) as such: <<
echo “1 -1” > File_Name.mtx and have never had issues, however I have
not used "[ ] " on my contrasts before...
Thank you so so much for your willingness to help and your time!
On Wed, Nov 15, 2023 at 6:47 PM Douglas N. Greve
wrote:
Can you send
/data/
Internally, samseg uses partial volume to compute a more accurate
volume. They should still be very close though.
On 11/16/2023 6:46 AM, reza razmara wrote:
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Hi freesurfer team
I use samseg for lesion segmentation. In the result of .stats i see
the
I answered it yesterday. Check your inbox
On 11/16/2023 4:08 AM, Spapens, Jeltje (NP) wrote:
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Hello Freesurfer Developers,
I have never received an answer to my problem, maybe it was lost in
the e-mails.
Kind regards,
Jeltje Spapens
*From: *"Spapens,
You have to know the coordinate system of the matrix. See, eg, here
https://surfer.nmr.mgh.harvard.edu/fswiki/CoordinateSystems
Once you know the coordinate system, I would use lta_convert to generate
an appropriate file, eg,
lta_convert --inlta identity.nofile --src preop.mgz --trg postop.mgz
Can you run it with --debug as the first option and send the resulting
terminal output?
On 11/9/2023 12:54 PM, Mirsol Choi wrote:
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Hello Freesurfers,
I am trying to segment the hippocampus into its subfields and take the
FA values from each subfield
Caution
Hi Douglas,
Thank you for your reply.
Yes, find attached the fsgd file, the contrast is [1 1 1 -1 -1 -1 0 0
0 0]/3
As well as the code I am running and the whole output from the terminal.
Thank you so much for your help!
On Thu, Nov 9, 2023 at 6:35 AM Douglas N. Greve
wrote
You can map the curvature from fsaverage to the individual (or reverse)
and then load both on the surface to see if they agree. I think that CVS
will/can save intermediate registrations, so you might check those to
see if the problem is cropping up at a particular step.
On 11/9/2023 8:18 AM,
Several things
- don't use --init-fsl. If you don't specify, then it will use
mri_coreg, which will work better. You can also try --init-header
- your movable scan appears to be t2 weighted, so use --t2 instead of --t1
- look at the cost file (or send it). It is hard to say what the cost
Yes, that looks right (assuming that cortisol is your first variable)
On 11/7/2023 3:49 PM, Laura Willers de Souza wrote:
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Hello FreeSurfer Developers,
Following the FSGD examples on the website, I built the following test:
Question: Is there an
ANTs denoising is not used by default. Ants N4 is used to crfeate nu.mgz
On 11/6/2023 11:46 AM, Alexopoulos, Dimitrios wrote:
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To which anatomical volume is ANTs denoising applied to for generating
the orig surface?
We do ANTS denoising to the input T1
Can you send the command line, all the terminal output, and your fsgd file?
On 11/3/2023 11:51 AM, Ludmila Midrigan wrote:
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Hi dear FS experts,
I am having issues with ( I am assuming) the design matrix for my GM
analysis.
I am getting the error:
"error:
26q%3Dsubject%3A%2522Re%255C%253A%2B%255C%255BFreesurfer%255C%255D%2BMean%2BGyrification%2Bindex%2522%26o%3Dnewest>
Douglas N. Greve
<https://secure-web.
So you are trying to predict the neuropsych battery from brain
measurement? This is not how mri_glmfit is usually used, but it is just
a GLM so it is possible. You'd have to set up a table for the --table
input. You can try running asegstats2table to get an example table, then
you'd just set
On 10/30/2023 9:50 PM, Mirsol Choi wrote:
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Hi there,
I am currently going through the dt_recon tutorial on your website and
I just have a quick question regarding the recon-all and dt_recon
commands on freesurfer.
For me to process dt_recon, my
My experience is that it is extremely robust with respect to defacing
(and even skull stripping).
On 10/30/2023 12:02 PM, Iglesias Gonzalez, Juan E. wrote:
Dear Dawn,
Integrating the hippocampal subfields into SynthSeg in on the to-do
list, but it’s tricky due to differences in resolution.
