Hi Maedeh
there are a bunch of steps involved in the topology correction that you
will need to run (e.g. surface inflation, quasi-homeomorphic spherical
mapping, etc...). If you can synthesize a T1-ish image you can just run it
through recon-all and it should do the right thing. Otherwise you
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We run on our freesurfer through singularity/docker container, and we are
currently using Centos7 as the base image to build our freesurfer
container, but we can run it on any other Linux based OSes. As far as our
hardware goes, we run on variety of har
Hi freesurfers,
I am currently using freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 and I
need to run $mri_vol2label which I have been informed works with fs v6.0. Is
there any way I can use this command or a is there a similar command on v5.3?
Thanks in advance,
Zeynab Alshelh, PhD
the name of the program in 5.3 is mri_cor2label
On 8/5/2019 11:41 AM, Alshelh, Zeynab wrote:
Hi freesurfers,
I am currently using freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 and I
need to run $mri_vol2label which I have been informed works with fs v6.0. Is
there any way I can use this com
can you give more info on the error? Eg, command line, terminal output, log file
On 7/31/2019 6:55 PM, Gregory Mierzwinski wrote:
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Hello,
Even though this is an old post, the entire solution to this has not been
posted and I couldn’t find it anywhere.
I hit
Can you upload the input (ie, argument to --y) here:
ftp://surfer.nmr.mgh.harvard.edu/transfer/incoming
Also, send your mri_glmfit command line.
On 8/2/2019 9:41 AM, Reza Rahmanzadeh wrote:
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yes, I have the page below for all patients.
I think it means all
?Hi all,
For the sake of time, for one dataset we have that we want to extract
hippocampal/amygdala/thalamus subfields from, we ran it without manually
editing any portions of the brain. We're going to visually QC it, but do you
anticipate any trouble with the accuracy of the segmentation cons
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Is there a way to extract the gray matter intensity value at each vertex of a
surface file (lh/rh.curv/pial/etc)?
Notice: This UI Health Care e-mail (including attachments) is covered by the
Electronic Communication
There is no set value for surface or volume. Typically we apply 5-10mm.
Surface-based smoothing is more gentle than volume-based, so you can apply
larger kernels.
On 8/5/2019 2:59 AM, Matthieu VANHOUTTE wrote:
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Hi Douglas,
I was talking about the FWHM smoot
Use mri_vol2surf, something like
mri_vol2surf --mov norm.mgz --hemi lh --projfrac 0.5 --regheader subject --o
lh.norm.mgz
On 8/5/2019 11:57 AM, Axelson, Eric D wrote:
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Is there a way to extract the gray matter intensity value at each vertex of a
surface file
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Hi,
I am beginner for FreeSurfer... I want to run recon-all on my MRI T1 data.
I have a series of dcm files for an individual and these dcm files are
archived in a tgz file. What should I import to FreeSurfer for recon-all? A
single dcm file, or some s
You should untar your tar file so that the individual dicoms are available.
You will see many (more than 150) dicom files.
If you know for sure that there is only a single T1 volume in the group, you
can just run
recon-all -s yoursubjectname -all -i path/to/dicom/one_dicom_file
where one_dicom
That mostly looks good.
I would suggest is to change your smoothing command to something like
mris_fwhm --smooth-only --s fsaverage --hemi lh --fwhm 5 --cortex --prune --i
allgrp1.rlhmgxctx.fsaverage.sm00.nii.gz allgrp1.lhmgxctx.fsaverage.sm05.nii.gz
The only difference will be that any vertices
you will need to extract them from the archive into a directory, then
give recon-all a *single* dicom file from each T1-weighted series that you
want to motion correct and average (if you only hae one, then just specify
one). Something like:
recon-all -i -sd \
-s -all
cheers
Bruce
On
Hi experts
I appreciate if you could help me with this question.
Thanks
Zahra (Mona) Nasiriavanaki
Postdoctoral Research Fellow
Martinos Center for Biomedical Imaging
Massachusetts General Hospital
149 13th Street, 149-2615
Charlestown, MA, USA, 02129
what is your registration command?
On 8/2/2019 12:17 PM, Nasiriavanaki, Zahra wrote:
Dear Freesurfers
Hi
I have a subject that the registration is not done correctly in two runs (run
12 and run 15) .
