Dear mailing list,
I am trying to run a LME model using the matlab tools, but I’m unsure how to
specify the model we wish to run. We have a qdec file that contains the
following columns:
fsid, fsid-abse, years between scans, age at baseline, gender, group
We want to specify a model where we can
Probably not. Probably you the cerebellum is still attached. You should
check the wm.mgz volume.
On 2/24/17 11:21 AM, Shane Schofield wrote:
Hi Freesurfer Team,
I am running recon-all on Freesurfer version 6. A few of my subjects
have “XL defect detected …” and their recon-all have been runn
If the alignment looks good, you can just close the transform window (or
just kill freeview)
On 2/26/17 4:06 PM, miracoo...@gmail.com wrote:
Hello Antonin,
Thank you for your quick reply. Does this mean I should close the
transform window when it opens? The alignment looks good to me, I was
you can ignore the warning as you are working with volumes and not
surfaces or ROIs or way points. The "INFO" is only for informational
purposes
On 2/26/17 2:48 PM, miracoo...@gmail.com wrote:
Sent from my BlackBerry 10 smartphone.
*From: *miracoo...@gmail.com
*Sent: *Sunday, February 26,
Hello Antonin, Thank you very much for you help. I shall do it tomorrow and provide an update. Best, Paul.
Dear Paul,
I think that the transform window in freeview opens by default to enable manual
refinement of registration if needed.
If you are not sure, try also tkregister2. It should work to simply replace
tkregisterfv by tkregister2, the command would be
tkregister2 --mov your_moveable --targ
Hello Antonin, Thank you for your quick reply. Does this mean I should close the transform window when it opens? The alignment looks good to me, I was worried because the transform window opened and the info on th
Dear Paul,
LTA means transformation matrix stored in .lta format.
This matrix can encode transformation between various coordinate spaces.
What coordinate systems transform this .lta from and to is specified by string
in the .lta file. Typically this type could be vox2RAS, RAS2vox, vox2vox or
Hi Eugenio,
Thanks for getting back to me and yes it is version 5.1-5.3. I will speak to my
IT department about upgrading to version 6.0, but can you let me know about the
processing details for the older version in the meantime? We have already
processed a group of subjects and my Investigator
Hello Freesurfer, While checking the Coregistration step of PETsurfer using tkregisterfv, I encountered an issue (not sure if it was an error). The transform GUI simultaneously opened with freeview and I received this message in the terminal window ( warning : transformation can only apply to vol
Hi everyone,
I segmented with Mantis, a toolbox of spm, MRI T2-weighted images of infants
. Now I have to compute cortical thickness. How can I do it with Freesurfer? I
know there's the recon-all function that segments and does this but is
based on T1-weighted images. There is a way to be able to a
Dear Shane,
the "topological defect" in FreeSurfer jargon means that the estimated surface
contains errors like "holes" or "handles".
See
PPT from FreeSurfer course
http://surfer.nmr.mgh.harvard.edu/pub/docs/freesurfer.failure_modes.ppt
or
https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/T
Dear experts,
I was wondering what is your opinion on the fact, that, according to the
mindboggle paper
http://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1005350
it is beneficial to use ANTS volume-based gray matter segmentation to refine
gray matter segmentation in FreeSur
Dear Doug,
If I want to create a new volume that is registered to the MNIspace (using
mni1525reg), can I mask out other voxels that are not part of the mni template
brain? It is a PET volume (already in individual space using bbregister) that
has noisy signals in non-brain regions.
Thank you.
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