Freesurfer July 2016

freesurfer@nmr.mgh.harvard.edu

143 participants
252 discussions

Bug in Freesurfer Installation
by Sherryse Corrow 19 Jul '16

19 Jul '16

Hello freesurfer developers, I installed FreeSurfer on my computer today using the instructions found here: https://surfer.nmr.mgh.harvard.edu/fswiki/DownloadAndInstall. After installation, I proceed to the “test your FreeSurfer Installation” section. Upon trying the first test, I ran the following and code and received the following error. Sherryses-iMac:~ sherrysecorrow$ cd $FREESURFER_HOME/subjects Sherryses-iMac:subjects sherrysecorrow$ mri_convert sample-001.mgz sample-001.nii.gz mri_convert sample-001.mgz sample-001.nii.gz $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from sample-001.mgz... TR=7.25, TE=3.22, TI=600.00, flip angle=7.00 i_ras = (-0, -1, -0) j_ras = (-0, 0, -1) k_ras = (-1, 0, 0) writing to sample-001.nii.gz... niiWrite(): error opening file sample-001.nii.gz ERROR: failure writing sample-001.nii.gz I’ve searched the list and was unable to find someone with the same error in the archives. Any thoughts on how to fix this? freesurfer-Darwin-lion-stable-pub-v5.3.0 Mac OS X version 10.9.5 uname -a Darwin Sherryses-iMac.local 13.4.0 Darwin Kernel Version 13.4.0: Mon Jan 11 18:17:34 PST 2016; root:xnu-2422.115.15~1/RELEASE_X86_64 x86_64 Thanks, Sherryse

2 1

T2 vs. T2-FLAIR update
by Michelle T Kassel 19 Jul '16

19 Jul '16

Hello, I am beginning a new study and would like to determine the optimal T2 acquisition parameters for improved pial surface results from FreeSurfer. I am wondering if there is a difference in using a T2 or T2-FLAIR. I have found a discussion post from 2014 which provided useful information (https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2014-July/039580.html) however, it seems from reading the post that newer developments were underway, and I was wondering if I could get an updated answer to the question: is there any difference from freesurfer's perspective of using T2-space or T2-space-flair? Thank you for your help! Michelle

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Request for new mri_tessellate (error: max vertices 1000000 exceeded)
by Ferguson, B. 19 Jul '16

19 Jul '16

Dear Freesurfer team, I am running Falk Luesebrinks hires recon<https://surfer.nmr.mgh.harvard.edu/fswiki/HiResRecon>, and am running into the error of "mri_tessellate: max vertices 1000000 exceeded" when I run the command line "recon-all -maskbfs -segmentation -fill -tessellate -s $SUBJECT" on a 0.5mm T1 structural volume. I have seen an earlier e-mail conversation<https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg42045.html>, and would like to request: is a similar mri_tesselate that is easier about the number of vertices available for my platform? FREESURFER_HOME = /Applications/freesurfer Build stamp: freesurfer-Darwin-lion-stable-pub-v5.3.0 Mac version: OS X Yosemite 10.10.5 Kernel info: Darwin Kernel Version 14.5.0: Thu Apr 21 20:40:54 PDT 2016; root:xnu-2782.50.3~1/RELEASE_X86_64 x86_64 Thanks in advance, best wishes, Bart Ferguson PhD candidate | Department of Psychiatry | Brain Division | University Medical Center Utrecht Post: A01.126 kantoortuin 1 | Visit: A01.504| Heidelberglaan 100 | 3584 CG UTRECHT T +31 (0)88 75 555 55 | M +31 (0)6 1191 6897 | www.umcutrecht.nl ------------------------------------------------------------------------------ De informatie opgenomen in dit bericht kan vertrouwelijk zijn en is uitsluitend bestemd voor de geadresseerde. Indien u dit bericht onterecht ontvangt, wordt u verzocht de inhoud niet te gebruiken en de afzender direct te informeren door het bericht te retourneren. Het Universitair Medisch Centrum Utrecht is een publiekrechtelijke rechtspersoon in de zin van de W.H.W. (Wet Hoger Onderwijs en Wetenschappelijk Onderzoek) en staat geregistreerd bij de Kamer van Koophandel voor Midden-Nederland onder nr. 30244197. Denk s.v.p aan het milieu voor u deze e-mail afdrukt. ------------------------------------------------------------------------------ This message may contain confidential information and is intended exclusively for the addressee. If you receive this message unintentionally, please do not use the contents but notify the sender immediately by return e-mail. University Medical Center Utrecht is a legal person by public law and is registered at the Chamber of Commerce for Midden-Nederland under no. 30244197. Please consider the environment before printing this e-mail.

2 1

DeMean Flag
by Clara Kühn 19 Jul '16

19 Jul '16

Dear Freesurfer experts, is there an explanation somewhere for the DeMeanFlag? I can't find it in the wiki but I would like to use it to demean my covariates for the GLM and LME. Cheers 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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mri_segstats
by Alshikho, Mohamad J. 18 Jul '16

18 Jul '16

Dear FS experts, I have PET image "pet.anat.mgz" in subject space. I want to calculate the mean PET signal for every parcellate and segment in the atlas "wmparc.mgz". Which one of the following commands is more accurate? 1. mri_segstats --seg $SUBJECTS_DIR/${subj}/mri/wmparc.mgz --ctab $FREESURFER_HOME/FREESURFERColorLUT.txt --i PET.anat.mgz --sum PET.wmparc.stats 2. mri_segstats --seg mri/wmparc.mgz --sum stats/wmparc.stats --pv mri/norm.mgz --excludeid 0 --brainmask mri/brainmask.mgz --in mri/ PET.anat.mgz--in-intensity-name norm --in-intensity-units MR --subject ${subj} --surf-wm-vol --ctab /usr/local/freesurfer/stable5_3_0/WMParcStatsLUT.txt --etiv Best, Mohamad

