Freesurfer April 2017

freesurfer@nmr.mgh.harvard.edu

123 participants
217 discussions

freesurferstats2table_bash
by shi yao wang 24 Apr '17

24 Apr '17

Dear FS experts: Would you pls provide freesurferstats2table_bash script? The link of http://surfer.nmr.mgh.harvard.edu/fswiki/freesurferstats2table does not work. thanks Shiyao

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How are Vertex RAS coordinates calculated in TKsurfer
by Zhiliang Long 24 Apr '17

24 Apr '17

Dear FS experts: I am studying the coordinate system in FS. I met a problem that confused me. I run tksurfer: tksurfer fsaverage lh inflated. Then I chose a point on surface. It showed that the Vertex Index is 80321, and the Vertex RAS is (-38.53 9.05 40.01). I thought that the Vertex RAS is just obtained from the lh.inflated file. But I run: mris_info --v 80321 .\fsaverage\surf\lh.inflated. It showed that coordinate is (-18.4 40.8 32.7). I have no idea that how the Vertex RAS is calculated in Tksurfer. Maybe is there a transform matrix between the two coordinates ? If so, how can i get the transform matrix ? Best, Zhiliang

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Worse determination of ?h.white with v6.0 in comparison to v5.3 - worse GM/WM contrast
by Antonin Skoch 24 Apr '17

24 Apr '17

Dear experts, I am sending just one more example to illustrate issue with white surface estimation in v6.0. See the attached screenshots: In v6.0 there seems to be insufficient contrast in brain.finalsurfs.mgz, so the white surface is leaking at three spots dramatically outwards towards pial surface. The white surface in v5.3 looks much more anatomically relevant in the same spot. Could you please comment on how to avoid such issues in v.6.0? Regards, Antonin Skoch

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Cognomics conference: poster and advertisement
by X K 24 Apr '17

24 Apr '17

This message contained a link to a web site whose IP address has recently been associated with malicious activity. Due to that activity the site is not accessible from within the Partners Network. The link has been modified in the message below. If you feel this is an error please contact the IS Service Desk and open a ticket with the network security - phs assignment group. IS Service Desk numbers BWH 617-732-5927 BWH-RICS 617-525-0848 DFCI 617-632-3399 FALK 617-983-7454 LCC 857-307-4150 MCL 781-416-8940 MGH 617-726-5085 NHP 617-643-2020 NSMC 978-354-2014 NWH 617-243-6001 PCHI 781-433-3757 PHH 617-726-0790 PHS 617-726-5085 SRH 617-952-5555 ********************************* *FYI:* Dear all, We are happy to announce the COGNOMICS Conference 2017 with the topic of “Neurogenomics: the road ahead”! This conference will be held on the 7th and 8th of September 2017 at the Donders Institute for Brain, Cognition and Behaviour in Nijmegen, the Netherlands. The program includes a keynote lecture by the world-leading neuroscientist and founder of the worldwide ENIGMA Consortium, Paul Thompson (University of Southern California), and several invited talks by top-researchers in the field, covering the state-of-the-art on imaging genetics and novel developments in phenotyping and genomics. It also includes a panel discussion on the future of imaging genetics and several stimulating oral and poster sessions. Participants will compete for a Best Poster award. Please find the program, as well as a further information about registration on our website BLOCKEDcognomics[.]nlBLOCKED. We invite you and your colleagues to submit abstracts for oral and poster presentations (max. 250 words excluding the title, author names, and references). Abstract submission deadline is June 15, 2017 Max number of participants is 120, so sign-up now! We hope to see you in September! Kind regards, on behalf of the Cognomics Board Barbara Franke Professor of Molecular Psychiatry Radboud University Medical Center Nijmegen Dr. Xiangzhen Kong (孔祥祯) Language and Genetics Department, Max Planck Institute for Psycholinguistics http://www.mpi.nl/people/kong-xiangzhen

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Weighted Average of Cortical Thickness
by Michael Kranz 24 Apr '17

24 Apr '17

Hi, I had 2 questions relating to measuring global mean cortical thickness with the weighting factor of surface area bh.thickness = ( (lh.thickness * lh.surfarea) + (rh.thickness * rh.surfarea) ) / (lh.surfarea + rh.surfarea) 1.) If this weighting is recommended, then shouldn't it be performed for each vertex in an exploratory whole brain group analyses (e.g., for one vertex in left hemi: lh.thickness*lh.surfarea)/(lh.surfarea). 2.) Are there any references that come to mind to cite in regards to this normalization technique? I see that this following paper uses normalization (but was wondering if you would recommend any others): Vuoksimaa, E., Panizzon, M. S., Chen, C.-H., Fiecas, M., Eyler, L. T., Fennema-Notestine, C., … Kremen, W. S. (2015). The Genetic Association Between Neocortical Volume and General Cognitive Ability Is Driven by Global Surface Area Rather Than Thickness. *Cerebral Cortex (New York, NY)* , *25*(8), 2127–2137. http://doi.org/10.1093/cercor/bhu018 Best, Mike

