Freesurfer

freesurfer@nmr.mgh.harvard.edu

18 participants
30131 discussions

apply inverse transform
by Martin Chadwick 24 Jun '09

24 Jun '09

Dear freesurfers, I'm new to freesurfer and have a problem using --apply_inverse_transform with the .m3z warp. Any help would be greatly appreciated: I've been running a multivariate fmri decoding study, and have used freesurfer to generate anatomical masks which I've used as ROIs for the multivariate analysis in the native space of each subject. I then took the pattern of informative voxels from each subject as a binary mask, and warped it into standard space using the freesurfer high-dimensional warp (I am looking at subcortical structures, so this level of registration accuracy is quite important) with the following command: mri_convert -ot nifti1 ~/inputimage --apply_transform ~/transforms/talairach.m3z ~/outputimage.img Which seems to have worked fine. I've then performed some overlap analyses on these warped binary images, and created a new binary image representing the between-subject overlap. What I really want to do next is to warp this back into the native space for each subject and use as an ROI for further multivariate analyses. To do this I tried the following command: mri_convert -it nifti1 -ot nifti1 ~/inputimage.img --apply_inverse_transform ~/transforms/talairach/m3z ~/outputimage.img which gave me the following error message: mriBuildVoronoiDiagramFloat: incorrect input type(s) Any ideas on what I'm doing wrong here? Many thanks, Martin

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make_average_subject error about limit
by Feng-Xian 24 Jun '09

24 Jun '09

Hi, I have a problem with make_average_subject. After running all commands about running QDEC, I found that QDEC could not analysis my group. Because the group I want to analysis have 1 factor and three levels, QDEC can't run. So, I want to change the method of analysis from QDEC to FSGD. But, I have a problem about FSGD. When I type: make_average_subject --subects <subjid1> <subjid2> ... the terminal show that: limit: descriptors: Can't remove limit (此項操作並不被允許) What's wrong about the command I type? And, how to solve the problem? Thank you in advance! Feng-Xian ------------------------------------------------- Chang Gung University Mail Server Web Mail system By Chang-Gung University Information Center (http://www.cgu.edu.tw/ic/)

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volume group analysis
by Anita di Iasio 23 Jun '09

23 Jun '09

Hi all, I follow the tutorial on group analysis. But the example is surface-based. I looked for something similar in freesurfer archive, but I can't find anything. Can someody helps me to do a volume-based group-analysis? which flag do I use with mris_preproc and mri_glmfit? for example I need to compare white matter volume....I think should be similar with other volumes, don't I? In the end....to visualize the results, what shall I use? perhaps the tkmedit command? Thanks, Anita

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R: Re: R: Re: [Freesurfer] Qdec
by free_surfer＠virgilio.it 23 Jun '09

23 Jun '09

Dear Nick, we were able to use Qdec upon your suggestions. Many thanks. Since we are going to download the last version of FS (with a newer Qdec) on another workstation, would you suggest to use the new Qdec for our data processed by FS 4.0.2. If yes, can you briefly tell us which are the main differences and advantages of the newer Qdec? Many thanks, Antonio >----Messaggio originale---- >Da: nicks(a)nmr.mgh.harvard.edu >Data: 22-giu-2009 12.49 >A: "free_surfer(a)virgilio.it"<free_surfer(a)virgilio.it> >Cc: "Freesurfer Mailing List"<freesurfer(a)nmr.mgh.harvard.edu>, "Allison Stevens"<astevens(a)nmr.mgh. harvard.edu> >Ogg: Re: R: Re: [Freesurfer] Qdec > >Antonio, > >The Generate Stats Data Table feature was added in the v4.3.0 release of >freesurfer. Its not necessary to perform an analysis, only to aid in >the import of the morphometric measures from the recon-all stream (like >hippocampal volume). > >You should be able to goto to the Design tab and conduct and analysis >with your age and white covariates. > >Nick > > >On Mon, 2009-06-22 at 10:03 +0200, free_surfer(a)virgilio.it wrote: >> Hi Allison, >> I send you the snapshot of qdec. >> Thanks, >> Antonio >> >> Antonio, >> Can you >> describe what qdec is showing that's wrong or send a screenshot >> of >> it? >> Thanks, >> >> Allison >> >> -- >> >> On Thu, 18 Jun 2009, free_surfer(a)virgilio.it wrote: >> >> > Dear >> Freesurfer users, >> > We are experiencing a problem using Qdec (FS version >> > >> 4.2.0; Qdec 1.0) for group data analysis. >> > Indeed, the qdec display [after >> > >> creating the qdec.table.dat and the <factor>.levels files] >> doesn't visualize >> > >> properly (as in the tutorial) the Data Table View and other >> window-options that >> >> > should allow us to select "Generate Stats Data Table" and >> proceed with the >> > >> group analysis. >> > >> > Any suggestion would be greatly appreciated. >> > >> > Many >> Thanks in >> > advance for your help, >> > >> > Antonio Gallo, MD, PhD >> > Department of >> Neuroscience >> > >> > Second University of Naples >> > Ph: +39-081-5665090 >> > >> > >> > >> _______________________________________________ >> > Freesurfer mailing list >> > >> Freesurfer(a)nmr.mgh.harvard.edu >> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>>> > >> > >> >> _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > >_______________________________________________ >Freesurfer mailing list >Freesurfer(a)nmr.mgh.harvard.edu >https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>

