Freesurfer May 2019

freesurfer@nmr.mgh.harvard.edu

95 participants
141 discussions

Spatial smoothing kernel in fsfast
by Zhi Li 15 May '19

15 May '19

External Email - Use Caution Dear Freesurfer experts. Now I am using preproc-sess to preprocess functional MRI data. I would like to smooth the data first and then resample them into the standard space. Hence I run 'preproc-sess -s sub001 -fsd func -stc odd -fwhm 0 -per-run' first, and then 'spatialsmooth-sess -s sub001 -fsd func -i fmcpr.odd -o fmcpr.odd.sm5 -fwhm 5', finally 'preproc-sess -s sub001 -fsd func -stc odd -surface fsaverage lhrh -mni305 -fwhm 0 -per-run' (I have already renamed the stem of smoothed file from fmcpr.odd.sm5 to fmcpr.odd). However, the preprocessed data 'fmcpr.odd.sm0.mni305.2mm.nii.gz' contains both cortical and subcortical data. If I use '-fwhm 1' this file only contains the subcortical area. May I know why and how to fix it? About each stage embedded in 'preproc-sess', if I would like replace one stage with other software/algorithms, can I just change the name of the generated file by other software/algorithms to the name of file in this stage of 'prepoc-sess', and them rerun 'preproc-sess' while keep the flag '-update' on? For example, if I would like to use FSL/SPM to register the functional image to structural data, can I just rename the mat-file which describes the affine registration generated by FSL/SPM to 'register.dof6.mat'? Looking forward to your kind suggestions. Thanks and best wishes, Lizhi

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Issue with vol2surf
by Martin Juneja 15 May '19

15 May '19

External Email - Use Caution Hi FS experts, I am interested in displaying my ROI: ROI.nii (which is in standard space: avg152T1.nii.gz) on to fsaverage space. For that, I performed following steps: (1). Registered my template to fsaverage and saved the transformation matrix TT.dat as following: fslregister --s fsaverage --mov ROIs/avg152T1.nii.gz --reg TT.dat (2). Mapped my ROI to fsaverage using the transformation matrix TT.dat as following: mri_vol2surf --mov ROIs/ROI.nii --reg TT.dat --projdist-max 0 1 0.1 --interp nearest --hemi lh --out ROIs/ROI_Trans.mgh This works for 12 out of my 14 ROIs, but two of the ROIs are not displaying properly, and after the transformation when I displayed those on fsaverage space, these ROIs cover the whole hemisphere (please see attached: e.g. overlaying an ROI_Trans on fsvaerage space). I confirmed that both of these (non-working) ROIs (in .nii form) look fine on avg152T1.nii.gz, and on fsaverage when applying the transformation as following: tkmedit fsaverage T1.mgz -overlay ROIs/ROI.nii -overlay-reg TT.dat -fthresh 0.5 -surface lh.white -aux-surface lh.white I would really appreciate any help. Thanks.

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Control Points to Include Hyperintensity in WM Surface
by Rachel Hoel 15 May '19

15 May '19

External Email - Use Caution Dear Freesurfer Developers, We're still struggling with editing a subject where a hyperintensity in the right temporal lobe leads to poor white and grey matter segmentation. The coordinates are [83, 163, 139]. Our study is using the longitudinal processing pipeline with version 6.0. Even after adding several control points and running recon-all, the white matter is still not fully being included in the surface. I've also tried filling in the wm voxels instead of adding control points, but no luck there either. We are performing white and grey matter edits starting at the cross sectional. I was wondering what would be the best way to go about editing this subject? If it helps, I just ftp'ed the subject and attached some screenshots of the error. Please let me know if there's any other information I can provide you with. Thanks in advance, Rachel

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Voxel to Surface Coordinates
by Song, Da-Yea 15 May '19

15 May '19

External Email - Use Caution Hello, We have an anatomical atlas that we have incorporated in the FreeSurfer pipeline. Is it possible to convert this voxel based atlas into MNI152 surface coordinates? Any suggestions or comments would be greatly appreciated. Thank you, Da-Yea ---------------------------------------------------------------------- Disclaimer: The materials in this e-mail are private and may contain Protected Information. Please note that e-mail communication is not encrypted by default. You have the right to request further emails be encrypted by notifying the sender. Your continued use of e-mail constitutes your acknowledgment of these confidentiality and security limitations. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying, distribution, or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this e-mail in error, please immediately notify the sender via telephone or return e-mail.

