[Freesurfer] make_average_subject error about limit
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/) ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[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@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] fdr thresholds in tksurfer compared to Nichol's function
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 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
RES: [Freesurfer] volume group analysis
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@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@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] ADC units after dt_recon
Hi All, After running the dt_recon processing stream on a standard diffusion tensor image, does any body know the units on the resulting adc.nii volume? Thanks Greg -- ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] RE: fdr thresholds in tksurfer compared to Nichol's function
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: lari...@gmail.com To: freesurfer@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 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] RE: fdr thresholds in tksurfer compared to Nichol's function
Use the fast_fdrthresh matlab function provided in the fsfast/toolbox directory
in freesurfer. It gives the same results as tksurfer.
Cheers
Jorge Luis Bernal Rusiel
Phd Student
Laboratory of Functional Neuroscience.
University of Pablo de Olavide. Seville. Spain
--- El jue, 25/6/09, Lars M. Rimol lari...@gmail.com escribió:
De: Lars M. Rimol lari...@gmail.com
Asunto: [Freesurfer] RE: fdr thresholds in tksurfer compared to Nichol's
function
Para: FS maling list freesurfer@nmr.mgh.harvard.edu
Fecha: jueves, 25 junio, 2009 4:18
#yiv1972015953 .hmmessage P
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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: lari...@gmail.com
To: freesurfer@nmr.mgh.harvard.edu
Subject: fdr thresholds in tksurfer compared to
Nichol's function
Date: Thu, 25 Jun 2009 14:07:08 +0200
#yiv1972015953 .ExternalClass .EC_hmmessage P
{padding:0px;}
#yiv1972015953 .ExternalClass body.EC_hmmessage
{font-size:10pt;font-family:Verdana;}
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
-Adjunto en línea a continuación-
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[Freesurfer] labels
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 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] labels
1. Not really, although you can dilate a label, which will be somewhat circular. 2. No, sorry. 3. You can save it and reload it as a new one I guess. 4. Not sure, I'll leave this one for Doug Bruce On Thu, 25 Jun 2009 adrze...@nmr.mgh.harvard.edu wrote: 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 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] make_average_subject error about limit
Feng-Xian, It appears that you do not have permission on your system to change the limits. So you will have to edit the scripts make_average_volume, make_average_surface and make_average_subject to comment out the 'limit' line, so that it looks like this: #limit descriptors unlimited Nick On Thu, 2009-06-25 at 15:51 +0800, Feng-Xian wrote: 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/) ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] make_average_subject error about limit
Feng-xian, I should also mention that i dont think creating your own average subject will solve the problem you describe, where you need to work with three levels in your group. for that, you wont be able to use qdec, but will need to run things manually. these pages give examples: http://surfer.nmr.mgh.harvard.edu/fswiki/FsgdExamples and note one of them is 1 Factor, 3 Levels. Nick On Thu, 2009-06-25 at 11:55 -0400, Nick Schmansky wrote: Feng-Xian, It appears that you do not have permission on your system to change the limits. So you will have to edit the scripts make_average_volume, make_average_surface and make_average_subject to comment out the 'limit' line, so that it looks like this: #limit descriptors unlimited Nick On Thu, 2009-06-25 at 15:51 +0800, Feng-Xian wrote: 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/) ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: RES: [Freesurfer] volume group analysis
Anita, to add to that comment, you would use asegstats2table to create the text file of data of your subjects and their stats of volumetric data, which can be imported into any stats package. see this page: http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/VolumetricGroupAnalysis while its possible to perform volumetric analysis using mri_glmfit, its kind of cumbersome compared to just using a stats package. qdec will eventually support doing such an analysis though. Nick On Thu, 2009-06-25 at 12:31 +, p...@netfilter.com.br wrote: 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@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@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Errors in qdec/Analyze
It means that you have an ill-conditioned design matrix. It is probably the case that your discrete or continuous variables are redundant or that you don't have members in all your classes. doug Toh Hock Wong wrote: 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 11.00 2.112000 /// /Input SCoward genderFemale-diagnosisnonepileptic 13.00 1.979000 /// /Input JConigrave genderMale-diagnosisnonepileptic 10.00 2.47 /// /Input AConigrave genderFemale-diagnosisnonepileptic 5.00 2.268000 /// /Input KBleasel genderFemale-diagnosisnonepileptic 9.00 2.292000 /// /Input MBleasel genderFemale-diagnosisnonepileptic 16.00 2.181000 /// /Input CMcintosh genderFemale-diagnosisnonepileptic 15.00 2.107000 /// /Input OJohanssen genderMale-diagnosisnonepileptic 6.00 2.033000 /// /Input MJohanssen genderFemale-diagnosisnonepileptic 6.00 2.037000 /// /Input GHerbert genderFemale-diagnosisnonepileptic 4.00 2.209000 /// /Input JRathmell genderMale-diagnosisnonepileptic 11.00 2.287000 /// /Input ARathmell genderMale-diagnosisnonepileptic 14.00 2.223000 /// /Input ZTucker genderFemale-diagnosisepilepsy 11.00 2.415000 /// / / / / Your advice and tips will be most appreciated! Toh Wong (Sydney, Australia) / / / / / / / / / / / / / / / / / / ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center
Re: [Freesurfer] averaging fMRI data across multiple scan sessions
Can you be more specific? I would not recommending pooling them together. doug Krishna Srihasam wrote: 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 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@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 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] do I have to include age as covariate in qdec analysis?
