Re: [Freesurfer] Qdec image considering multiple variables

Not in FS, sorry. On 10/13/17 3:59 AM, 박경일 wrote: So, I'm wondering if there is another way to draw statistical map considering multiple factors including missing variables. Thanks a lot. Kyung 2017-10-10 6:09 GMT+09:00 Douglas Greve

Re: [Freesurfer] PETSURFER: MRTM2 volumes?

do you mean you want to map the surface-based data into the volume? If so, you can use mri_surf2vol. If you want to analyze your pet data in the volume you can just do that with mri_glmfit On 10/5/17 4:59 PM, Elijah Mak wrote: > Hi Doug, > > Referring to the PETSURFER tutorial for dynamic PET

Re: [Freesurfer] mris_anatomical_stats: segmentation fault core dumped

Does this happen repeatedly? You don't have to rerun recon-all again, just that last mris_anatomical_stats command to see if it seg faults again. If it does, first check your disk space, then load the left hemi in freeview along with the annot and the cortex.label On 10/13/17 11:05 AM, Keiko

Re: [Freesurfer] cortical surface area

Thank you for the input. Jim -Original Message- From: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Douglas Greve Sent: Friday, October 13, 2017 10:09 AM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] cortical surface

Re: [Freesurfer] mris_anatomical_stats: segmentation fault core dumped

Hi Doug! I just ran the mris_anatomica_stats on its own- and it ran successfully? Do you know what may have caused it to fault? Thank you very much! Keiko On Fri, Oct 13, 2017 at 12:17 PM, Douglas Greve wrote: > Does this happen repeatedly? You don't have to rerun

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

That subcort mask is only GM (sorry, should have indicated that when I named it). On 10/13/17 11:15 AM, Elijah Mak wrote: Hi Doug, Yes, but I am using the GM rather than the subcortical volume. How can we get a similar GM mask on CVS 2mm space? Thanks for your help. Best Wishes, Elijah

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

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 looking for a similar mask that also includes the GM regions. Any idea? Best Wishes,

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

Got it. Thanks, Doug! :) Best Wishes, Elijah > On 13 Oct 2017, at 17:06, Douglas Greve wrote: > > That subcort mask is only GM (sorry, should have indicated that when I named > it). > > On 10/13/17 11:15 AM, Elijah Mak wrote: >> Hi Doug, >> >> Yes, but I am using

Re: [Freesurfer] PETSURFER: MRTM2 volumes?

Hi Doug, I wonder what is the difference between this approach (mri_surf2vol) as opposed to doing the MRTM2 modelling on the MGX GM output (58 frames), which will give us the bp.nii.gz in volume space? Thanks. Best Wishes, Elijah > On 13 Oct 2017, at 16:19, Douglas Greve

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

I have applied the contrasts that we discussed in the previous mails but they produce doubt results. In summary, I aim to look at: A- Difference between groups without considerer the covariate effect (I suppose that the maps will be in the intercept folder) ---> ANOVA between 4 groups B-

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

Hi Doug, Yes, but I am using the GM rather than the subcortical volume. How can we get a similar GM mask on CVS 2mm space? Thanks for your help. Best Wishes, Elijah Dr. Elijah Mak, Research Associate Department of Psychiatry, Old Age Psychiatry Group | Cambridge Intellectual &

Re: [Freesurfer] dcmunpack

It should not take that long. For only that number of scans it should only take a few min. On 10/12/17 1:10 PM, Keiko McCreary wrote: Hi There, Could someone tell me how long approximately dcmunpack should take? (I have 243 files and it has been "interrogating" now for 2 hours. Thank you!

Re: [Freesurfer] cortical surface area

that is the area of the white matter surface in mm2 On 10/12/17 2:15 PM, Alexopoulos, Dimitrios wrote: What measure is for the cortical surface area? The measure in the aparc.stats file states ‘WhiteSurfArea’ Jim The

Re: [Freesurfer] cortical surface area

The 2nd is the one you want as the first one includes non cortical structures in the medial wall. On 10/12/17 6:35 PM, Alexopoulos, Dimitrios wrote: > Thanks. > > I ran this command: > mris_anatomical_stats subjectID lh pial > It gave me a total surface area of 115007 mm^2 > > I also tried the

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

Dear FreeSurfer community, I have a few questions regarding the usage of the LME matlab tools for longitudinal data analyses, and how to set up the model. We have patients and control data that we want to compare with respect to cortical changes over time (two time points: baseline and

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

Are you using mri_vol2vol to go into the cvs 2mm space? If so, then use $FREESURFER_HOME/subjects/cvs_avg35_inMNI152/mri.2mm/subcort.mask.mgz On 10/11/17 3:15 PM, Elijah Mak wrote: Hi Doug, Thanks. Could I check my workflow to perform the constrained smoothing of PET MGX-GM volumes? My

Re: [Freesurfer] cortical/subcortical volume based analysis

Hello Bruce,   Thank you for the response. I meant the latter ( making maps etc). I want to do something similar to the subcortical volume based analysis on PETSurfer page however, on freesurfer T1. Freesurfer doesn't perform VBM hence, why should there be a problem with interpretation? 

Re: [Freesurfer] cortical/subcortical volume based analysis

Hi Paul we typically do this type of analysis by looking at scatter plots of structure volumes (e.g. hippocampus). Alternatively, you can make maps, but that opens up all the problems/difficulties of interpretation of VBM. Which did you mean? cheers Bruce On Fri, 13 Oct 2017, miracle

[Freesurfer] cortical/subcortical volume based analysis

Hello FreeSurfer experts, I want to perform a whole brain volume based group analysis for cortical and subcortical regions. That's something very similar to surface based group analysis for cortical thickness however, for volume. Is there a tutorial on how to do it? if yes, please can i get the

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

Hi all, I was just wondering if there was any further insight into what I might be doing wrong on this. Thanks again! On Thu, Oct 12, 2017 at 10:30 AM, Neuro Lists wrote: > Hi Doug and Bruce, > I forgot to mention that I had tried that as well but without

Re: [Freesurfer] Qdec image considering multiple variables

So, I'm wondering if there is another way to draw statistical map considering multiple factors including missing variables. Thanks a lot. Kyung 2017-10-10 6:09 GMT+09:00 Douglas Greve : > You can't run it with missing variables > > On 10/9/17 12:40 AM, 박경일 wrote: > >

Re: [Freesurfer] mris_anatomical_stats: segmentation fault core dumped

not really. If you're running on a cluster, sometimes there can be communication issues where it can only read part of a file, but that is just a wild guess On 10/13/17 12:44 PM, Keiko McCreary wrote: Hi Doug! I just ran the mris_anatomica_stats on its own- and it ran successfully? Do you

Re: [Freesurfer] Errors on compiling FreeSurfer

Hi Aziz, The centos6-built packages seem to cause issues when building on ubuntu, particularly for tcltk apps. I would ignore this for now, or you could compile tcltk yourself. As a general fix, I’ll work on building a package distribution on ubuntu16 best, Andrew On Oct 9, 2017, at 2:02 AM,

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

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 rh.ROI.thickness.fsaverage.mgh) , could some one guide me how i could obtain such file. I have 120 subjects and I have done recon-all for all