Freesurfer

freesurfer@nmr.mgh.harvard.edu

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30076 discussions

Re: [Freesurfer] questions on optseq2
by peng 01 Jul '07

01 Jul '07

Thank you for your advice, Daniel. I think you may suggest the latter way I mentioned in your first piece of advice. I have two conditions with equal trials:for target(t),32*2(t15&t25); for standard(s),8*8(s11-14,21-24). Maybe my expression in the first email was not clear enough. I don't care the activation of the individual stimuli within certain conditions. I just need to balance them to make sure "I don't care" is reasonable. Now I am going to use the seqence generated by the first piece of code. But when evaluate it with seqefficiency, I would merge stimuli within conditions together. Then I would run more runs than needed, but not as much as consider the stimuli separately. Then I would be sure the two conditions were well randomized. The stimuli within condition were also reasonablely randomized. I am not sure whether I correctly understand your second piece of advice. But I can't change the ratio because I have to combine the fMRI data with a finished EEG experiment with the same paradigm. On 6/29/07, Daniel G. Wakeman <dwakeman(a)nmr.mgh.harvard.edu> wrote: > Hi Peng, > > I'm sure Doug and others will have very valuable advice, but why not just > keep the number of trials in the two conditions equal and separate out the > individual stimuli in the actual events (dividing to keep the number of > events per condition equal). That way you can keep your power and if you > want to do the other analysis later you can take a look at that. You > could of course, also fiddle with the ratios, so you use 1/2 (bottom most) > the time instead of 1/4. I'm not sure if all of this makes sense, but > according to this I believe the command would look like the one below > (Note! I kept the ratio of trials to null the same as in your examples). > > optseq2 --ntp 160 --tr 2 --psdwin 0 14 --ev s11 2 32 --ev s12 2 32 --ev 21 > 2 8 --ev s22 2 8 --ev s23 2 8 --ev s24 2 8 --ev s25 2 8 --ev s26 2 8 --ev > s27 2 8 --ev s28 2 8 > > optseq2 --ntp 160 --tr 2 --psdwin 0 14 --ev s11 2 16 --ev s12 2 16 --ev 21 > 2 12 --ev s22 2 12 --ev s23 2 12 --ev s24 2 12 --ev s25 2 12 --ev s26 2 12 > --ev s27 2 12 --ev s28 2 12 > > Dan > > > hi list, > > > > I have two conditions, one contain 2 stimuli and the other 8. The > > difference between stimuli within certain condition is vey small, and > > could be omitted in further analysis if they're treated equal. Now I > > have two choice: > > optseq2 --ntp 160 --tr 2 --psdwin 0 14 / > > --ev s11 2 8 --ev s12 2 8 --ev s13 2 8 --ev s14 2 8 / > > --ev t15 2 32 / > > --ev s21 2 8 --ev s22 2 8 --ev s23 2 8 --ev s24 2 8 / > > --ev t25 2 32 / > > --nkeep 6 --o pl1 --nsearch 10000 > > or > > optseq2 --ntp 160 --tr 2 --psdwin 0 14 / > > --ev s 2 64 --ev t 2 64 / > > --nkeep 6 --o pl2 --nsearch 10000 > > Obviously, the first one would need more test runs, which in fact was > > nearly 2 hours for the subjects . And the second one need only 1/4 > > time, but is risky. I am afraid it would induce difference between > > stimuli within condition. > > Do you have any suggestions on it? > > Thanks a lot. > > > > Peng > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer(a)nmr.mgh.harvard.edu > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > > > >

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make_average_subject
by Lars M. Rimol 01 Jul '07

