Freesurfer

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30080 discussions

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.

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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

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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*

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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

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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.

2 1

mri_glmfit error
by Chatzi, Vasiliki 18 Jul '16

18 Jul '16

Dear Developers, I am trying to run the mri_glmfit command and I get two different errors for two different subjects. Please find details below. I would be really grateful if you could provide any advice. Error1 setenv SUBJECTS_DIR ./ mri_glmfit --glmdir ./ --y lh.10.lgi.mgh --fsgd fsgd_test2.txt --no-contrasts-ok --surf subject1 lh gdfReadHeader: reading fsgd_test2.txt INFO: gd2mtx_method is dods Reading source surface .//subject1/surf/lh.white Number of vertices 167703 Number of faces 335402 Total area 108706.031250 AvgVtxArea 0.648206 AvgVtxDist 0.881642 StdVtxDist 0.250483 $Id: mri_glmfit.c,v 1.196.2.8 2012/11/01 18:51:41 greve Exp $ cwd /home/test cmdline mri_glmfit --glmdir ./ --y lh.10.lgi.mgh --fsgd fsgd_test2.txt --no-contrasts-ok --surf subject1 lh sysname Linux hostname machine x86_64 user FixVertexAreaFlag = 1 UseMaskWithSmoothing 1 OneSampleGroupMean 0 y /home/test/lh.10.lgi.mgh logyflag 0 usedti 0 FSGD fsgd_test2.txt labelmask .//subject1ii/label/lh.cortex.label maskinv 0 glmdir ./ IllCondOK 0 ReScaleX 1 DoFFx 0 Creating output directory ./ Loading y from /home/test/lh.10.lgi.mgh INFO: gd2mtx_method is dods Saving design matrix to .//Xg.dat Normalized matrix condition is 1 Matrix condition is 1 Found 158404 points in label. ERROR: mri_reshape: number of elements cannot change nv1 = 167703, nv1 = 163842 Pruning voxels by thr: 0.000000 Found 163842 voxels in mask Saving mask to .//mask.mgh Reshaping mriglm->mask... ERROR: mri_reshape: number of elements cannot change nv1 = 163842, nv1 = 167703 search space = 108705.102552 DOF = 0 ERROR: DOF = 0 Error 2 setenv SUBJECTS_DIR ./ mri_glmfit --glmdir ./ --y lh.10.lgi.mgh --fsgd fsgd_test2.txt --no-contrasts-ok --surf subject2 lh gdfReadHeader: reading fsgd_test2.txt INFO: gd2mtx_method is dods Reading source surface .//subject2/surf/lh.white Number of vertices 129318 Number of faces 258632 Total area 86174.742188 AvgVtxArea 0.666379 AvgVtxDist 0.893985 StdVtxDist 0.260921 $Id: mri_glmfit.c,v 1.196.2.8 2012/11/01 18:51:41 greve Exp $ cwd /home/test cmdline mri_glmfit --glmdir ./ --y lh.10.lgi.mgh --fsgd fsgd_test2.txt --no-contrasts-ok --surf subject2 lh sysname Linux hostname machine x86_64 user FixVertexAreaFlag = 1 UseMaskWithSmoothing 1 OneSampleGroupMean 0 y /home/test/lh.10.lgi.mgh logyflag 0 usedti 0 FSGD fsgd_test2.txt labelmask .//subject2/label/lh.cortex.label maskinv 0 glmdir ./ IllCondOK 0 ReScaleX 1 DoFFx 0 Creating output directory ./ Loading y from /home/test/lh.10.lgi.mgh INFO: gd2mtx_method is dods Saving design matrix to .//Xg.dat Normalized matrix condition is 1 Matrix condition is 1 Found 121215 points in label. ERROR: mri_reshape: number of elements cannot change nv1 = 129318, nv1 = 163842 Pruning voxels by thr: 0.000000 Segmentation fault Bets wishes, Vasiliki

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Comparing between a group of subject
by Aman Montazeri 18 Jul '16

18 Jul '16

Hi Freesurferes, Sorry for my simple and rookie question, I'm a new user and couldn't find my answer after a bit googling. I have a group of subjects and want to compare their thickness with a baseline (average of my subjects). I thought to use the mri_avarage to make the baseline (Average of all of my subjects), but don't know how to compare them with the baseline after making the baseline. Any help would be highly appreciated Thanks, Aman Ps. I have looked into GLM and longitudinal processing tutorials; GLM doesn't work for me as I don't have any variable to regress against; longitudinal processing is also for comparing different time shots of the same subject (my case are 40 different subjects).

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