There is not an easy way to do this yet. If you have your segmentations
in the conformed anatomical space, you can merge them with gtmseg.mgz
with something like
mri_vol2vol --interp nearest --mov yoursegs.mgz --targ gtmseg.mgz --o
yoursegs-in-gtmseg-space.mgz
mergeseg --src gtmseg.mgz --merge
This usually means that you edited a recon, then reran recon-all but
only partially leaving the surfaces out of sync.
On 10/25/2023 11:40 AM, Huang, Yujing wrote:
Hi Nicole,
The error message indicated the number of vertices or the number of
triangles don’t match in the two surface files it
fsxvfb is just a script that sets up an env for running Xvfb. I wrote
this script and got it working, but I'm not an expert on Xvfb, so you'll
have to figure it out yourself. You can try to running another program
that brings up an image (eg, fsxvfb glxgears) to make sure it is not a
freeview
I'm not sure what happened. Have you checked the surface-based
registration? Also check the talairach reg.
On 10/19/2023 11:35 AM, Antonín Škoch wrote:
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Dear experts,
I have encountered an failure of
mri_cvs_register --mov my_subject --mni
The resulting
Hi Corinna, the two files should give the same vol2vol output. Can you
send your command lines and pics of how they are different? The fscale
was only used by the old tkregister program to control the brightness.
doug
On 10/18/2023 1:44 PM, Corinna Bauer wrote:
External Email - Use
The UNI scan will likely fail for the talairach. One thing you can try
is -samseg-reg, which will compute the tal reg using samseg (which will
be much more robust). However, it wont surprise me to see it fail
somewhere else along the stream.
On 10/18/2023 8:57 AM, Hensenne, Eva (Stud. FHML)
I'm not sure what you mean. Can you elaborate?
On 10/17/2023 5:36 PM, Daniel Gutstein wrote:
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Is there a methodology in FreeSurfer for creating atrophy maps and
displaying them on individual coronal slices?
Thank you.
*Daniel Gutstein*
Research Data
See https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis
On 10/17/2023 11:55 AM, Alberto Del Cerro Leon wrote:
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Good morning, I would be interested in observing regional differences
in cortical thickness without using predefined regions.
This looks like an error inside of fmriprep to me. If you want our help,
please recreate the error using just the FS tools
On 10/11/2023 2:08 PM, Xingyu Liu wrote:
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Dear freesurfer experts,
I was trying to segment thalamic nuclei using
Not sure what is going wrong here. Try looking at the images and the
initial segmentation, eg,
freeview norm.mgz aseg.presurf.mgz
Does anything look off?
On 10/8/2023 11:05 AM, Massimo Valerio wrote:
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Il giorno dom 8 ott 2023 alle ore 16:58 Massimo Valerio
Do you just need to change the voxel size for that dimension? If so, you
can use mri_convert, something like
mri_convert -iis newvoxsize input.mgz output.mgz
where -iis means the change the voxel size of the first dimension. Use
-ijs or -iks for the 2nd and 3rd. You may have to play with it to
You are on the right track. First, you need a registration matrix. You
can get this with
bbregister --mov mtr.nii.gz --reg reg.lta --s subject --t2
The above command assumes that GM is brighter than WM in MTR. If this is
not the case, then use --t1
View your registration with
tkregisterfv --mov
have you looked here
https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/SkullStripFix_freeview
?
On 10/4/2023 4:20 PM, Carly McIntyre-Wood wrote:
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Hi there,
I have recently been looking at the aseg.mgz file in several of the
participants I have ran
That is correct for DOSS (note that you don't need to do the pos and neg
separately as you can handle that at the next stage; in the sig maps,
the pos will show up as red/yellow and neg will show up as blue). For
DODS you would need 0 0 0 0 0.5 0.5
On 10/4/2023 10:34 AM, Steve Petersen
:* freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of Douglas N. Greve
*Sent:* 24 September 2023 05:22:56
*To:* freesurfer@nmr.mgh.harvard.edu
*Subject:* Re: [Freesurfer] [FreeSurfer] regeneration of aseg.stats
from manually edited aseg.mgz
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Ideally, you
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I tried adding the –no-surfs (e.g. tkregisterfv --s PI163_noflair
--no-surfs),however receive the below error message:
ERROR: must spec a moveable volume
Many thanks,
Viki
*From: *freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of Douglas N. Greve
*Date: *Monday, July
You can also try editing the wm.mgz or filled.mgz to remove the defect.
