Freesurfer November 2018

freesurfer@nmr.mgh.harvard.edu

121 participants
189 discussions

Pial sueface error
by Miguel Ángel Rivas Fernández 06 Dec '18

06 Dec '18

External Email - Use Caution Hi Freesurfer devs, I´m doing a visual quality control of my pial and white matter segmentation using freeview and I noticed that several subjects could present an error in pial surface segmentation. I have attached two images. Is this an pial surface error? in that case, How can I fix it? maybe adding control points in order to extend the pial surface limit? Thanks Cheers,

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Question regarding mri_label2label and mris_anatomicalstats
by Wang, Xiaoyu 06 Dec '18

06 Dec '18

External Email - Use Caution Dear Freesurfer Experts, I am currently doing a Longitudinal LME comparison between early and late onset Parkinson's Patients. After the Matlab analysis, I view the resulting sig.mgh file in tksurfer and create a label based on regions that pass FDR 0.05. I then use the mri_label2label on the label I created to resample it back onto my subject pool using the following loop. for i in `less ./list` do echo $i mri_label2label \ --srcsubject fsaverage \ --srclabel fsaverage/label/ReFront.label \ --trgsubject $i \ --trglabel $i/label/ReFront.label \ --hemi lh \ --regmethod surface \ done However, the resulting labels have a different shape and surface area from the one I first created, and the data I obtained from mris_anatomical_stats conflicts with the results from LME. What am I doing wrong? Sincerely, Xiaoyu Wang

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CerebralWhiteMatterVol
by Song, Da-Yea 06 Dec '18

06 Dec '18

External Email - Use Caution Hello, Does the CerebralWhiteMatterVol (from the aseg.stats) include the cerebellum? Thank you so much in advance for your help! Best, 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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mean LGI per hemisphere
by C.P.E. Rollins 06 Dec '18

06 Dec '18

External Email - Use Caution Dear Freesurfer developers, I have a quick question regarding calculating mean LGI (Marie Schaer's measure) per hemisphere. I believe that I can get the mean LGI per hemisphere with a command like: mri_segstats --slabel subject_ID lh $SUBJECTS_DIR/subject_ID/label/lh.cortex --i $SUBJECTS_DIR/my_subject_id/surf/lh.pial_lgi --sum lh.aparc.pial_lgi_lh.stats which gives me a file like this: # SUBJECTS_DIR /lustre/group/p00355/REST_Beijing_SCZ/Freesurfer # subjectname Sub_010 # Label Sub_010 lh /lustre/group/p00355/REST_Beijing_SCZ/Freesurfer/Sub_010/label/lh.cortex # InVolFile /lustre/group/p00355/REST_Beijing_SCZ/Freesurfer/Sub_010/surf/lh.pial_lgi # InVolFileTimeStamp 2018/11/13 16:38:05 # InVolFrame 0 # ExcludeSegId # Only reporting non-empty segmentations # VertexArea_mm2 0.678865 # TableCol 1 ColHeader Index # TableCol 1 FieldName Index # TableCol 1 Units NA # TableCol 2 ColHeader SegId # TableCol 2 FieldName Segmentation Id # TableCol 2 Units NA # TableCol 3 ColHeader NVertices # TableCol 3 FieldName Number of Vertices # TableCol 3 Units unitless # TableCol 4 ColHeader Area_mm2 # TableCol 4 FieldName Area # TableCol 4 Units mm^2 # TableCol 5 ColHeader StructName # TableCol 5 FieldName Structure Name # TableCol 5 Units NA # TableCol 6 ColHeader Mean # TableCol 6 FieldName Intensity Mean # TableCol 6 Units unknown # TableCol 7 ColHeader StdDev # TableCol 7 FieldName Itensity StdDev # TableCol 7 Units unknown # TableCol 8 ColHeader Min # TableCol 8 FieldName Intensity Min # TableCol 8 Units unknown # TableCol 9 ColHeader Max # TableCol 9 FieldName Intensity Max # TableCol 9 Units unknown # TableCol 10 ColHeader Range # TableCol 10 FieldName Intensity Range # TableCol 10 Units unknown # NRows 2 # NTableCols 10 # ColHeaders Index SegId NVertices Area_mm2 StructName Mean StdDev Min Max Range 1 0 7509 5068.1 Seg0000 2.6260 0.3824 1.8121 3.0658 1.2537 2 1 134787 91531.4 Seg0001 3.3455 0.8431 1.9459 5.7739 3.8280 I was wondering which row corresponds to the mean LGI for the left hemisphere (and what the other row corresponds to? Many thanks, Colleen