01 Jul '07

Hi Bruce, Oh yes, I see that now! And the problem is that FS looks for the FSGDF under SUBJECTS_DIR//space/emc1/3/data/TOP/Analysis_lmr/, but SUBJECTS_DIR and Analysis_lmr are both in the same directory, i.e. /space/emc1/3/data/TOP. I thought that by giving the full path to the FSGDF I had taken care of that: make_average_subject --fsgd /space/emc1/3/data/TOP/Analysis_lmr/TOPtest.fsgdf --out /space/emc1/3/data/TOP/Analysis_lmr/average_TOPtest Is there a way around that, or do I have to put the FSGDF inside the SUBJECTS_DIR? The reason I would like to keep them separate is that lab techs are doing scan workups inside the SUBJECTS_DIR, and I don't want to create new directories and files inside there all the time. I guess this is a general question, is it possible to run make_average_subject, mris_preproc and surf2surf and get the FSGDF from a dir that is not a subdirectory of the subjectsdir, and also write the output to that dir? It seems if you give the full path, FS assumes that it should be added to the path of the subjects dir. Thank you! Lars Hi Lars, it looks like no input subjects are defined. Bruce On Wed, 27 Jun 2007, Lars M. Rimol wrote: > Hi, > Trying to run make_average_subject but getting an error message. Any idea > what may be wrong? > > Thank you! > Lars M. Rimol > > > > make_average_surface --fsgd > /space/emc1/3/data/TOP/Analysis_lmr/TOPtest.fsgdf --out > /space/emc1/3/data/TOP/Analysis_lmr/average_TOPtest > $Id: make_average_surface,v 1.27.2.2 2006/06/09 15:46:28 nicks Exp $ > Wed Jun 27 18:06:43 PDT 2007 > /space/emc1/3/data/TOP/Analysis_lmr > setenv SUBJECTS_DIR /space/emc1/3/data/TOP/Containers > output sdir is /space/emc1/3/data/TOP/Containers > uid=7266(lmr) gid=7266(lmr) groups=7266(lmr),7450(topproj) > context=user_u:system_r:unconfined_t > ==================== > make_average_surface > ==================== > input subjects: > output subject: /space/emc1/3/data/TOP/Analysis_lmr/average_TOPtest > mri_add_xform_to_header -c auto -- yours, LMR

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questions on optseq2
by peng 29 Jun '07

29 Jun '07

hi list, I have two conditions, one contain 2 stimuli and the other 8. The difference between stimuli within certain condition is vey small, and could be omitted in further analysis if they're treated equal. Now I have two choice: optseq2 --ntp 160 --tr 2 --psdwin 0 14 / --ev s11 2 8 --ev s12 2 8 --ev s13 2 8 --ev s14 2 8 / --ev t15 2 32 / --ev s21 2 8 --ev s22 2 8 --ev s23 2 8 --ev s24 2 8 / --ev t25 2 32 / --nkeep 6 --o pl1 --nsearch 10000 or optseq2 --ntp 160 --tr 2 --psdwin 0 14 / --ev s 2 64 --ev t 2 64 / --nkeep 6 --o pl2 --nsearch 10000 Obviously, the first one would need more test runs, which in fact was nearly 2 hours for the subjects . And the second one need only 1/4 time, but is risky. I am afraid it would induce difference between stimuli within condition. Do you have any suggestions on it? Thanks a lot. Peng

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[Freesurfer] 3D volume generation, ROI selection, subvolume analysis
by Greg Soltis 28 Jun '07

28 Jun '07

Good morning, We have been working on Slicer and have been able to read in our stack of images. I can view them at the desired cross-sections by moving the three planes at will. But now we would like to be able to generate a 3D volume (in this case a rectangular prism) that contains all of these images in the stack. Once this is assembled, we are interested in being able to have Slicer/Free Surfer select ROI's or do so ourselves and be able to analyze these subvolumes from within the prism itself. Before I delve to deeply into FreeSurfer, I just wanted to make sure that it was capable of providing these capabilities and that Slicer cannot do them on its own. Are there any resources that I could access to aid me that are not accessible through the main FreeSurfer site: http://surfer.nmr.mgh.hardvard.edu/fswiki ? Could you give me a few quick pointers to get me started? Thanks a lot. Greg _________________________________________________________________ Picture this share your photos and you could win big! http://www.GETREALPhotoContest.com?ocid=TXT_TAGHM&loc=us

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Problems with surface topologies
by jorge luis 28 Jun '07

28 Jun '07

Hello all I have the freesurfer automatic hippocampus segmentation for some subjects. It seems that the segmentation is not bad. I have produced the binary masks (after labels generation in tksurfer)with the following command: mri_label2vol --label label/lefthipoca.label --temp mri/orig.mgz --o lefthipoca.img I have loaded the lefthipoca.img mask in matlab and used the standard matlab isosurface algorithm to triangulate the contours of the binary mask. The problem is that the resulting surface although no topological defects and no boundaries does not have spherical topology (euler number<2). Is it a consequence of imperfections in the freesurfer segmentation? How can I correct it? I have seen that with litter volumetric smoothing of the mask I get surfaces with spherical topology after the triangulation, but the structure volume is remarkable increased after the smoothing. Any tip is welcome In advance Thank you Jorge ____________________________________________________________________________________ ¡Descubre una nueva forma de obtener respuestas a tus preguntas! Entra en Yahoo! Respuestas. http://es.answers.yahoo.com/info/welcome

