There might be a couple things happening. First, I would try adding a
few control points in that area; make sure they are in true WM in voxels
that have a value less than 110 on the brain.mgz file. This might help
push the white surface further out (the WM in that gyrus is very thin).
It might
Can you check the registration of the FLAIR and T1?
cd subject/mri
tkregisterfv --mov orig/FLAIRraw.mgz --reg transforms/FLAIRraw.lta
--targ orig.mgz
On 5/20/2021 4:33 PM, Mark Wagshul wrote:
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Hi. I’m trying to run
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The command I used is in load_untouch_nii.png and the dimension shown in
this file is in the dimension.png. It seems that the dimension used matlab
command is 1*1*1*120.
Thank you
Mingyang Xia
On Thu, May 27, 2021 at 3:00 PM Douglas N. Greve
wrote:
You definitely do not want to use mni152.register.dat for this (I'm
surprised it even got close). Instead, register the orig.mgz to the
HCP842 template space, eg, with
mri_coreg --mov orig.mgz --targ HCP842.template.nii.gz --dof 12 --reg
reg.HCP842.lta
This will print out a tkregisterfv command
Try removing the trailing slash from the subject name, ie,
10100_S2654UFQ, not 10100_S2654UFQ/
On 5/26/2021 1:18 PM, Zeng, Victor (BIDMC - Keshavan - Psychiatry) wrote:
Hi all,
I am trying to extract LGI measures as prescribed in *MailScanner has
detected a possible fraud attempt from
you'll need to supply us with more information, eg, command lines and
why do you think it has the wrong dimensions
On 5/25/2021 11:53 PM, Mingyang Xia wrote:
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Dear freesurfer expert:
My name is Mingyang. I want to preprocess fmri image and map the
There is not one file for CSF or GM, but you can extract them from other
files. Eg,
mri_binarize --i aparc+aseg.mgz --ventricles --o ventricles.mgz
mri_binarize --i aparc+aseg.mgz --gm --o gm.mgz
You can use aparc+aseg.mgz as your brain mask
On 5/25/2021 6:14 PM, Camargo, Aldo wrote:
I see, it does look like they are in the cortex in 3D view. Although I tried to
keep them in white matter in 2D planes as possible. I will try deleting some.
Thank you,
Manorama
From: freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of Douglas N. Greve
Sent:
run it with -autorecon2 and -autorecon3
On 5/25/2021 1:47 PM, Camargo, Aldo wrote:
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Hi Bruce,
I was wondering if there is way to continue the process to recon-all
once I have done the recon-all with the option
If the tkregisterfv command works without the --surf option, then just
use that
On 5/18/2021 12:04 PM, Gabor Perlaki wrote:
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Dear all,
I tried to check the talairach transformation under Freesurfer 7 linux
version
No, not just volume. Example 5 has a surface example. If you want help
with your mri_segstats command, send the command and the terminal output
On 5/24/2021 2:29 PM, Jensen, Alexandria wrote:
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My apologies if I am missing something obvious, but isn't
On 5/24/2021 12:32 PM, Francisca Ferreira wrote:
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Dear Experts,
I am new to FS. I'm trying to run mri_glm fit
I've created FSGD with 2 classes -responders vs non-responders to a
given intervention- and 3 variables to be regressed out-according age,
No, not really
fov is field of view = voxelsize*number of voxels
frames are the number of frames in the file (ie, the 4th dimension)
dof = degrees of freedom we never use
xyz-start - edge of the volume
voxel to ras transform converts a column-row-slice into a
right-anterior-superior coordinate
Generally, control points are the way to go here. It looks like you have
put a bunch of them in cortex though
On 5/21/2021 12:14 PM, Kadwani, Manorama wrote:
Hi,
I am trying to correct the white matter segmentation in the second
image shown below. It doesn't include chunks of the temporal
If I understand you correctly, you have an ROI defined in the volume and
you want to transfer it to the surface. Is that right? First you should
look at the ROI in the volume along with the surfaces and make sure that
they pass through the ROI. I would generally use the projfrac-max option
for
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It seems that the dim in the header is -1 1 1 120. If I use Matlab command
load_untouch_nii to read the file, the header shows dimension is 1 1 1 120
and will get a 1×1×1×120 img
thank you
Mingyang
Douglas N. Greve 于 2021年5月27日周四 14:12写道：
> Are you
Some how the Yeo dimensions got flipped. Usually, this does not matter,
but in mri_glmfit it does. You can get around this by running
mri_convert lh.Yeo2011_17NetworksConfidence_N1000.mgz --reorder 2 1 3
lh.Yeo2011_17NetworksConfidence_N1000.reordered.mgz
and using the reordered in
You could also run recon-all on the mni152 template, then run the
hippo/amyg seg on the output. It will give you the same bad segmentation:)
On 5/20/2021 9:21 AM, Iglesias Gonzalez, Juan E. wrote:
Hi Jessica,
There’s no direct way of doing this, since the atlas lives it its own
space and
This is more of a question for the PALM developer (whom I have cc'ed).
On 5/19/2021 8:15 AM, Marina Fernández wrote:
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Dear experts,
I used the function fspalm to run permutations with the following options:
fspalm --glmdir /my_glmdir/ --cft 1.3 --name palm
The easiest thing to do is to create a new stats file that has the same
basic format as the aseg.stats but with your desired measures in them.
Then specify the new stats file with --stats=newstatsfile when you run
long_stats_slopes
On 5/19/2021 1:06 AM, AJ wrote:
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Just create a text file (not bfloat) where each row is a different time
point. You can have multiple columns and can specify how many of them to
use in the analysis.
On 5/18/2021 5:03 PM, Eli Bulger wrote:
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Hello,
I am working with task-based functional
Are you sure those are the dimensions? They do not look right. It should
be something more like ~12x1x1x120
Try running
mri_info --dim fmcpr.up.sm5.self.lh.nii.gz
On 5/18/2021 1:26 PM, Mingyang Xia wrote:
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Dear freesurfer expert:
I am sorry to
I'm not sure what is going wrong with it, but you can do this yourself with
mri_binarize --i aparc+aseg.mgz --match 7 --o bin7.mgz
Then do the same with 8, 46, 47
On 5/17/2021 6:39 PM, A.R. Sekar wrote:
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Hello
On 5/17/2021 10:16 AM, Ellen JOOS wrote:
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Dear Freesurfer team,
I am currently preparing my first fMRI study and used OptSeq2 for
creating the trial sequence. Since I am not experienced with the study
design in MRI (I mainly conducted EEG studies so far), I would
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Hi users,
We're having some issues with running some of our 2-3yo data (0.8mm isotropic)
through FS7 with and without the -hires flag.
There are persistent issues with the frontal lobe regions where the pial has
not extended to outer surface as
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Dear Experts,
Is it possible to use the SUITS labels (#601-628) in the LUT to make masks and
extract volume measures. I ultimately want to use the masks for tractography
purposes. Can I use the mri_extract to pull out the specific ROI's and if so do
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Dear Andrew,
Thank you for your reply. I shared with you the recon-all.cmd file via
Drive, since I could not upload it directly to the mail. I also copy here
(down) the last lines in this file.
I checked the resulting volumes and surfaces up to that
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