[Freesurfer] question about Correction for Multiple Comparison

2012-03-26 Thread ZhiLiangLong
Hi all: A few days ago, i have asked about some questions about Correction for Multiple Comparison. But i'm still confused about it. The version of FS is 5.1.0. when i performed Correction for Multiple Comparison using command line with 'mris_glmfit-sim', it usually took many hours to

[Freesurfer] TR mismatch between analysis and data analysis

2012-03-26 Thread Kiley Seymour
Dear Doug, Thanks for your earlier reply. I have installed fsl on my machine, and have progressed a little further through the retinotopy analysis. However, I now have the following error.  ERROR: TR mismatch between analysis and data analysis TR = 2, data TR = 0 I used mri_convert f.nii

Re: [Freesurfer] TR mismatch between analysis and data analysis

2012-03-26 Thread Douglas N Greve
You'll have to re-run the preprocessing (or change all the .nii files). doug Kiley Seymour wrote: Dear Doug, Thanks for your earlier reply. I have installed fsl on my machine, and have progressed a little further through the retinotopy analysis. However, I now have the following error.

Re: [Freesurfer] make_average_subject

2012-03-26 Thread Douglas N Greve
It might be failing on the aseg, so try it with --no-aseg doug Bruce Fischl wrote: Hi Sonya did you run out of RAM? How much is on your machine? cheers Bruce On Fri, 23 Mar 2012, sonya kaur wrote: Dear all,I'm getting an error with the make_average_subject command on freesurfer.

Re: [Freesurfer] question about FSGD file

2012-03-26 Thread Douglas N Greve
Hi ZhiLiangLong, what you have set up probably does not make sense. By using gender as a covariate (male=1 and female=2), you are saying that you expect females to be twice as thick as males. doug ZhiLiangLong wrote: Hi, FS experts: I'm scanning freesurfer pages about FSGD files here:

Re: [Freesurfer] question about Cluster-wise Correction for Multiple Comparisions

2012-03-26 Thread Douglas N Greve
ZhiLiangLong wrote: Hi all: I'm performing the group analysis on my own data using command line on FS5.1.0 and i'm a little confused about the Clusterwise Correction for Multiple Comparisions. the command is as follows: mri_glmfit-sim \ --glmdir lh.gender_age.glmdir \ --sim mc-z 1 4

Re: [Freesurfer] Displaying FSL zstats onto FreeSurfer

2012-03-26 Thread Douglas N Greve
Zurcher Nicole wrote: Hi everyone, I have two questions regarding FreeSurfer and FSL interoperation and it would be great if someone could help. 1) When displaying subject-level FSL FEAT data onto the FS volume using the command tkmedit blobby orig.mgz lh.white -overlay

Re: [Freesurfer] Freesurfer coordinate problem

2012-03-26 Thread Douglas N Greve
which MNI coordinate system? We don't know anything about surfstat. Can you tell us what you want to do without using the surfstat commands? doug xiaoning wu wrote: Hi all, Recently I have a problem about coordinate of freesurfer. I have reprocessed the MRI data to get the cortical

Re: [Freesurfer] [BUG] epidewarp.fsl

2012-03-26 Thread Douglas N Greve
what does it do? What is the terminal output? Satrajit Ghosh wrote: epidewarp.fsl does not take non-integer smoothing kernel sizes. cheers, satra ___ Freesurfer mailing

Re: [Freesurfer] [BUG] epidewarp.fsl

2012-03-26 Thread Satrajit Ghosh
hi doug, here is the error, it told me there was a problem in an if statement somewhere. if you use smooth = 2.0 instead of 2 you will get the error. cheers, satra --- [snip] fslmerge -t /mindhive/gablab/users/keshavan/scripts/BrainImagingPipeline s/utils/test/fmunwarp/temp/ph.nii.gz

Re: [Freesurfer] about QAtools

2012-03-26 Thread Louis Nicholas Vinke
Hi Chunhui, The wm-anat-snr missing step is misleading. That file gets created when QAtools generates the SNR/WM measures using the wm-anat-snr command. It is not part of the recon-all stream. If you specify the default status log file included with the scripts you should not get that error

Re: [Freesurfer] normal vector projection

2012-03-26 Thread Douglas N Greve
You don't need to do that registration. Instead, use --identity xDS with mri_surf2vol. doug Seok Lew wrote: Hi, After freesurfer reconstruction, I tried to project surface normal vectors on the ribbon. I used the following scripts, but the projected vectors were out of the ribbon when I

Re: [Freesurfer] volume mapping

2012-03-26 Thread Anastasia Yendiki
Hi Johnson - The aparc+aseg.mgz is in the same space as the T1 used as input to freesurfer. a.y On Mon, 26 Mar 2012, Johnson wrote: Hi FS expert I need to know the transformation matrix itself since I will do the transformation in matlab. I successfully transformed white matter fibers

Re: [Freesurfer] volume mapping

2012-03-26 Thread Johnson
Hi I found it in a 256x256x256 space while the T1 we use is in different space, I found this page on the registration step: http://surfer.nmr.mgh.harvard.edu/fswiki/FsAnat-to-NativeAnat I wish to know how this script work? mri_label2vol --seg aseg.mgz --temp rawavg.mgz --o aseg-in-rawavg.mgz

