Freesurfer

freesurfer@nmr.mgh.harvard.edu

30132 discussions

white matter edit
by Abazid, Leen 26 Feb '19

26 Feb '19

External Email - Use Caution ??Hello, I am a PhD student at the University of Texas in San Antonio. I am working on the PTSD project and we used the FreeSurfer to clean the MRI images of the patients. After we were done cleaning, the statistics analysis of the cingulate structure in the brain was not accurate, this part of the brain is one of the most important structure in the pathogenesis of PTSD. We believe that the FreeSurfer is messing the white matter with the gray matter and interpret what is supposed to be a gray matter as a white matter. So the values are not accurate which is affecting our results. We tried to use the command to edit the white matter but we are not sure if we are doing the correct thing. After the edit and re-running the FreeSurfer again on the white matter, the gray matter values are slightly increasing but the white matter values are increasing and decreasing, so we are not sure what the FreeSurfer is doing exactly and if our edit is correct. This is the command we are using to edit the white matter: freeview -v mri/brainmask.mgz \ mri/wm.mgz:colormap=heat:opacity=0.4 \ -f surf/lh.white:edgecolor=blue \ surf/lh.pial:edgecolor=red \ surf/rh.white:edgecolor=blue \ surf/rh.pial:edgecolor=red \ surf/rh.inflated:visible=0 \ surf/lh.inflated:visible=0 After done cleaning the white matter recon-all -autorecon2-wm -autorecon3 -subjid# Leen F. Abazid Ph.D. Student Neuroscience Imaging at the Research Imaging Institute UT Health Science Center at San Antonio (210) 823-3532

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MRISalloc error during automatic reconstruction
by Julia Ströhlein 26 Feb '19

26 Feb '19

External Email - Use Caution Dear experts, while running one of my subjects, I got this error: MRISalloc(732595, 480): could not allocate vertices Cannot allocate memory Linux xubuntu-VirtualBox 3.2.0-23-generic #36-Ubuntu SMP Tue Apr 10 20:41:14 UTC 2012 i686 i686 i386 GNU/Linux recon-all -s P_04 exited with ERRORS at Mon Feb 4 16:40:03 EST 2019 Do you know what went wrong and how I can fix this? Best regards, Julia

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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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