Re: [Freesurfer] Qdec - thickness-age correlation - Interpretation

Thank you Doug ! regards, alex. --- En date de : Lun 14.3.11, Douglas N Greve a écrit : Hi Alex, you can compute the difference in those slopes using an appropriate contrast matrix passed to mri_glmfit. QDEC should do so autotmatically (this would be an interaction between group and age).

[Freesurfer] display multiple functional overlays simultaneously

Hi, I have 2 functional maps (Patient > Controls and Controls > Patients) and I would like to view both maps simultaneously on the surface (one with "normal" values and the other using the "inverse" values so that I get a "warm" and "cool" map simultaneously displayed on the surface). I'm using FS

[Freesurfer] Re-post: Fixated brain

Dear Users, Is there a way to process fixated brain (after autopsy) with Freesurfer? I have read somewhere that I should just "invert" the image, but what does it mean? And would it not increase the noise and the signal from the CSF? Of course, the brain is without any skull, pia and dura mat

Re: [Freesurfer] Re-post: Fixated brain

Tibor, We are working to put some exvivo wm segmentation methods into the next FreeSurfer release although I'm not sure where that stands. We do process our exvivo scans with FreeSurfer but we use scripts that use different parameters than recon-all since the contrast is different and as you sai

Re: [Freesurfer] display multiple functional overlays simultaneously

Hi Scott, I'm not sure what you are trying to do. How can you display two different z-values at the same voxel at the same time? Or do you want to merge the maps in some way? doug Scott Hayes wrote: > Hi, > I have 2 functional maps (Patient > Controls and Controls > Patients) > and I would like

Re: [Freesurfer] results visualization

Hi Nadia, You can follow instructions on how to check data using our tutorials: https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/OutputData and https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/TroubleshootingData Allison On Tue, 15 Mar 2011, nadia merhoum wrote: > Hello > > I have just

Re: [Freesurfer] normal vector in gm

Hi Seok, Try using "--projfac .01" in the surf2vol command. doug Seok Lew wrote: > Thank you ! > > I successfully projected the pial surface normals in the volume. Now > I wanted to project the normals in the inner gm boundary voxels (i.e. > gm boundary voxels with wm). What I tried is scali

[Freesurfer] CUDA installation

Hi: I tried to install CUDA to use with freesurfer, but I got some errors that I sent to freesurfer list sometime ago... Could you please send how can I install CUDA and freesurfer in a Ubuntu platform ?... Sincerely, Gonzalo Rojas Costa Laboratory for Advanced Medical Image Processing

Re: [Freesurfer] Homologous Right Left ROIs

Hi Lena, we don't have tools released yet to do this. They should be available in the spring. dopug Lena Palaniyappan wrote: > Hi all > > I have a ROI label on left hemisphere – I need to map this ROI onto > right hemisphere to get a homologous region (for testing hemispheric > differences). Wh

Re: [Freesurfer] display multiple functional overlays simultaneously

No, you'll have to merge them into one map (and you'll probably want it to be an annotation). To do this, you'll need to run several programs. 1. mri_binarize -- threshold your two raw maps, give one a "--binval 1" the other "--binval 2" 2. Add them together: fscalc binmap1.nii add binmap2.nii -

Re: [Freesurfer] mri_mask problem

Hello Bruce and Nick, I've tryed these options you said and still not works, I must say that is not in all my subjects, I've tryed both brain.mgz and brainmask.mgz. The commands I've used are: A1) mri_vol2vol --mov brain.mgz --targ rawavg.mgz --out brain2raw.mgz --regheader A2) mri_mask

Re: [Freesurfer] mri_mask problem

Have you checked brainmask2raw.mgz? It looks like you've checked brain2raw.mgz, but you're not using it for some reason. Make sure the background has values less than 2. doug Gabriel Go.Es. wrote: > > Hello Bruce and Nick, I've tryed these options you said and still not > works, I must say that

[Freesurfer] V1 prediction

Dear Freesurfer List, I ran the script for predicting V1 location on the surface: http://surfer.nmr.mgh.harvard.edu/fswiki/V1 According to the paper, the output should be a probability map, but the script only seems to produce a label file: $SUBJECT_DIR/label/?h.v1.prob.label . When I load this

