Dear FreeSurfer experts,
Thanks again for a great FreeSurfer forum.
I have been trying to run the linear mixed effects model on a longitudinal
dataset. However, i get the an error in matlab: "matlabpool has been
removed. Use PARPOOL instead". I can see in the forum that others have
experienced th
Hi Kaspar,
I had the same problem. The last version that supports matlabpool is Matlab
8.2. Maybe try it with that version.
Cheers, Clara
- Ursprüngliche Mail -
Von: "Kasper Jessen"
An: "Freesurfer support list"
Gesendet: Mittwoch, 23. März 2016 09:41:51
Betreff: [Freesurfer] Matlabpo
Hi Clara,
Your right, an older version of Matlab, could be a solution. However, i am
thinking that there must be a fix?
Cheers,
Kasper
2016-03-23 11:16 GMT+01:00 Clara Kühn :
> Hi Kaspar,
>
> I had the same problem. The last version that supports matlabpool is
> Matlab 8.2. Maybe try it with that
Hi Doug,
Thanks!
I manually tweaked the registration of the PET to T1 on a number of
subjects to bring the mincost down to < 0.5. After saving the pet2free
volume in Freeview, I noticed that a new .lta is produced in the same
directory (i.e. pet2free_fsl.mgz.lta).
Will the option --regheader te
Hi Kasper,
the fix is that someone needs to sit down and port all matlabpool to
parpool, which is straightforward. It needs to be done in a way that is
backward compatible, as not everyone has the new version of Matlab.
Maybe someone on the list want's to take this on, should only be a
couple
mri_concat --f pib_lh_fsaverage (textfile of subjects and their images) --o
concat_lh_pet.mgh
Should I add -mean here for the GLM?
mri_glmfit --y concat_lh_pet.mgh --fsgd pib_fsgd --C group1.group2.mtx
--surf fsaverage lh --cortex --glmdir lh.pet.glmdir
My simple 2 group-no-covariates FS
On 3/23/16 1:04 AM, Reema Jayakar wrote:
Hi Dr. Greve,
Thank you very much for getting back to me so promptly. If memory
serves me right, I am pretty sure that the orientations were incorrect
in tkmedit but will double check soon. Based on what you are saying
and based on what I read in the
On 3/23/16 9:07 AM, Elijah Mak wrote:
mri_concat --f pib_lh_fsaverage (textfile of subjects and their
images) --o concat_lh_pet.mgh
Should I add -mean here for the GLM?
No, that is handled by glmfit
mri_glmfit --y concat_lh_pet.mgh --fsgd pib_fsgd --C
group1.group2.mtx --surf fsaver
No, you'll need to pass the new registration to mri_vol2surf. You should
also check that freeview is producing the correct registration file.
We've had several problems with it that are definitely fixed in 6.0, but
not sure about 5.3. Try loading it in tkregister (--lta your.lta --reg
your.reg
Dear FreeSurfer experts,
I would like to analyze my longitudinal data also cross-sectionally at single
time points. I am a little confused as to how to register my data to the
template and smooth it accordingly.
So far, I have registered my longitudinal data to my template to use in LMEs
with
Hi Clara,
1) You'd create a different table for your time point with fsid being
the longitudinal directories s1.long.sbase , no fsid-base column. then
you can map and stack these using cross sectional commands (mris_preproc
--qdec ...)
2) You should use Qdec or glm_fit for cross sectional anal
Hi Doug,
Thanks. I was wondering if you think this would do the job: 1) use
fmcpr.nii.gz 2) split it to 3d volumes 3) do mri_vol2vol for all the
volumes separely 4) concatenate the resampled volumes together to get a 4d
volume. If you don't think this is a good approach, I appreciate it if you
Hi,
I'm using mri_label2vol with the parameters below but the output .nii volume
has the shape 163842x1x1 while the input volume is 27307x1x6. This dimension
mismatch is causing issues in our gPPI pipeline.
How can I generate a .nii output file with the 27307x1x6 dimension?
mri_label2vol
-
Trying to integrate freesurfer data with our XNAT database.
Are there any freesurfer schemas for XNAT available, or is it pretty much I
have to try to make my own?
Thanks,
--
Elijah Rockers
Research Data Analyst
Houston Methodist Neurological Institute
O: 713 363 7729
Houston Methodist. Leadin
hello doug,
i performed a group analysis and after correction for multiple comparisons when
i tried to load the corrected clusters the whole hemisphere was completely
yellow. what should i do?
Best,
Miracle
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Freesurfer@nmr.
Dear. Freesurfer experts.
Hi. How are you?
I'd appreciate it a lot if you can help me with this problem.
I'm trying to check the ROI (.nii) after creating it by using mri_label2vol
command.
I used the command:
mri_label2vol --label $SUBJECTS_DIR/$SUBJECT/label/lh.v1vt.label --label
$SUBJECTS_D
Dear. Experts.
Please ignore the previous email.
It works.
Thank you.
Best,
Ji Won
2016-03-23 17:24 GMT-04:00 Ji Won Bang :
> Dear. Freesurfer experts.
>
> Hi. How are you?
>
> I'd appreciate it a lot if you can help me with this problem.
>
> I'm trying to check the ROI (.nii) after creating
I too am puzzled as to why you would want to do this. In terms of getting
improvement in the alignment across subjects TBSS is one way to approach
this. Another would be to use the fiber orientations in the registration
like these folks have done:
http://dti-tk.sourceforge.net/pmwiki/pmwiki.php?n
Hi Matt,
I highly appreciate your input on this!!
Actually my goal is to study the difference in FA values between groups within
the cortex. I know that diffusivities ( MD, AD and RD) can be used to evaluate
gray matter and many people claim that it is much better to use diffusivities
to evalua
Right but what do you think FA, MD, AD, RD, etc are telling you
neurobiologically in the grey matter?
Matt.
On 3/23/16, 7:18 PM, "Alshikho, Mohamad J."
wrote:
>Hi Matt,
>I highly appreciate your input on this!!
>
>Actually my goal is to study the difference in FA values between groups
>within t
It can explain one thing "tissue integrity"
It will tell us neurobiologically exactly what can tell us in tissues other
than the brain such as liver, lung, heart, joints, etc
Mohamad
-Original Message-
From: freesurfer-boun...@nmr.mgh.harvard.edu
[mailto:freesurfer-boun...@nmr.mg
FA or fractional anisotropy explains the fraction of the diffusion that is
along the long axis of the diffusion tensor. In so far as the diffusion
tensor is an accurate model of the underlying structural architecture,
what you say might be true (e.g. in the small number of white matter
regions wit
This is theoritically correct!
If we do DTI to study the liver. How these measures can explain the tissue? It
is not only white matter and gray matter!
All DTI measures can explain how much space we have between the cells. More
space means low FA and high RD. The opposit correct as well.
Given
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