Freesurfer August 2017

freesurfer@nmr.mgh.harvard.edu

145 participants
233 discussions

Map of covariance
by stdp82＠virgilio.it 05 Sep '17

05 Sep '17

Hi list,by applying a design e.g. 4GV1 in fsgd I could assess the dependence of group differences taking in account the effect of covariate.Anyway, where I should look if I want assess the the map showing the clusters in which the dependent variable is associated to covariate, tacking in account the group difference? Please could you suggest my the path?Thanks Stefano

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upsampling ?h.curv
by shahin＠nmr.mgh.harvard.edu 05 Sep '17

05 Sep '17

Dear Freesurfers, I want to project a map on up-sampled inflated brain. Up-sampled inflated brain has been generated using mris_mesh_subdivide command (without any problem). But when I apply the same command to ?h.cuv I get an error message that: ERROR: MRISread: file 'surf/rh.curv' has many more faces than vertices! Probably trying to use a scalar data file as a surface! I even tried to regenerate ?h.curv files using mris_make_surfaces as below: mris_make_surfaces -c -white rh.white_upsampled subjid ?h But this command automatically down-sample rh.curv after down-sampling rh.white. Regards

3 4

Interpretting Brain Segmentation Volume to eTIV ratio
by Mehta, Chintan 05 Sep '17

05 Sep '17

Dear FreeSurfer community, I wanted to interpret the BrainSegVol.to.eTIV ratio that is outputted from FreeSurfer version 5.2.0. In my sample of normally developing adolescents of ages 8 to 21, this ratio is between 0.65 and 0.85 for 98% of subjects. However, the value is less than 0.65 for 2% of subjects. Could this reflect actual feature of brain volume to eTIV? Or is this a reflection of poor scans, poor overall FreeSurfer processing, or inaccurate eTIV estimates for these subjects? Subjects with BrainSegVol.to.eTIV ratios less than 0.65 tended to all be females. They had Brain Segmentation volumes falling in normal ranges of females in the full sample. However, their eTIV was on the upper-end among eTIVs of females in the sample. If the eTIVs for these subjects were over-inflated, then it makes sense the ratios are especially low. Thank you. Best, Chintan

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group interaction with one continuous covariate and three nuisance variables (two continuous, one dichotomous)
by Ines Mürner-Lavanchy 05 Sep '17

05 Sep '17

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Multi-Subject Comparison in FreeSurfer
by Sherrill, John T 05 Sep '17

05 Sep '17

I am a new grad student and have been assigned a project in our Brain Imaging Research Center. I would be taking the time to push through and find these answers on my own but our program gives us 5 weeks of half days in a lab for a trial. So I am in a bit of a time crunch. I have been given a database of about 500 .nii files and been asked to find duplicates or likely duplicates. (Some subjects were duel-consented so they may have multiple scans.) What is the best way to recon-all all of the files? Individually, in small groups, or in one larger group? If I do it in groups do I need to list each file or can I just recon-all the entire directory? And if a recon-all on 1 file takes 6-20hr, will doing a recon-all on the entire data set take 500*(6-20hr)=3000-10,000hr? Any help is greatly appreciated. John Sherrill jtsherrill(a)uams.edu john_sherrill(a)me.com (870) 761-0580 ---------------------------------------------------------------------- Confidentiality Notice: This e-mail message, including any attachments, is for the sole use of the intended recipient(s) and may contain confidential and privileged information. Any unauthorized review, use, disclosure or distribution is prohibited. If you are not the intended recipient, please contact the sender by reply e-mail and destroy all copies of the original message.

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mris_anatomical_stats error: missing ", " in "Measure Cortex, CortexVol Total cortical gray matter volume, ..."
by Ernst Schwartz 05 Sep '17

05 Sep '17

Hi! It seems that in FreeSurfer 6, the comma between “CortexVol” and “Total cortical gray matter volume” is missing here’s the relevant part of one of my stats-files: # Table of FreeSurfer cortical parcellation anatomical statistics # # CreationTime 2017/08/23-20:19:44-GMT # generating_program /software/easybuild/software/FreeSurfer/6.0.0-centos6_x86_64/bin/mris_anatomical_stats # cvs_version $Id: mris_anatomical_stats.c,v 1.79 2016/03/14 15:15:34 greve Exp $ # mrisurf.c-cvs_version $Id: mrisurf.c,v 1.781.2.6 2016/12/27 16:47:14 zkaufman Exp $ # cmdline /software/easybuild/software/FreeSurfer/6.0.0-centos6_x86_64/bin/mris_anatomical_stats -mgz -cortex /data/datasets/pediatric/CLG//sub-A00057725_ses-CLG2/label/lh.cortex.label -a /data/datasets/pediatric/CLG//sub-A00057725_ses-CLG2/label/lh.aparc.a2009s.annot -b -f /data/datasets/pediatric/CLG//sub-A00057725_ses-CLG2/stats/lh.aparc.a2009s.pial.stats sub-A00057725_ses-CLG2 lh pial # sysname Linux # hostname cn4.cir.meduniwien.ac.at <http://cn4.cir.meduniwien.ac.at/> # machine x86_64 # user ernst # # SUBJECTS_DIR /data/datasets/pediatric/CLG/ # anatomy_type surface # subjectname sub-A00057725_ses-CLG2 # hemi lh # AnnotationFile /data/datasets/pediatric/CLG//sub-A00057725_ses-CLG2/label/lh.aparc.a2009s.annot # AnnotationFileTimeStamp 2017/08/23 22:18:44 # Measure Cortex, NumVert, Number of Vertices, 121790, unitless # Measure Cortex, PialSurfArea, Pial Surface Total Area, 105158, mm^2 # Measure Cortex, MeanThickness, Mean Thickness, 2.80672, mm # Measure BrainSeg, BrainSegVol, Brain Segmentation Volume, 1051285.000000, mm^3 # Measure BrainSegNotVent, BrainSegVolNotVent, Brain Segmentation Volume Without Ventricles, 1040194.000000, mm^3 # Measure BrainSegNotVentSurf, BrainSegVolNotVentSurf, Brain Segmentation Volume Without Ventricles from Surf, 1039128.584538, mm^3 # Measure Cortex, CortexVol Total cortical gray matter volume, 532907.136355, mm^3 # Measure SupraTentorial, SupraTentorialVol, Supratentorial volume, 926570.584538, mm^3 # Measure SupraTentorialNotVent, SupraTentorialVolNotVent, Supratentorial volume, 918874.584538, mm^3 # Measure EstimatedTotalIntraCranialVol, eTIV, Estimated Total Intracranial Volume, 1254280.104289, mm^3 cheers, Ernst ~ Ernst Schwartz Computational Image Research (CIR) Lab Department of Biomedical Imaging and Image-guided Therapy Medical University Vienna, Austria ----------------------------------------------------------------------

