /Volumes/DANIEL/dti_freesurf/diffusion_recons/${subj}.${cond}/mri/wmparc2diff.mgz --reg $subj_dir/dtrecon/${subj}.${cond}./register.dat --no-save-reg mri_vol2vol --mov $subj_dir/dtrecon/${subj}.${cond}./lowb.nii.gz --targ $subj_dir/diffusion_recons/${subj}.${cond}/mri/aseg.mgz --inv --interp nearest --o $subj_dir/dtrecon/${subj}.${cond}./aseg2diff.nii.gz --reg $subj_dir/dtrecon/${subj}.${cond}./register.dat --no-save-reg However, one of my subjects shows a major issue with the mri_vol2vol registration (for most of the subject scans it seems to work no problem). When looking at the wmparc2diff.mgz I created, it is apparent that the registration of the wmparc to wmparc2diff space actually causes wmparc2diff.mgz to be further from the lowb than wmparc is (the brain is shifted severely to the right). This same registration issue occurs for aseg.mgz. When I look at fa-tal.nii.gz it is poorly registered (again worse than FA overlayed on aseg or wmparc which happens to be pretty close without dt_recon). I assume this means there is an issue with the register.dat file for this subject? If so is there any way to troubleshoot the issue and get a correct register.dat file from dt_recon? For reference, the following commands and registration steps have worked for other subjects, as well as this same subject's scans under a different condition. At first glance there don't seem to be any specific issues with the anatomical or diffusion images before the registration attempt. Any advice with troubleshooting would be greatly appreciated. Best, *Daniel Callow* *PhD Student, Neuroscience and Cognitive Science* Exercise for Brain Health Lab University of Maryland, College Park *ddcc2442(a)gmail.com <ddcc2442(a)gmail.com>* 443-254-6298 *Daniel Callow* *PhD Student, Neuroscience and Cognitive Science* Exercise for Brain Health Lab University of Maryland, College Park *ddcc2442(a)gmail.com <ddcc2442(a)gmail.com>* 443-254-6298

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Partial Volume Correction for FA map
by Daniel Callow 25 Feb '19

25 Feb '19

External Email - Use Caution Hello, I am currently trying to run PVC for my adc images using the following script. mri_gtmpvc --i /Volumes/DANIEL/dti_freesurf/dtrecon/${subj}.${cond}./adc-masked.nii.gz --reg /Volumes/DANIEL/dti_freesurf/dtrecon/${subj}.${cond}./register.lta --psf 0 --seg /Applications/freesurfer/subjects/Freesurfer_output/${subj}.${cond}.fsoutput/mri/gtmseg.mgz --default-seg-merge --auto-mask PSF .01 --mgx .25 --o /Volumes/DANIEL/dti_freesurf/dtrecon/${subj}.${cond}./adc.gtmpvc.output --no-rescale What would I need to change in order to accurately perform PVC on FA images? Would the --mgx flag need to be changed? Best, *Daniel Callow* *PhD Student, Neuroscience and Cognitive Science* Exercise for Brain Health Lab University of Maryland, College Park *ddcc2442(a)gmail.com <ddcc2442(a)gmail.com>* 443-254-6298

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Re: [Freesurfer] downsampling orig.mgz
by Ella Hanns 25 Feb '19

25 Feb '19

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Mapping between fsaverage_sym hemispheres
by Alon Baram 25 Feb '19

25 Feb '19

External Email - Use Caution Hello, I would like to get a mapping (preferably in Matlab) where for a given vertex in the left hemi of fsaverage_sym returns the vertex of the exact same cortical location, but on the right hemisphere. Is that possible? Thanks for the help.