See
https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/TopologicalDefect_freeview
On 10/3/2023 5:23 AM, Pål Gunnar Larsson wrote:
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OK.
Did make a new setup with 16Gb. Restarted.
You can use mri_segstats, eg,
mri_segstats --seg seg.mgz --sum summary.txt
If the seg.mgz has an embedded color table that lists all the
segmentatons, then the names will appear in the summary. If you have
such a color table you can pass it with --ctab
On 10/18/2023 10:34 AM, Iglesias
This is the kind of thing that happens with clusterwise corrections. It
is hard to predict what happens. When you raise the threshold, you lose
some of the activation in your real map (ie, clusters become smaller).
But in the Null map, clusters also become smaller. So, at the lower
threshold,
On 9/28/2023 4:13 PM, Lesage, Anne-Cecile wrote:
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Dear Freesurfer teams
I am working on sEEG data to help localize the epileptogenic zone at UTMB.
We were wondering with Dr Karas if we could use the *.inflated surface
to view better the electrodes in
If that is a volume label, then you will have to sample it on the
surface, eg, with mri_vol2surf. This will create a segmentation on the
surface (not a label). You can use vol2surf to map it all the way to
fsaverage, or you can map it on the native surface then use
mris_apply_reg or
By default, mri_glmfit will "prune" voxels. Ie, if it finds any subject
that is zero at a given voxel, then that voxel is set to zero in the
output and in the mask. I suggest you load up your data
(lh.cbf.fsaverage.proj0.5sm00.nii.gz) as an overlay in freeview and
scroll through the subjects
.
Thank you for any suggestions you can give me.
Il giorno mar 26 set 2023 alle ore 16:03 Douglas N. Greve
ha scritto:
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I'm not sure what problem you are describing. Can you elaborate?
On 9/25/2023 9:16 AM, Matteo Parodi wrote
That is a bug in mri_compute_volume_fractions. That seg (29) has not
been given a tissue type. Probably there are like 5 voxels in there with
that label. In the short term, you can just replace it with another
label, eg 2 for left white matter or 41 for right white matter. You can
do this with
Yes, we have depricated the TclTk stuff. You should not have gotten that
error when using tkregisterfv. Can you send the command line and full
terminal output?
On 9/19/2023 7:02 PM, Nadvar, Negin wrote:
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Good afternoon,
I’m trying to run “tkregister2”
yes, I think so too
On 9/19/2023 5:07 PM, gabriel robert wrote:
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Dear experts in longitudinal neuroimaging
We carefully read the papers about possible biases introduced by
treating timepoints images differently (Reuter and Fischl NI 2011, for
example) to
In general, I would recommend treating sex as a categorical rather than
continuous variable. To do this, you would have 6 groups (your 3 x 2
sex). I'm not sure what you are trying to test for. Eg, are you
interested in the difference between groups regressing out the effects
of age, DD, and
I doubt it. Have you tested it and found otherwise?
On 6/14/2023 3:23 PM, ruifen...@gmail.com wrote:
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Hi all,
I am running Freesurfer 7.3.2 on T1 images (LPI orientation) with
176*256*256 FOV, 1mm isotropic resolution.
I saw that the Ants N4 bias
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I'm not sure what problem you are describing. Can you elaborate?
On 9/25/2023 9:16 AM, Matteo Parodi wrote:
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Hello,
I'm trying to perform a pet ROI analysis on an image recon from a T1.
