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Hi Lauri,
You can also try this:
https://github.com/ThomasYeoLab/CBIG/tree/master/stable_projects/registration/Wu2017_RegistrationFusion
Regards,
Thomas
On Tue, Jul 30, 2019 at 5:20 AM Greve, Douglas N.,Ph.D. <
dgr...@mgh.harvard.edu> wrote:
> Hi La
look in subject/scripts/build-stamp.txt
you should see something like
freesurfer-Linux-centos7_x86_64-stable-v6-20161229-80ac5eb
On 7/29/2019 6:40 PM, FAST Study wrote:
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Hi!
I am re-running all recon-all using version 6.0. I was running a full list of
subje
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Hello,
I have recently used segmentHA_T1_long.sh and was pleased with the
segmentation results. However, I now have a longitudinal data set that has
additional T2 high-resolution scans of the hippocampus as well as T1's. I
know there is a segmentHA_T2.
Hi Daniel - TRACULA uses manually labeled examples of tracts to learn from.
That template simply defines the coordinate space in which those training
examples live. If you were to provide a different set of manually labeled
tracts that lived in a different space, that's when you'd provide a diff
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Thank you for your response. We may have some children slightly younger so
I am not sure if the method would still apply. Does that mean my suggested
edit of changing the mni template to a different template wouldn’t work. I
appreciate your input and qu
Hi Daniel - What is the age range you're interested in? We have used tracula
with children as young as 5 (see example ref below). Keep in mind that tracula
is not a traditional template-based approach that needs perfect alignment to a
template, because it finds tracts based on their relative pos
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Hi!
I am re-running all recon-all using version 6.0. I was running a full list
of subjects when our server crashed - and I would like to begin where it
stopped.
How do I check which subjects have been run on the latest version (v. 6)?
Thanks so!
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Hello,
Is it possible to run TRACULA on baby/children brain scans? If so how would
one go about doing this?
Could I just change
set mnitemp = $FSLDIR/data/standard/MNI152_T1_1mm_brain.nii.gz
to a different baby/child atlas? If not how would I go abo
Have you seen this tutorial?
https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/MultipleComparisonsV6.0Perm
it uses permutation (which does not work with weighted least squares),
but you could change it to use the old monte carlo stuff.
On 7/29/19 2:15 PM, FAST Study wrote:
>
> Externa
Oh, I guess that's a problem! I've created a new version here
https://gate.nmr.mgh.harvard.edu/safelinks/greve/mris_preproc
See if that works. You should compare the output to using the max or
-projfrac 0.5 to make sure they are at least similar since I have not
run it even once:)
On 7/29/19 5:
Hi Lauri, try example 8b in
https://surfer.nmr.mgh.harvard.edu/fswiki/CoordinateSystems
I just created it, so please let me know if something seems not right:)
doug
On 7/29/19 1:41 PM, Lauri Tuominen wrote:
> External Email - Use Caution
>
> Dear Freesurfers,
> I am targeting the MNI152
Does it run correctly outside of Nipype?
On 7/29/19 10:50 AM, Pratik Kashyap wrote:
>
> External Email - Use Caution
>
> Hello experts,
>
> I'm running recon-all by wrapping it in a Nipype workflow.
> (cmdline:
> recon-all -all -i {data/T1_files(iterfield)} -openmp 64 -sd . -s seg )
> The
one computes the average, the other computes the maximum
On 7/29/19 9:03 AM, Reza Rahmanzadeh wrote:
>
> External Email - Use Caution
>
> Dear Doug,
>
>
> I appreciat if you reply my question in the previous e-mail with this:
>
>
> can not i use projfrac-avg in mris_preproc? Is --projfrac-
Sort of. mri_glmfit will take a design matrix (--X) and contrast
matrices (--C), but they need to be in the right format (simple text
table). So, you'll have to convert the output of design_ttest2 into that
format.
On 7/26/19 8:55 AM, Reza Rahmanzadeh wrote:
>
> External Email - Use Cau
I'm not sure that is a way to do this as it is quite tricky managing the
exchangeability in longitudinal data. Maybe PALM can do it. I'm cc'ing
Anderson in case he wants to weigh in.
