Freesurfer

freesurfer@nmr.mgh.harvard.edu

16 participants
30084 discussions

labels
by adrzezga＠nmr.mgh.harvard.edu 25 Jun '09

25 Jun '09

Hi I have four questions on label-design: 1.) Is there a way do design labels of a certain geometric form (e.g. a circle or a square with a standardized diameter) in tksurfer ? 2.) Can I move an existing label from one positition to another defined position (e.g. center it on some particular vertex) ? 3.) Can I copy and duplicate a label in tksurfer ? 4.) I wonder if there is some option to "mirror" a label which I designed on the surface of one cortical hemisphere (in tksurfer) to the corresponding areo on the other cortical hemisphere ? Alex

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volume group analysis
by Anita di Iasio 25 Jun '09

25 Jun '09

Hi all, I have 2 groups of subjects and I want to do a volume group analysis to compare volumes of subcortical structures. I have to run my analysis with the command-line methods but I don't know the correct flags to use with the commands (mris_preproc and mri_glmfit). Can you help me? Can you give me some suggestion? thank you in adavanced, Anita

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make_average_subject error about limit
by Feng-Xian 25 Jun '09

25 Jun '09

Hi, I have a problem with make_average_subject. After running all commands (including ln -s $FREESURFER_HOME/subjects/fsaverage and recon-all -s <subjid> -qcache for all my subjects) about running QDEC, I found that QDEC could not analysis my group. Because the group have 1 factor and three levels, QDEC can't run. So, I want to change the method of analysis from QDEC to DODS. I had a fsaverage file when I running QDEC, but the fsaverage did not use my subjects to make. So, can I use the fsaverage file to run DODS? If not, I should make a new fsaverage with my subjects. But, I encounter the problem about make_average_subject. When I type: make_average_subject --subects <subjid1> <subjid2> ... the terminal show that: limit: descriptors: Can't remove limit 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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group analysis with one factor and three levels
by Feng-Xian 25 Jun '09

25 Jun '09

Hi, I have a problem of group analysis with QDEC. Now, I want to analysis a group with one factor and three levels. When I run QDEC with this group, the terminal shows error with too many levels. So, how can I do to analysis this group with one factor and three levels? Would you tell me what to do? If not, would you suggest me any other way to get the group analysis? 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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do I have to include age as covariate in qdec analysis?
by 류철형 25 Jun '09

25 Jun '09

Dear all I'm trying to compare the cortical thickness between the neurodegenerative disease patient group and normal controls. To match the age, I selected subjects from both groups and finally included age-matched groups into freesurfer thickness analysis (similar mean age, same age distribution from 40-73, 70 normal controls and 91 patients) In 1st qdec analysis, direct comparison between two groups without age covariate showed thickness of temporoparietal cortex of patient group was smaller than that of normal controls (uncorrected P<0.001 or FDR corrected P<0.05). However, when the age was included in the model as a covariate, the significant surface vertices almostly disappearred and some unexpected vertices emerged as significant, in which mean thickness were not so much different between two groups. My question is... 1) Is there any possibility that disease-related cortical thinning area is quite similar to the age related cortical thinning area and resulted in the disappearance of significant vertices? 2) Do I have to include age covariate in that model even if I clearly matched the age distribution? 3) The area "does the average thickness differ between normal and patient?" was just same as the area "does the thickness--age correlation differ between normal and patient?", except for the color of blobs (e.g. red -> blue, blue -> red). Then, what do those question mean? >From Lyoo

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averaging fMRI data across multiple scan sessions
by Krishna Srihasam 25 Jun '09

25 Jun '09

Hi, We had collected a lot of data in our first few scan sessions trying different TR/TE/voxel size/REPs combinations in order to get the optimal values. Now, I would like to do a joint analysis of all those scans. Is it possible ? regards, Krishna

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Errors in qdec/Analyze
by Toh Hock Wong 25 Jun '09