[Freesurfer] Label Orientation

Hi, I am having a bit of a problem with the orientation of a label produced by mri_cor2label. I have an old analyze ROI that I have converted to a nifti volume and then registered to T1.mgz. When I load the ROI volume in tkmedit , the registration looks fine. The label and T1.mgz are in the sam

Re: [Freesurfer] V1 prediction

In tksurfer, try going to Tools->Label->Threshold Selected Label. Then choose a threshold between 0 and 1. doug Thesen, Thomas wrote: > > Dear Freesurfer List, > > I ran the script for predicting V1 location on the surface: > > http://surfer.nmr.mgh.harvard.edu/fswiki/V1 > > According to the pape

Re: [Freesurfer] Label Orientation

So the difference is that one label was created from the ROI resampled in the T1 space and the other was created from the original ROI volume? If so, then this behavior is as expected. Why not use the first label? doug Tyler Blazey wrote: > Hi, > > I am having a bit of a problem with the orient

[Freesurfer] corpus calosum volume ?...

Hi: The CC_Posterior, CC_Central, etc, volumes in "aseg.mgz" are the complete CC volume, or it includes only some sagital slices ?... How can I meassure the CC volume for some sagital slices only (5 in total for example) ?... When I tried using "mri_cc" I got an error (for example) in th

Re: [Freesurfer] mri_mask problem

Yes, I did check the brainmask2raw.mgz, Im using brain2raw.mgz and/or brainmask2raw.gz to mask the rawavg.gz on the mri_mask. "mri_mask -T 2 -keep_mask_deletion_edits rawavg.mgz brain2raw.mgz outbrain.mgz" And actually the brain.mgz and brainmask.mgz have values of one on edited voxels, but

Re: [Freesurfer] mri_mask problem

For mri_vol2vol try using --interp nearest doug Gabriel Go.Es. wrote: > > Yes, I did check the brainmask2raw.mgz, Im using brain2raw.mgz and/or > brainmask2raw.gz to mask the rawavg.gz on the mri_mask. "mri_mask -T 2 > -keep_mask_deletion_edits rawavg.mgz brain2raw.mgz outbrain.mgz" > And actual

Re: [Freesurfer] Re-post: Fixated brain

we do have a procedure but it involved a fair amount of manual intervention and isn't terribly well documented (and it's evolving). It depends on Andre van der Kouwe's multi-echo flash sequence, which you would need to get as well cheers Bruce On Tue, 15 Mar 2011, Auer, Tibor MD. Ph.D. wrote

Re: [Freesurfer] Label Orientation

Hi Doug, Thanks for your reply. There is actually only one label, which was created from the ROI resampled in T1 space. The problem is that the label only has the correct orientation in tkmedit when the resampled ROI is loaded as the main volume. When I load T1.mgz as the main volume, the label

Re: [Freesurfer] results visualization

try: tkmedit tpidNtpidN norm.mgz lh.white -aux wm.mgz -aseg -aux-surface rh.white cheers Bruce On Tue, 15 Mar 2011, nadia merhoum wrote: > Hello > > I have just started using FreeSurfer (version 4.5) and performed the > following script: > > ?recon-all -i tpidN.nii -subjid tpidN -all? > > I w

[Freesurfer] tksurfer error

Hi, In response to the message below, I have been getting the exact same error when running tksurfer on a particular workstation. tksurfer does display correctly, but the drawing is very slow, as if running remotely (or not using the video card). This happens with versions 3.0.5 and 4.5.0. I tr

Re: [Freesurfer] tksurfer error

A quick update on my earlier posting: After disabling the "Composite" extension, I no longer get the UBB warning in the Xorg.0.log, but I still get the error and slow drawing with tksurfer. From: dhagle...@hotmail.com To: freesurfer@nmr.mgh.harvard.edu Date: Tue, 15 Mar 2011 12:07:56 -0700 Sub

Re: [Freesurfer] V1 prediction

Hi Thomas, there is a tksurfer menu item to transfer the label stat field to an overlay, and you can go from there. cheers Bruce On Tue, 15 Mar 2011, Thesen, Thomas wrote: > Dear Freesurfer List, > > I ran the script for predicting V1 location on the surface: > http://surfer.nmr.mgh.harvard.ed

Re: [Freesurfer] corpus calosum volume ?...