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Checking segmentations with aseg.mgz
by Reema Jayakar 18 Jul '16

18 Jul '16

Hello FS Listserv members, With regard to checking amygdala segmentation, is it appropriate to overlay the aseg.mgz file on the brainmask.mgz? Or should I be overlaying aseg.mgz on norm.mgz? I am aware of the general rule of thumb that editing the subcortical segmentations generally is not recommended. Also, where can I find documentation on the Freeview options "Resample to standard RAS space" and "Apply registration file". I am trying to understand whether or not it is necessary for me to use any of these options for what I am doing with the subcortical segmentations. Thanks in advance for your help! Reema -- *Reema Jayakar, M.A.* Doctoral Candidate - Clinical Neuropsychology Health Resources and Services Administration (HRSA) Fellow Department of Psychology Georgia State University Email: rjayakar1(a)student.gsu.edu

2 1

FSGD error: class Input not defined
by Jarek Rokicki 18 Jul '16

18 Jul '16

Dear Freesurfer experts, I am trying to perform the resting state fMRI analysis as in: http://surfer.nmr.mgh.harvard.edu/fswiki/FsFastFunctionalConnectivityWalkth… I got stuck with the STEP8, when I tried to use my own fsgd file. I tried to test for two group difference, no covariance as in: https://surfer.nmr.mgh.harvard.edu/fswiki/Fsgdf2G0V But I am getting this error: mri_glmfit --y fc.lpccseed.surf.lh/L_PCC/ces.nii.gz --wls fc.lpccseed.surf.lh/L_PCC/cesvar.nii.gz --fsgd ../glm_file.fsgd --C ../group.diff.mtx --surface fsaverage lh --glmdir my-glm.wls --nii.gz gdfRead(): reading ../glm_file.fsgd Input line 1, subjid = HM-HR10-002Rest Group1, class Input not defined FSGDF Format Error: file = ../glm_file.fsgd, tag=Input I am testing the pipeline so just 8 subjects so far. I've checked the ces.nii.gz and cesvar.nii.gz and both of them have correct dimensions of 163842 x 1 x 1 x 8. Thank you for your help in advance. *fsdg_file is:* GroupDescriptorFile 1 Title OSGM Class Group1 Class Group2 Input HM-HR10-002Rest Group1 Input HM-HR10-005Rest Group1 Input HM-HR10-007Rest Group1 Input HM-HR10-010Rest Group1 Input PD0001Rest Group2 Input PD0002Rest Group2 Input PD0004Rest Group2 Input PD0005Rest Group2 *mtx file is:* 1 -1 宜しくお願い致します。 Sincerely, Jarek Rokicki, Ph.D. Integrative Brain Imaging Center (IBIC) National Center of Neurology and Psychiatry (NCNP) *4-1-1 Ogawahigashi-chyo, Kodaira, Tokyo 187-8551 Japan* TEL: +81-80-6628-5709 国立精神・神経医療研究センター脳病態統合イメージングセンター(IBIC) 臨床脳画像研究部画像情報解析研究室 *〒187-8551 東京都小平市小川東町4-1-1*

2 1

FS-FAST "If: Expression Syntax" Error
by Hibert, Matthew Louis 18 Jul '16

18 Jul '16

Hi All, I'm running into an error analyzing some fMRI data with FS-FAST in Freesurfer version 5.3. The analysis runs fine until it gets to the register-sess part, which quits before actually starting to do any registration. The last line of the log file, attached, is "if: Expression syntax", but there are no other errors prior to that. The command I'm using, analysis, and contrasts have all worked on several other similar data sets. Has anyone encountered this problem before, or know what's causing it? Thanks, Matt Clinical Research Coordinator Stufflebeam Lab Athinoula A. Martinos Center Massachusetts General Hospital 149 13th Street, Room 1115S Charlestown, MA 02129

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Question about NULL event with Optseq2
by Feng Zhou 18 Jul '16

18 Jul '16

Dear experts, I'd like to use optseq2 to optimize the order of events as well as inter stimulus intervals. My experiment contains 3 runs and each run contains 3 events, say Cp, Cn and Pobe events Each stimulu will be presented 4, 4 and 1 sec and the numbers of times that each event type will be presented during the course of the run are 12 12 and 4 respectively, and interstimulus interval ranges from 8–12 sec. So each run would last around 380 sec. I used the following code: optseq2 --ntp 380 --tr 1 --psdwin 0 20 1 --ev Cp 4 12 --ev Cn 4 12 --ev Prob 1 3 --evc 1 -1 0 --tnullmin 8 --tnullmax 12 --nkeep 3 --o IAPS --nsearch 10000 However, the durations of some NULL events were more than 12 sec and the last NULL events were more than 30 sec. Did I use optseq2 in the right way? How could I fix it? Thanks in advance & Best regards, Feng Zhou

2 1

Inquiries about thickness and lgi group analysis
by Mahtab Farahbakhsh 18 Jul '16

18 Jul '16

Dear FreeSurfer, I am doing group analysis for thickness and LGI values. I have just got the output and the output of both analyses (sig.mgh file view in Freeview) are exactly the same. Would you please guide me with this? Best Regards, Mahtab.

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Freesurfer July 2016