On 7/28/19 7:24 PM, Mark Wagshul wrote:
>
> External Email - Use Caution
>
> Doug,
>
> Thanks. Unfortuna
The label file has much less info than the surface file (eg, does not
have neighborhood relations). mri_label2vol requires that a full surface
file be provided. It might not be obvious because it usually finds the
surface based on the subject name.
On 7/25/19 3:29 PM, Sam W. wrote:
>
>
The registration matrix maps an XYZ coordinate in the diffusion space to
an XYZ coord in the anatomical space. This appears to be counter
intuitive. In the end, the direction is not very important because you
can just invert the matrix to go the other way. It only really becomes
important if yo
did you run recon-all -qcache ... on all your subjects?
On 7/25/19 3:35 PM, Renew Andrade wrote:
>
> External Email - Use Caution
>
> Dear FreeSurfer experts:
> I am processing in qdec 3 subjects with the GUI and I have this
> terminal output.
>
>
> Error in Analyze: Couldn't open
> /App
what is your mri_segstats command? If you want area in mm2, you'll need
to pass an area file to mri_segstats as input (--i) and use
--accumulate. If this is on fsaverage, you can use
$SUBJECTS_DIR/fsaverage/surf/lh.white.avg.area.mgh
On 7/24/19 7:55 AM, Mark Wagshul wrote:
> External E
That is a little strange. Can you tar up the data and upload it to
ftp://surfer.nmr.mgh.harvard.edu/transfer/incoming
Let me know when it is there and what the file name is
On 7/24/19 4:53 AM, Agnieszka Sabisz wrote:
>
> External Email - Use Caution
>
> Dear Freesurfer Team,
> I checked sk
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Hi all,
I have installed freesurfer and when I type in “dcmunpack -src . -scanonly
scan.log”, I get “command not found.” Please advise. Thank you!
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Freesurfer@nmr.mgh.harvard.edu
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Dear Freesurfers,
I am trying to calculate distances using mris_pmake with Freesurfer Version
6.0.0. When using the command line the following error appears:
mris_pmake: unrecognized option '—surface0'
In January the similar question
(https://www.
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Dear Freesurfers,
I am targeting the MNI152 coordinate -38,44,26 with TMS. I would like to use
this target as an ROI/seed in surface based analyses.
How would I:
1. Transfer the coordinate onto fsaverage surface?
2. Expand the coordinate into a 5m
we got it. I'm out of town but will try to look at it soon
cheers
Bruce
On Mon, 29 Jul
2019, Brian Biekman wrote:
>External Email - Use Caution
>
> Hi Bruce, I uploaded a subject's output via the Martinos Center File Drop.
> Let me know if there is anything else you need.
> --
> Brian Bi
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Hi Bruce, I uploaded a subject's output via the Martinos Center File Drop. Let
me know if there is anything else you need.
--
Brian Biekman
Graduate Student, University of Houston
Clinical Psychology, Neuropsychology Concentration
Laboratory of Early E
Hi Brian
usually this is fixable by changing some default parameters in recon-all.
You can try this yourself (the intensity bounds used in mri_segment and
mris_make_surfaces - look at the help), or you can upload a subject
to our ftp site and we can recommend some
cheers
Bruce
On Su
Dear Freesurfers,
Can anyone please help me with mris_curvature_stats? Anyone was using or
testing it and encountered the same parameter problem or errors?
Thanks and best
Maria
On 24.07.19 10:03, Maria Kalemanov wrote:
> Hello FreeSurfer developers,
>
> I have three issues with mris_curvature_s
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Dear Doug,
I appreciat if you reply my question in the previous e-mail with this:
can not i use projfrac-avg in mris_preproc? Is --projfrac-max min max delta
just the same?
Best,
Reza
From: freesurfer-boun...@nm
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Dear Doug,
Thanks, the tutorial was super helpful. As i would compare the MWF value in
cortex between control subjects and patients. Now my problem is how to make the
contrast matrix for mris_preproc to do the comparison in both direction (in 1,
th
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