Re: [Freesurfer] PCA on PET / Thickness in Freesurfer

Hi Doug, I have pasted the correspondences below. My question is, if I want to identify the PCs in a group for a single modality (PET), how should I run the mri_glmfit? A single group design with A contrast of 1 0 (for a nuisance covariate)? Thanks ! Elijah Doug: For within modality,

Re: [Freesurfer] PCA on PET / Thickness in Freesurfer

sorry, can you repost with previous correspondence? On 12/01/2016 06:30 PM, Foo Keat Mak wrote: > Thanks Doug. Does that mean that a one group design? With a contrast > of 1 0 (adjusting for one variable)? > > > > > ___ > Freesurfer mailing list >

Re: [Freesurfer] PCA on PET / Thickness in Freesurfer

Thanks Doug. Does that mean that a one group design? With a contrast of 1 0 (adjusting for one variable)? ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this

Re: [Freesurfer] white matter segmentation incorrect after intensity change

sure, good luck Bruce On Thu, 1 Dec 2016, Rizvi, Batool wrote: > Sounds great, thanks again for your help and will try out your > recommendations. > Have a great day! > > B > > > From: freesurfer-boun...@nmr.mgh.harvard.edu >

Re: [Freesurfer] white matter segmentation incorrect after intensity change

Sounds great, thanks again for your help and will try out your recommendations. Have a great day! B From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Bruce Fischl [fis...@nmr.mgh.harvard.edu] Sent:

Re: [Freesurfer] white matter segmentation incorrect after intensity change

yes, you can remove the control.dat file and run autorecon2-cp and autorecon3. Should only take a couple of hours depending on your processor On Thu, 1 Dec 2016, Rizvi, Batool wrote: > > Hi Bruce, > Thanks so much for the feedback, that is very helpful. We'll try deleting the > control points

Re: [Freesurfer] white matter segmentation incorrect after intensity change

Hi Bruce, Thanks so much for the feedback, that is very helpful. We'll try deleting the control points then. Is there a quick way to rerun recon-all without having it take up to 5-8 hours? Also, a separate question, when running autorecon, after edits to the white matter and pial surfaces,

Re: [Freesurfer] white matter segmentation incorrect after intensity change

the problme is that you have several control points in voxels that aren't entirely wm. For example, 129, 134, 173 is a control point and it has no wm in it. This causes the intensity in that region to go up way too high, as we will normalize the control points to the desired wm intensity (110).

Re: [Freesurfer] white matter segmentation incorrect after intensity change

I mean to tar and gzip the entire subject dir, which will be too big to email. You can put it on our ftp site: https://surfer.nmr.mgh.harvard.edu/fswiki/FtpFileExchange On Thu, 1 Dec 2016, Rizvi, Batool wrote: > Hi Bruce, > Thanks for your reply. It is actually brighter on the brainmask.mgz

Re: [Freesurfer] white matter segmentation incorrect after intensity change

Hi Bruce, Thanks for your reply. It is actually brighter on the brainmask.mgz than the orig.mgz when I checked. I'm uploading the freesurfer subject here. Thanks! BR From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu]

Re: [Freesurfer] white matter segmentation incorrect after intensity change

hmmm, that's awfully bright. Is it also bright on the orig.mgz? It's not really possible to diagnose from a single slice from a single subject. If you tar, gzip and upload the subject one of us will take a look cheers Bruce On Thu, 1 Dec 2016, Rizvi, Batool wrote: Hi FreeSurfer experts,  

Re: [Freesurfer] PCA on PET / Thickness in Freesurfer

For within modality, you can add --pca to mri_glmfit (run it with --help to get more info). We do not have ICA tools in FS. On 12/01/2016 02:04 PM, Foo Keat Mak wrote: > Hi Freesurfer Team, > > For a given group, I want to look at the covariance patterns between > thickness and PET. Within

[Freesurfer] PCA on PET / Thickness in Freesurfer

Hi Freesurfer Team, For a given group, I want to look at the covariance patterns between thickness and PET. Within Freesurfer, what are some general workflow tips on how I could go about performing PCA (within modality) or joint ICA analyses looking at the covariance patterns across

Re: [Freesurfer] Demeaning variables

If you want to find the effect of group regressing out the effect of age and there is truly a difference in the age slopes, then you have a problem. Imagine a scatter plot of thickness vs age. Each group gets it's own best fit line (offset and slope). If the slopes are the same, then the two

Re: [Freesurfer] Longitudinal stream : LME and limits of model

Dear FS's experts, Could you answer me about questions from below inline precedent mail ? Best regards, Matthieu 2016-11-22 21:31 GMT+01:00 Matthieu Vanhoutte : > Hi Martin, > > Please see inline below: > > Le 22 nov. 2016 à 17:04, Martin Reuter

Re: [Freesurfer] DTI Multi band sequence?

Thanks a lot Dr. Harms and Dr. Wakeman for the help. This is really helpful. On Wed, Nov 30, 2016 at 10:24 AM, Harms, Michael wrote: > > That would be yet another way. > For those that are curious, the field is “MosaicRefAcqTimes”. > > cheers, > -MH > -- > Michael Harms, Ph.D.

Re: [Freesurfer] obtain fa FA data from the white matter ROIs in WMParcStatsLUT.txt. or FreeSurferColorLUT.txt.

If you want to use the FA map, it's dmri/dtifit_FA.nii.gz From: Knut J Bjuland [knutjor...@outlook.com] Sent: Wednesday, November 30, 2016 4:40 PM To: Yendiki, Anastasia Cc: Freesurfer support list Subject: Re: [Freesurfer] obtain fa FA data from the white matter

[Freesurfer] Pegasus workflows?

Hi, Somewhat off-topic, but are there Freesurfer users on this list who might use the Pegasus WMS for executing workflows? If so, I’d like to hear about your use cases. I’m part of an NSF-funded project to incorporate data integrity and security assurances into Pegasus for scientific

[Freesurfer] Postdoctoral position in early onset adolescent psychosis study

Dear All, At the NORMENT – K.G. Jebsen Research Centre for Psychosis Research, a Centre of Excellence, Institute of Clinical Medicine, University of Oslo, Norway, there is a position available as a postdoctoral student funded by the Research Council of Norway. The research area is psychiatric