The tkregister-sess values for this subject is shown below.
Subject 1 10 0.2628
Subject 1
Hi Soichi, you can update mri_deface with:
curl
https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/dev_binaries/centos7_x86_64/mri_deface
-o $FREESURFER_HOME/bin/mri_deface
chmod +x $FREESURFER_HOME/bin/mri_deface
Then, before running mri_deface, set the env variable:
export FS_HISTO_STD_T
Thanks for your reply.
preproc-sess -s $subj -per-run -nostc -fwhm 0 -surface fsaverage lhrh -fsd bold
-init-header -d .
Zahra (Mona) Nasiriavanaki
Postdoctoral Research Fellow
Martinos Center for Biomedical Imaging
Massachusetts General Hospital
149 13th Street, 149-2615
Charlestown, MA,
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Dear Lilla,
Thanks for your help.
I have used the same command in the recon-all.log file (seen bellow), but I
have a doubt for the highlighted part in the command:
"mri_aparc2aseg --s SBJ1 --volmask --aseg aseg.presurf.hypos --relabel
mri/norm.mgz
Can you send a pointer to the data so I can have a look? Include the folder
were you run tkregister-sess from as well as the $SUBJECTS_DIR
On 8/5/2019 1:33 PM, Nasiriavanaki, Zahra wrote:
Thanks for your reply.
preproc-sess -s $subj -per-run -nostc -fwhm 0 -surface fsaverage lhrh -fsd bold
-i
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Hi Doug, I just wanted to follow up on this last message I sent. What do you
suggest that we do about the spots where the white surface "leaks" in the gray
surface?
--
Brian Biekman
Graduate Student, University of Houston
Clinical Psychology, Neuropsy
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I am also using pediatric brains and am also interesting in using your defacing
algorithm. I downloaded your updated script and changed the environment
variable but it leaves a lot of the jaw and chin. Is this something that can be
fixed by changing
In general, this would be handled by manual editing, but we are
looking into whether a parameter adjustment can be used instead. The
problem is that adjustments often result in underlabeling in other places.
On 8/5/2019 1:53 PM, Brian Biekman wrote:
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>
>
no, the env variable won't change that. You can try changing the radius
with:
-radius
where n=7 by default. Smaller will make it more aggressive.
cheers
Bruce
On Mon, 5 Aug
2019, Brian Biekman wrote:
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>
> I am also using pediatric brains and am also inter
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Got it, thank you for your help, Doug!
--
Brian Biekman
Graduate Student, University of Houston
Clinical Psychology, Neuropsychology Concentration
Laboratory of Early Experience and Development (LEED)
bdbiek...@uh.edu
brian.biek...@times.uh.edu
___
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Hello Doug,
Thanks very much for your help. Your assumption was right in that i want to
run a group comparison (i.e. test for a difference in amyloid-thickness
slopes between the two groups). However, I am having a hard time creating
the correct mri_gl
Yes, that contrast is correct.
On 8/5/2019 3:11 PM, miracle ozzoude wrote:
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Hello Doug,
Thanks very much for your help. Your assumption was right in that i want to run
a group comparison (i.e. test for a difference in amyloid-thickness slopes
between the tw
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Thanks Doug. How about the mri_glmfit commands? Since the contrasts are
correct, I think the commands should be right. Best, Paul. Sent from my Samsung
Galaxy smartphone.
Original message From: "Greve, Douglas N.,Ph.D."
Date: 2019-0
It still looks like you are using a group specific input (--y). The input
should be a simple file with both groups (same input as you would use without
pvr)
On 8/5/2019 4:39 PM, miracooloz wrote:
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Thanks Doug. How about the mri_glmfit commands? Since the con
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I think i got it now. Something like this:
## group1 comes first in my fsgd file. removing the effects of age and
education
##amyloid-thickness. first pet pvr = 1 for group1 and 0 for group 2.
mri_glmfit --y lh.thickness.15.mgh --fsgd project.fsgd dods
I think there is still something not right. You should just have one mri_glmfit
command for each hemisphere in which the input is ?h.thickness.15.mgh, the
fsgdfile is project.fsgd, you then specify the pvrs for both groups (--pvr
?h.pvr_grp1_pet.nii.gz --pvr ?h.pvr_grp2_pet.niigz) and then use t
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