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What do you recommend should I use dcm2nixx or use mri_concat in order to deal
with multi frame t1 mri?
Knut j Bjuland
Sent from my iPad
On 25 Feb 2022, at 19:47, Douglas N. Greve wrote:
I'm not sure what question you are asking
On 2/25/2022
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Hi Dr. Greve,
Thank you for your response. I uploaded the .mgh, .fsgd, and .mtx files
that I used to run the mri_glmfit command. I can upload the recon-all
outputs of the individual samples as well, if needed. The files are
uploaded in google drive,
Can you upload the data to me somewhere? I'd need the input volume and
the fsgd and any contrasts
On 2/21/2022 10:24 PM, 정현우 wrote:
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Hi Dr. Greve,
Thank you for your suggestion. Unfortunately, the same problem
occurred when I ran the command with
This is a bit tricky as you need a volume as a template that has the
dimensions/resolution you want. One fast and dirty way to do it is to
upsample the orig to 0.5mm, eg
mri_convert --upsample 2 orig.mgz orig.us2.mgz
You can then run
mri_vol2vol --mov T2.nii.gz --lta reg.lta --targ orig.us2.mgz
You can't tell from the image whether the wm in cerebellum or dura is
attached. you need to look at the wm.mgz volume to see. You can load the
?h.orig.nofix as well. In the terminal output of recon-all/topofix, it
should give a vertex number of the topodefect. Go to that vertex n the
nofix
yes, it does
On 2/25/2022 5:14 PM, Jennifer Bramen wrote:
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Hi Doug
I want to confirm that the signal any region flagged as cortex is
restricted to gray matter. If that is the case, then I finally have
what I need. Thank you.
Warm regards,
Jennifer
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Hi Doug
I want to confirm that the signal any region flagged as cortex is restricted to
gray matter. If that is the case, then I finally have what I need. Thank you.
Warm regards,
Jennifer Bramen, PhD
(she/her/hers)
Senior Research Scientist,
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Replication is essential for progress in science. There are several reasons
why findings may not replicate, including sampling variability, limited
statistical power, cultural/population influences, and improvements in data
acquisition and analysis
It's running quite a long time, with this repeating message:
"
This often happens because cerebellum or dura has not been removed from wm.mgz.
This may cause recon-all to run very slowly or crash.
if so, see
https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/TopologicalDefect_freeview
"
I think
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Hi all,
We are reprocessing some of our data with FS 7.2 to evaluate the new updates to
Tracula, however, we are getting errors from
the trac-all -prep -c configfile step.
The last 20 lines of output are shown below. Anyone have any comments on how
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Sending the info to your email shortly.
- R.
On Feb 25, 2022, at 13:06, Rihab Bayoudhi bayoudhiri...@gmail.com
wrote:External Email - Use
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Email - Use CautionHi guys!I have followed the virtual machine setup for
virtual box
I'm not sure what question you are asking
On 2/25/2022 1:17 PM, Knut J Bjuland wrote:
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DearFreesurferexperts,
IgetthiserrorwhenIamrunning FreeSurfer.
Checkingfor(invalid)multi-frameinputs...
ERROR:input(s)cannothavemultipleframes!
Are you doing an ROI analysis or a voxel-wise analysis? If an ROI
analysis, then use mri_gtmpvc (with or without PVC). This will give you
GM, WM, and CSF ROIs. Or do you mean you want a single average across
all GM?
On 2/24/2022 1:15 PM, Jennifer Bramen wrote:
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Dear Freesurfer experts,
I get this error when I am running FreeSurfer.
Checking for (invalid) multi-frame inputs...
ERROR: input(s) cannot have multiple frames!
/home/knutjb/subjects/test/mri/orig/001.mgz has 4 frames
If this is a
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If you are using high resolution T1w and T2w images with FreeSurfer, you might
just run the HCP Pipelines that depend upon such data and take care of all of
this. Alternatively, you can see how FreeSurfer is called by the HCP Pipelines:
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Hi all,
Thanks again for all the help so far with getting my data registered and
surfaces extracted. I have one further issue that I'm hoping to get help with.
I've used bbregister to align my T2 scan with the surfaces from my T1 scan.
However, the
Hi Jee Won and Priyanka,
I created a bit of a hack that I'd like y'all to test out. Go to
https://gate.nmr.mgh.harvard.edu/safelinks/greve/ (user guest, pwd
collab) and download dngtester and ventfix (you may need to chmod a+x
both of them). Run ventfix with --help to see how to run it. I've
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