I have to perform the
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Ideally, you should have edited the aseg.presurf.mgz, then rerun
recon-all starting just after the aseg. That said, if you edited the
aseg.mgz and then re-ran that mri_segstats command, the stats should
have changed.
On 9/15/2023 4:05 AM, Krystal
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Yes, that is all correct. There is a tutorial on the wiki. You can use
multiple covariates. See
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what problem? There is nothing else in your email and I don't have the
previous threads.
On 9/12/2023 10:51 AM, Glass, John wrote:
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Hello,
I am running into the exact same problem at my local site running
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Have you tried doing the tutorial? I think all these questions will be
answered there.
On 9/11/2023 7:33 AM, Le Prieult, Yéléna wrote:
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Good afternoon,
I have some questions about the analysis of the structural
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I just tried to run mideface on a CT scan, and it failed; probably just
needs some parameter adjustments. If you have an MRI scan for that same
person, you can run mideface on that, then apply it to the CT scan. See
the mideface wiki page.
On
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I'm not sure what you are asking for. The freeview command allows you to
view volumes in 3D
On 9/6/2023 12:50 PM, Pukovisa Prawiroharjo wrote:
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anyone have suggestion data visualization from freesurfer
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No, unfortunately not. You can easily convert back to native space with
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It looks like there is a huge defect which you will probably have to
fix by hand if you want to use this case. See
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Have you looked at this page
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What command are you using to generate the surfaces? I don't think this
is done by default in recon-all
On 9/3/2023 1:22 PM, Srishyla, Diksha wrote:
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Hello FreeSurfer Developers,
I am attempting to produce
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Try mkheadsurf
On 9/1/2023 6:46 AM, Giulio Siracusano wrote:
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Dear Experts,
I'm trying to understand what is the best approach
to reconstruct the face of the patient from the MRI scan.
I'm well aware that with
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Which annot files are you comparing? Some of them (eg, aparc) have an
extra procedure where the labels boundaries are fine-tuned, so that
could cause the difference. Your command looks right.
On 8/30/2023 1:28 PM, Leonardo Cardoso Saraiva wrote:
oc(675792816): could not allocate xforms
I tried renaming the run4to1 registration file to run4to1.xfm and
nothing changes (no error but the registration still does not seem to
be applied).
Any idea what's going on?
Thanks a lot for your help and
Good evening!
Sebastien
Douglas N. Greve Mon, 28 Aug
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You can try
mri_binarize --i aseg.mgz --csf --o csf.mgz
to get a binary map
Note that the aseg does not have sulcal CSF labeled. But you can get
that with something like
samseg --i orig.mgz --o samseg
Then run mri_binarize on the seg.mgz file
On
External Email - Use Caution
Sorry, I don't have your previous email so I don't know what the context
is. Can you resend this email with the previous exchanges included at
the bottom? Also, please remember to send to the FS list instead of us
personally.
thanks!
doug
On
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It looks like you are transforming it to fsaverage space before
computing the statistics. If this is correct, then that will explain the
differences as that transform will involve some interpolation which will
change the values. But they should be
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You can also use mri_binarize, like
mri_binarize --dilate-vertex vno lh.white radius out.mgz
where radius is the radius in mm. This will start with your seed vertex,
then keep adding vertices in a ring until the desired area (pi*r^2) is hit
On
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You can try something like
mri_volsynth --dim 1 1 1 1 --vox-size size size size --p0 x y z --pdf
const --o voxel.mgz
where size is the size of the MRS voxel
x y z are the center of the voxel in scanner space
Load voxel.mgz onto the anatomical to make
. So will the following command work?
mri_convert t2.nii.gz --flair 002.mgz
or is it:
mri_convert --flair t2.nii,gz 002.mgz
Thanks,
Alan
On Sun, Aug 20, 2023 at 4:17 PM Douglas N. Greve
wrote:
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How did you set up the T2? Did you set 001.mgz
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SVM is a segmentation/classification algorithm and does not give the
inference that the GLM gives. Not sure what other models you are talking
about
On 8/21/2023 9:28 AM, 林 耀云 wrote:
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Hi Freesurfer Team,
I have
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There is no way to do this. All the fsfast commands are going to expect
things to be in the fsfast directory structure.
