[Freesurfer] Warping a significance map to MNI space

Hi I have proceed my data and produced a significance map across all my subjects and this looks fine on the fsaverage inflated brain. To compare to some other results, I really need to wrap this map into standard MNI152 space. To do this, I have used the following commands but with a problem at

[Freesurfer] convert sig.mgh into *.nii

Hi FS experts, I want to extract time course from sig.mgh. But the *.y.ocn.mgh cannot be created. So I want to view it in other formats, such as nii. So how to convert it into nii format. Thanks. All the best. Rujing Zha 2014-03-11 charujing123___ F

[Freesurfer] view time course in freeview

Hi FS experts, For the sig.mgh, can I see the time course vertex by vertex in freeview? Thanks. All the best. Rujing Zha___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The informati

[Freesurfer] Tksurfer + Histogram

Hello Freesurfer Expert, Can anyone help me with histogram plotting of different surfaces in tksurfer. I looking to calculate the thickness of cortex. Thanks in advance, Saurabh Thakur, ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https

[Freesurfer] adding time points to longitudinal base template

Dear FS experts, I have a serial study in which I have run cross-sectional and longitudinal analysis on 5 time points. Now, I want to add a 6th time point to my dataset. Do I have to rerun my base template creation step from scratch or is there a way to just add further time points t

Re: [Freesurfer] Tksurfer + Histogram

what is it that you want to histogram? If the thickness, tksurfer will do this for you if you load it as an overlay. Or you can read it into matlab and show it there On Tue, 11 Mar 2014, Saurabh Thakur wrote: > Hello Freesurfer Expert, > > Can anyone help me with histogram plotting of differe

Re: [Freesurfer] Brain Segmentation blurred at the interhemisphere surface

Hi Louis, Thanks, so should this be amended or can be simply left there which may not influence the stats results and further comparison? Great thanks, Kaiming On Mon, Mar 10, 2014 at 8:01 PM, Louis Nicholas Vinke < vi...@nmr.mgh.harvard.edu> wrote: > Hi Kaiming, > I'm almost certain you are r

Re: [Freesurfer] Brain Segmentation blurred at the interhemisphere surface

Hi Kaiming, I can't say for certain looking at that one slice, but I'm pretty sure it's fine. What you can do is make the surfaces for one hemi a different color than the other hemi, then pan through in the sagittal view and you should see one set of surfaces go out as the other comes in. Als

[Freesurfer] Tracula multiple subjects error

Hello- I'm having a consistent problem running multiple subjects through tracula. I am able to run single subjects through all steps but whenever I try to run it on multiple subjects I get the same error about a syntax error and one of the items it wants to copy being a directory so its not being

Re: [Freesurfer] primary auditory cortex ROI

If you're asking whether we have tools that do myelination-based segmentation from T1, the answer is no. I've found from fMRI that the transversetemporal label does pretty well. doug On 03/10/2014 11:34 AM, Ritobrato Datta wrote: > Hi Doug, Wow, telepathy…Just resent my email and got this repl

Re: [Freesurfer] project locations from template to individual MRIs

Hi Peng, there's a lot going on there, and it is not specific enough for me to make recommendations. Take a look at the docs we have on our coordinate systems http://surfer.nmr.mgh.harvard.edu/fswiki/CoordinateSystems?action=AttachFile&do=get&target=fscoordinates.pdf you might get the answer y

Re: [Freesurfer] Warping a significance map to MNI space

Almost right. Try this command (reversed mov and targ and added --inv): mri_vol2vol --inv –targ SIG.fsspace.mgz –mov /$FSL_DIR$/data/standard/MNI152_T1_2mm.nii.gz –o SIG_MNI.nii –interp nearest –reg /$FS_DIR$/average/mni152.register.dat I know, it is a little confusing doug On 03/11/2014 04

Re: [Freesurfer] convert sig.mgh into *.nii

mri_convert file.mgh file.nii doug On 03/11/2014 05:55 AM, charujing123 wrote: > Hi FS experts, > I want to extract time course from sig.mgh. But the *.y.ocn.mgh cannot > be created. So I want to view it in other formats, such as nii. So how > to convert it into nii format. > Thanks. > All the

Re: [Freesurfer] view time course in freeview

the time course of what? On 03/11/2014 07:18 AM, charujing123 wrote: > Hi FS experts, > For the sig.mgh, can I see the time course vertex by vertex in freeview? > Thanks. > All the best. > Rujing Zha > > > ___ > Freesurfer mailing list > Freesurfer@nmr.mg

[Freesurfer] ERROR: matrix is ill-conditioned or badly scaled, condno = 1e+08

Hello, I would like to conduct an analysis using mri_glmfit but I'm getting this error: ERROR: matrix is ill-conditioned or badly scaled, condno = 1e+08 My command was: mri_glmfit --y lh.area.fwhm10.fsaverage.mgh --fsgd finalgroupanalysis.fsgd dods --C group_effect.mtx --surf fsaverage lh --corte

Re: [Freesurfer] Tracula multiple subjects error

Hi Sarah - The best way to troubleshoot the configuration file is to source it, make sure that there are no errors, and then echo each variable to make sure it contains what you intended. For example once you run "source Tracula_config" you'll get an error, and you'll find that you have to c

Re: [Freesurfer] ERROR: matrix is ill-conditioned or badly scaled, condno = 1e+08

The fsgd file appears to have been created using a windows program (or mac program that saves in windows format). Is that correct? I've attached a linux-compatible version. Let me know if that works. doug On 03/11/2014 12:19 PM, Wanda Truong wrote: Hello, I would like to conduct an analys

Re: [Freesurfer] Tksurfer + Histogram

try configure->functional overlay or something like that after loading the thickness into a functional overlay On Tue, 11 Mar 2014, Saurabh Thakur wrote: > I am referring one paper. > It mentioned about the freesurfer and cortical thickness they hv got in > tksurfer. > > I m just want to know h

Re: [Freesurfer] project locations from template to individual MRIs

what template? When discussing coordinate systems you have to be very specific. A template could be a volume template or a surface template. If a volume template it could be MNI305 or MNI152. If MNI152 it could be the 1mm version or the 2mm version. All of these things are important and the qu

Re: [Freesurfer] ERROR: matrix is ill-conditioned or badly scaled, condno = 1e+08

Hi Doug, Thanks for the new fsgd file - it solved the error. However, now I get a different error: ERROR: dimension mismatch between y and X. y has 46 inputs, X has 71 rows. which is similar to the error I got when I tried to do this analysis in QDEC. I've attached my Xg.dat. I'm not sure what

Re: [Freesurfer] ERROR: matrix is ill-conditioned or badly scaled, condno = 1e+08

how did you create the input lh.area.fwhm10.fsaverage.mgh? How many subjects does it have in it? The error means that the FSGD file has a different number of Input lines than the lh.area file has subjects On 03/11/2014 02:45 PM, Wanda Truong wrote: > Hi Doug, > > Thanks for the new fsgd file -

Re: [Freesurfer] Group Analysis Age slopes

Hi Doug, Thanks for your reply. Just to be clear, I need to ask some trivial questions: 1) I need to do that subtraction in the fsgd file right? (In which case there will be negative numbers as well) 2) I ran the analysis and the resulting significant clusters when looking at the results of [1 -

Re: [Freesurfer] project locations from template to individual MRIs

Thanks for your reply. I am using *ICBM 2009a Nonlinear Asymmetric 1×1x1mm template. *I did not expect that it will make much difference in the algorithm. Does freesurfer favor certain template than others? btw: the individual mri is also 1 mm resolution. On Tue, Mar 11, 2014 at 8:46 PM, peng wr

Re: [Freesurfer] project locations from template to individual MRIs

Hi Doug, With the terminology in the document you provided, I can summarize what I want to do exactly as part of the flow chart in page 7. I listed it as between==. As described in the document, I can get Ta, Tb by ; and R from a file ; am I right? Practically, I may put my template as a subjec

[Freesurfer] wm.mgz and lh.orig.nofix not matching

Hi guys, I was wondering if someone could take a look at a subject that I just uploaded (L217_100908.zip). An RA was editing wm.mgz to attempt to fix a topology problem in the LH visual cortex.  The edited wm.mgz that she created looks fine to me, but after re-running FS, the surfaces still ar

Re: [Freesurfer] wm.mgz and lh.orig.nofix not matching

Hi Mike mri_pretess that is causing this behavior. I guess we delete the pretess output after ceating the surfaces, which makes it harder to diagnose this kind of thing. I ran (which I got from the recon-all.log): mri_pretess ../mri/filled.mgz 255 ../mri/norm.mgz ../mri/filled-pretess255.mgz

Re: [Freesurfer] view time course in freeview

Hi doug, sig.mgh is my result for two group t-test on pial thickness of whole brain. So I want to see the time course of thickness of rh.ttest.thickness.10.mgh vertex by vertex. Thanks. All the best. Rujing Zha 2014-03-12 charujing123 发件人：Douglas N Greve 发送时间：2014-03-12 00:16 主题：Re: [Frees

[Freesurfer] Combining scans with different scanning parameters

Hi, I'm interested in comparing CT differences between 2 different groups, and in order to increase my sample size I'm contemplating combining 3 datasets with different scanning parameters. Some scans were collected with a 3T1 with fmri head coil, while others were collected with a 3T2 magnet wit

Re: [Freesurfer] convert sig.mgh into *.nii

Hi Bruce, Thanks Bruce. I knew that code, but I have no idea to deal with my problem after reading the help. Would you please tell me how to use mri_surf2vol after I describe my problem details? I have a file named rh.36sb.score.thickness.10.mgh which is created from the "mris_preproc --fsgd $FS

Re: [Freesurfer] Combining scans with different scanning parameters

Hi Ashley that is probably trouble unless your groups are perfectly balanced across the datasets (that is, the same # in each group were scanned on each configuration). cheers Bruce On Tue, 11 Mar 2014, Ashley Shurick wrote: Hi, I'm interested in comparing CT differences between 2 diffe

Re: [Freesurfer] convert sig.mgh into *.nii

try mri_surf2vol with the output volume named .nii cheers Bruce On Wed, 12 Mar 2014, charujing123 wrote: Hi doug, Thanks doug. I try this code, but it represent two dimension for each subject data when loaded in the AFNI. Is there any code to volume-based conversion from mgh to nii? All the b

Re: [Freesurfer] convert sig.mgh into *.nii

Hi doug, Thanks doug. I try this code, but it represent two dimension for each subject data when loaded in the AFNI. Is there any code to volume-based conversion from mgh to nii? All the best. Rujing Zha 2014-03-12 charujing123 发件人：Douglas N Greve 发送时间：2014-03-12 00:16 主题：Re: [Freesurfer]