25 Jun '09

Hi to all, I have been having troubles with qdec and several error messages appear. The first message appeared when clicking 'analyze'. It doesn't matter if i use one or two discrete plus one or two continuos factors, i get the same error message. What does it mean by codno=1e+08? Creating output directory /Applications/freesurfer/subjects/qdec/ lh_postcentral_thickness Loading y from /Applications/freesurfer/subjects/qdec/ lh_postcentral_thickness/y.mgh Matrix condition is 1e+08 ERROR: matrix is ill-conditioned or badly scaled, condno = 1e+08 Possible problem with experimental design: Check for duplicate entries and/or lack of range of continuous variables within a class. Another error message that appeared earlier when i include age, gender, diagnosis(epilepsy/nonepileptic) and ln_postcentral_thickness is as follow: $Id: mri_glmfit.c,v 1.138.2.3 2008/08/27 13:33:05 greve Exp $ cwd /Applications/freesurfer cmdline mri_glmfit --y /Applications/freesurfer/subjects/qdec/ lh_postcentral_thickness/y.mgh --fsgd /Applications/freesurfer/ subjects/qdec/lh_postcentral_thickness/qdec.fsgd dods --glmdir / Applications/freesurfer/subjects/qdec/lh_postcentral_thickness --surf fsaverage lh --label /Applications/freesurfer/subjects/fsaverage/label/ lh.cortex.label --C /Applications/freesurfer/subjects/qdec/ lh_postcentral_thickness/contrasts/lh-Avg-Intercept-thickness.mat --C / Applications/freesurfer/subjects/qdec/lh_postcentral_thickness/ contrasts/lh-Avg-thickness-age-Cor.mat --C /Applications/freesurfer/ subjects/qdec/lh_postcentral_thickness/contrasts/lh-Avg-thickness- lh_postcentral_thickness-Cor.mat --C /Applications/freesurfer/subjects/ qdec/lh_postcentral_thickness/contrasts/lh-Diff-Male-Female-Intercept- thickness.mat --C /Applications/freesurfer/subjects/qdec/ lh_postcentral_thickness/contrasts/lh-Diff-Male-Female-Cor-thickness- age.mat --C /Applications/freesurfer/subjects/qdec/ lh_postcentral_thickness/contrasts/lh-Diff-Male-Female-Cor-thickness- lh_postcentral_thickness.mat --C /Applications/freesurfer/subjects/ qdec/lh_postcentral_thickness/contrasts/lh-Diff-nonepileptic-epilepsy- Intercept-thickness.mat --C /Applications/freesurfer/subjects/qdec/ lh_postcentral_thickness/contrasts/lh-Diff-nonepileptic-epilepsy-Cor- thickness-age.mat --C /Applications/freesurfer/subjects/qdec/ lh_postcentral_thickness/contrasts/lh-Diff-nonepileptic-epilepsy-Cor- thickness-lh_postcentral_thickness.mat --C /Applications/freesurfer/ subjects/qdec/lh_postcentral_thickness/contrasts/lh-X-gender-diagnosis- Intercept-thickness.mat --C /Applications/freesurfer/subjects/qdec/ lh_postcentral_thicknesss/contrasts/lh-X-gender-diagnosis-Cor- thickness-age.mat --C /Applications/freesurfer/subjects/qdec/ lh_postcentral_thickness/contrasts/lh-X-gender-diagnosis-Cor-thickness- lh_postcentral_thickness.mat Can the above error occur because one of the two groups has only one subject (epilepsy and female). I have also attached fsgd1 generated by freesurfer as below: GroupDescriptorFile 1 Title lh_postcentral_thickness MeasurementName thickness Class genderMale-diagnosisnonepileptic Class genderFemale-diagnosisnonepileptic Class genderMale-diagnosisepilepsy Class genderFemale-diagnosisepilepsy Variables age lh_postcentral_thickness Input RCoward genderMale-diagnosisnonepileptic 11.000000 2.112000 Input SCoward genderFemale-diagnosisnonepileptic 13.000000 1.979000 Input JConigrave genderMale-diagnosisnonepileptic 10.000000 2.470000 Input AConigrave genderFemale-diagnosisnonepileptic 5.000000 2.268000 Input KBleasel genderFemale-diagnosisnonepileptic 9.000000 2.292000 Input MBleasel genderFemale-diagnosisnonepileptic 16.000000 2.181000 Input CMcintosh genderFemale-diagnosisnonepileptic 15.000000 2.107000 Input OJohanssen genderMale-diagnosisnonepileptic 6.000000 2.033000 Input MJohanssen genderFemale-diagnosisnonepileptic 6.000000 2.037000 Input GHerbert genderFemale-diagnosisnonepileptic 4.000000 2.209000 Input JRathmell genderMale-diagnosisnonepileptic 11.000000 2.287000 Input ARathmell genderMale-diagnosisnonepileptic 14.000000 2.223000 Input ZTucker genderFemale-diagnosisepilepsy 11.000000 2.415000 Your advice and tips will be most appreciated! Toh Wong (Sydney, Australia)

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RE: fdr thresholds in tksurfer compared to Nichol's function
by Lars M. Rimol 25 Jun '09