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FSGD File
by Larissa Bechtle 06 Dec '18

06 Dec '18

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mkcontrast-sess and mkcontrast2 matlab errors
by Emily Levin 06 Dec '18

06 Dec '18

External Email - Use Caution Hi FreeSurfer experts, I'm trying to run mkcontrast-sess using the newest development version of freesufer from Nov 30th, 2018, and I am getting a matlab permission denied error (see mkcontrast-sess_error text file). It seems to be happening around line 150-160 of mkcontrast2. However, when I copy the old mkcontrast-sess and mkcontrast2 scripts from freesurfer 6.0.0 (non-development version), it works fine in the development version. The two versions in question are the stable release 6.0.0 and the development release for centos7 Nov 30th, 2018. Any insight into why I'm getting permission denied would be really helpful. There don't seem to be any changes between the two scripts so I'm a little confused. Thanks, Emily -- Emily J. Levin Lab Manager Attention & Perception Neuroimaging Lab Boston University Lab: 617-358-1737

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Map image in MNI onto fsaverage
by john Anderson 05 Dec '18

05 Dec '18

External Email - Use Caution Dear Freesurfer experts, I have the mean PET images for a number of subjects in MNI152 space. For visualization purposes, I would like to map this mean image onto brain surface. How can I do it. I appreciate any suggestion you may provide. Thanks! John

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Recon-all - mghRead could not read rawavg.mgz
by Diamond, Bram Ryder 03 Dec '18

03 Dec '18

Hi Batuhan, Can you please upload the BE2 subject data using our ftp file exchange and let me know the exact command and terminal output when you ran mri_convert? Info on our ftp file exchange: https://surfer.nmr.mgh.harvard.edu/fswiki/FtpFileExchange Thanks, Bram Bram R. Diamond, BSc Research Technician II Laboratory for Computational Neuroimaging Martinos Center for Biomedical Imaging Massachusetts General Hospital 149 13th Street Charlestown, MA 02129 (p): 617-726-6598

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trouble in manual editing of pial surface
by 박경일 02 Dec '18

02 Dec '18

External Email - Use Caution Dear experts I met a problem during manual editing. My version is 5.3. Following FS tutorial, freeview process was run, which loaded T1, brainmask and apar+aseg images. Then, I clicked 'voxel edit', checked 'recon-edit' and clicked a part of image which had been excluded from cortex (outside the pial line). I saved it and also re-ran the recon-all process. The saved images were as follows. I compared the values before and after editing, but, the values of total cortical volume, e-TIV and the volume of temporal pole and sup temporal gyrus, were not changed. I have no idea whether some steps were skipped and why my editing did not reflect the numerical values of this areas. Thanks always. Sincerely yours Kyung

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Triangular mesh sampling problem
by 1013364183 01 Dec '18

01 Dec '18

External Email - Use Caution Dear FS We now have high and low resolution images, we want to resample each triangular surface mesh generated from low-resolution data onto the corresponding triangular surface mesh generated from high-resolution data and vice versa as follows: For every vertex in a low-resolution surface mesh we found the closest point on the high-resolution surface mesh (which typically fell within a triangle face of the mesh), and defined a point at that location on the high-resolution surface mesh (subsequently referred to as “sparse” meshes).What should we do to use freesurfer to do the above? Thanks in advance yours yujunjie

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Freesurfer November 2018