Freesurfer

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30098 discussions

Re: [Freesurfer] eTIV question
by Jared Tanner 22 Feb '16

22 Feb '16

My experience with eTIV is that it's great with a perfect Talairach transform but otherwise is less accurate than other measures. Manually fixing the transforms and reprocessing as necessary will result in great eTIVs but requires quite a bit of manual work. What we do instead is just use the brainmask volume (but our data are MRIs of non-demented older adults so there's not typically extensive atrophy). We've found that brainmask has a Dice Similarity Coefficient of 0.95 and an ICC of 0.92 with manually traced intracranial masks (inferior termination on a straight line between the lowest portion of the clivus and occipital bone). eTIV had an ICC of 0.67 with our manual masks (but we didn't fix the transformations). Jared ____ Jared Tanner, Ph.D. Research Assistant Professor Clinical and Health Psychology University of Florida > ---------- Forwarded message ---------- > From: "Harms, Michael" <mharms(a)wustl.edu> > To: "freesurfer(a)nmr.mgh.harvard.edu" <freesurfer(a)nmr.mgh.harvard.edu> > Cc: > Date: Sun, 21 Feb 2016 18:10:12 +0000 > Subject: Re: [Freesurfer] eTIV question > > Hi, > Why not use a measurement of brain size rather than “eTIV”? > > cheers, > -MH > > -- > Michael Harms, Ph.D. > > ----------------------------------------------------------- > Conte Center for the Neuroscience of Mental Disorders > Washington University School of Medicine > Department of Psychiatry, Box 8134 > 660 South Euclid Ave.Tel: 314-747-6173 > St. Louis, MO 63110Email: mharms(a)wustl.edu > >

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Re: [Freesurfer] mri_convert Ubuntu 14.04 LTS not working (neither is freeview) (Z K)
by Veronica.Popescu 22 Feb '16

