Freesurfer

freesurfer@nmr.mgh.harvard.edu

19 participants
30132 discussions

TIV corrected
by Guang Zeng 20 Oct '09

20 Oct '09

Hi, there, Have those volume of ROIs in aseg.stats been TIV corrected? Thanks a lot! Guang _________________________________________________________________ Hotmail: Free, trusted and rich email service. http://clk.atdmt.com/GBL/go/171222984/direct/01/

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T1 scanning parameters and mean curvature
by Narly A Golestani 20 Oct '09

20 Oct '09

Hello all, I would like to know whether the T1 parameters such as TR, TE, TI, and flip angle can systematically influence mean curvature values obtained by recon-all -all. I have processed 2 data sets with the following T1 parameters, and am noticing that the mean curvature values systematically bigger in the former compared to the latter data set in 78% of the brain regions segmented in the default (Desikan) atlas. data set 1: TR=12.24, TE=3.56, TI=530.00, flip angle=23.00 Original Data has (1, 1, 1) mm size and (240, 256, 176) voxels data set 2: TR=20.66, TE=8.42, TI=640.00, flip angle=25.00 Original Data has (1, 1, 1) mm size and (224, 256, 176) voxels More generally, I would like to confirm that it's not recommended to combine data based on different scanning parameters in one study, due to possible systematic differences in the segmentation output related to scanning parameters. thanks in advance and all the best, Narly.

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optseq2 questions
by 杨宏宇 20 Oct '09

20 Oct '09

Hi list, I am using optseq2 to design my fMRI study. These are my scripts: optseq2 --ntp 500 --tr 2 --psdwin 0 40 1 --ev star 12 9 --ev star 13 8 --ev star 14 8 --ev diamond 12 9 --ev diamond 13 8 --ev diamond 14 8 --tnullmin 5 --tnullmax 7 --nkeep 3 --o ex.event12.13.14s --nsearch 5000 I have 2 events, which last for 12,13, and 14s. I found that the schedule documents I got had many null events more than 7s, however, I have set the maximam as 7s. In the sum logfile, I found that my script was recorded correctly, so could you please tell me the reason, and how to solve the problem? Many thanks, Hongyu Division on Addiction, Psychiatry Department, UT Southwestern Medical Center

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Creating FSGD file
by Weisinger, Brian (NIH/OD) [E] 20 Oct '09

20 Oct '09

I am trying to follow the directions to create a FSGD file put I am having trouble. I used open office to make the file which looks like the one in the example. Is this where I am supposed to create it? Do I create it in as a text file? Do I save it as an .odt file? If all this is correct I have a question of where do I place the file so when I put in mris_preproc --target fsaverage --hemi lh \ --meas thickness --out lh.paired-diff.thickness.mgh \ --fsgd pairs.fsgd --paired-diff It finds it? Thanks for the help.

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mgz file is tilted
by Jay Ives 20 Oct '09

20 Oct '09

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out of space
by Ahmed, F, Me <fahmed＠sun.ac.za> 20 Oct '09

20 Oct '09

Hello, I'm trying to get my dicom images into my VMware desktop but I have run out of space so can't continue to copy files over. I am trying desperately to make space on the desktop and had a question regarding that. I have 2 freesurfer folders; 1 is on my desktop and 1 is located in /usr/local. I'm wondering if I need to have both, or if I can delete the one on my desktop (as it's taking up space) and if so, will that cause any problems in using fs? Any advice you can give will be greatly appreciated. Thank you, Fatima

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mri_motion_correction to average DTI sequences?
by Francisco Costela 20 Oct '09

20 Oct '09

Hi all, I want to get the average DTI from 2 DTI sequences (obtained from the same subject with the same configuration data). I am using mri_motion_correct to get it but I wonder whether I can apply the original diffusion direction file to this average image or I need to rotate the diffusion direction accordingly (due to the motion introduced). Thanks for your help, Francisco

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Re: [Freesurfer] out of space
by Ahmed, F, Me <fahmed＠sun.ac.za> 20 Oct '09