류철형 wrote: 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 P0.001 or FDR corrected P0.05). 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? Yes, it is possible. It looks like it might be that there is an interaction between group and age, based on what you say in #3. This can complicate looking for differences between group thickness means as the difference itself becomes age dependent. 2) Do I have to include age covariate in that model even if I clearly matched the age distribution? Technically, you do not, but it should be a good idea to do so. You can try one of these things: (a) use DOSS (fits the same slope to both groups), or (b) stay with DODS and demean the ages. This is the same as what you are doing already, but it tests for the difference at the mean of your group instead of at 0. 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? This is sort of expected if there is an interaction. With DODS, you have two lines (one for each group). If they are not parallel (ie, the slopes are different, indicating an interaction) then they will cross at some age. If that age is to the right of age=0, then they will have different signs. doug From Lyoo ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@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 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] wmparc.mgz average
The easiest thing would be to binarize the aparc+aseg like: mri_binarize --i aparc+aseg.mgz --wm --o whitematter.mgz You can the resample this to mni305 with: mri_convert --apply_transform transforms/talairach.xfm whitematter.mgz whitematter.mni305.mgz -oc 0 0 0 Not sure what you want to do now. You can then mri_concat the whitematter.mni305.mgz files from you different subjects into one file, or create a mean. doug muet0...@umn.edu wrote: Hi FreeSurfers, I was wondering if it is possible to obtain an average wmparc.mgz file for a group of subjects that have been processed through freesurfer? We have 72 cases that have been independently processed through freesurfer, and we would like to generate a representative white-matter atlas that could potentially be aligned to some standard space (e.g., MNI). Would this be possible? If this isn't possible, could we obtain this from fsaverage? I noticed that $FREESURFER_HOME/subjects/fsaverage does have an aparc+aseg.mgz --- is there also a way to get wmparc.mgz (e.g, using mri_aparc2aseg)? Thanks in advance for any suggestions! -Ryan Muetzel ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@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 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] group analysis with one factor and three levels
You will have to do it with the command-line stream. Ie, set up your own FSGD file with classes and covariates, run mris_preproc, create your own contrasts, then run mri_glmfit. There are examples on the wiki. doug Feng-Xian wrote: 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/) ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@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 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] make_average_subject error about limit
You don't *have to* to run make_average_subject to do your analysis, only if you want to view the results on a map with the curvature patterns averaged over your subjects. As for the limit error, how old is your version of freesurfer? That line was removed about 1.5 years ago... doug Feng-Xian wrote: 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/) ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@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 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] volume group analysis
You can use mris_preproc or mri_glmfit. Instead, use asegstats2table. This will create a text table that you can load into a stats program. See the wiki tutorial for examples. doug Anita di Iasio wrote: 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@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@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 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] ADC units after dt_recon
They are the inverse of the units that you used to spec the b-values. doug Gregory Dierksen wrote: Hi All, After running the dt_recon processing stream on a standard diffusion tensor image, does any body know the units on the resulting adc.nii volume? Thanks Greg -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@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 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] labels
#4. Not yet, though I have started working on this again, but it will be a while before it is ready. Carl Schwartz gave a solution a while ago, search the archives. It's not great, but you can do it now. doug Bruce Fischl wrote: 1. Not really, although you can dilate a label, which will be somewhat circular. 2. No, sorry. 3. You can save it and reload it as a new one I guess. 4. Not sure, I'll leave this one for Doug Bruce On Thu, 25 Jun 2009 adrze...@nmr.mgh.harvard.edu wrote: 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 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@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 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