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make_average-subject
by Lars M. Rimol 27 Jun '07

27 Jun '07

Hi, Trying to run make_average_subject but getting an error message. Any idea what may be wrong? Thank you! Lars M. Rimol make_average_surface --fsgd /space/emc1/3/data/TOP/Analysis_lmr/TOPtest.fsgdf --out /space/emc1/3/data/TOP/Analysis_lmr/average_TOPtest $Id: make_average_surface,v 1.27.2.2 2006/06/09 15:46:28 nicks Exp $ Wed Jun 27 18:06:43 PDT 2007 /space/emc1/3/data/TOP/Analysis_lmr setenv SUBJECTS_DIR /space/emc1/3/data/TOP/Containers output sdir is /space/emc1/3/data/TOP/Containers uid=7266(lmr) gid=7266(lmr) groups=7266(lmr),7450(topproj) context=user_u:system_r:unconfined_t ==================== make_average_surface ==================== input subjects: output subject: /space/emc1/3/data/TOP/Analysis_lmr/average_TOPtest mri_add_xform_to_header -c auto /space/emc1/3/data/TOP/Containers//space/emc1/3/data/TOP/Analysis_lmr/average_TOPtest/mri/mni305.cor.mgz /space/emc1/3/data/TOP/Containers//space/emc1/3/data/TOP/Analysis_lmr/average_TOPtest/mri/mni305.cor.mgz INFO: extension is mgz #@# Making rh annotation --------------------- Wed Jun 27 18:06:47 PDT 2007 mris_ca_label -ml-annot rh.curvature.buckner40.filled.desikan_killiany.gcs 7 label/rh.aparc.annot /space/emc1/3/data/TOP/Containers/space/emc1/3/data/TOP/Analysis_lmr/average_TOPtest ML Label: rh.curvature.buckner40.filled.desikan_killiany.gcs 7 label/rh.aparc.annot Reading icosahedron /space/monkeys/1/pubsw/packages/freesurfer/RH4-x86_64-R304/lib/bem/ic7.tri Reading gcsa from /space/monkeys/1/pubsw/packages/freesurfer/RH4-x86_64-R304/average/rh.curvature.buckner40.filled.desikan_killiany.gcs reading color table from GCSA file.... average std = 35.0 0.3 using min determinant for regularization = 0.011 0 singular and 829 ill-conditioned covariance matrices regularized Building most likely labels Filtering labels 2 filter iterations complete (2 requested, 376 changed) writing colortable into annotation file... mris_ca_label -ml-annot rh.atlas2005_simple.gcs 7 label/rh.aparc.a2005s.annot /space/emc1/3/data/TOP/Containers/space/emc1/3/data/TOP/Analysis_lmr/average_TOPtest ML Label: rh.atlas2005_simple.gcs 7 label/rh.aparc.a2005s.annot Reading icosahedron /space/monkeys/1/pubsw/packages/freesurfer/RH4-x86_64-R304/lib/bem/ic7.tri Reading gcsa from /space/monkeys/1/pubsw/packages/freesurfer/RH4-x86_64-R304/average/rh.atlas2005_simple.gcs reading color table from GCSA file.... average std = 1.0 0.2 using min determinant for regularization = 0.000 0 singular and 827 ill-conditioned covariance matrices regularized Building most likely labels Filtering labels 2 filter iterations complete (2 requested, 1935 changed) writing colortable into annotation file... #@# Making average rh.orig surface --------------------- Wed Jun 27 18:07:06 PDT 2007 /space/emc1/3/data/TOP/Containers/space/emc1/3/data/TOP/Analysis_lmr/average_TOPtest mris_make_average_surface -i 7 -o orig -sdir-out /space/emc1/3/data/TOP/Containers rh orig_avg sphere.reg/space/emc1/3/data/TOP/Analysis_lmr/average_TOPtest reading vertex positions from orig... mris_make_average_surface [options] hemi outsurfname cansurfname outsubject subj1 subj2 subj3 ... Run with -help for more info -- yours, LMR

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OASIS Freesurfer Data
by Daniel Marcus 27 Jun '07

