Freesurfer

freesurfer@nmr.mgh.harvard.edu

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30131 discussions

Incorrect results after re-run.
by zheng.hui＠singhealth.com.sg 25 Oct '07

25 Oct '07

Hi, I did some editing, add in control points and edit pial surface on one set of our data on the left hand side of the screenshot attached, and re-run recon-all -autorecon2 -autorecon3 -s subjID The result turned out to be wrong as shown in the right hand side of the screenshot. The algorithm worked well at the temporal lobe where control points were added, but it failed at the superior part. Can you suggest why it is so? Thanks Zheng Hui

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Re: {Spam?} 答复: [Freesurfer] thickness difference map
by Nick Schmansky 24 Oct '07

24 Oct '07

Can you send along the output text that shows the error? On Wed, 2007-10-24 at 21:10 -0400, Wang, Xin wrote: > Thank you for your response, Doug. I attached all the commends I > modified from Han's note. I worked through step1 & 2. But the step3 is > the problem now. step4 hasn't been tried. I look forward to hearing > your suggestions. > > Thank you again, > > Xin > > > ______________________________________________________________________ > From: Doug Greve [mailto:greve@nmr.mgh.harvard.edu] > Sent: 2007-10-24 (星期三) 19:12 > To: Wang, Xin > Cc: Nick Schmansky; Freesurfer Mailing List > Subject: RE: [Freesurfer] thickness difference map > > > > > > What is your cmd line and what is the terminal output? > > > > On Wed, 24 Oct 2007, Wang, Xin wrote: > > > Thank you very much, Nick. I ran into a problem when I ran the step > 3 of Han's note of thickness repeatability. The --tfmt of > mri_surf2surf is curv. The step can not be completed. > > > > Please help me. > > > > Thank you again, > > > > Xin > > > > ________________________________ > > > > From: Nick Schmansky [mailto:nicks@nmr.mgh.harvard.edu] > > Sent: Sat 10/20/2007 5:34 PM > > To: Wang, Xin > > Cc: Freesurfer Mailing List > > Subject: Re: [Freesurfer] thickness difference map > > > > > > > > Xin, > > > > Have a look at this wiki page written by Xiao (the author of the > paper): > > > > http://surfer.nmr.mgh.harvard.edu/fswiki/ThicknessRepeatibility > > > > It describes the procedure for how Figure 2 was created. > > > > Nick > > > > On Fri, 2007-10-19 at 15:42 -0400, Wang, Xin wrote: > >> Hello, Group, > >> > >> We want to make a figure as Fig2 in Han X et al. 2006 reliability > >> paper. Does anyone kindly share his/her way to make a map of > >> difference in average thickness between two groups? > >> > >> Thank you in advance, > >> > >> Xin Wang > >> _______________________________________________ > >> Freesurfer mailing list > >> Freesurfer(a)nmr.mgh.harvard.edu > >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > > > > > > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > greve(a)nmr.mgh.harvard.edu > Phone Number: 617-724-2358 > Fax: 617-726-7422 > > In order to help us help you, please follow the steps in: > surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > > > >

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thickness difference map
by Wang, Xin 24 Oct '07

24 Oct '07

Hello, Group, We want to make a figure as Fig2 in Han X et al. 2006 reliability paper. Does anyone kindly share his/her way to make a map of difference in average thickness between two groups? Thank you in advance, Xin Wang

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orientation
by Nurunisa Neyzi 24 Oct '07

24 Oct '07

Hi, I have these analyze files with wrong orientation I can change their orientation using fslswapdim but when I convert them to mgz files using mri_convert, the orientation is wrong again. i tried the following reading from 001.mgz... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (0, 0, -1) j_ras = (1, 0, 0) k_ras = (0, -1, 0) reordering axes... MRIreorder: incorrect dst width error reordering axes so not sure what i should do, can you please help me on this?

