Freesurfer May 2017

freesurfer@nmr.mgh.harvard.edu

145 participants
219 discussions

Two stage model question
by Clara Kühn 09 May '17

09 May '17

Dear FreeSurfer experts, I have a longitudinal design with 3 groups and 3 time points. For one group the intervention did not work so for now I would like to look at 2 groups only. Can I do this with the Longitudinal Two Stage Model by looking at the spc from tp1 to tp2 and then looking at the spc from tp2 to tp3? Are there statistical reasons that forbid this procedure of comparing the change across time between groups? Thanks for your help! Clara -- Clara Kühn, Phd Student Max-Planck-Institute for Human Cognitive and Brain Science Department of Neuropsychology Stephanstrasse 1A 04103 Leipzig, Germany Phone: +49 341 - 9940 2271 Fax: +49 341 - 9940 2260 Web: www.cbs.mpg.de E-Mail: ckuehn(a)cbs.mpg.de

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Probabilistic atlas illustration
by Julian Jäckle 09 May '17

09 May '17

Dear all In the paper "A computational atlas of the hippocampal formation using *ex vivo*, ultra-high resolution MRI" (DOI:10.1016/j.neuroimage.2015.04.042 <https://deref-web-02.de/mail/client/_I-kyDlKQj4/dereferrer/?redirectUrl=htt…> ;2015) you have two illustrations Fig4&6 showing the probabilistic atlas and mesh deformation. Can I create such an image myself using freeview /tkmedit? If so could you explain to me how to do it? I've attached an example image Thanks a lot Julian

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Surface area
by John Anderson 08 May '17

08 May '17

Dear Freesurfer experts, I know that the grey or white matter volume measures for the ROIs reported in "wmparc.mgz" can be adjusted for the total intracranial volume.... Is is correct to do the same for surfaces? I mean can the surface of an ROI (e.g. precentral) be adjusted to total surface area? If yes, this must be done for total white right or total left depending on the ROI if it is left or right, correct? Thank you John

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Re: [Freesurfer] perform group analysis on user defined maps
by Ladan Shahshahani 08 May '17

08 May '17

Hi Doug, I asked you about how to perform group analysis on maps created using an index I calculated. You suggested using mri_concat to concatenate the maps and then perform the analysis using mri_glmfit. I then asked about NaN values in the maps and how freesurfer treat these values. You said "It will probably crash. I does nothing to find NaNs and handle them in an appropraite way" When concatenating maps with NaN values, the following lines are printed out in the terminal: *Invalid argument* *WARNING: #number NaNs found in subjid.map.mgh* but it creates the concatenated mgh file. However, if maps from all subjects contain NaN values, it does not create the corresponding mgh file. My question is: Does it mean that it discards subjects with NaN values?? Ladan

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submillimeter resolution
by Annie Duchesne 08 May '17

08 May '17

Dear experts, We are currently developing a MRI protocol for a longitudinal study that will take over in the next 3 years using a Siemens Prisma 3T. We are interested in structural changes within cortical and sub cortical regions, we will also be acquiring DTI and a FLAIR scans. I have seen that for HC subfields .6 mm iso T1 seems to be the gold standard. Being a new user of freesurfer and trying to make an educated decision regarding our scanning parameters, I was wondering if you have any recommendations regarding the T1 parameters. Thank you very much, Annie

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Re: [Freesurfer] Statistical analysis
by Laura Ferrero Montes 08 May '17

08 May '17

Hi Joost, Thank you for the information, that course would be great. However, I would need to know if the analysis I am doing is OK to continue with my study. Joost Janssen <joost.janssen76(a)gmail.com> escribió: > Hi Laura, > > There is an upcoming FreeSurfer course in Barcelona this summer. Please > contact Susana Carmona > susannacarmona(a)gmail.com > > Op 7 mei 2017 19:17 schreef "Laura Ferrero Montes" <lauferm2(a)etsii.upv.es>: > >> >> Dear FS team, >> >> Thank you very much for your help. Just a few more questions. >> >> I want to perform a statistical analysis between two groups:controls >> and patients, using age and IQ as covariates. First I have to test if >> there is an interaction between group and covariate using DODS. >> >> My questions are: >> >> Q1) Do I have to test age and IQ separately, or together? >> >> Q2) In case that there is not interaction in any of the covariates, >> can I use the same FSGD file but do I have tu run it as DOSS? How it >> could be done? >> I would appreciate if you could give me some hints or examples about >> the matrices and contrast files that I must use. >> >> Thank you, >> All the best, >> >> Laura >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer(a)nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> >> The information in this e-mail is intended only for the person to whom it >> is >> addressed. If you believe this e-mail was sent to you in error and the >> e-mail >> contains patient information, please contact the Partners Compliance >> HelpLine at >> http://www.partners.org/complianceline . If the e-mail was sent to you in >> error >> but does not contain patient information, please contact the sender and >> properly >> dispose of the e-mail. >> >>

