Leticia,

In the interim until the new longitudinal stream is released, you can run all your timepoints through the regular stream (recon-all -all), as this is required in the new stream. Doing so was not required in the existing (old) longitudinal stream (only the first timepoint was required, now all timepoints must be processed).

Nick

On Tue, 2009-05-12 at 14:09 -0400, Bruce Fischl wrote:

Hi Leticia,

the recon-all -long stuff is not quite ready yet. Hopefully we'll have something to distribute within a week or so.

cheers, Bruce On Tue, 12 May 2009 l.gutierrez@ion.ucl.ac.uk wrote:

...

Hi,

We have installed the 4.0.1 version and we are starting the longitudinal analysis. I have some problems with -base flag( recon-all -base <baseid> -base-insubj <tp1subjid> -base-insubj <tp2subjid> ... -all). Should 4.0.1 version be one problem in order to do that?

Many thanks

Leticia

...

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Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

no, probably not, since we're still sorting out the details. We'll be happy to chat about it in person if you like though

On Wed, 13 May 2009, James Porter wrote:

As a tangential follow-up question, will the longitudinal analysis stream be discussed and demonstrated in the upcoming FSL/FreeSurfer course in San Francisco?

---

Jim Porter Graduate Student Clinical Science & Psychopathology Research University of Minnesota

Nick Schmansky wrote:

Leticia,

In the interim until the new longitudinal stream is released, you can run all your timepoints through the regular stream (recon-all -all), as this is required in the new stream. Doing so was not required in the existing (old) longitudinal stream (only the first timepoint was required, now all timepoints must be processed).

Nick

On Tue, 2009-05-12 at 14:09 -0400, Bruce Fischl wrote:

Hi Leticia,

the recon-all -long stuff is not quite ready yet. Hopefully we'll have something to distribute within a week or so.

cheers, Bruce On Tue, 12 May 2009 l.gutierrez@ion.ucl.ac.uk wrote:

Hi,

We have installed the 4.0.1 version and we are starting the longitudinal analysis. I have some problems with -base flag( recon-all -base <baseid> -base-insubj <tp1subjid> -base-insubj <tp2subjid> ... -all). Should 4.0.1 version be one problem in order to do that?

Many thanks

Leticia

---

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---

Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

The easiest thing would be to binarize the aparc+aseg like:

mri_binarize --i aparc+aseg.mgz --wm --o whitematter.mgz

You can the resample this to mni305 with:

mri_convert --apply_transform transforms/talairach.xfm whitematter.mgz whitematter.mni305.mgz -oc 0 0 0

Not sure what you want to do now. You can then mri_concat the whitematter.mni305.mgz files from you different subjects into one file, or create a mean.

doug

muet0005@umn.edu wrote:

Hi FreeSurfers,

I was wondering if it is possible to obtain an average wmparc.mgz file for a group of subjects that have been processed through freesurfer? We have 72 cases that have been independently processed through freesurfer, and we would like to generate a representative white-matter "atlas" that could potentially be aligned to some standard space (e.g., MNI). Would this be possible?

If this isn't possible, could we obtain this from fsaverage? I noticed that $FREESURFER_HOME/subjects/fsaverage does have an aparc+aseg.mgz --- is there also a way to get wmparc.mgz (e.g, using mri_aparc2aseg)?

Thanks in advance for any suggestions!

-Ryan Muetzel

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Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Hi Ryan,

is this only in the longitudinal stream? Sounds like a bug. If you upload the whole subject directory we'll take a look.

Bruce On Thu, 10 Sep 2009 muet0005@umn.edu wrote:

Hello,

I am running the longitudinal processing using version 4.5 and was wondering if there are any data quality checks specific to the longitudinal stream (other than the standard ones listed for the cross-sectional analysis)? For example, is there a way to check the registration between TP1 & TP2 when creating the base?

Also, in two of my 36 subjects (one in creating the base, one TP->base longitudinal processing), the final step that creates wmparc.mgz was taking extremely long to finish (I let it go 18hrs before killing the process, and only 25 slices were complete). After looking at the aparc+aseg.mgz file, I noticed that part of the right hemi, and all voxels outside of the brain received a value of 41, corresponding to right cerebral white matter. The aseg.mgz appears to be fine, and the pial & inflated + annotation file appeared OK in tksurfer. Any ideas on what may be going wrong with these cases?

Thanks! -Ryan

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Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Jim,

No, I dont think there will be time, other than maybe a brief mention, as the existing freesurfer material must fit in one day, which makes things quite packed, as there is a ton of stuff to learn before even thinking about longitudinal analysis.

However, maybe that day we'll ask for a show-of-hands on interest and then maybe spend more time, or at the very least some one-on-one time to answer questions. We have long term plans in the longitudinal analysis stream that perhaps could benefit from your feedback.

Nick

On Wed, 2009-05-13 at 13:34 -0500, James Porter wrote:

As a tangential follow-up question, will the longitudinal analysis stream be discussed and demonstrated in the upcoming FSL/FreeSurfer course in San Francisco?

---

Jim Porter Graduate Student Clinical Science & Psychopathology Research University of Minnesota

Nick Schmansky wrote:

...

Leticia,

In the interim until the new longitudinal stream is released, you can run all your timepoints through the regular stream (recon-all -all), as this is required in the new stream. Doing so was not required in the existing (old) longitudinal stream (only the first timepoint was required, now all timepoints must be processed).

Nick

On Tue, 2009-05-12 at 14:09 -0400, Bruce Fischl wrote:

...

Hi Leticia,

the recon-all -long stuff is not quite ready yet. Hopefully we'll have something to distribute within a week or so.

cheers, Bruce On Tue, 12 May 2009 l.gutierrez@ion.ucl.ac.uk wrote:

...

Hi,

We have installed the 4.0.1 version and we are starting the longitudinal analysis. I have some problems with -base flag( recon-all -base <baseid> -base-insubj <tp1subjid> -base-insubj <tp2subjid> ... -all). Should 4.0.1 version be one problem in order to do that?

Many thanks

Leticia

---

Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

---

Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

---

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