20 Oct '09

How do I increase the size of my vmware disk image? I managed to get enough space on the desktop for the time being (after deleting the duplicate freesurfer folder) but for future reference, it'd be good to know how to increase the space should I need to. Thanks -----Original Message----- From: Rudolph Pienaar [mailto:rudolph.pienaar@childrens.harvard.edu] Sent: 20 October 2009 15:14 To: Ahmed, F, Me <fahmed(a)sun.ac.za> Cc: Freesurfer Mailing List Subject: Re: [Freesurfer] out of space You can also increase the size of your vmware disk image, or add another "blank" vmware disk to your virtual machine. It requires some admin, but is doable. Google will help. Alternatively, you can also "share" folders on your Windows host and have them accessible from your CentOS guest. Essentially you need to get 'samba' running on your CentOS guest. 'Samba' allows Linux machines to share network folders with Windows machines. -=R On Oct 20, 2009, at 06:05 , Ahmed, F, Me <fahmed(a)sun.ac.za> wrote: > Hello, > > I'm trying to get my dicom images into my VMware desktop but I have > run out of space so can't continue to copy files over. I am trying > desperately to make space on the desktop and had a question > regarding that. > > I have 2 freesurfer folders; 1 is on my desktop and 1 is located in / > usr/local. I'm wondering if I need to have both, or if I can delete > the one on my desktop (as it's taking up space) and if so, will that > cause any problems in using fs? > > Any advice you can give will be greatly appreciated. > > Thank you, > Fatima > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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The uncertainty of final stats from repeated runs on the same subject
by leemon albert 20 Oct '09

20 Oct '09

Hi, We run the freesurfer stable v4.4.0 on our Linux computer (Ubuntu 9.04). The program finishes without any error. However, we find the stats files (in the /subject/stats) from repeated runs on the same subject vary widely in final outcome. Meanwhile, we notice the item of the stable v4.5.0 release notes, which's about the flag of -norandomness. It's said that the binaries in the recon-all stream are subject to variability due to usage of a random number generator (mris_smooth, mris_sphere, mris_topology_fixer, mris_topo_fixer and mris_ca_label). Is this realtive with our problem? Have anyone met this problem? Do the data need to rerun using Stable v4.5.0? To take into account the number of the subjects, is there any other method to fix it? For example: tail -2 'thickness.lh.MT.songjunyi.txt' # ColHeaders StructName NumVert SurfArea GrayVol ThickAvg ThickStd MeanCurv GausCurv FoldInd CurvInd lh.MT.songjunyi.label 2330 1564 4584 2.548 0.684 0.146 0.062 52 6.5 tail -2 thickness.lh.MT.songjunyi_re1.txt # ColHeaders StructName NumVert SurfArea GrayVol ThickAvg ThickStd MeanCurv GausCurv FoldInd CurvInd lh.MT.songjunyi_re1.label 2409 1631 4786 2.539 0.698 0.146 0.075 78 7.7 tail -2 thickness.lh.MT.songjunyi_re2.txt # ColHeaders StructName NumVert SurfArea GrayVol ThickAvg ThickStd MeanCurv GausCurv FoldInd CurvInd lh.MT.songjunyi_re2.label 2341 1576 4659 2.558 0.694 0.143 0.058 39 6.0 Any help would be appreciated. Thanks.

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Re: [Freesurfer] FDR correction (fwd)
by Doug Greve 19 Oct '09

