[Freesurfer] ERROR: matrix is ill-conditioned or badly scaled, condno = 18696.1

External Email - Use Caution Hi freesurfer community, I am trying to do QDEC with a data for 2 groups but stuck in this error for many hours now. Tried and checked everything I could think of. Also went through the old threads and checked those recommneded but still could not solv

Re: [Freesurfer] Lobe parcellation without cingulate from --lobesStrict

External Email - Use Caution Dear Douglas, how should the input for mri_mergelabels be? Should I use the name of the file, or the number of the label (from https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/AnatomicalROI/FreeSurferColorLUT )? Thank you very much, Fernanda On T

Re: [Freesurfer] ERROR: matrix is ill-conditioned or badly scaled, condno = 18696.1

The main problem is the 4th group where you only have two subjects and they are almost exactly the same age. This makes it hard to estimate the age slope and is causing the ill-conditioned error. You can try normalizing the ages (ie subtract the mean and divide by the stddev), you can remove ag

Re: [Freesurfer] Using a cluster as an ROI for further analysis

Hi Martin create a label for X1, then use mri_label2label to map it to each of your subjects in P2 and P3 cheers Bruce On Mon, 13 Aug 2018, Martin Juneja wrote: External Email - Use Caution For instance, if there is any way to extract spatial location of cluster X1 and use

Re: [Freesurfer] Using a cluster as an ROI for further analysis

First, run mris_preproc and mri_surf2surf commands as before to create a stack of P2 and P3. If you ran mri_glmfit-sim on P1,  then you will have an "ocn" output file. You can run mri_segstats --i P2P3.stack.mgh --seg ocn.mgh --id N --avgwf P2P3.means-in-clusterN.dat where N is the number of yo

Re: [Freesurfer] Using a cluster as an ROI for further analysis

External Email - Use Caution Hi experts, How to create the stack of P2P3.stack.mgh after mris_preproc and mir_surf2surf? Great thanks. Regards, Ting > On Aug 14, 2018, at 10:51 AM, Douglas Greve wrote: > > First, run mris_preproc and mri_surf2surf commands as before to creat

[Freesurfer] Flipped left to right hemisphere subjects

Dear Freesurfer group, We have some scans that have been processed using Freesurfer 5.1 and the measures have already been extracted from the DKT atlas. We've realized that some of the scans have been flipped left to right before proceeding through recon-all. Assuming we cannot reprocess these

Re: [Freesurfer] Surface Area in Toddlers/Children

Hi Derek, We do not use the standard FS pipeline for the analysis of the age group of your interest. In general, we have seen it being successfully used on subjects down to 4.5yrs of age, but 25 mo is quite young to be analyzed by the adult template. I assume, without seeing your data, that yo

Re: [Freesurfer] Flipped left to right hemisphere subjects

Hi Olivia yes, the DKT (and other internal atlases) will probably have asymmetries Bruce On Tue, 14 Aug 2018, Lutz,Olivia (BIDMC - Psychiatry) wrote: Dear Freesurfer group, We have some scans that have been processed using Freesurfer 5.1 and the measures have already been extracted from t

Re: [Freesurfer] Flipped left to right hemisphere subjects

To clarify, you cannot just swap the left and right results and get the same thing as if you had analyzed the unflipped data. On 08/14/2018 12:31 PM, Bruce Fischl wrote: > Hi Olivia > > yes, the DKT (and other internal atlases) will probably have asymmetries > Bruce > On Tue, 14 Aug 2018, Lutz,Ol

[Freesurfer] cannot execute mri_aparc2aseg

External Email - Use Caution Dear Freesurfer Developers and Experts, I am trying to patch freesurfer 6.0 to run make_average_subject on Mac OSx 10.13.3 I am having a problem executing the updated mri_aparc2ase

Re: [Freesurfer] Using a cluster as an ROI for further analysis

External Email - Use Caution Dear Bruce and Doug, Thank you so much. Its working perfectly fine. Best, MJ On Tue, Aug 14, 2018 at 8:51 AM, Douglas Greve wrote: > First, run mris_preproc and mri_surf2surf commands as before to create a > stack of P2 and P3. If you ran mri_glmfi

Re: [Freesurfer] cannot execute mri_aparc2aseg

External Email - Use Caution Dear Freesurfer Developers and Experts, I was able to locate an answer to this problem here. Apologies for the redundant post, the old thread did not return in my initia

Re: [Freesurfer] coregistering with bbregister

Hi Ben, please remember to post the list. Answers below On 08/14/2018 02:22 PM, Ben M wrote: > > External Email - Use Caution > > Hi Doug, > > Thanks again for your help! > > | It reslices the mov into the anatomical space. What do you mean when > you "load" them? > > I mean when I view t

[Freesurfer] SNR for PET images

External Email - Use Caution Hi Freesurfer team, I would like to use "mri_segstat" to compute SNR for regions of interest. My question is, if I use PET images as input does this mean that SNR will be computed for the PET signal in the ROIs? Thanks for any help John__

[Freesurfer] hardware needs for fMRI

External Email - Use Caution Folks, I am a computer administrator trying to put together a proposal for a new University shared resource compute cluster. Some fMRI image analysts have suggested that GPUs are frequently used in the field and that in particular, double precision G

Re: [Freesurfer] SNR for PET images

Yes, but know that the "SNR" as computed there is the spatial mean divided by the spatial standard dev. This is likely not the SNR that you want On 08/14/2018 05:07 PM, James Brown wrote: > > External Email - Use Caution > > Hi Freesurfer team, > I would like to use "mri_segstat" to comp

Re: [Freesurfer] SNR for PET images

External Email - Use Caution Hi Doug, thank you for the response. I would appreciate if you advice any better method to compute the SNR for PET signal within an ROI (e..g. thalamus)? I used spmregister to move my PET images to Freesurfer space then I am thinking of using mri_segs