22 Feb '16

Dear Zeke, This is the output: "Mon Feb 22 18:27:05 CET 2016 /usr/local/freesurfer/subjects/myscan /usr/local/freesurfer/bin/recon-all -s myscan -i myscan.nii.gz subjid myscan setenv SUBJECTS_DIR /usr/local/freesurfer/subjects FREESURFER_HOME /usr/local/freesurfer Actual FREESURFER_HOME /usr/local/freesurfer build-stamp.txt: freesurfer-Linux-centos4-stable-pub-v5.3.0 Linux MSveronica 3.19.0-49-generic #55~14.04.1-Ubuntu SMP Fri Jan 22 11:24:31 UTC 2016 x86_64 x86_64 x86_64 GNU/Linux cputime unlimited filesize unlimited datasize unlimited stacksize 8192 kbytes coredumpsize 0 kbytes memoryuse unlimited vmemoryuse unlimited descriptors 1024 memorylocked 64 kbytes maxproc 15308 maxlocks unlimited maxsignal 15308 maxmessage 819200 maxnice 0 maxrtprio 0 maxrttime unlimited total used free shared buffers cached Mem: 3940392 3452568 487824 223760 262988 2343920 -/+ buffers/cache: 845660 3094732 Swap: 2023420 77288 1946132 ######################################## program versions used $Id: recon-all,v 1.379.2.73 2013/05/12 23:15:37 nicks Exp $ $Id: mri_motion_correct.fsl,v 1.14 2011/03/02 20:16:39 nicks Exp $ $Id: talairach_avi,v 1.9 2011/03/02 18:38:06 nicks Exp $ Program nu_correct, built from: Package MNI N3, version 1.10, compiled by nicks@fishie (i686-pc-linux-gnu) on 2010-02-20 at 20:19:13 ####################################### GCADIR /usr/local/freesurfer/average GCA RB_all_2008-03-26.gca GCASkull RB_all_withskull_2008-03-26.gca AvgCurvTif average.curvature.filled.buckner40.tif GCSDIR /usr/local/freesurfer/average GCS curvature.buckner40.filled.desikan_killiany.2010-03-25.gcs ####################################### /usr/local/freesurfer/subjects/myscan mri_convert /usr/local/freesurfer/subjects/myscan.nii.gz /usr/local/freesurfer/subjects/myscan/mri/orig/001.mgz Linux MSveronica 3.19.0-49-generic #55~14.04.1-Ubuntu SMP Fri Jan 22 11:24:31 UTC 2016 x86_64 x86_64 x86_64 GNU/Linux recon-all -s myscan exited with ERRORS at Mon Feb 22 18:27:07 CET 2016 To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting" It creates the directory myscan but the folders myscan/mri/orig and myscan/mri/transforms are empty. Before running I changed the rights -R a+w for /usr/local/freesurfer/subjects. I tried to use mri_convert myscan.nii.gz myscan.mgz and it doesn't do anything, no error message it just skips to a new line. mri_convert -h or mri_convert --help also don't have any output. And recon-all -s bert -autorecon1 gives: "Subject Stamp: freesurfer-Linux-centos4-stable-v5.3.0beta-20130503 Current Stamp: freesurfer-Linux-centos4-stable-pub-v5.3.0 INFO: SUBJECTS_DIR is /usr/local/freesurfer/subjects Actual FREESURFER_HOME /usr/local/freesurfer -rwxrwxrwx 1 root root 472994 Feb 8 16:54 /usr/local/freesurfer/subjects/bert/scripts/recon-all.log Linux MSveronica 3.19.0-49-generic #55~14.04.1-Ubuntu SMP Fri Jan 22 11:24:31 UTC 2016 x86_64 x86_64 x86_64 GNU/Linux INFO: current FREESURFER_HOME does not match that of previous processing. Current: /usr/local/freesurfer Previous: /space/freesurfer/centos4.0/stable #-------------------------------------------- #@# MotionCor Mon Feb 22 18:24:35 CET 2016 Found 3 runs /usr/local/freesurfer/subjects/bert/mri/orig/001.mgz /usr/local/freesurfer/subjects/bert/mri/orig/002.mgz /usr/local/freesurfer/subjects/bert/mri/orig/003.mgz Checking for (invalid) multi-frame inputs... ERROR: input(s) cannot have multiple frames! /usr/local/freesurfer/subjects/bert/mri/orig/001.mgz has frames Linux MSveronica 3.19.0-49-generic #55~14.04.1-Ubuntu SMP Fri Jan 22 11:24:31 UTC 2016 x86_64 x86_64 x86_64 GNU/Linux recon-all -s bert exited with ERRORS at Mon Feb 22 18:24:35 CET 2016" I tried to use If I try to run: "freeview -v $SUBJECTS_DIR/bert/mri/brainmask.mgz -v $SUBJECTS_DIR/bert/mri/aseg.mgz:colormap=lut:opacity=0.2 -f $SUBJECTS_DIR/bert/surf/lh.white:edgecolor=yellow -f $SUBJECTS_DIR/bert/surf/rh.white:edgecolor=yellow -f $SUBJECTS_DIR/bert/surf/lh.pial:annot=aparc:edgecolor=red -f $SUBJECTS_DIR/bert/surf/rh.pial:annot=aparc:edgecolor=red" as indicated on the website nothing happens, no error message. -----Origineel Bericht----- > Van: freesurfer-request(a)nmr.mgh.harvard.edu > Aan: freesurfer(a)nmr.mgh.harvard.edu > Datum: 10-02-2016 17:28 > Onderwerp: Freesurfer Digest, Vol 144, Issue 14 > > Send Freesurfer mailing list submissions to > freesurfer(a)nmr.mgh.harvard.edu > > To subscribe or unsubscribe via the World Wide Web, visit > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > or, via email, send a message with subject or body 'help' to > freesurfer-request(a)nmr.mgh.harvard.edu > > You can reach the person managing the list at > freesurfer-owner(a)nmr.mgh.harvard.edu > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of Freesurfer digest..." > > > Today's Topics: > > 2. Re: mri_convert Ubuntu 14.04 LTS not working (neither is > freeview) (Z K) > > > > ---------------------------------------------------------------------- > > > > Message: 2 > Date: Tue, 9 Feb 2016 12:55:18 -0500 > From: Z K <zkaufman(a)nmr.mgh.harvard.edu> > Subject: Re: [Freesurfer] mri_convert Ubuntu 14.04 LTS not working > (neither is freeview) > To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> > Message-ID: <56BA2806.6060106(a)nmr.mgh.harvard.edu> > Content-Type: text/plain; charset=windows-1252; format=flowed > > I just did a tst of mri_convert of freesurfer v5.3 on my Ubuntu 14.04 > machine and it ran successfully. Freeview also ran (after typing the > libjpeg symlink command). > > Can you provide any error or terminal output information? > > -Zeke > > On 02/08/2016 12:41 PM, Veronica.Popescu wrote: > > Dear all, > > I have just installed FreeSurfer 5.3.0. on Ubuntu 14.04 LTS (64-bit). > > The mri_convert doesn't work with no error message. which mri_convert > > gives /usr/local/freesurfer/bin/mri_convert. Of course neither does > > recon-all (which exits with errors with no error message in the log). > > I made sure all the paths are 777. I did the recommended "sudo ln -s > > libjpeg.so.8 libjpeg.so.62 sudo ln -s libtiff.so.4 libtiff.so.3" in > > x86_64-linux-gnu. > > The same problem with freeview, nothing happens. > > Thank you in advance! > > Veronica > > > > > > End of Freesurfer Digest, Vol 144, Issue 14 > ******************************************* -- Revalidatie & MS Centrum VZW | Overpelt Boemerangstraat 2 B-3900 Overpelt Tel.: 011 / 809 100 Fax: 011 / 66 28 86 http://www.msreva.be info(a)msreva.be Disclaimer: http://www.msreva.be/default.aspx?main