19 Oct '09

Here's Tom Nichols explanation. He points out that you use the maximum i, not the minimum, so you don't have to get past i=1. Thanks Tom! ---------- Forwarded message ---------- Date: Fri, 16 Oct 2009 23:11:09 +0100 From: Thomas Nichols <t.e.nichols(a)warwick.ac.uk> To: Doug Greve <greve(a)nmr.mgh.harvard.edu> Cc: Donna Dierker <donna(a)brainvis.wustl.edu> Subject: Re: [Freesurfer] FDR correction (fwd) Dear Doug, Great discussion! But I think it misses the point. Can you forward the following to the list? The Benjamini-Hochberg (BH) FDR procedure uses the inequality P(i) <= i / V * q for the ordered P-values P(1)<=P(2)<=...<=P(V) and desired level-q FDR control, which suggests that one will never get significance unless P(1)<q/V, just like Bonferroni. HOWEVER, the key element of BH-FDR is that you get to search over i and find the *largest* P-value that satisfies the inequality and use that P-value as a threshold. Hence when considering changing resolutions (i.e. increasing V, but increasing resolution/smoothness and roughly keeping the information content of the images the same) the magic of BH-FDR is that if the 5-th %ile of uncorrected P-values is FDR-significant at one resolution, i.e. i' = 0.05*V satisfies P( i' / V ) <= i' / V * q then one would expect that the 5-th %ile of P-values after up-sampling would have a similar value, and thus would also satisfy the inequality even though V has changed. That is the motivation that FDR is resilient to changes in resolution. However, I should note that in my own experience, leaving V fixed but changing smoothness, often changes the distribution of P-values dramatically, and thus changes the FDR result. But that should be a different beast that up-interpolation. Hope this helps! -Tom On Fri, Oct 16, 2009 at 5:43 PM, Doug Greve <greve(a)nmr.mgh.harvard.edu>wrote: > > Tom, here's an FDR question for you. It appears that the FDR > correction is dependent on the number of voxels (need p < fdr/N just > to get past i=1). Meaning that as N grows, the min p-value must also > shrink to get past i=1. Any way to get around this? > > thanks > > doug > > > > > ---------- Forwarded message ---------- > Date: Fri, 16 Oct 2009 11:30:59 -0500 > From: Donna Dierker <donna(a)brainvis.wustl.edu> > To: Michael Harms <mharms(a)conte.wustl.edu> > Cc: freesurfer(a)nmr.mgh.harvard.edu, Yulia WORBE <yulia.worbe(a)upmc.fr> > Subject: Re: [Freesurfer] FDR correction > > Regardless: FDR's sensitivity appears resolution-dependent to me. > > On 10/16/2009 10:39 AM, Michael Harms wrote: > >> Interesting post Donna, but my understanding of FDR is that it sets the >> p-value threshold based on the LARGEST p-value that satisfies the FDR >> relationship. >> >> That is, steps 3 and 4 in Genovese et al. (2002) are: >> 3) Let r be the largest i for which p <= i/V*q (assuming c=1) >> 4) Threshold the image at the p-value p(r). >> >> So, it isn't the case that you require the most significant p-value to >> satisfy p <= 0.05/V "just to get past i=1" as you put it in your post. >> >> Rather, you pick the largest p-value that satisfies the relationship, >> meaning that lower (more-significant) p-values may not have necessarily >> satisfied p <= i/V*q for their particular position in the sorted list of >> p-values. >> >> cheers, >> Mike H. >> >> >> On Fri, 2009-10-16 at 10:13 -0500, Donna Dierker wrote: >> >> I never heard anything on my post here, but it might just be high >>> surface resolution: >>> >>> >>> http://www.mail-archive.com/neuro-mult-comp@brainvis.wustl.edu/msg00026.html >>> >>> On 10/16/2009 09:58 AM, Michael Harms wrote: >>> >>> Your FDR analysis sounds correct. You probably have a rather small >>>> number of "marginally" significant vertices, which is why none survive >>>> FDR. You could try increasing the "q" value from say 0.05 to 0.1, in >>>> which case 10% of the surviving vertices would be expected to be false >>>> positives. >>>> >>>> cheers, >>>> Mike H. >>>> >>>> On Fri, 2009-10-16 at 12:03 +0200, Yulia WORBE wrote: >>>> >>>> >>>> Dear Freesurfer team, >>>>> >>>>> We are currently doing a cortical thickness studies between a group of >>>>> psychiatric patients (n=60) and controls (n=30). We tested several >>>>> smoothing levels (15mm, 20mm, 25mm) >>>>> >>>>> When setting an uncorrected threshold (such as p<0.005), we obtained >>>>> several regions of decreased thickness, which are consistent with the >>>>> pathology. >>>>> >>>>> However, when trying to correct for multiple comparisons using FDR >>>>> ("Set Using FDR" button in qdec), the computed threshold is very high >>>>> (e.g. 4.3 for 20mm smoothing) and, obviously, no significant regions >>>>> are left. >>>>> >>>>> Did we do anything wrong in the analysis ? >>>>> >>>>> Thank you very much for your help, >>>>> Yulia >>>>> >>>>> >>>>> >>>>> _______________________________________________ >>>>> 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 >> >> > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > -- ____________________________________________ Thomas Nichols, PhD Head of Neuroimaging Statistics Applied Neuroimaging Group University of Warwick Senior Research Fellow Oxford University FMRIB Centre

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