Re: [Freesurfer] Extracting labels using mri_watershed

Interesting.. would you mind sending me the command you ran and file drop the input and output volumes to me?: https://gate.nmr.mgh.harvard.edu/filedrop2/ Emma From: freesurfer-boun...@nmr.mgh.harvard.edu on behalf of

Re: [Freesurfer] Constrain smoothing to GM for PET data

Hi Doug, I am looking for a total GM mask that includes cortical and subcortical regions. Best Wishes, Elijah Dr. Elijah Mak, Research Associate Department of Psychiatry Old Age Psychiatry Group | Cambridge Intellectual & Developmental Disabilities Research Group University of Cambridge

Re: [Freesurfer] Constrain smoothing to GM for PET data

You can mri_binarize --gm --i aparc+aseg.mgz --o gm.mask.mgz On 10/16/17 12:41 PM, Elijah Mak wrote: Hi Doug, I am looking for a total GM mask that includes cortical and subcortical regions. Best Wishes, Elijah *Dr. Elijah Mak, Research Associate *Department of Psychiatry Old Age

Re: [Freesurfer] PETSURFER: MRTM2 volumes?

it comes down to have you smooth it. If you do it in the volume, then you need to smooth it in the volume, and that is an invalid analysis with MG. On 10/13/17 8:42 PM, Elijah Mak wrote: > Hi Doug, > > I wonder what is the difference between this approach (mri_surf2vol) as > opposed to doing

Re: [Freesurfer] register.dof6.dat file missing with register-sess

which version of FS are you using? Is this a new analysis done from scratch or had you preprocessed before? On 10/15/17 4:10 PM, Yagmur Ozdemir 19 wrote: Hello Freesurfer experts, After I run preproc-sess with this command (  preproc-sess -surface self lhrh -fwhm 5 -fsd Retinotopy -per-run

[Freesurfer] Fw: cortical/subcortical volume based analysis

Re: [Freesurfer] lta_convert does not produce ITK transforms that are correctly applied by antsApplyTransforms

Not sure I understand. If the two transforms are only off by less than the 5th decimal, then why are the registrations off so much. As for why it would be off at the 5ht dec, it probably has to do with the way we store the matrix. When a volume is read in, the matrix is decomposed into

Re: [Freesurfer] Fwd: Adding control points to aparc+aseg

what is the index (ie, col, row, slice) where you are seeing a problem? On 10/16/17 11:44 AM, Nicholas Goh wrote: Hi, I am not sure if this email got lost in the process or is still awaiting approval, but I was asked to tar and gzip the images that I was having no luck with fixing the white

Re: [Freesurfer] R: Re: R: Re: R: Re: R: Re: R: Re: R: Re: R: Re: Map of covariance

they all look ok except that these should be C13) gr1+gr2-vs-gr3+gr4.intercept 0.5 0.5 -0.5 -0.5 0 0 0 0 C14) gr1+gr2-vs-gr3+gr4.slope 0 0 0 0 0.5 0.5 -0.5 -0.5 On 10/13/17 11:30 AM, std...@virgilio.it wrote: > I have applied the contrasts that we discussed in the previous mails but they >

[Freesurfer] New Openings for Postdoctoral Fellows

Dear Everyone, My lab has new openings for postdoctoral fellows. Please see job descriptions here: https://yeolab.weebly.com/jobs.html Thanks, Thomas ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu

Re: [Freesurfer] How to obtain a label for Custom ROI mask

run the juelich atlas through recon-all, then use mri_vol2surf On 10/14/17 3:38 PM, Dev vasu wrote: Dear all, I have custom ROI mask ( MNI Space )  that i have prepared from Jülich atlas , I would be like to obtain corresponding surface label file, Could you please guide me necessary the

Re: [Freesurfer] Generating Mean thickness surface file for volume ROI mask

May the ROI to the surface using mri_vol2surf, then use mri_segstats to extract the mean value On 10/13/17 4:09 PM, Dev vasu wrote: Dear all, I have a   ROI mask volume file and i would like to generate Mean cortical thickness surface file (i.e lh.ROI.thickness.fsaverage.mgh and

Re: [Freesurfer] Problem flipping a label into other hemisphere

Sorry, try this mris_apply_reg --src-label lh.BA45.label --trg lh_flip.BA45.label --streg ../surf/lh.sphere.left_right ../surf/rh.sphere.left_right On 10/13/17 2:58 PM, Neuro Lists wrote: Hi all, I was just wondering if there was any further insight into what I might be doing wrong on

Re: [Freesurfer] Fwd: Adding control points to aparc+aseg

I don't know what coordinates those are. Can you give indices? indices are non-neg On 10/16/17 12:59 PM, Nicholas Goh wrote: An example of the aparc+aseg not covering all that it needs to can be found around [-7, 114, 133] On Mon, Oct 16, 2017 at 12:47 PM, Douglas Greve

Re: [Freesurfer] register.dof6.dat file missing with register-sess

I am using version 6.0.0 and this is made from scratch. Just a couple of days ago I processed a different subject but used the special retinotopy procedure and didn't come across this problem. I first noticed this error in selxavg-sess and went back and used mkbrainmask, register-sess and

Re: [Freesurfer] PETSURFER: MRTM2 volumes?

