Re: [Freesurfer] TRACULA bvecs question

Dear Priti, Anastasia, Thank you for your help, I created bvec and bval files and it went fine. But now I have another error in preprocessing step. I attach a log file. Could you please take a look at that? Thank you, Tanja. trac-preproc exited with ERRORS at Fri Feb 10 10:52:37 CET 2012 O

Re: [Freesurfer] Comparing Cortical Thickness

Hi Jeff, I think you want to use Doug's tools for this (mri_glm and such). He'll probably comment in an hour or two cheers Bruce On Mon, 13 Feb 2012, Jeff Sadino wrote: Hello FreeSurfers, I want to compare cortical thickness differences between my two groups.  Is this the correct pipeline

Re: [Freesurfer] Comparing Cortical Thickness

Hi Jeff, you should use mris_preproc to stack the subjects into one file, mri_surf2surf to smooth them, and mri_glmfit to analyze them (including computing the difference between groups and other stats). See the group tutorial on the web page. You could probably do what you are suggesting, but

Re: [Freesurfer] Comparing Cortical Thickness

Hi Jeff, make_average_subject is just if you want to visualize results on a surface presenting the average of your own subjects, rather than using the provided 'fsaverage'. It is not necessary (and not related) to performing group statistical comparisons per se. You can use the 'qdec' utility to

Re: [Freesurfer] Clusters locations

Hi Antonella, what level of detail do you want? I think that most people are reporting MNI coordinates. doug On 2/13/12 2:44 PM, Antonella Kis wrote: Hi Doug, I will be very grateful if you give me some directions regarding how I can get my clusters location ( my output is too general telling

[Freesurfer] mri_volcluster register.dat question

Hello all, I'm trying to run mri_volcluster on our third-level functional data and one of the required flagged arguments is the register.dat file. Our data preprocessing/registration was done in FSL, not Freesurfer, so we don't have this particular file. Is there anything we can do to get around t

[Freesurfer] mri_vol2surf

Dear FreeSurfers, To get a better view on the pial surface of the Heschl' Gyri I used the command mri_vol2surf after having created the suitable label with (label2vol). My goal is to get My Command was: *mri_vol2surf --src pf_lh_vol.mgz --hemi lh --srcreg register.dat --out_type paint --o A1surf

Re: [Freesurfer] TRACULA bvecs question

You need to set the nb0 parameter (number of low-b volumes in the beginning of your DWI series). On Tue, 14 Feb 2012, Tetiana Dadakova wrote: > Dear Priti, Anastasia, > > Thank you for your help, I created bvec and bval files and it went fine. > But now I have another error in preprocessing ste

Re: [Freesurfer] TRACULA bvecs question

PS: The info on what you need to set it here: https://surfer.nmr.mgh.harvard.edu/fswiki/dmrirc # Number of low-b images # Must be specified if inputs are not DICOM # Default: Read from DICOM header # set nb0 = 10 On Tue, 14 Feb 2012, Tetiana Dadakova wrote: > Dear Priti, Anastasia, > > Thank

Re: [Freesurfer] mri_volcluster register.dat question

Hi Huiting, you don't need to give it a register.dat. That only gives you access to label locations of your clusters. If this is something you want, you can use $FREESURFER_HOME/average/mni152.register.dat. doug Huiting Liu wrote: > Hello all, > > I'm trying to run mri_volcluster on our third-le

Re: [Freesurfer] Clusters locations

Antonella Kis wrote: > Hi Doug, > > 1) I would like to report the MNI coordinates and also a more exactly > region I mean if possible tto find exactly where in the > Left-Cerebral-White-Matter and Right-Cerebral-White-Matter my cluster > is located. What do you me by "exactly where"? The neare

[Freesurfer] (no subject)

Hi, I am trying to use selxavg3-sess function and getting this error. Below is the error I get. I actually have this fingertap.par file but freesurfer somehow does not see it. Any help would be appreciated. Thanks! Meryem Yucel PMI Lab Extension format = nii.gz ERROR: opening /autofs/space/m

[Freesurfer] Extraction of vertex identifiers from a significant cluster

Dear all, We have performed a cluster analysis in Qdec and found a significant vertex-cluster after correction for multiple testing using the Monte Carlo simulation. Now, we would like to extract the (unique) identifiers of all vertices that form the significant cluster. We then would like to

Re: [Freesurfer] TRACULA bvecs question

I see, thank you :) On Tue, Feb 14, 2012 at 6:50 PM, Anastasia Yendiki wrote: > > PS: The info on what you need to set it here: > > https://surfer.nmr.mgh.harvard.edu/fswiki/dmrirc > > # Number of low-b images > # Must be specified if inputs are not DICOM > # Default: Read from DICOM header > #