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volume in native space of .vtk file in mni152 space
by Corinna Bauer 23 Apr '17

23 Apr '17

Dear all, I have a series of .vtk files in MNI152 1mm space from an external thalamus atlas outlining specific thalamic nuclei. I would like to put these into native subject space and calculate the volume from each nuclei. I would imagine that I would do the following: 1. run mni152reg --s --1 on each subject 2. mri_vol2vol --mov mni152space_atlas_file.nii.gz -- targ subject/mri/orig.mgz --reg subject/mri/mni152.orig.mgz.reg --inv --o newoutputfile_subject_space But then I am not certain how to calculate the volume of the new output file. Suggestions? Thanks! Corinna

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Difference between lh.thickness file and lh.thickness.fsaverage.mgh file
by Zhiliang Long 23 Apr '17

23 Apr '17

Dear FS experts: I conducted recon-all analysis on my own subjects, and found that there are several kinds of thickness files, such as the lh.thickness file and lh.thickness.fsaverage file. By using MATLAB scripts implemented in FS, different numbers of vertex were found between the two files. What I am thinking is that the lh.thickness file is the individual thickness map (It has not been transformed into fsaverage space), while the lh.thickness.fsaverage.mgh is the thickness map in fsaverage space. Is that correct? Best, Zhiliang

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R: R: Re: R: Re: Hipposubfields in FreeSuerferColorLUT.txt
by stdp82＠virgilio.it 23 Apr '17

23 Apr '17

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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mris_label2annot not creating annot file
by Das S. 23 Apr '17

23 Apr '17

Hi, I was using the mris_label2annot to create .annot file before but now couldn't figure out why the .annot file is not being created. The mris_label2annot is giving the below output but not creating the label files. My label file names are as node-lh-xx.label and the content of ctab file as below: 0 node-lh-0 25 5 25 0 1 node-lh-1 70 0 180 0 2 node-lh-2 245 245 245 0 3 node-lh-3 205 62 78 0 4 node-lh-4 120 18 134 0 5 node-lh-5 196 58 250 0 6 node-lh-6 0 148 0 0 7 node-lh-7 220 248 164 0 8 node-lh-8 230 148 34 0 9 node-lh-9 0 118 14 0 10 node-lh-10 70 118 14 0 11 node-lh-11 122 186 220 0 12 node-lh-12 236 13 176 0 13 node-lh-13 12 48 255 0 14 node-lh-14 204 182 142 0 *********************************************************** mris_label2annot --s 100307 --h lh --no-unknown --ctab label/eq_parcellation_label/MyColorLUTleft01.txt --a eq40left --ldir label/eq_parcellation_label/left/ Reading ctab label/eq_parcellation_label/MyColorLUTleft01.txt Number of ctab entries 41 INFO: no labels specified, generating from ctab $Id: mris_label2annot.c,v 1.20 2016/01/07 23:28:11 greve Exp $ cwd /home/koushik/Parcellation/100307 cmdline mris_label2annot --s 100307 --h lh --no-unknown --ctab label/eq_parcellation_label/MyColorLUTleft01.txt --a eq40left --ldir label/eq_parcellation_label/left/ sysname Linux hostname koushik-DQ77MK machine x86_64 user koushik subject 100307 hemi lh SUBJECTS_DIR /home/koushik/Parcellation ColorTable label/eq_parcellation_label/MyColorLUTleft01.txt AnnotName eq40left nlables 0 LabelThresh 0 0.000000 Loading /home/koushik/Parcellation/100307/surf/lh.orig Writing annot to /home/koushik/Parcellation/100307/label/lh.eq40left.annot Thanks Sarbani

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aparc files missing a comma
by Mike Schmidt 22 Apr '17

22 Apr '17

Hello FreeSurfer Developers, I'm attempting to parse stats files with regular expressions. Everything seems to work in all of the aseg and wmparc files, but the {lh,rh}.aparc{,a2009s,DKTatlas,pial}.stats files are missing a comma after "CortexVol" on line 25. This causes my regex to miss that measurement on each pass. All other lines match my regex perfectly, only CortexVol misses the comma. This is a new field in version 6; it does not exist in versions 5.2.0 and 5.3.0. This is consistent across all subjects I've viewed, and there are no errors to dig into, but I've attached the recon-all.log file and a few stats files from one of them in case they're of any use. 1) FreeSurfer version: freesurfer-Linux-centos6_x86_ 64-stable-pub-v6.0.0-2beb96c 2) Platform: external linux cluster, unsure exactly 3) uname -a: Linux sequoia 3.12.67-60.64.24-default #1 SMP Fri Dec 9 14:35:11 UTC 2016 (8154761) x86_64 x86_64 x86_64 GNU/Linux 4) recon-all.log: see attached, along with a few aparc files. I have added the comma using sed to all of the aparc files in our system, but I hope this is helpful in removing bugs for future use. Best wishes, Mike Schmidt

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Freesurfer April 2017