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Re: [Freesurfer] concerning my posting: curvature file'lh.area.mid' has wrong magic number - add logfile
by Oliver Grimm 23 Jun '09

23 Jun '09

Hi! Thanks for the replies! 1. I think, I need some help with the stats output of mris_calc: e. g. mris_calc lh.area stats gives me mris_calc lh.area stats mris_calc: Insufficient number of arguments. You should specify '<curvFile1> <ACTION> <curvFile2>' Use a '-u' for full usage instructions. which is a quite humiliating error message, isn't it ... 2. A look into the /surf/ directory shows that lh.area.mid has a size of zero byte. That does not look very sensible. 3. Disk-Space: I am running my experiments on a NAS with >300 MB free diskspace. Even my local computer has some GB's left and I don't see anything written locally. Memory and processor speed should be enough (4 MB quad-core). 2009/6/23 Grimm, Oliver <Oliver.Grimm(a)zi-mannheim.de> > > ------------------------------------------- > *Von:* freesurfer-bounces(a)nmr.mgh.harvard.edu im Auftrag von Nick > Schmansky[SMTP:NICKS@NMR.MGH.HARVARD.EDU<SMTP%3ANICKS(a)NMR.MGH.HARVARD.EDU>] > > *Gesendet:* Dienstag, 23. Juni 2009 01:04:35 > *An:* Grimm, Oliver > *Cc:* Freesurfer Mailing List > *Betreff:* Re: [Freesurfer] concerning my posting: curvature > file'lh.area.mid' has wrong magic number - add logfile > *Diese Nachricht wurde automatisch von einer Regel weitergeleitet.* > > Oliver, > > That's a strange error. Did you run out of disk space? I can only > think of that as a reason for a corrupted curvature file. > > Nick > > On Mon, 2009-06-22 at 14:00 +0200, Oliver Grimm wrote: > > Hi! > > > > I just mentiones my error > > > > curvature file 'lh.area.mid' has wrong magic number > > > > on a openSUSE 11.1 system: > > > > /data/MOODS2/freesurfer/1005/surf > > > > mris_calc -o lh.area.mid lh.area add lh.area.pial > > > > > > mris_calc -o lh.area.mid lh.area.mid div 2 > > > > > > mris_calc -o lh.volume lh.area.mid mul lh.thickness > > > > > > mris_calc: curvature file 'lh.area.mid' has wrong magic number. > > > > Linux impsy-pc4 2.6.27.19-3.2-default #1 SMP 2009-02-25 15:40:44 +0100 > > x86_64 x8 > > 6_64 x86_64 GNU/Linux > > > > recon-all exited with ERRORS at Sat Jun 20 00:17:58 CEST 2009 > > > > > > I forgot to attach the recon-all.log for further details. I attached > > it. > > > > Thank you for your held, > > > > Oliver Grimm > > > > > > > > -- > > Dr. med. Oliver Grimm > > Zentralinstitut für Seelische Gesundheit > > Institut für Neuropsychologie und Klinische Psychologie & > > AG Imaging in der Psychiatrie > > J5 > > 68159 Mannheim > > > > Tel: +49-621-1703-6341 > > Fax: +49-621-1703-6305 > > email oliver.grimm(a)zi-mannheim.de > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer(a)nmr.mgh.harvard.edu > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > -- Dr. med. Oliver Grimm Zentralinstitut für Seelische Gesundheit Institut für Neuropsychologie und Klinische Psychologie & AG Imaging in der Psychiatrie J5 68159 Mannheim Tel: +49-621-1703-6341 Fax: +49-621-1703-6305 email oliver.grimm(a)zi-mannheim.de

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How to rerun recon-all after modifying talairach registration manually?
by Zhen Zonglei 22 Jun '09