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Re: [Freesurfer] CAT12 surfaces on tkregister2 and Freeview
by Loucao, Ricardo 25 Feb '19

25 Feb '19

External Email - Use Caution Thanks for the reply! I tried the --vol-geom orig.mgz option but to no avail. Small update: I inspected the metadata on the surface files using mris_info and discovered that the ctr property was different between the CAT generated surface and the pial surface that was produced from recon-all, while all the other transforms where the same. So I figured the difference in the ctr should be compensated by a translation. To do that, I first created a CAT2FS.fslmat transform of the form: 1 0 0 (CAT.ctr(1)-FS.ctr(1)) 0 1 0 (CAT.ctr(3)-FS.ctr(3)) 0 0 0 (CAT.ctr(2)-FS.ctr(2)) 0 0 0 1 (NOTE: Im sure the order of the translation portion of the matrix has something to do with the orientation convention but I couldnt be bothered to dig deeper - I got this by trial and error) and then converted it to LTA using lta_convert: lta_convert --infsl CAT2FS.fslmat --outlta CAT2FS.lta --src orig.mgz --trg orig.mgz and then applied this transformation using mris_transform: mris_transform ?h.CAT CAT2FS.lta ?h.CATreg sure enough when I load CATreg on tkregister2 I see everything perfectly aligned, but after doing mri_vol2surf the surface overlay is still messed up in Freeview. Any suggestions? Thanks in advance for the help! Ricardo ------------------------------------------------------------------------------------------------ ------------------------------------------------------------------------------------------------ Forschungszentrum Juelich GmbH 52425 Juelich Sitz der Gesellschaft: Juelich Eingetragen im Handelsregister des Amtsgerichts Dueren Nr. HR B 3498 Vorsitzender des Aufsichtsrats: MinDir Dr. Karl Eugen Huthmacher Geschaeftsfuehrung: Prof. Dr.-Ing. Wolfgang Marquardt (Vorsitzender), Karsten Beneke (stellv. Vorsitzender), Prof. Dr.-Ing. Harald Bolt, Prof. Dr. Sebastian M. Schmidt ------------------------------------------------------------------------------------------------ ------------------------------------------------------------------------------------------------

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Post-Doctoral Fellowship in Whole Brain Modelling
by John Griffiths 25 Feb '19

25 Feb '19

External Email - Use Caution Post-Doctoral Fellowship in Whole Brain Modelling The Whole Brain Modelling Group (PI Dr. John Griffiths; www.grifflab.com) at the Krembil Centre for Neuroinformatics, Toronto, is looking to hire a Post-Doctoral Fellow with a strong background in neuroimaging and/or computational neuroscience. The successful candidate shall spearhead the group's efforts in computational modelling of large-scale brain dynamics, with a particular focus on brain stimulation (TMS, TDCS), EEG, neural plasticity, and macro-connectomics. The fellow will have the opportunity to shape the details of the project based on their specific interests, as well as to contribute to other ongoing projects on a range of topics, including: neuroinformatics of whole-brain modelling, mapping and modelling anatomical connectivity and microstructure with DWI in relation to ageing and stroke, and multi-scale modelling of the thalamocortical system in relation to sleep, pharmacological neuromodulation, and neuropsychiatric disease. The successful candidate will have a PhD in neuroscience, engineering, physics, psychology, or related area, a track record for independent research, and a strong publication record. Strong programming skills and familiarity with neuroimaging data analysis (s/d/fMRI and/or M/EEG) are required; experience with computational modelling using numerical simulations (particularly modelling of neural population activity with mean-field/neural mass/neural field techniques) would be advantageous. Full details of the position and application instructions can be found at www.grifflab.com/positions/ For informal inquiries, please email Dr. John Griffiths at john.griffiths(a)camh.ca with the title “Post-Doctoral Fellowship in Whole Brain Modelling” in the subject line. -- Dr. John D. Griffiths Independent Scientist @ Krembil Centre for Neuroinformatics, CAMH, Toronto Assistant Professor @ Department of Psychiatry, University of Toronto www.grifflab.com

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overlay cortical thickness estimates
by forsteca＠hu-berlin.de 25 Feb '19

25 Feb '19

External Email - Use Caution Thank you for your reply. I saved the estimates in a 4D matfile (I calculate the standard deviation over the cortical thickness values and get a 1638421xdouble for right hemisphere and left hemisphere each). I tried to use the save_mgh command to overlay them on the surface, but that doesn't work. Thank your for your help. Carina

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Freesurfer February 2019