On 8/11/2023 12:19 PM, Noah Lee wrote:
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Hello!
I am trying to run some freesurfer commands
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mri_glmfit-sim outputs several files that may be helpful. If you run it
with --help, you will get more info, but is this the final file you want?
csdbase.y.ocn.dat - this is a summary of the input (y) over each
cluster. It has a column for each
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yea, this can be a big bookkeeping headache. I would suggest just
modeling the missed trials as an event in the par file. If some subjects
don't have a missed trial, then just take one of the unmissed ones and
call it missed. Not perfect, but it
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Can you try the 7.4.1 version? Can you also send your full command line
and terminal output?
On 8/20/2023 2:57 PM, Jacobs, Heidi I.,PHD wrote:
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Hello FreeSurfer team,
I am trying to run the sclimbic tool on our
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Do the two align in freeview if you just load both of them? If so, then
you can use something like
mri_vol2vol --mov vol1.mgz --targ vol2.mgz --regheader --no-resample --o
new.vol1.mgz
If they do not but you have a registration, then you can use a
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when you convert to fsaverage space, there is some interpolation that
will cause the two to be not exactly the same. They should be very close
though
On 8/17/2023 11:27 AM, 1500787798 wrote:
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Dear FreeSurfer
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Do any of these examples
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On 8/14/2023 12:38 PM, Qian Chu wrote:
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Correction: tal_mat is 3x4. Sorry for the typo.
*From:* freesurfer-boun...@nmr.mgh.harvard.edu
on
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where did the functional data come from? Are you trying to map the time
courses? That usually does not work that well as your resulting image
will be huge. One thing to do is to map it to a cropped volume (most of
the 256^3 is outside the brain) and
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How did you set up the T2? Did you set 001.mgz to be the T1 and the
002.mgz to be the T2FLAIR? If so, that will not work. You should pass
the FLAIR with the --flair flag. recon-all will register them together.
Or do you just want to register them
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On 8/9/2023 5:03 AM, inbal paran wrote:
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Dear FreeSurfer developers,
Thank you for your response to my previous questions, I have a few
more (I'm inexperienced with both Freesurfer and Linux):
1. Can I
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you can use mri_surf2vol
also you can try mris_skeletonize to label the fundi
run both with --help to get more info
On 8/8/2023 11:34 AM, Bluye Demessie wrote:
> External Email - Use Caution
>
> Dear FreeSurfers,
>
> I am hoping to do an
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It is going to list the cluster=0 value as the first value. cluster=0
are all the voxels not in a cluster. If you want to exclude this, just
add --excludeid 0
On 8/10/2023 7:58 PM, Lara Foland-Ross wrote:
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Hi
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Hmm, it does not look like that option was ever added (ie, that wiki
page is incorrect).
On 8/6/2023 8:13 AM, Woo-Suk Tae wrote:
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Dear Freesurfer developer.
According to the explanation in the *MailScanner has
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It is worse -- we do not support qdec anymore
On 8/5/2023 6:04 AM, inbal paran wrote:
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Hello FreeSurfer Developers, I have a question regarding group
analysis: When I followed the instructions on how to build my
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You'll have to do it by hand or maybe in matlab; you can use
fast_ldtable.m to load in the tables in matlab
On 8/5/2023 4:54 AM, inbal paran wrote:
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Hello FreeSurfer Developers, I need to compute the volume of
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we are not supporting tkmedit anymore (and have not for a long time).
Have you tried using freeview (or tkmeditfv which is a frontend for
freeview that takes tkmedit-like options). FV is not available in 5.3,
but you can still use it on 5.3 data.
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Can you send the full terminal output?