Got it, thanks! I have already performed smoothing on the MGX surfaces so I’d like to proceed with mri_surf2vol. According to the “hidden secrets of success” for mri_surf2vol, there are 2 methods. Is the command below correct? mri_surf2vol --so lh.bp.nii.gz (the PET surface BPNDs) --so

Re: [Freesurfer] mri_aparc2aseg output file values

I don't think you can use the mris_label2annot ctab. What happens if you run freeview using the default ctab? On 10/10/17 3:19 PM, Sims, Sara A wrote: Freesurfer people, *I have a label file that I want to make into a volume file only in the white matter to use in diffusion tractography.*

Re: [Freesurfer] register.dof6.dat file missing with register-sess

I don't know what might be going wrong here. Have you tried to re-run it from scratch? Are you out of disk space? On 10/16/17 12:59 PM, Yagmur Ozdemir 19 wrote: I am using version 6.0.0 and this is made from scratch. Just a couple of days ago I processed a different subject but used the

Re: [Freesurfer] Fwd: Adding control points to aparc+aseg

An example of the aparc+aseg not covering all that it needs to can be found around [-7, 114, 133] On Mon, Oct 16, 2017 at 12:47 PM, Douglas Greve wrote: > what is the index (ie, col, row, slice) where you are seeing a problem? > > On 10/16/17 11:44 AM, Nicholas Goh

Re: [Freesurfer] PETSURFER: MRTM2 volumes?

You have to do it one hemi at a time, eg, mri_surf2vol --hemi lh --so lh.bp.nii.gz --subject fsaverage --o smoothed.bpnd.in.volume.nii.gz mri_surf2vol --hemi rh --so rh.bp.nii.gz --subject fsaverage --merge smoothed.bpnd.in.volume.nii.gz  --o smoothed.bpnd.in.volume.nii.gz On 10/16/17

Re: [Freesurfer] lta_convert does not produce ITK transforms that are correctly applied by antsApplyTransforms

Doug, Sorry if I muddied things by going into the significant digits - accurate to 5 seems reasonable. I was simply meaning to say that the rotation and scaling parameters are not the issue, to save the reader time inspecting them. The translations (final three parameters) are off by anywhere

[Freesurfer] LGI calculation

Dear All, I designed an adaptive filter according to local gyrification index values and then want to see the lgi histogram of new smoothed brain volume. However freesurfer gave an error as: ERROR: mritotal failed, see transforms/talairach.log It seems that the input volume orientation has

Re: [Freesurfer] Constrain smoothing to GM for PET data

that includes GM regions. not sure what you want On 10/13/17 8:58 PM, Elijah Mak wrote: Hi Doug, That subcort mask is only GM (sorry, should have indicated that when I named it). I just looked at the subcort mask in the cvs 2mm folder and it looks like it is only subcortical? I am

Re: [Freesurfer] Normalize to mni

I'm not sure what you mean/want. If you run preproc-sess with the -mni305 flag, it will resample to mni305 space and mask out non-subcortical structures On 10/12/17 11:14 AM, Jan Willem Koten wrote: Normalize to mni Dear Doug, We have a very simple question. In a first step we segmented

Re: [Freesurfer] Longitudinal analysis using data with only two timepoints and LME

Hi Christoph, 1) I would use only intercept as random effect. I like to keep the model simple and - as you say - there is only a max of 2 time points. If you like you can do a model comparison (see wiki page) to compare the two models. 2) I would use the exact time in years (as float with

[Freesurfer] TRACULA bedpostx step with gpu

Dear FreeSurfer users, I am using Freesurfer 6.0 and Tracula 6.0 for processing MRI and DTI scans. The second step of the trac-all pipeline performs the ball-and-stick fit with the bedpost function from FSL. Documentation for FSL suggests that the use of GPUs can considerably speed this

Re: [Freesurfer] TRACULA bedpostx step with gpu

Hi Chintan - Freesurfer is open source, so all of our source code is available, but trac-all is actually a shell script, so you can find it under $FREESURFER_HOME/bin/. TRACULA just expects the output files of bedpostX, and does not care if they were generated on GPUs or CPUs. Just provide the

[Freesurfer] R: Re: R: Re: R: Re: R: Re: R: Re: R: Re: R: Re: R: Re: Map of covariance

Thanks. The maps produced in slope and intercept folders are very similar and opposite in colors. I have already applied this contrast but I think that they did not fit with my goals. Why the intercept did not produce the same results of G4VO? The slope effect is very similar to the inverse of

Re: [Freesurfer] Questions about the transformation of DKatlas from surface to volume

do you really want the atlas in MNI space or do you want an individual subject parcellation mapped to MNI? If the atlas, I think it already is, or at least it lives on the fsaverage surface which has associated MNI coords. Doug can confirm. cheers Bruce On Mon, 16 Oct 2017, cain wrote: