Freesurfer

freesurfer@nmr.mgh.harvard.edu

15 participants
30064 discussions

problems with group analysis (mri_glmfit?)
by Lars M. Rimol 30 May '06

30 May '06

Hi, I did a group analysis on 10 subjects (as a test run) following the steps of the updated tutorial. I get no error messages, however, when I load the y.fsgd, there are no data points. These 10 subjects were chosen randomly, solely for the purpose of running through the group analysis procedure, so I don't necessarily expect significant findings but at least there shold be some datapoints, right? Make_average_subject, mris_preproc and mri_surf2surf went fine without error messages but the mri_glmfit script took less than 1 minute to run, which I think seems a little suspicious. What should "Matrix condition" be? Here, it was 1. And DOF? (It was 8). Is "OneSampleGroupMean 0" a sign that something has gone wrong? There was a warning message during mri_glmfit, but the fsgdf is in accordance with the tutorial: [lmr@ip45 ovelse]$ mri_glmfit --y rh.IQ.txt.thickness.10.mgh --fsgd IQ.txt--glmdir rh.IQ.txt.glmdir --pca --surf average rh --C contrast.mat gdfReadHeader: reading IQ.txt WARNING: gdfReadV1: no variables on 'Variables' line found INFO: gd2mtx_method is dods Reading source surface /home/subjects/average/surf/rh.white reading group avg surface area 948 cm^2 from file Reading in average area /home/subjects/average/surf/rh.white.avg.area.mgh Number of vertices 163842 Number of faces 327680 Total area 78857.140625 AvgVtxArea 0.481300 AvgVtxDist 0.814244 StdVtxDist 0.276731 $Id: mri_glmfit.c,v 1.78.2.5 2006/03/10 23:27:29 greve Exp $ cwd /home/subjects/ cmdline mri_glmfit --y rh.IQ.txt.thickness.10.mgh --fsgd IQ.txt --glmdir rh.IQ.txt.glmdir --pca --surf averageja rh --C contrast.mat sysname Linux hostname ip45.ucsd.edu machine x86_64 user lmr FixVertexAreaFlag = 1 OneSampleGroupMean 0 y /home/subjects/rh.IQ.txt.thickness.10.mgh FSGD IQ.txt glmdir rh.IQ.txt.glmdir Creating output directory rh.IQ.txt.glmdir Loading y from /home/subjects/rh.IQ.txt.thickness.10.mgh Matrix condition is 1 search space = 94836.7 DOF = 8 Starting fit and test 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Fit completed in 0.0191 minutes Computing spatial AR1 on surface Residual: ar1mn=0.995564, ar1std=0.004225, gstd=6.106113, fwhm=14.378798 Writing results contrast maxvox sig=-3.35122 F=32.6872 at index 22070 0 4 seed=1149137562 Computing PCA (10) mri_glmfit done ------------ This is my FSGDF: $ cat IQ_fsgdf.txt GroupDescriptorFile 1 Title Gruppesammenligning Class lowIQ Class highIQ Variables Input TOP_161 lowIQ Input TOP_162 lowIQ Input TOP_163 lowIQ Input TOP_164 lowIQ Input TOP_165 lowIQ Input TOP_166 highIQ Input TOP_167 highIQ Input TOP_175 highIQ Input TOP_188 highIQ Input TOP_189 highIQ -- yours, LMR

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mri_vol2surf problem
by adam walczak 30 May '06

30 May '06

Hello, I am trying to overlay my own ROIs onto the pial surface using mri_vol2surf. this is my command line: mri_vol2surf --src wrawKH_MAE3_4/Agap1_2_gap-nogap_p05u-05u --src_type analyze --srcreg wrawKH_MAE3_4/register.dat --fwhm 3 --hemi lh --surf pial --surfreg /cajal/public/programs/freesurfer/subjects/wrawKH_MAE3_4/surf/lh.pial --out wrawKH_MAE3_4/surf/lhpialoverlaytest --out_type paint --trgsubject wrawKH_MAE3_4 and this is my output: INFO: output format is paint srcvol = wrawKH_MAE3_4/Agap1_2_gap-nogap_p05u-05u srctype = analyze srcreg = wrawKH_MAE3_4/register.dat srcregold = 0 srcwarp unspecified surf = pial hemi = lh trgsubject = wrawKH_MAE3_4 surfreg = /cajal/public/programs/freesurfer/subjects/wrawKH_MAE3_4/surf/lh.pial interp = nearest float2int = round INFO: float2int code = 0 INFO: reading as a two-file NIFTI INFO: using NIfTI-1 sform Done loading volume INFO: smoothing volume at fwhm = 3 mm (std = 1.27398) Reading surface /cajal/public/programs/freesurfer/subjects/subject-unknown/surf/lh.pial MRISread(/cajal/public/programs/freesurfer/subjects/subject-unknown/surf/lh.pial): could not open file No such file or directory mri_vol2surf: could not read surface /cajal/public/programs/freesurfer/subjects/subject-unknown/surf/lh.pial No such file or directory the program seems to read the input images correctly, but can't read the surface images. I don't know what is up with the 'subject-unknown.' I specified the subject and it still doesn't know the path. I am kind of at a loss. Adam adam --------------------------------- Yahoo! Messenger with Voice. PC-to-Phone calls for ridiculously low rates.

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Segmentation
by Joao Pereira 30 May '06

30 May '06

Hi, I tried to test FS cortical thickness analysis by using a batch of 10 subjects whose grey matter I manually deleted in the temporal lobes (a significant part at least). When I compared it to the original 10 images, little or none changes were significant! I checked the segmentation and I noticed that the grey/white boundary in the original subjects was too conservative, hence no changes were detected (at least I believe it is the only explanantion). Is it possible to change the segmentation parameters to make it more "agressive" or am I overlooking something? Thank you! Joao Pereira

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regarding slice timing
by Sebastian Moeller 27 May '06

27 May '06

Dear fellow FreeSurfers, does anybody know how to account for interleaved slice acquisition of functionals in fs-fast? Basically all my scans were taken interleaved instead of linear ordered, so I think it might be a good idea to tell the system (even though the block design used should not be too sensitive). selxavg2 does sort of know a parameter acqorder that will be passed to fast_selxavg.m, but selxavg-sess does not allow to specify this parameter, and on first impression there seems to be no auto-detection. And the 3.0.2 version of fast_selxavg does not use the SliceDelay in any way. Ahoi Sebastian -- Sebastian Moeller Tel.: 04 21 - 2 18 - 78 38 oder 96 91 Fax.: 04 21 - 2 18 - 90 04 GSM: 01 62 - 3 25 45 59 moeller(a)brain.uni-bremen.de AG Kreiter / FB 2 Institut fuer Hirnforschung III Abteilung Theoretische Neurobiologie Universitaet Bremen Biogarten Hochschulring 16a Postfach 33 04 40 28359 Bremen

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updated tutorial and data
by Nick Schmansky 26 May '06

26 May '06

Freesurfers, An updated Freesurfer tutorial is now online at: http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial and the data that accompanies it (processed by stable v3.0.2) is available through: http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Data The outline is setup for a two-day course (to align with tutorial sessions typically found at a conference). Each of the four sessions should take no more than 90 minutes to complete. Comments and suggestions are appreciated. The Freesurfer team

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troubleshooting
by Amanda Dow 26 May '06

26 May '06

I ran one of my brains through recon-all and the skull strip and talairach were normal. When I checked the white matter edits with tkmedit, the right hemisphere wm and pial surface lines are including some of the left hemisphere, and the right temporal lobes are not included as white matter or in the pial surface. I thought it may be a tailarach problem, but it looks normal. Any suggestion on what could be wrong. I may try using control points and re-running it with <recon-all -autorecon2-cp...> Thanks!

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colortable
by Satrajit Ghosh 26 May '06

26 May '06

1. Is there a matlab function to read the colortable from an annot file? 2. Is there a reason why several of the annotvalues generated by the classifier using rh.atlas2005_simple.gcs do not have corresponding names in surface_labels.txt? I remember there was a release where there was a separate colortable for that atlas, but it doesn't exist in the current download, so I was assuming they have been merged into a single file. Thanks, Satra

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scalp surfaces - mri_watershed vs betsurf
by Darren Weber 25 May '06

25 May '06

Dear Bruce, Steve, et al, have you compared the output of mri_watershed with betsurf? I ran a T1 volume through mri_watershed with the -surf output options. I also ran the same volume through betsurf. When comparing the two volumes, I specified an offset of -128 for the betsurf output. I expected a close correspondence between these surfaces. There is a slight rotation difference (see image attached). Have you seen this before? Steve, is there some reason the betsurf output could be rotated? Thanks, Darren -- Darren L. Weber, Ph.D. Postdoctoral Scholar Dynamic Neuroimaging Laboratory, UCSF Department of Radiology, 185 Berry Street, Suite 350, Box 0946, San Francisco, CA 94107, USA. Tel: +1 415 353-9444 Fax: +1 415 353-9421 www: http://dnl.ucsf.edu/users/dweber "To explicate the uses of the brain seems as difficult a task as to paint the soul, of which it is commonly said, that it understands all things but itself." Thomas Willis (The Anatomy of the Brain and Nerves, 1664)

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unable to run mc-sess with bert dataset
by Olivier Piguet 25 May '06

25 May '06

Good morning, I recently installed the new version of FreeSurfer and have been re-familiarising myself with the steps/procedures. I followed the FreeSurfer and FsFast tutorial which went fine until I tried the step described in the FsFastTutorial/700: Motion correct the data. When I ran the command: mc-sess -sf sessid -df sesspar I received the following error message: Logfile is /home/olivierp/BERT_TUTORIAL_ANALYSES/log/mc-bert-functional-bold.log ------------------------------------------- /home/olivierp/FreeSurfer_tutorial/bert-functional RunList: 007 008 009 Targ Stem is 007/f ------- ************************** ----------- ------- Motion Correcting Run 007 ----------- ------- ************************** ----------- sess = bert-functional Fri May 26 08:27:34 EST 2006 mc-afni -i 007/f -o 007/fmc -t 007/f -toff 0 -ipr 3.12500000000000000000 -bpr 6. 00000007484366104649 -TR 2 ERROR: cannot find AFNI command to3d Any help/suggestion on how to solve this problem would be greatly appreciated. Olivier Piguet -- Olivier Piguet, Ph.D. Prince of Wales Medical Research Institute Barker St Randwick NSW 2031 Australia

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smoothing kernel
by Sasha Wolosin 25 May '06

25 May '06

Dear all, In group analysis, how should I determine which value to use for the Gaussian fwhm smoothing kernel? Is there a recommended number? Thanks, Sasha Disclaimer: The materials in this e-mail are private and may contain Protected Health Information. Please note that e-mail is not necessarily confidential or secure. Your use of e-mail constitutes your acknowledgment of these confidentiality and security limitations. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying, distribution, or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this e-mail in error, please immediately notify the sender via telephone or return e-mail.

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