Hi Gonzalo mri_cc computes the optimal rotation. If the patient's head is not straight this can make it look like an inconsistent labeling, but in 3d it usually is correct. Bruce On Tue, 15 Mar 2011, Gonzalo Rojas Costa wrote: > Hi: > > The CC_Posterior, CC_Central, etc, volumes in "aseg.mgz

Re: [Freesurfer] display multiple functional overlays simultaneously

Thanks Doug. Does mri_seg2annot come w/ the latest FS distribution? It doesn't seem to be available (I can't launch the help and receive "command not found" when I try to run the command). mri_binarize worked fine. On Tue, Mar 15, 2011 at 12:33 PM, Douglas N Greve wrote: > No, you'll have to mer

[Freesurfer] Visualizing SPM Results on Template FreeSurfer Brain

Hello, I have second-level results in .img/.hdr format that I have just run through SPM. I was wondering whether there is a way to visualize these results onto a template FreeSurfer surface model in MNI space. Is this possible, or can you only visualize second-levels which have been processed th

[Freesurfer] Philips DICOM format problem

Hi All I'm new in freesurfer. I have a question regards Philips DICOM format. I tried to convert from dicom to .mgz using mri_convert but i get the following error message: MRIresample(): error inverting matrix; determinant is nan, matrix is: -0.000 -0.000 nan nan; 0.000 0.000 nan

Re: [Freesurfer] display multiple functional overlays simultaneously

Sorry, it should be mris_seg2annot (not mri_seg2annot). doug Scott Hayes wrote: > Thanks Doug. Does mri_seg2annot come w/ the latest FS distribution? > It doesn't seem to be available (I can't launch the help and receive > "command not found" when I try to run the command). mri_binarize > worked

Re: [Freesurfer] mri_glmfit allocate memory error

So you re-ran mris_preproc and you still get the error? If so, try running mris_preproc --debug |& tee mris_preprog.err.log Send me the mris_preprog.err.log, but don't email it as it will likely be huge. Instead drop it to me a the file drop listed at the end of this email. doug Andrew Mend

Re: [Freesurfer] Visualizing SPM Results on Template FreeSurfer Brain

After you've gone into MNI space with all of your subjects, then visualizing the results on the surface are of questionable value. If you just want to take a peek, then it's not a big deal, but I would not recommend reporting them in a publication. If your results are in the mni152 space, you c

Re: [Freesurfer] Philips DICOM format problem

Can you try running it with "-it dicom". It will probably still fail, but worth a shot. doug leonardo kay wrote: > Hi All > > I'm new in freesurfer. I have a question regards Philips DICOM > format. I tried to convert from dicom to .mgz > using mri_convert but i get the following error messag

Re: [Freesurfer] Philips DICOM format problem

Hi Leo: I have faced this problem before. Philips scanner's default output format is the PAR/REC format - but it also outputs in Dicom format. What I believe is the problem is that the images are oriented wrongly. Take a look at this in MRICRO and see how the images are oriented. You may need to r

Re: [Freesurfer] corpus calosum volume ?...

Hi Bruce: Thanks you very much for your answer... And, how can I get the volume of the new segmentation of the CC that I got with mri_cc command ?... Sincerely, Gonzalo Rojas Costa El 15-03-2011 21:27, Bruce Fischl escribió: > I mean that if the volume is rotated in any 2d slice it ca

[Freesurfer] Is there a way to obtain the thickness of every vertex of the whole brain?

Hi,all: Just as the title says,I wonder if there is a method to obtain the thickness of each vertex in the whole brain,and so,if we can,how do we kown which of the area is the vertex belong to? I am using the freesurfer 5.0. thanks in advance! wang___