22 Jun '09

Hi all: After autorecon1 was done, I corrected the talairach registration manually. Next, I rerun autorecon1 on the data, but tal_check still gave the same talAviQA and z-score as non-corrected. What's the problem? Is it necessary to rerun autorecon1? Can we skip autorecon1 and do autorecon2 directly? My version is FreeSurfer4.3. Thanks. Zonglei Zhen -- Zonglei Zhen, PhD Assistant Professor of Cognitive Neuroscience BNU Imaging Center for Brain Research, State Key Laboratory of Cognitive Neuroscience and Learning, P.R. China

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concerning my posting: curvature file 'lh.area.mid' has wrong magic number - add logfile
by Oliver Grimm 22 Jun '09

22 Jun '09

Hi! I just mentiones my error curvature file 'lh.area.mid' has wrong magic number on a openSUSE 11.1 system: /data/MOODS2/freesurfer/1005/surf mris_calc -o lh.area.mid lh.area add lh.area.pial mris_calc -o lh.area.mid lh.area.mid div 2 mris_calc -o lh.volume lh.area.mid mul lh.thickness mris_calc: curvature file 'lh.area.mid' has wrong magic number. Linux impsy-pc4 2.6.27.19-3.2-default #1 SMP 2009-02-25 15:40:44 +0100 x86_64 x8 6_64 x86_64 GNU/Linux recon-all exited with ERRORS at Sat Jun 20 00:17:58 CEST 2009 I forgot to attach the recon-all.log for further details. I attached it. Thank you for your held, Oliver Grimm -- Dr. med. Oliver Grimm Zentralinstitut für Seelische Gesundheit Institut für Neuropsychologie und Klinische Psychologie & AG Imaging in der Psychiatrie J5 68159 Mannheim Tel: +49-621-1703-6341 Fax: +49-621-1703-6305 email oliver.grimm(a)zi-mannheim.de

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qdec analyses
by Jose Soares 22 Jun '09

22 Jun '09

Hi all, I am a little bit confused about the qdec display. I have some simple questions about two groups A and B: 1- In the question, does the average thickness differ between A and B? How this average is calculated? By the difference between the A average and B average (avgA-avgB) ? The negative values (normally in blue) mean that the thickness (average of B) B is higher than A? 2- I want to analyze lh parahippocampal thickness. What is the difference between insert the values manually in the qdec.table.dat file (like the tutorial) or import ( in subjects - stats data import) the lh_parahippocampal_thickness from aparc? 3- In the question, does the thickness--lh_parahippocampal_thickness correlation differ between A and B? what for instance a positive value mean on display? I only expected results in the parahippocampal area... Thaks for the help, Miguel. Veja quais são os assuntos do momento no Yahoo! +Buscados http://br.maisbuscados.yahoo.com

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how to segment hippocampus using freesurfer
by Wenlu Yang 22 Jun '09

22 Jun '09

Hi all, I want to use freesurfer to segment hippocampus from MR images, but I don't know how to do it because I am a newcomer here. could you give me some advices? thanks. wyang

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Mris_thickness_diff and FS4.4
by Jürgen Hänggi 22 Jun '09

22 Jun '09

Dear FS experts I run the following command with longitudinal data from FS4.4, but I am not sure whether I specified the files properly (_base files?) and used the right transform (tp1_to_tp2.lta?), because files and transforms changed in FS4.4. mris_thickness_diff -xform tp2.long.tp2_base/mri/transforms/tp1_to_tp2.lta \ -src_type curv \ -out tp2.long.tp2_base/surf/lh.thickness_diff \ -nsmooth 30 \ -abs -S tp2.long.tp2_base \ -L tp2.long.tp2_base/surf/lh_thickness_diff.log \ tp1.long.tp1_base/surf/lh.white \ tp1.long.tp1_base/surf/lh.thickness \ tp2.long.tp2_base/surf/lh.white \ tp2.long.tp2_base/surf/lh.thickness Thanks in advance for clarification Regards Jürgen ---------------------------------------------------------------------------- Juergen Haenggi Ph.D. (Dr. des.) Division Neuropsychology Institute of Psychology University of Zurich Binzmuehlestrasse 14, PO Box 25 8050 Zurich, Switzerland 0041 44 635 73 97 (phone office) 0041 76 445 86 84 (phone mobile) 0041 44 635 74 09 (fax office) BIN 4.D.04 (office room number) j.haenggi[at]psychologie.uzh.ch (email) http://www.psychologie.uzh.ch/neuropsy/ (website) http://www.juergenhaenggi.ch (private website) This e-mail (and any attachment/s) contains confidential and/or privileged information. If you are not the intended recipient (or have received this e-mail in error) please notify the sender immediately and destroy this e-mail. Any unauthorised copying, disclosure or distribution of the material in this e-mail is strictly forbidden. ----------------------------------------------------------------------------

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