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Thalamus segmentation {Disarmed}
by 郑凤莲 15 May '19

15 May '19

External Email - Use Caution Dear Experts, When I used the recent FS version for thalamus segmentation, I have segmented it sucessfully. However, in the .txt file, there are no the volume of lateraldorsal and reticular nuclei. Is there any error in my processing steps? I don't know the reason for this cese. I am looking forward to your reply. Thanks very much in advance. Sincerely, Zheng | | 郑凤莲 | | 邮箱：zhengfenglian0105(a)163.com | 签名由网易邮箱大师定制

2 1

Download a sample dataset Failed
by Hui Xu 15 May '19

15 May '19

External Email - Use Caution Dear Professors, I began my study of FreeSurfer few days ago. So happy to learn and enjoy data analyses using FreeSurfer. Now, a problem happened when I wanna download a sample dataset which can be used to become familiar with the LME Matlab tools. The download always failed. Please help me to solve this problem. The website is https://surfer.nmr.mgh.harvard.edu/fswiki/LinearMixedEffectsModels, and please check here "An optional sample dataset which can be used to become familiar with the LME Matlab tools can be found here (485 MB)." This is the sample dataset I wanna download. Many thanks. Hui PhD Candiate, Medical Imaging and Psychology

1 0

Computing measures like area for a custom surface
by Tim Schäfer 15 May '19

15 May '19

External Email - Use Caution Dear list, I have created a custom surface at 50% thickness between the white and pial for my subjects (`mris_expand -thickness lh.white 0.5 lh.graymid`). Is there a way to compute measures like curv and area for this surface using FreeSurfer tools? An example to clarify: I would like to get a file named lh.area.midgray for my new midgray surface, just like I have lh.area and lh.area.pial for the white and pial surfaces, respectively. I have checked the recon-all devtable [1] and it looks like `mris_make_surfaces` is used to compute these measures. But it is not clear to me whether I could use it for a custom surface as well (and if so, how). Best, Tim [1] https://surfer.nmr.mgh.harvard.edu/fswiki/ReconAllTableStableV6.0 -- 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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A Question Regarding Smoothing a Surface
by Maedeh Khalilian 15 May '19

15 May '19

External Email - Use Caution Dear experts, I have a parcellation scheme (an annotation file). Now I wanna smooth the map for better visualization. The command "mri_surf2surf" can do it ,but it doesn't recognize .annot. Now I wonder how to do it. I would appreciate it if u could help me with that. Best wishes, Maedeh,

1 0

Freesurfer 5.3 flags
by Aaron Tanenbaum 14 May '19

14 May '19

External Email - Use Caution Hello freesurfers, Our lab has been using freesurfer 5.3 for a while. We use the following flag when we run the initial recon-all -mprage -hippo-subfields -qcache -cortparc3 -parcstats3 -cubic -pctsurfcon -custom-tal-atlas TRIO_PIB_NDC_as_mni_average_305 However i have found out that we do not use any of these flags when we have we rerun recon-all after making standard edits. So my question is do any of these flags need to be used when rerun recon-all?

2 1

aparcstats2table
by Alan Francis 14 May '19

14 May '19

External Email - Use Caution Hi Doug: I used the following command: [airhunger:Structural_for_7T] (nmr-stable6-env) aparcstats2table --subjects 100610 --hemi rh --meas thickness --tablefile aparc_stats.txt However, I got an error message: File "/usr/local/freesurfer/stable6/bin/aparcstats2table", line 156 print 'ERROR: atleast 1 subject must be provided' ^ SyntaxError: Missing parentheses in call to 'print'. Did you mean print('ERROR: atleast 1 subject must be provided')? I have used this command on several occasions without any problems, so this is quite puzzling. Could you please help. Thanks, Alan -- *|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|* *Alan N. Francis PhDInstructor in PsychiatryHarvard Medical School* *Louis V. Gerstner III scholarMartinos Center for Biomedical Imaging* *Massachusetts General Hospital* *149, 13th street, Charlestown, MA* *alanf(a)bwh.harvard.edu <ezra_wegbreit(a)brown.edu> * *afrancis(a)mclean.harvard.edu <afrancis(a)mclean.harvard.edu>*

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Freesurfer May 2019