25 Jun '09

Hi, Please disregard my previous mail. I was a little too trigger happy..., the 1.928 threshold set by tksurfer is too high for any vertex to survive so the two methods DO concur. I should actually look at the maps and not just the output... The reason I asked is that I'm combining images to obtain an overall FDR, either for both hemispheres or for several comparisons. I don't see how this can be done in tksurfer so I'm using Nichols' function, which works just fine. I just don't know how to get an FDR threshold when no vertex has a p-value that survives - but tksurfer obviously produces such a threshold. How do I obtain that threshold? (Or is it simply set just higher than the highest -log(p-value) in the image, for display purposes? It seems always to be just above.) thanks (and apologies for the confusion), LMR From: larilin(a)gmail.com To: freesurfer(a)nmr.mgh.harvard.edu Subject: fdr thresholds in tksurfer compared to Nichol's function Date: Thu, 25 Jun 2009 14:07:08 +0200 Hi, I've used the fdr function in tksurfer and compared the results to Tom Nichol's matlab function (http://www.sph.umich.edu/~nichols/FDR/) I use p = 10.^-abs(pfile), where "pfile" is 'sig.mgh'. I find that the p-threshold (pID, assuming positive dependence) is usually exactly the same as the one in tksurfer (probably because you use the same algorithm..?). But in some cases where pID is empty, which should mean that there is no suprathreshold vertex, I do get a threshold in tksurfer. Here's an example: For one contrast where pID was returned empty in Nichol's matlab function, I got a threshold of 1.927741 in tksurfer. Is this supposed to happen? The output is: MRISfdr2vwth(rate=0.05000, sign = 0, 1, only marked = 0) = 1.927741 surfer: MRISfdr2vwth with rate 0.05 and sign 0 returned threshold 1.927741 Thank you! yours, LMR

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[Fwd: Re: [Freesurfer] setting of fdr thresholds in qdec]
by Michael Harms 25 Jun '09

25 Jun '09

Lars, I had a similar question regarding the setting of the FDR p-value threshold back in Dec 2008 (search "fdr Harms" in the Archive), but for some reason, I see that Nick's reply to me didn't make it into the archive, even though he cc'ed the FS list. So, I'm forwarding Nick's response below, which I believe answers your question. cheers, -Mike H. -------- Forwarded Message -------- From: Nick Schmansky <nicks(a)nmr.mgh.harvard.edu> To: Michael Harms <mharms(a)conte.wustl.edu> Cc: Freesurfer Mailing List <freesurfer(a)nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] setting of fdr thresholds in qdec Date: Tue, 16 Dec 2008 18:06:24 -0500 Mike, I've attached the code that operates the "Set Using FDR" button in qdec. First have a look at the routine SetSurfaceScalarsColorsUsingFDR in vtkQdecWindow.cxx, which calls our FDR library and returns a threshold. Then, it calls the routine SetSurfaceScalarsColors after setting mid = threshold + 1.5, and max = threshold + 2.25. from there, SetSurfaceScalarsColors just checks min, mid and max against the current values (from prior run) and updates them if they differ. so basically, the 'algorithm' for mid and max appears to be just adding 1.5 and 2.25 to the threshold. I wasn't aware of this, or understand why (other than the need to set it to something!), so if you have an alternative, I'd like to hear. Also attached are mri2.c and sig.c, which contains the core fdr2vwth routine. It appears that "if no values meet the FDR criterion, then a value slightly smaller than the smallest p is returned." I've updated the code to print to the terminal the number of vertices having a P < the fdr min, although it seems to always be a large number of vertices because the fdr min is a positive value, and a typical result has both positive and negative P values. Nick On Thu, 2008-12-11 at 17:09 -0600, Michael Harms wrote: > Hello, > I'm curious, what algorithm is used for setting the "mid" and "max" > threshold values in QDEC when using the "Set Using FDR" button? > > And, what does the algorithm do for setting the "min" threshold when no > single p-value is significant enough to satisfy the necessary inequality > for the specified FDR Rate? > In that case, is the resulting "min" just set to the -log10(p) of the > most significant p-value? > > If easy to implement, it would be handy if the output to the terminal > reported the number of vertices with P < than the FDR determined "min" > threshold. > > cheers, > Mike H. > > _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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RES: [Freesurfer] volume group analysis
by ppj＠netfilter.com.br 25 Jun '09

25 Jun '09

To make analysis of volumetric data export volumetric data to csv and use your statistical package. -- Pedro Paulo Jr E71 Nokia -----Msg original----- De: Anita di Iasio Enviada: 25/06/2009 06:04:38 Para: freesurfer(a)nmr.mgh.harvard.edu Assunto: [Freesurfer] volume group analysis Hi all, I have 2 groups of subjects and I want to do a volume group analysis to compare volumes of subcortical structures. I have to run my analysis with the command-line methods but I don't know the correct flags to use with the commands (mris_preproc and mri_glmfit). Can you help me? Can you give me some suggestion? thank you in adavanced, Anita _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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