[Freesurfer] eTIV in qdec

Dear FreeSurfer experts, my idea was to put the eTIV as a variable in qdec. I have put this in my qdec.table.dat and when I run qdec and choose eTIV as variable I get the following error and qdec closes some seconds later automatically: Creating output directory /Users/dolphinede/Desktop/Proba

[Freesurfer] pial surface voxel shift

Hi After running several subjects (using trio siemens dicomfiles) with recon-all -all -nowmsa, we have observed an apparent shift of approximately one voxel to the left of the pial surface as compared to the brainmask.mgz in the TkMedit coronal view. This was observed in all of our subjects. Do you

[Freesurfer] MCSRCH ERROR

Hello All, While processing a brain image data(.mgz) through ver5.0.0, I got the following errors. I have no idea how to resolve them. I need outputs in stats directory, there are only lh.aparc.a2009s.stats, lh.aparc.stats, and lh.curv.stats. What caused them? How should I resolve them? IFLAG= -1

Re: [Freesurfer] MCSRCH ERROR

Are you sure they are errors? We see this mysterious message sometimes, but I don't think it is really an error, and usually things are fine cheers Bruce On Tue, 18 Oct 2011, Kenichiro Tanaka wrote: > Hello All, > > While processing a brain image data(.mgz) through ver5.0.0, I got the > followi

Re: [Freesurfer] pial surface voxel shift

eek, no, we definitely don't see this. Can you upload the subject? Bruce On Tue, 18 Oct 2011, Pernille Iversen wrote: > Hi > After running several subjects (using trio siemens dicomfiles) with recon-all > -all -nowmsa, we have observed an apparent shift of approximately one > voxel to the left

[Freesurfer] mri_ca_register error

Hello , I am running recon-all with -cm switch and getting following error. Is there any workaround? Without -cm switch , recon-all completes all the processing just fine. Thank you. Hiroyuki mri_ca_register -invert-and-save transforms/talairach.m3z mri passed volume size is different fro

Re: [Freesurfer] coregistration - FA to Freesurfer

Thanks Doug! It worked! Joana 2011/10/17 Douglas N Greve > No, use the register.dat that you manually created as the input to > bbregister with the --init-reg. You could move your register.dat to > regidster.man.dat and set the output to be register.dat. > > doug > > Joana Braga Pereira wrote:

Re: [Freesurfer] mri_ca_register error

can you check to make sure that the partition is not full? If you have space, upload the dataset and we'll take a look cheers Bruce On Tue, 18 Oct 2011, Oya, Hiroyuki (UI Health Care) wrote: Hello ,   I am running   recon-all with ?cm switch and getting following error. Is there any worka

Re: [Freesurfer] reg-feat2anat failure

The registration that should be used for all of these is anat2exf.register.dat found in feat/reg/freesurfer. Can you verify that that was the one that you manually changed? Look at the time stamp as compared to the other files in that folder. doug Michelle Umali wrote: > Hi Doug, > I am using r

[Freesurfer] Surface area measure

When I extract surface area data using the following commands, which measure of surface area am I getting, the pial surface, the WM surface, or the total of both combined? aparcstats2table --subjects 1 2 3 4 --parc aparc.a2009 --hemi rh --meas area --tablefile aparc_stats_rh.txt Thanks! Krista _

Re: [Freesurfer] QDec questions

krista kelly wrote: > Hi, just wondering if anyone has any advice on the following questions: > > I'm using QDEC to analyze cortical thickness differences between > groups and I have a few questions: > > 1) There are a few variables that I need to control for. First > variable is scanner - I us

Re: [Freesurfer] Surface area measure

The white surface. doug krista kelly wrote: > When I extract surface area data using the following commands, which > measure of surface area am I getting, the pial surface, the WM > surface, or the total of both combined? > > aparcstats2table --subjects 1 2 3 4 --parc aparc.a2009 --hemi rh > -

Re: [Freesurfer] label transformation to MNI space

The way the reg is set up, the targ is your mask. Try this cmd: mri_vol2vol --targ lh_entorhinal.nii.gz --mov MNI152_T1_2mm.brain.nii.gz --o lh_entorhinal_MNI.nii.gz --reg $FREESURFER_HOME/average/mni152.register.dat --inv doug Linda Douw wrote: > Hi all, > > I am trying to transform some labels

Re: [Freesurfer] eTIV in qdec

i'm not able to replicate this error you are seeing. to attempt to replicate, i used the 40 subjects included in our tutorial, loaded into qdec, then clicked 'Generate Stats Data Tables', then selected 'aseg.volume' in Stats Data Import, then selected IntraCorticalVol (which is eTIV) and 'add sele

Re: [Freesurfer] label transformation to MNI space

Hi Doug, Thanks for the reply. This cmd makes it slightly better I guess, but still definetely off target. It seems to be shift downward, towards inferior, and therefore sometimes outside the skull. Any other ideas? Linda > The way the reg is set up, the targ is your mask. Try this cmd: > mri_vol2

Re: [Freesurfer] QDec questions

Sorry, I meant to say that you cannot use QDEC with more than 2 discrete variables (you have 3). You do not need to extract data from the smoothed thickness files, but the results you get from your ROI analysis may then differ a bit from that you get from the QDEC analysis. doug krista kelly wr

Re: [Freesurfer] Surface area measure

I don't know if that has ever been explored. doug krista kelly wrote: > Great! Do you know if it is better to use one surface area (i.e. WM or > pial) over the other when investigating differences between groups? > > On Tue, Oct 18, 2011 at 2:24 PM, Douglas N Greve > mailto:gr...@nmr.mgh.harvard

Re: [Freesurfer] label transformation to MNI space

The problem appears to be with the label itself. Try this conversion: mri_label2label --srclabel lh.entorhinal.label --s fsaverage --regmethod surface --trglabel lh.entorhinal.new.label --hemi lh Also, you might want to use the entorhinal label define in the aparc+aseg since it fills in the rib

Re: [Freesurfer] QDec questions

Yes, see the answer to your first question below. doug krista kelly wrote: > Am I able to do vertex-by-vertex analyses using freesurfer if I have > more than 2 discrete variables? If so, how? > > Is it also ok to use the unsmoothed data when doing surface area label > analyses? > > Thanks! > > O

Re: [Freesurfer] label transformation to MNI space

This fixed the problem, thanks! > The problem appears to be with the label itself. Try this conversion: > > mri_label2label --srclabel lh.entorhinal.label --s fsaverage --regmethod > surface --trglabel lh.entorhinal.new.label --hemi lh > > Also, you might want to use the entorhinal label define in

Re: [Freesurfer] Group Average of Retinotopy Results

Hi Doug and the Freesurfers, Thanks for your help. I have 2 questions.: 1) I did the retinotopy analysis on the fsaverage surface as you suggested below and then ran isxconcat-sess for my eccen and polar data: e.g. isxconcat-sess -analysis rtopy.fsaverage.lh -contrast polar -sf sessid -o group