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Brodman areas using tksurfer/tkmedit
by Pratap Kunwar 24 Oct '07

24 Oct '07

Hi, Can tksurfer/tkmedit have Brodman arreas as well as talairach coordinates displayed? thanks pratap

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Sulcal CSF measure
by Morgan Hough 23 Oct '07

23 Oct '07

Hi there, I was wondering if sulcal CSF differences should be reported given the difficulty in its identification from T1 data? How is sulcal CSF defined by FS? Thanks in advance for your time. Cheers, -Morgan

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model for pair-T test
by Wang, Xin 23 Oct '07

23 Oct '07

Hello, group, Could anybody tell me how to do the pair T test and the repeat measurement F test? I will really appreciate if you can share the steps and GLM of the tests. I am using the old freesurfer group analysis. Thank you, very much, Xin Wang

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activation patterns and par files
by Cameron Ellis 23 Oct '07

23 Oct '07

Hi all, I have run two different group analyses in stable3. All of the analysis parameters between the two are identical except that one uses a paradigm file containing three conditions and the other uses a paradigm file containing five conditions. The first three conditions in the analysis using the five condition paradigm file are identical to those in the three condition paradigm files, meaning the timing and definitions are exactly the same. The five condition paradigm file just contains additional conditions that were not originally defined, as additions to the three condition paradigm files. The problem is that the activation patterns I receive for contrasts using only the first three conditions of the five condition paradigm files are different from the activation patterns of contrasts using the three condition paradigm files. I do not know why this would be. Is there something about not defining all events that would lead to differences of this sort? I have visually inspected all of my paradigm files so I am sure the only diffences between them are the additional 2 conditions in the five condition files. I have attached images of the differences and below are the paths to both analyses as well as the commands run to produce the 5 condition results. The three condition commands were identical except for calling the different analysis. Any help or insight would be much appreciated! Cameron 3condition: /space/troy/3/users/retrievalnewest/Controlssh+smvsnh/bold/retrievalSPMHRF/sphsmooth-rfx/sh+smvsnh 5condition: /space/troy/3/users/retrievalnewest/Controlssh+smvsnh/bold/retrievalSPMHRF_5cond/sphsmooth-rfx/sh+smvsnh mkanalysis-sess.new -analysis retrievalSPMHRF_5cond -TR 2.5 -paradigm paradigmmacro5 -designtype event_related -spmhrf 0 -nconditions 5 -timewindow 25 -prestim 5 -funcstem fmcsm -taumax 30 -polyfit 2 -inorm selxavg-sess -sf sessidall -df sesspar -analysis retrievalSPMHRF_5cond mkcontrast-sess -contrast -sh+smvsnh -analysis retrievalSPMHRF_5cond -ncond 5 -a 1 -a 2 -c 3 func2sph-sess -sf sessidall -df sesspar -analysis retrievalSPMHRF_5cond sphsmooth-sess -smoothsteps 20 -analysis retrievalSPMHRF_5cond -insphdir sph -outsphdir sphsmooth -hemi rh -sf sessidall -df sesspar isxavg-re-sess -analysis retrievalSPMHRF_5cond -contrast sh+smvsnh -group Controlssh+smvsnh -space sph -spacedir sphsmooth -hemi rh -sf sessidcontrolssh+smvsnh -df sesspar

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Create thickness map
by lan lin 22 Oct '07

22 Oct '07

Hello, Is it possible to create a thickness map and use functional image's value to replace thickness value? Thanks, Ines

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intrasubject segmentation variance
by Thomas Doering 22 Oct '07

22 Oct '07

Dear freesurfers, i was running Freesurfer on the same subject on two independent Computers. The first Computer PC1has 2 physical Intel processors with 2 logical each - (dual core) - 1.6GHz with 4Gb Ram and the second PC2 has 2 physical Intel processors with 4 logical - (quad core) - 3 GHz with 8 Gb Ram. After running on these two Computers - i start at the exactly same time - i got a surprising result: My faster Computer PC2 took 41h to run the subject and the slower Computer took 31h. I wonder if somebody have some comment on this, because i have no idea what is wrong ( When i have the Linux System Monitor on, watching the CPU History, it seems that the slower PC hat a more effective occupation/usage than the faster - switching faster between one CPU and the other one...) Another small question: In the final segmentation table, i noticed that there are some small diferences between the results of PC1 and PC2: for ex.: PC1:ctx - rh-caudalmiddle frontal = 5029 5029 PC2:ctx - -"- 5360 5360 , so a diference of ~6%. I guess these are variations due to the algorithm.. Are there some established limits for that diferences? Thanks for help, Thomas

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