Freesurfer December 2018

freesurfer@nmr.mgh.harvard.edu

109 participants
175 discussions

How to run GLM FIT simulation in parallel?
by Sahil Bajaj 06 Dec '18

06 Dec '18

External Email - Use Caution Hello experts, I was trying to run mri_glmfit-sim --glmdir XY.glmdir --perm 1000 1.3 abs --cwp 0.05 --2spaces command, but its taking forever even if I reduce # of permutations from 1000 to 10. I was just wondering if there’s a version of FreeSurfer for Slurm parallel processing clusters. Thanks ! Sahil

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fMRI time series extraction
by Zhi Li 06 Dec '18

06 Dec '18

External Email - Use Caution Hello FreeSurfer Experts, Now I have a custom annotation file (only the cortical surface). May I ask how could I use it to extract the mean time series from the fsfast-preprocessed fMRI data? I have tried to transform this annotation file into anatomical volume first: mri_aparc2aseg --s fsaverage --annot test --o test.mgz It seems I cannot do it to the left and right surface respectively, right? How should use this .mgz file next? Any suggestions would be appreciated. Best wishes, Zhi Li

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Overall maxima is high and still no significant cluster
by Martin Juneja 06 Dec '18

06 Dec '18

External Email - Use Caution Hi FS experts, I am estimating the group-behavioral thickness interaction using contrast 2 FSGD file: https://surfer.nmr.mgh.harvard.edu/fswiki/Fsgdf2G2V at CFT < 0.01 and CWT < 0.05 at FWHM of 12 mm. I do not find any significant clusters and my output summary text file looks like the following. This file shows that overall maxima is 4.58212 (which corresponds to p < 0.0001 because -log (0.0001) = 4, so I am just wondering despite the fact that maxima is > 4, why I do not see this cluster in the summary/output *.mgh file? I would really appreciate any clarification and tips to modify my input thresholds so that I do not miss any significant findings here. Thanks. ----------------------------- # SearchSpace_mm2 76467.1 # SearchSpace_vtx 149953 # Bonferroni 2 # Minimum Threshold 2 # Maximum Threshold infinity # Threshold Sign abs # AdjustThreshWhenOneTail 1 # CW PValue Threshold: 0.05 # Area Threshold 0 mm^2 # CSD thresh 2.000000 # CSD nreps 10000 # CSD simtype null-z # CSD contrast NA # CSD confint 90.000000 # Overall max 4.58212 at vertex 10608 # Overall min -2.84277 at vertex 75476 # NClusters 0 # FixMNI = 0 # # ClusterNo Max VtxMax Size(mm^2) MNIX MNIY MNIZ CWP CWPLow CWPHi NVtxs WghtVtx Annot

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Surface based paired t test
by john Anderson 06 Dec '18

06 Dec '18

External Email - Use Caution Dear Freesurfer experts, I would like to run surface based paired t test of PET data on surface. For every subject I have visit pre treatment and post treatment. I tried to follow the instructions here https://surfer.nmr.mgh.harvard.edu/fswiki/PairedAnalysis but the toturial seems to be for cortical thickness data. How can i modify the command mris_preproc to do paired test of PEt data on brain surface mris_preproc --target fsaverage --hemi lh \ --meas thickness --out lh.paired-diff.thickness.mgh \ --fsgd pairs.fsgd --paired-diff thanks for any suggestion John

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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.

2 3

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

2 1

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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Freesurfer December 2018