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mris_make_surfaces dimensions error
by Corinna Bauer 22 Feb '16

22 Feb '16

Hello all, I am attempting to reshape the pial surfaces to fill the new boundaries in my edited ribbon.mgz file. I am using mris_make_surfaces with the -cover_seg flag but keep getting this error: ERROR: mris_make_surfaces-MRIcheckVolDims: volume1 height=256 != volume2 height=1. Any suggestions? Thanks! Corinna FYI: I am trying to reshape the pial boundary based off this previous thread. https://mail.nmr.mgh.harvard.edu/pipermail///freesurfer/2014-November/04134…

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Variations in results between qdec GUI and Command Line
by Vikas Bandalli 22 Feb '16

22 Feb '16

Dear Freesurfer Team, I am facing a discrepancy in the result when I run a Monte Carlo Z simulation. I have a group with 3 levels(normal,Non-psychotic and psychotic).I tried running an analysis to c the variation in cortical thickness between the same groups in the QDEC GUI,but since iit was impossible to do so and reading a few similar instances on the Freesurfer mailing list,I decided to run the analysis in Command line using mri_glmfit after mris_preproc.The detailed instructions I followed was from the below mentioned page https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis However,Published literature with similar cases has ran the simulation using pairing method i.e, lets say in this case between normal-psychotic,normal-non-psychotic and psychotic-non-psychotic. I have done both the methods to compare,However,I have the opposite results and discrepancy in results. (If there was a negative correlation between normal-psychotic in GUI, there was a positive correlation between normal-psychotic in the Command line analysis). Kindly note that the simulation was run for MC-z 1.3(0.05) in both GUI and Command line. Please help me with this issue and which is the TRUE result. -- Vikas B. R. Medical student Bangalore Medical College and Research Institute (BMCRI), Bangalore,India, Ph : +918904286825