2 1

time.dat file in Kinetic Modelling MRTM1 step - Petsurfer processing
by M Janani 05 Sep '17

05 Sep '17

Hi team, Could anyone please tell how to create the time.dat file in the Kinetic Modelling MRTM1 step mri_glmfit --y km.hb.tac.nii.gz --mrtm1 km.ref.tac.dat time.dat --o mrtm1 --no-est-fwhm --nii.gz Regards, Janani ::DISCLAIMER:: ---------------------------------------------------------------------------------------------------------------------------------------------------- The contents of this e-mail and any attachment(s) are confidential and intended for the named recipient(s) only. E-mail transmission is not guaranteed to be secure or error-free as information could be intercepted, corrupted, lost, destroyed, arrive late or incomplete, or may contain viruses in transmission. The e mail and its contents (with or without referred errors) shall therefore not attach any liability on the originator or HCL or its affiliates. Views or opinions, if any, presented in this email are solely those of the author and may not necessarily reflect the views or opinions of HCL or its affiliates. Any form of reproduction, dissemination, copying, disclosure, modification, distribution and / or publication of this message without the prior written consent of authorized representative of HCL is strictly prohibited. If you have received this email in error please delete it and notify the sender immediately. Before opening any email and/or attachments, please check them for viruses and other defects. ----------------------------------------------------------------------------------------------------------------------------------------------------

2 1

Freesurfer PIB PET image processing
by M Janani 05 Sep '17

05 Sep '17

Hi Team, I apologize, I am new to Freesurfer . Currently we are processing PIB PET images. When we compare the SPM data along with FREESURFER outputs. We were able to see a large variation in the values. Could you please guide us in processing PIB PET images in Freesurfer? Since the signal of a PET image is very weak, we used MRI image as a guide to map it to Standard brain. How does Freesurfer process in this case? Your help would be grateful. Regards, Janani ::DISCLAIMER:: ---------------------------------------------------------------------------------------------------------------------------------------------------- The contents of this e-mail and any attachment(s) are confidential and intended for the named recipient(s) only. E-mail transmission is not guaranteed to be secure or error-free as information could be intercepted, corrupted, lost, destroyed, arrive late or incomplete, or may contain viruses in transmission. The e mail and its contents (with or without referred errors) shall therefore not attach any liability on the originator or HCL or its affiliates. Views or opinions, if any, presented in this email are solely those of the author and may not necessarily reflect the views or opinions of HCL or its affiliates. Any form of reproduction, dissemination, copying, disclosure, modification, distribution and / or publication of this message without the prior written consent of authorized representative of HCL is strictly prohibited. If you have received this email in error please delete it and notify the sender immediately. Before opening any email and/or attachments, please check them for viruses and other defects. ----------------------------------------------------------------------------------------------------------------------------------------------------

2 7

aparc.DKTatlas+aseg.mgz
by John Anderson 05 Sep '17

05 Sep '17

Dear experts, looking into the output of Freesurfer in this page https://surfer.nmr.mgh.harvard.edu/fswiki/ReconAllOutputFiles I see that there should be a file named "aparc.DKTatlas+aseg.mgz". Do I need FLAIR images to get this file. I ran the command recon-all --s subj --all and I can';t find this file thank you for any clarification John

4 7

Contrast matrix for PVR
by Sahil Bajaj 05 Sep '17

05 Sep '17

Hi everyone, >From FreeSurfer manual and discussion forum, I found that volume and LGI can be correlated using mri_glmfit command with -pvr flag. For that, my fsgd file has age, gender as covariates and the file is as following: GroupDescriptorFile 1 Class Male Class Female Variables Age Input zerek1 Male 21 Input zerek2 Male 25 etc. My concern is: To run mri_glmfit command, I am not sure how to define my contrast matrix if I am interested in removing the effect of age and sex. 1st option I tried is: 0 0.5 0.5 0 1 Here, I think first 0 regresses out age, 0.5 0.5 should be averaging over males and females and last 0 1 correlates between volume and LGI. But this looks like it is not giving me correct correlations maps, although there is no error. 2nd option I tried is: 0 0 0 0 1 This looks like its working and maps look correct to me but I want to make sure this is the correct contrast matrix and I am not sure how this matrix is regressing out age and gender or 1st option is correct contrast matrix? Thank you so much ! Best, Sahil

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Freesurfer August 2017