Dear Freesurfer experts,
I am currently trying to obtain mean thickness values for certain
sub-regions of the cortex. I have previously used this command
asegstats2table --subjects X_* --meas thickness --tablefile aseg_stats.txt
however now (Ive updated to v 5.3) I receive this error
Dear Freesurfer experts, I am currently trying to do a cortical
thickness group analysis with one factor, three levels . I have run
mri_preproc and mri_surf2surf, and am now trying to run
mri_glmfit --y lh.group.thickness.10B.mgh --fsgd easy2.file --C
contrast1.mtx --surf fsaverage lh
Dear Jorge/freesurfer group,
I am using the scripts you sent me that do not require the newer
version of matlab, and now using a computer that has the Statistics
toolbox. I can get the scripts (with the suffix 1) to run with;
lhstats = lme_mass_fit_vw(X[1 2],ni,lhcortex);) however it fails
Hi,
Thank you for your response. I am actually using two random effects
(time and intercepts), and have fixed my design matrix to incorporate
this. We are actually running R2011b Matlab, however I just realised
that we do not have the Statistics toolbox. Could this be what is
causing the
Dear Freesurfer experts,
I have a question about fitting linear mixed models to mass-univariate
data using the lme tools in matlab.
I am currently trying to compute the initial vertex-wise temporal
covariance estimates by [lhTh0lhRe] =
lme_mass_fit_EMinit(X,[2],ni,lhcortex,3]
However, I
Dear Freesurfer experts,
I am trying to prepare my data for linear mixed modeling using the
matlab add ons, with this command
mris_preproc --qdec-long qdec.table.dat --target fsaverage --hemi lh
--meas thickness --out lh.thickness.mgh
However I keep getting this error message ERROR: flag
Dear Freesurfer experts,
I am trying to conduct the long_mris_slopes --qdec qdecfinal --meas
thickness --hemi lh --do-avg --do-rate --do-pc1 --do-spc --do-stack
?do-label ?time time --qcache fsaverage command for my longitudinal
processing. However I keep getting the error message:
Hi all,
I was trying to create an average subject however received this error
message. I temporarily removed that subject however I was wondering
what a possible cause for this error is?
Applying LTAtransformInterp (resample_type 1)
writing to
Dear all,
I have a question;
I am trying to load data into qdec; the data table is loaded fine
(although it lists age as continuous for some region, rather than
discreet). However, When i try to generate the stats table, this error
comes up. Does this mean I somehow have to manually set
Dear all,
I have a question;
I am trying to load data into qdec; the data table is loaded fine
(although it lists age as continuous for some region, rather than
discreet). However, When i try to generate the stats table, this error
comes up. Does this mean I somehow have to manually set
Sorry, just to clarify; it lists age as a discreet variable rather
than continuous for some reason, not the other way round as I
accidentally wrote=)
Regards
Quoting Catherine Bois c.b...@sms.ed.ac.uk on Tue, 12 Feb 2013
14:58:45 +:
Dear all,
I have a question;
I am trying
Hi,
I am considering using qdec, however due to our large dataset (and
different individuals having been in charge at different times) I just
realized that the folders fsaverage etc are missing. As these are
necessary for the qdec use, is there anything else I can do? Eg a
command line to
Hi, I am trying to extract stats files from my subjects using this command
aparcstats2table --hemi lh --subjects EHRS_* --skip --meas thickness
--parc --aparc --tablefile lh.thick.table
however I keep getting this error message
Parsing the .stats files
Skipping
Hi,
I am currently editing some scans (ie adding control points etc),
however I keep finding that after the editing often the brains look
worse than they did before; especially the medial temporal lobe
area. I have taken care not to put too many control points in/made
sure not to place
Hi, just to clarify,
When beginning longitudinal analysis, the first step is the same as
cross-sectional processing, eg just the normal recon-all command,
for each subject, and each individual time point? Then the norm.mgz
files are used?
Thanks
--
The University of Edinburgh is a
?
Thanks,
- Forwarded message from c.b...@sms.ed.ac.uk -
Date: Wed, 09 Jan 2013 13:35:12 +
From: Catherine Bois c.b...@sms.ed.ac.uk
Subject: longitudinal processing
To: freesurfer@nmr.mgh.harvard.edu
Hi, just to clarify,
When beginning longitudinal analysis
Hi,
when reconstructing the brains including manual edits, does the step that
incorporates control points come before the white matter edits? Ie so if
I do both control points and white matter edits, will the white matter
edits be take into account even if I just use -autorecon -cp , and not -wm?
I have noticed that when I reconstruct the brains (with edits) three files
appear; fsaverage, lh/EC_average and rh.EC_average...I only recently
noticed these and have before then been under the impression that all the
useful data for analysis is in each individual's subject folder. Therefore
I
Hi,
I am currently in the process of reconstructing my brains after edits.
However, the brains keep being reconstructed with large portions of brain
missing/cerebellum missing; ie they are much worse than before I edited
them. However, I am sure that I have only put control points in white
matter
Hi, sorry I have an additional question; when reconstructed 9with edits),
if the scan seemingly is worse off than before the edits were made; is
there a recon clean command; that one can use that takes away all the
edits and starts from scratch?
Thank you,
Cathy
Hi,
I am currently in the process of reconstructing my brains after performing
edits. I am submitting them to a system named condor, which allows them to
be processed in parallel, reducing time. However, I am unsure of how to
best use the script that takes into account all the changes made. Is it
Hello,
I have a question re reconstructing brains (ie after doing the edits and
running them again to ensure the edits went through). Before the
reconstruction, the whole brain was there, however afterwards, large chunks
of the brain is missing. Im worried whether this is something to do with
the
, Catherine Bois clb...@york.ac.uk wrote:
Hello,
I have a question re reconstructing brains (ie after doing the edits and
running them again to ensure the edits went through). Before the
reconstruction, the whole brain was there, however afterwards, large chunks
of the brain is missing. Im
Hi, I am trying to use freeview to look at wm/brainmask etc however the
command wont work. The command Im suing is
freeview -v wm1_edits_before/mri/wm.mgz:colormap=heat:opacity=0.4
wm1_edits_before/mri/brainmask.mgz \
-f wm1_edits_before/surf/lh.white:edgecolor=blue
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