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Freesurfer tool to automatically generate label surrounding a given vertex?
by Martha Shiell 22 Feb '16

22 Feb '16

Hello Freesurfer community, I am looking for a way to automatically generate a surface label file of a specific dimension (e.g. a circle with a specific diameter, or a square), given a specific vertex and some measure of the desired size. I have considered to do so by starting with a label file consisting of a single vertex, and then expanding this label with the mri_label2label tool, using the --dilate option. I wanted to know though if anyone has any better suggestions. Thank you, Martha -- Martha M. Shiell, PhD

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Longitudinal results questions
by Hutton, Seth 22 Feb '16

22 Feb '16

Hello FreeSurfers, My lab has been using the longitudinal processing stream for our data set and seem to be getting some potentially troublesome results. The attached images present a snap shot of the issues we are encountering. As you can see in the left image, there seems to be some kind of shifting going on. However, when you view each individual T1 with their corresponding boundary maps they look spot on. My question is whether or not this will have any major implication when we are trying to do a longitudinal analysis of cortical thickness? The more troublesome issue which is shown on the right is an overall "messiness" that seems to occur in some scans. When looking back at the template and the original FreeSurfer images there doesn't appear to be any issue. It's only when the longitudinal image is constructed that there seems to be some exaggerated blur as well as some over inclusions of dura (this isn't shown in the image but has happened in a handful of our subjects). Has anyone else experienced these kinds of issues? Only a quarter of our subjects that look as good "quality wise" as the examples posted on your wiki. Thanks, Seth Hutton ********************************************************** Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues

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Use of gcs altlas with freesurfer on T1 image
by Thomas Jacquemont 22 Feb '16

22 Feb '16

Dear FreeSurfer experts, I would like to use the P. Hagmann atlas (Lausanne 2008 available here https://github.com/LTS5/cmp/tree/master/cmp/data/colortable_and_gcs) on my subjects. I ran Recon all on their T1 images and then these two commands to get the Hagmann parcellation for my subject: mris_ca_label -dir ../subject_dir/003_S_2374 rh sphere.reg /aramis/home/jacquemont/DataAramis/Atlas/Hagmann/myatlas_250_rh.gcs ./test_sub_003_S_2374.rh.Hagmann500.annot mri_label2vol --subject 003_S_2374 --hemi rh --annot ./test_sub_003_S_2374.rh.Hagmann500.annot --temp ../subject_dir/003_S_2374/mri/orig/001.mgz --o annoted_volume_Hagmann500_003_S_2374.mgz --identity I have two questions. First, looking at the recon all log file I saw that the command is used this way: #@# Cortical Parc lh mardi 19 janvier 2016, 23:32:45 (UTC+0100) mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.mgz -seed 1234 NameSubject_M0 lh ../surf/lh.sphere.reg /path/to/freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0/average/lh.curvature.buckner40.filled.desikan_killiany.2010-03-25.gcs ../label/lh.aparc.annot I would like to know what is the "seed" option? Do I need it? Secondly, By surperimposed the resulting parcellation file (output of the mri_label2vol command) to the repective T1 image it seems that they are not in the same space. How could I have the pacellated file in the same space as the T1 image? Is the way I am using these two command good? What inputs should I change? The sphere file (for mris_ca_label), the --temp (for mri_label2vol), etc... Thank you for your help, Yours faithfully, Thomas

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Reference about: MeanCurv, GausCurv, FoldInd, CurvInd?
by Karas, Marta 22 Feb '16

22 Feb '16

H! I am working with data which is an output from the FreeSurfer processing. I would like to kindly ask you to refer me to materials / precise "mathematical" definitions that could help to understand what are the following parameters: * ?MeanCurv - Integrated Rectified Mean Curvature, * GausCurv - Integrated Rectified Gaussian Curvature, * FoldInd - Folding Index, * CurvInd - Intrinsic Curvature Index. (I have been trying to google but not been successful, unfortunately.) Kind regards, Marta Karas, M.S. Research Assistant, Department of Biostatistics Richard M. Fairbanks School of Public Health and School of Medicine Indiana University tel: 317-665-4551 email: mkaras(a)iu.edu<mailto:harezlak@iu.edu>