Re: [Freesurfer] (no subject)

Hi Meryem, it looks like it is looking for "fingertap" not "fingertap.par". Could that be the problem? doug Meryem Ayse Yucel wrote: > Hi, > > > I am trying to use selxavg3-sess function and getting this error. Below is > the error I get. I actually have this fingertap.par file but freesurfer > s

Re: [Freesurfer] Extraction of vertex identifiers from a significant cluster

Hi Florian, you can save the cluster as a label. This is a text file with xyz values for each vertex. The xyz values are in mni305 space. doug Florsek wrote: > Dear all, > > We have performed a cluster analysis in Qdec and found a significant > vertex-cluster after correction for multiple testin

[Freesurfer] ERROR mri_volcluster

Dear Doug, Can I run the mri_volcluter without --reg ? I am asking this because when I run: mri_glmfit-sim \       --glmdir GroupAnalysis_ADC.glmdir \       --grf 3 neg \       --cwpvalthresh .05 \       --overwrite gives me the following error (I also attached the log file): Also, does neg

Re: [Freesurfer] Extraction of vertex identifiers from a significant cluster

You can do it in tksurfer using the Tools->CustomFill, then select fill to threshold (or something like that). I think there's a way to do it in QDEC too. Try looking at the tutorial. doug Florsek wrote: > Hi Doug, > > do I have to manually draw the new label or can I somehow custom fill > the

Re: [Freesurfer] (no subject)

Hi, Now it seems to be working with the par file but I am getting this error. Any help will be appreciated. Thanks, Meryem Computing compensation for resdual AR1 bias 1 -0.5 -0.473129(t=0.192235) 2 -0.25 -0.238292(t=1.09283) 3 0 -0.00411884(t=1.27811) 4 0.25 0.228971

Re: [Freesurfer] (no subject)

The mask used to compute the global mean does not have any voxels in it because the field of view is so small. Try running mkbrainmask-sess -s session -nero 1 -fsd bold Then run selxavg again. The above mkbrainmask command tells it to only erode the mask by one voxel (the default in preproc-sess

Re: [Freesurfer] (no subject)

I tried this. It is still giving the same error. Should I check my mask files? Thanks. > The mask used to compute the global mean does not have any voxels in it > because the field of view is so small. Try running > mkbrainmask-sess -s session -nero 1 -fsd bold > Then run selxavg again. The above

[Freesurfer] Question about hippocampal-subfield probability map

Dear experts, The hippocampal-subfield are expressed as probability maps. For each subfield, each voxel is assigned a probability of inclusion on a scale of [0-255]=[0-1]. However, If I were to select only voxels from each subfield's probability map corresponding to a >50% chance (i.e. mri_binariz

Re: [Freesurfer] Question about hippocampal-subfield probability map

Ha nevermind. While true, I can just mask the masks with each other and drop the over lapped regions. - Josh On Tue, Feb 14, 2012 at 3:59 PM, Joshua Lee wrote: > Dear experts, > > The hippocampal-subfield are expressed as probability maps. For each > subfield, each voxel is assigned a probabili

[Freesurfer] make average subject error

Hello, I have run into an error while trying to make an average subject using 200 scans. When I ran this command I got an error: *make_average_subject --xform talairach.xfm --out 200avgsub --subjects* The error: Allocing output mri_concat(40491) malloc: *** mmap(size=262144) failed (error code=

[Freesurfer] TRACULA question: pathstats.byvoxel.txt

Hello Tracula Developer & User, I found a few subjects have pathstat.overall.txt information but with blank voxel information in pathstats.byvoxel.txt. For such tracts, they usually len_min = len_max = len_avg. Anyone know what happened for the fiber tracking? Is it possible to extract the byvoxel

Re: [Freesurfer] Question about hippocampal-subfield probability map

That is, I can use fslmaths from fsl suite to subtract my binarized subfield rois. - Josh On Tue, Feb 14, 2012 at 4:58 PM, Joshua Lee wrote: > Ha nevermind. While true, I can just mask the masks with each other and > drop the over lapped regions. > - > Josh > > > On Tue, Feb 14, 2012 at 3:59 PM

[Freesurfer] recon-all error (nu_correct problem)

Hello, Freesurfers, I got an error message when I trying to use recon-all function in freesurfer on the XUbuntu system installed on the VirtualBox on a Windows 7 machine. I searched the e-mailing list but I can't find any answers. My problem is related to the nu_correct and nu_estimate_np_and_em.