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Differences in aseg volumes between FreeSurfer 5.3.0 and FreeSurfer 6.0
by Knut J Bjuland 07 May '17

07 May '17

Dear FreeSurfer expert, I have compared the aseg volume between FreeSurfer 5.3 and FreeSurfer 6.0 with asegstatsdiff from FreeSurfer 6.0 for each subject in my data set. I have enclosed the range for some of the volume. I found the largest differences in subcortical structures, especially in Corpus callosum(CC). I found that FreeSurfer 6.0 CC posterior volume was 525.51 % larger than in FreeSurfer 5.3. Nevertheless, these differences were much smaller for lhCortex, but also here FreeSurfer 6.0 was on average larger than FreeSurfer 5.3. I ran the FreeSurfer 6.0 using the same option as FreeSurfer 5.30. Both versions of FreeSurfer were run on Centos. I am also enclosing a table with mean values along with min and max for differences between FreeSurfer 5.3 and FreeSurfer 6.0 aseg volumes. Best regards Knut Jørgen Bjuland PhD NTNU Left-Lateral-Ventricle 7.4 (-0.13,130.72) Left-Cerebellum-White-Matter 0.64 (-22.9,56.15) Left-Cerebellum-Cortex 7.56 (-10.3,19.17) Left-Thalamus-Proper 0.12 (-16.31,32.42) Left-Caudate -4.25 (-12,33.64) Left-Putamen -16.72 (-27.99,8.3) Left-Pallidum 16.23 (-22.94,84.75) Left-Hippocampus -1.74 (-13.53,15.93) Left-Amygdala 2.29 (-19.28,41.04) Right-Lateral-Ventricle 4.6 (-24.77,102.12) Right-Cerebellum-White-Matter -3.2 (-20.87,49.37) Right-Cerebellum-Cortex 4.88 (-12.99,14.36) Right-Thalamus-Proper 1.06 (-22.34,19.99) Right-Caudate -6.08 (-14.59,6.13) Right-Putamen -12.87 (-31.37,10.17) Right-Pallidum 14.01 (-27.79,89.19) Right-Hippocampus -1.71 (-9.29,12.02) Right-Amygdala 3.74 (-18.6,51.01) Right-Accumbens-area -9.14 (-37.89,61.02) CC_Posterior 22.07 (-47.04,525.51) CC_Mid_Posterior 53.59 (-11.3,537.3) CC_Central 36.77 (-21.36,317.24) CC_Mid_Anterior 24.09 (-18.86,128.31) CC_Anterior 10.64 (-33.71,152.33) lhCortexVol 3.13 (-1.31,12.37) rhCortexVol 3.16 (-0.36,14.2) CortexVol 3 (-4.47,13.26) EstimatedTotalIntraCranialVol 0.65 (-0.05,26.52)

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cortex parcellation
by james pardon 07 May '17

07 May '17

Hello, I was wondering whether the number of subjects used for segmentation and parcellation of cortex has changed from the original 36 MRI volumes explained in (Fischl et al, Cortex, 2004)? If so, how many subjects are now used in Freesurfer for segmenting and parcellating? Can you also explain what pathology these subjects have? Where can I find these? Thank you, James Pardon

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R: R: R: R: Re: R: Re: Hipposubfields in FreeSuerferColorLUT.txt
by stdp82＠virgilio.it 07 May '17