On 8/4/2023 1:20 PM, Sun, Wendy wrote:
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Good afternoon,
We are encountering an issue with getting non-integer values (input
file has all integers) when using the “nearest”
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it still generates accurate thresholds
On 8/1/2023 4:07 PM, Finn, Quentin wrote:
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Freesurfer experts,
I have a surface overlay that represents -log_10(p) for a statistical
test that I ran using tools other than
uwCMgEVszYME1u78YwHQVyqxKs3LXVSrZZth3cHJ7tNqycV-NWxDwXSMAT75oTv4Q/https%3A%2F%2Ftranslationalpsychiatry.de%2Falexandra-korda%2F>
------------
*From:* freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of Douglas N. Greve
*Sent:* 20 July 2023 22:53:23
*To:* freesurfer@nmr.mgh.harv
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The argument to -tp should be the cross subject (run earlier with
recon-all), not the input volume
On 8/1/2023 4:58 AM, Bernis SÜTÇÜBAŞI wrote:
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Hello FreeSurfer experts,
I'm attempting to follow the
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That should be enough RAM. What is your command line? Can you send the
log file?
On 8/1/2023 7:52 AM, MANSSOUR Wassima wrote:
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Hello FreeSurfer Developers,
I'm conducting the *Surface Based Group Analysis*
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does 004/mri/wm.mgz exist?
On 7/31/2023 6:40 PM, Rachel Wagner wrote:
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Hello,
I am looking to cortically project onto a pial surface and am trying
to use the following code in the freeview GUI to do so:
/lh.white
file is created and therefore an error is produced that this file
can’t be found. Seems like with tkregisterfv the default is for it to
require the lh.white file?
Many thanks,
Viki
*From: *freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of Douglas N. Greve
*Date: *Friday, July 21
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there is not an easy way to do it, but there is a way
1. convert the annot to labels using mri_annotation2label
2. for each label, run mri_label2label with the --erode option to create
a new set of labels (different folder)
3. use mris_label2annot to
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there are not options to autorecon1 specifically. You can pass some
watershed args on the command line, but it is probably easier to use an
expert options file, eg, create a text file (eg, xopts.txt) with
something like
mri_watershed -less
then run
ttps%3A%2F%2Ftranslationalpsychiatry.de%2Falexandra-korda%2F>
*From:* freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of Douglas N. Greve
*Sent:* 20 July 2023 22:53:23
*To:* freesurfer@nmr.mgh.harvard.edu
*Subject:* Re:
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tkregister2 is pretty old at this point; try using tkregsiterfv with the
same option.
On 7/20/2023 7:06 PM, Viktorija Pratuseviciute wrote:
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Hello,
We are trying to process a scan with a failed talairach. We
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I'm not sure I understand what you are asking for. Do you want to
compute the distance from a given point in the volume to the closest
point on cortex?
On 7/20/2023 7:09 AM, alexandra.ko...@uksh.de wrote:
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I'm not sure what you mean, like some kind of service where you upload
your image and it returns a freesurfer analysis? Not that I know of
On 7/19/2023 1:09 AM, Gonzalo Rojas Costa wrote:
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Hi:
Is there a
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I don't know what you mean. can you elaborate?
On 7/18/2023 11:51 AM, Magang Visa wrote:
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can we use freeview for comparing 2 MRI in a overlaying 3D model in
one windows ?
best regards
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Can you load the wmparc along with the surface in freeview? Also send
the recon-all.log file. Is it possible that you ran recon-all several
times on this subject? Eg, the surfaces might not have been good in that
chunk, so you fixed them and reran,
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yes
On 7/14/2023 4:15 PM, Carlos Alcocer wrote:
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Thank you for your response. If I wanted to calculate the surface area
of this cortical ROI, would i pass lh.area.pial into ? Do i still
use --accumulate flag?
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YOu can cite
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On 7/10/2023 10:00 AM, Maria Czarnecka wrote:
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Dear Sisters and Brothers in neuroscience,
I have a problem with conjunction analysis. I do my analysis using:
/mri_concat --i con1/sig.nii.gz --i con2/sig.nii.gz
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First of all, you are not going to get the same answer from these
different programs. For ento, recon-all will zero the thickness in some
areas around ento, and clinical is probably not doing that. Still a
factor of 4 seems pretty large. Maybe
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