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comparison between two hemisphere in single
by Ashkan Faghiri 22 Feb '16

22 Feb '16

Thank you doug for you answer. So now I have two other question. 1- how can I check the inter hemisphere registration quality? e.g. can I check if the parcellation for the two hemisphere are matched well? or there is other ways? 2- how can I correct for multiple correction for single subject? calculate the p vale for each vertex (to find significant difference between the two hemisphere) and correct these for multiple correction. Regards, Ashkan > What is your mris_preproc command line? If you run mris_preproc with > --xhemi, it should give you two frames (left hemi and right hemi). If > you want to compute left-right, then add --paired-diff to the command > line. The output will be on the lh of fsaverage_sym. This can be > displayed on the white, pial, or inflated of fsaverage_sym. You can use > mris_apply_reg to map this back to the subject's native surface if you > want to display it there. > doug > > On 2/19/16 9:18 AM, Ashkan Faghiri wrote: > > Hello, > > > > sorry for asking this again > > > > I want to calculate the difference between the thickness of one > > subjects different hemispheres and show this on pial (left or right or > > even fsaverage_sys). so I have ran : > > > > surfreg --s $subject --t fsaverage_sym --lh > > surfreg --s $subject --t fsaverage_sym --lh --xhemi > > > > for my one subject. now I have two .reg files: > > shahi/xhemi/surf/lh.fsaverage_sym.sphere.reg > > shahi/surf/lh.fsaverage_sym.sphere.reg > > > > If I am understanding this right, these two are the transform matrix > > for both hemisphere of my one subject to fsaverage_sym (*right?*) > > > > if I run mris_preproc with xhemi option I will get a vector which have > > the length equal to number of vertexes. it's values are left-right > > (*or right-left?*). how can I convert this vector to pial or inflated > > surface? and how can I use lh.fsaverage_sym.sphere.reg to register my > > pial directly to fsaverage_sym? > > > > Regards, > > Ashkan > > -- > > -- > > Ashkan Faghiri > > MSc student of Bioelectrical Engineering > > Department of Electrical Engineering > > Sharif University of Technology > > > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer(a)nmr.mgh.harvard.edu > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > -- > -- Ashkan Faghiri MSc student of Bioelectrical Engineering Department of Electrical Engineering Sharif University of Technology

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longitudinal analysis Repeated Measures ANOVA 2x2
by María Díez Cirarda 22 Feb '16

22 Feb '16

Dear FS experts, I am trying to do a longitudinal analysis with a Repeated Measures ANOVA 2x2, with two groups (experimental and control group) and two times (pre and post treatment). First, I have followed the Longitudinal Processing Tutorial: 1) I have 2 acquisitions per subject so, I created a subject template (BASE) for each pair of subjects 2) I created the two longitudinal runs Now I am confused, because I don´t know wether I have to: 1) do a Longitudinal QDEC table with two columns (time and group) or 2) create a FSGD File, (or a DOSS file?) and create the contrasts. If I have to create the FSGD file, Would this be OK? GroupDescriptorFile 1 Class Subject 1 Class Subject 2 Variables Tp1vsTp2.Gr1Exp Tp1vsTp2.Gr2Control Input Subject1-tp1 Subject1 1 0 Input Subject1-tp2 Subject1 -1 0 Input Subject2-tp1 Subject2 0 1 Input Subject2-tp2 Subject2 0 -1 Contrasts: Mtx file: 0 0 1 0 0 0 0 -1 0 0 1 -1 Were do I have to create the FSGD file? In subjects folder or inside qdec folder? The group descriptor file must be "subject1" "subject2", or should I introduce the specific names of the folders from the subjects of my study? Thank you in advance, Maria.

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