27 Jun '07

Hi folks- The Freesurfer processing of the OASIS cross-sectional data set is now available for download via anonymous FTP. The whole set will also be available at the OASIS website in the coming weeks. Check out www.oasis-brains.org for more information on the OASIS project. Download instructions: -ftp to www.oasis-brains.org -login as anonymous (use email address as password) -cd to data -mget oasis_cs_freesurfer* The full set is ~150 GB. It is divided into 11 separate .tar.gz files. This data set falls under the same Data Usage Agreement as the core OASIS data (http://www.oasis-brains.org/app/template/UsageAgreement.vm) Most importantly, please make sure to properly acknowledge its origin. Again, thanks to Bruce, Jenni, and the rest of the folks at MGH for generating this very cool data set and for making it widely available. Dan Marcus dmarcus(a)wustl.edu Neuroinformatics Research Group Washington University School of Medicine http://nrg.wustl.edu

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Making labels from the commandline
by Morgan Hough 27 Jun '07

27 Jun '07

I was wondering if I can make a cortical label from a volume ROI from the commandline. I would like to extract thickness values from a region defined in each subject's volume space. Thanks in advance. Cheers, -Morgan

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RE: [Freesurfer] ROI of SI cortex
by Rahul Desikan 27 Jun '07

27 Jun '07

Hi Xin, I will Doug handle this one. And please email the list in your replies. Best, rahul On Mon, 30 Apr 2007, Wang, Xin wrote: > Many thanks, Rahul. I found readings in /stats/*h.aparc.stats. I am a freesurfer beginner. I have another question. I want to compare the cortical thickness between two small groups (2X2). I can not work through the steps in the tutorial on my data. The mri_glmfit commend always returns with "bad design, ill-constructed," and stops. Do you have any detail instructions of two group comparison? > Thank you again, > > Xin > > ________________________________ > > From: Rahul Desikan [mailto:rahul@nmr.mgh.harvard.edu] > Sent: Mon 4/30/2007 4:06 PM > To: Wang, Xin > Cc: freesurfer(a)nmr.mgh.harvard.edu > Subject: RE: [Freesurfer] ROI of SI cortex > > > > Hi Xin, > > Within the *h.aparc.annot files for each subject, there should be > individual label files for *h.precentral.label and *h.postcentral.label. > If you take a look at your *h.aparc.stats, there should be a value for the > thickness and volume. You can, of course, take this *h.aparc.stats file > and upload it into matlab, spss or any other stats package and do > statistics on these values. > > Best, > > rahul > > On Mon, 30 Apr 2007, Wang, Xin wrote: > >> Dear Rahul >> The SI is primary somatosensory cortex (or postcentral gyrus) and MI is primary motor cortex (or precentral gyrus). I want to compare the thickness and volume of these two areas from left side to right side. >> Thank you, >> >> Xin >> >> ________________________________ >> >> From: Rahul Desikan [mailto:rahul@nmr.mgh.harvard.edu] >> Sent: Mon 4/30/2007 3:52 PM >> To: Wang, Xin >> Cc: freesurfer(a)nmr.mgh.harvard.edu >> Subject: Re: [Freesurfer] ROI of SI cortex >> >> >> >> Hi Xin, >> >> What exactly do SI and MI cortices refer to? >> >> rahul >> >> On Mon, 30 Apr 2007, Wang, Xin wrote: >> >>> Hello, group >>> I need to compare thickness of left v.s. the right SI and MI cortices. I saw some matlab tools for comparsion of left and right hippocampus in Lundervold.pdf. I could not find similar tools in the matlab folder of Freesurfer stable release 3.0.5 that I just installed. Could anybody kindly tell me the tools I could use for my study? >>> Thank you in advance. >>> Xin Wang >>> >> >> -- >> >> >> >> >> >> >> >> >> >> > > -- > > > > > > > > > > --

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(no subject)
by duhanjian＠sohu.com 27 Jun '07

27 Jun '07

hi ,I have solved the the probelm.Now, I have some new question, just as belows:1  In the GUI interface, I can't type the letters ,I don't know why?2 when I choose the volume in the Morphometric-----Measure, the Qdec runs error. how to solve it ? the screenshot on the attachment.3 In the terminal command window, I type the make_average_subject command,It runs errors , show as :limit:decriptors:can't remove limite(operation not permition), how to deal with this bug?Thank you very much!!!

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