Dear Sir/Madame
I have written a script that calculates the cortical thickness for the
whole hemisphere of the brain. I have some question if there are any
ways to improve the script. I can quite easily write a script in Python
that runs through the file I have created and append it to a coma
sepa
Hello,
I've tried running mris_expand on several different surfaces, with or
without the -thickness flag, and while it ends without error and creates
the output file, the output looks identical to the input. I've tried even
expanding by large amounts, large percentages of thickness values, but
wit
Hello!
About synthesising a volume using mri_volsynth with direction cosines
and RAS from mrs header:
In the mrs header I have:
- VOI position in the 3 views (sag, cor and tra) which are from the
left upper corner of the voxel (these are the RAS coordinates that I
need to feed into mri_vols
Ji Jessica,
that's pretty low contrast. I would also bet that it's low bandwidth and
hence you have big temporal lobe B0 distortions that will change with
subject positioning. Are you stuck with this data going forward, or can you
change the acquisition parameters? If not, I think you will hav
Hi Reza,
what version are you running, and what is your command line? In the current
version, this works for me:
mris_expand -n 11 -thickness \
/homes/4/fischl/local_subjects/bruce/surf/lh.white 1 \
/homes/4/fischl/local_subjects/bruce/surf/lh.mid \
this will create surfaces nam
Hi,
I got the error running "trac-all -path -c configure.txt"
ERROR: Could not open
${SUBJECTS_DIR}/$Subject/dlabel/diff/lh.cst_AS_avg33_mni_flt_cpts_5.txt
I can only find only image files in the "dlabel/diff" directory, but
not text files.
Which step(s) create the lh.cst_AS_avg33_mni_flt_cpts
Hi Ping,
The text files get created in the trac-all -prior stage. Maybe something
went wrong in that step. Is this the case for all the tracts or just for
this tract? If you can send us the trac-all.log file under the scripts
directory it'll be easier to troubleshoot as to what went wrong.
-Priti
Hi all,
I'm running FreeSurfer v4.0.5 and keep getting the following error:
###
#-
#@# EM Registration Thu Jul 28 16:09:51 EDT 2011
/home/pnlstaff/freesurfer/subjects/ucsd_20110726/mri
mri_em_register -mask brainmask.mgz n
Hi Tali
did you check the skull stripping to make sure it didn't fail?
Bruce
On Fri, 29 Jul 2011, Tali Swisher wrote:
Hi all,
I'm running FreeSurfer v4.0.5 and keep getting the following error:
###
#-
#@# EM Registrat
Hi all,
When I run isxconcat-sess, I am experiencing an error finding a 'dof' file
in my analysis directories within the FSD files.
subjects directory: /cluster/manoach/milton/subjects
command line: isxconcat-sess -sf sessid_all -analysis mstmct_v_base -c
type_v_rest_vol -o /cluster/manoach/milt
Dear Bruce,
1). What is the minimum value/the range for the intensity in order to be
considered acceptable? I know the value in wm should be very close to 110 but
what is the accepted value closed to this?
If is not exactly 110 (foe example if is 101) do I need to add control points
in order to
Hi Antonella,
I'll leave 2) for others. For 1), it's only worth intervening/adding
control points if the white surface doesn't extend all the way out to the
end of a white matter strand (or if the gray matter over it doesn't get all
the way out either)
cheers
Bruce
On Fri, 29 Jul 2011, Anton
Hello everyone,
I was trying to create a table with my statistical results (the cortical
thickness and the number of vertices) and I was running:
aparcstats2table --hemi lh --subjects bert NPI001 --meas thickness -t
lh.aparcstas.THICKNESS.txt
When I tried to also get the number of vertices
Hi All,
I was trying to use the registration file that is created by
mri_robust_register with mri_vol2vol - but it is in a different format than
registration files created by bbregister or tkregister. Is it fsl format? Is
there an easy way to use this registration file with other freesurfer fu
Hi Kami
mri_robust_register should create .lta files (linear transform arrays,
although in practice they are almost always just single linear transforms),
which is our preferred xform file format as it has all the necessary info
to figure out coordinate systems and such. The current version of
Hi Antonella,
what do you mean by no. of vertices? The total # in the surface? You can
get that with mri_info. It's loosely related to surface area, but not that
interested a quantity.
Bruce
On Fri, 29 Jul 2011, Antonella Kis wrote:
Hello everyone,
I was trying to create a table with m
Hello Everyone,
We just installed Freesurfer on Mac and the software got installed
successfully.
But when I am running my data, it just gets stuck in between and shows me
the error.
The command I used was: /Applications/freesurfer/bin/recon-all-s 002 -i
/Users/kashou/Desktop/fMRI/Anesthetics/002
Hi Joanna,
can you send us the contents of the file transforms/talairach_avi.log?
Bruce
On
Fri, 29 Jul 2011, joanna floria wrote:
Hello Everyone,
We just installed Freesurfer on Mac and the software got installed successfully.
But when I am running my data, it just gets stuck in between an
Hi,
I was trying to create a table with my statistical results (the cortical
thickness and the number of vertices) and I was running:
aparcstats2table --hemi lh --subjects bert NPI001 --meas thickness -t
lh.aparcstas.THICKNESS.txt
When I tried to also get the number of vertices a table by
Hi Kami,
I usually use mri_convert -at nameof.lta source.mgz mapedsource.mgz
it simply works (w/o the need to specify a target-template volume)
because the information is stored in the lta file.
mri_vol2vol should work also w/o problems. I guess we should add a
--lta flag to it at some point, b
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