07 May '17

I have added-segid 222 fcseed-config -seg subj/mri/lh.perirhinal.nii.gz -segid 222 -fcname L_Perirhinal.dat -fsd rest -mean -cfg mean.L_Perirhinal.config -overwrite and runningselxavg3-sess -s subj_folder -a fc.rperiseed.surf.rhthis error is producedINFO: key nSliceGroups unrecognized, line 11, skipping ERROR: cannot find volume matching $SUBJ_DIR/subj/rest/001/R_Perirhinal.dat ERROR: loading nonpar reg $SUBJ_DIR/subj/rest/001/R_Perirhinal.dat ------------------------------------------ ERROR: fast_selxavg3() failed\n Thanks Stefano ----Messaggio originale---- Da: stdp82(a)virgilio.it Data: 1-mag-2017 22.04 A: <freesurfer(a)nmr.mgh.harvard.edu> Ogg: [Freesurfer] R: R: R: Re: R: Re: Hipposubfields in FreeSuerferColorLUT.txt Dear list and Eugenio, I have run for each subject mri_label2vol --label SUBJ/label/rh.perirhinal_exvivo.thresh.label --regheader SUBJ/mri/norm.mgz --fill-ribbon --subject SUBJ --hemi rh --o SUBJ/mri/rh.perirhinal.nii.gz next, to use FS-FAST on perihrinal.nii.gz, I have run fcseed-config -seg SUBJ/mri/lh.perirhinal.nii.gz -fcname L_Perirhinal.dat -fsd rest -mean -cfg mean.L_Perirhinal.config This error occurs: ERROR: no segmentations IDs (-segid) or ROI (-roi) specified What's should I do? Thanks Stefano On Mon, 06 Feb 2017 13:59:38 -0800 Do you mean to use them as seeds in FSFAST? You'll need to map them into the conformed space using mri_label2vol with the --regheader option (see the --help); view the volume to make sure it looks ok. Then run fcseed-config specifying the volume with -seg and the code with segid ----Messaggio originale---- Da: stdp82(a)virgilio.it Data: 6-feb-2017 22.27 A: "Freesurfer support list"<freesurfer(a)nmr.mgh.harvard.edu> Ogg: [Freesurfer] R: Re: R: Re: Hipposubfields in FreeSuerferColorLUT.txt Thank you very much.Could you provide me any suggestion to extract CA1 left or CA1 right?And how can I use them in FAST? By codes?Regards,Stefano ----Messaggio originale---- Da: "Iglesias Gonzalez, Eugenio" <e.iglesias(a)ucl.ac.uk> Data: 6-feb-2017 17.42 A: "stdp82(a)virgilio.it"<stdp82(a)virgilio.it>, "Freesurfer support list"<freesurfer(a)nmr.mgh.harvard.edu> Ogg: Re: [Freesurfer] R: Re: Hipposubfields in FreeSuerferColorLUT.txt You would extract CA1 left from lh.hippoSfLabels-T1.v10.mgz and CA1 right from rh.hippoSfLabels-T1.v10.mgz (assuming you’ve used T1s to segment the subfields). Cheers, /E Juan Eugenio Iglesias ERC Senior Research Fellow Translational Imaging Group University College London http://www.jeiglesias.com http://cmictig.cs.ucl.ac.uk/ On 6 Feb 2017, at 16:17, stdp82(a)virgilio.it wrote: Thanks Eugenio for your response. My apologies but this matter is unclear to me. If I would use results for FS-FAST how I can identify for example CA1 right from CA1 left? Additionally, for enthorinal which is the correct code in FAST? Stefano ----Messaggio originale---- Da: "Iglesias Gonzalez, Eugenio" <e.iglesias(a)ucl.ac.uk> Data: 6-feb-2017 15.54 A: "stdp82(a)virgilio.it"<stdp82(a)virgilio.it>, "Freesurfer support list"<freesurfer(a)nmr.mgh.harvard.edu> Ogg: Re: [Freesurfer] Hipposubfields in FreeSuerferColorLUT.txt Ciao Stefano, The results for the left and right hippocampi are in different files, so there’s no ambiguity despite the fact that they indeed share the same label codes. Cheers, /Eugenio Juan Eugenio Iglesias ERC Senior Research Fellow Translational Imaging Group University College London http://www.jeiglesias.com http://cmictig.cs.ucl.ac.uk/ On 6 Feb 2017, at 13:18, stdp82(a)virgilio.it wrote: Hi list, within FreeSuerferColorLUT.txt, do the numbers between 200-226 descrived the hippo-subfield outputs? Additionally, how can I obtain separate right and left masks? Thanks Stefano _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.

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How to calculate the surface area of a vertex ?
by Zhiliang Long 06 May '17

06 May '17

Hi FS experts: I am studying the vertex-level group analysis on surface area between groups. I know that the cortical thickness of a vertex is computed as the distance between white matter surface and pial surface. But I have no idea how to calculate the surface area of a vertex. In my understanding, surface area is a measurement of a face instead of a vertex. Best, Zhiliang

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Freesurfer May 2017