Re: [Freesurfer] volume mapping

2012-03-26 Thread Anastasia Yendiki
If you want to register your DWI to T1, you should register to mri/brain.mgz. You can do this with bbregister, or with any affine registration tool of your choice. On Mon, 26 Mar 2012, Johnson wrote: Hi I found it in a 256x256x256 space while the T1 we use is in different space, I found

Re: [Freesurfer] volume mapping

2012-03-26 Thread Johnson
Hi Let me re-phrase my question: I already did registration from DWI to T1, this step is OK. Now I want to go from T1 to FreeSurfer space (aparc+aseg.mgz file not the aparc+aseg-in-rawavg file). I know I have two choices: 1) do registration using bbregister 2) since Freesurfer during processing

Re: [Freesurfer] Cortical Normalization Questions

2012-03-26 Thread Anderson Winkler
Hi Jeff and all, For normalization (i.e., divide the measurement under study by some global measurement), I would not argue favourably, as this procedure can bias the results in the opposite direction if a global effect is present. Instead, include it as a covariate is not as harmful. My

Re: [Freesurfer] volume mapping

2012-03-26 Thread Anastasia Yendiki
Actually, (1) should be more accurate, because bbregister uses the surface reconstruction obtained from the T1 to optimize the contrast across the gray/white boundary in the registered DWI. However if you want to convert to the 1mm, 256^3 voxel size that was used as input to freesurfer, see

Re: [Freesurfer] calculating DLPFC or frontal lobe grey and white matter volumes

2012-03-26 Thread Douglas N Greve
Try this cd $SUBJECTS_DIR/subject mri_aparc2aseg --s subject --labelwm --hypo-as-wm --rip-unknown --volmask --o mri/wmparc.a2009s.mgz --a2009s --ctxseg aparc.a2009s+aseg.mgz mri_segstats --seg mri/wmparc.a2009s.mgz --sum stats/wmparc.a2009s.stats --pv mri/norm.mgz --excludeid 0

Re: [Freesurfer] mri_vol2surf failed, segmentation error

2012-03-26 Thread Douglas N Greve
Can you run it outside of the pipeline to assure that it is not a pipeline issue? doug On 03/18/2012 08:54 AM, Qingyang Li wrote: Hi all, I am new to the freesurfer world. I was running a pipeline where I met an error. Here is the command I run and the error message: Command:

Re: [Freesurfer] volume mapping

2012-03-26 Thread Johnson
OK T1 space is the space acquired from the machine, original anatomical space regards JG On 03/26/2012 2:25 PM, Bruce Fischl wrote: can you post to the list so others can answer? And can you clarify what you mean by T1 space? On Mon, 26 Mar 2012, Johnson wrote: Hi well, I had to transfer

Re: [Freesurfer] mri_vol2surf failed, segmentation error

2012-03-26 Thread Satrajit Ghosh
hi Qingyang, you can simply copy and paste the command line into the shell. cheers, satra On Mon, Mar 26, 2012 at 3:12 PM, Douglas N Greve gr...@nmr.mgh.harvard.eduwrote: Can you run it outside of the pipeline to assure that it is not a pipeline issue? doug On 03/18/2012 08:54 AM,

Re: [Freesurfer] mri_vol2surf failed, segmentation error

2012-03-26 Thread Qingyang Li
Thank you Doug and Satra, I ran the same pipeline on another machine after I post the question and it went through with no problem... On the machine which the pipeline failed, I have freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0. And on the machine that the pipeline went through, I have

[Freesurfer] segmentation of the dural sinuses

2012-03-26 Thread Jonathan A Winawer
Are there any tools associated with freesurfer to aid in segmentation of the dural sinuses (e.g., superior sagittal sinus, transverse sinus, straight sinus, etc) from a T1-weighted anatomical scan? Many thanks, Jon *** Jonathan Winawer Stanford University

Re: [Freesurfer] segmentation of the dural sinuses

2012-03-26 Thread Bruce Fischl
not that I know of, sorry On Mon, 26 Mar 2012, Jonathan A Winawer wrote: Are there any tools associated with freesurfer to aid in segmentation of the dural sinuses (e.g., superior sagittal sinus, transverse sinus, straight sinus, etc) from a T1-weighted anatomical scan? Many thanks, Jon

Re: [Freesurfer] Cortical Normalization Questions

2012-03-26 Thread jorge luis
I think we must be careful about including noisy large scale measurements as global nuisance covariates in the General Linear Model (GLM). The GLM assumes that the independent variables are measured almost without error (eg. see http://en.wikipedia.org/wiki/Errors-in-variables_models).  For

Re: [Freesurfer] about QAtools

2012-03-26 Thread chenchunhuichina
Got it. Thanks Louis! 2012-03-27 Chunhui Chen _ State Key Laboratory of Cognitive Neuroscience and Learning Beijing Normal University Beijing, China 100875 发件人: Louis Nicholas Vinke 发送时间: 2012-03-26 23:27:09 收件人: chenchunhuichina 抄送: freesurfer 主题: Re: Re: