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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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Hello,
'timepoints' refers to the individual scan sessions that make up a longitudinal
dataset for a subject.
i.e. If a subject was scanned 3 times, say in 2010, 2015, and 2020, this
subject would have 3 timepoints. One from each year they were
Not sure. I think those distortions are the surface folding back in on
itself, so you may need more cuts.
On 5/25/2022 9:26 AM, Alberto Pisoni wrote:
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Hi all, I am trying to flatten a whole hemisphere, and i created the
cut patch following the tutorials.
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Thank you for the answer.
So the averaged MRI has the size of the mni305.
Is there a way to give it its true size?
This can be problematic for children's MRIs.
> Le 2 mai 2022 à 21:33, Douglas N. Greve a écrit :
>
> It will remain in talairach space
It will remain in talairach space ( actually mni305)
On 5/2/2022 1:08 PM, Sébastien Daligault wrote:
> External Email - Use Caution
>
> Hi support,
> I have a naive question about the make_average_subject function.
> I want to average MRIs to create a template.
> This process uses the
Just give freeview the path to whatever volume or surface you want to visualize
Cheers
Bruce
From: freesurfer-boun...@nmr.mgh.harvard.edu
On Behalf Of Jabeur Mouna
Sent: Wednesday, April 27, 2022 5:45 AM
To: Freesurfer support list
Subject: [Freesurfer] (no subject)
External Email -
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Hello,
Can you please clarify the following:
Do we use subcortical QC rating for all subcortical measures such as
accumbens as well measures such as total white matter volume. We do not use
it for estimated total intracranial volume as this is
No, it should not
On 6/22/2021 4:12 PM, miracle ozzoude wrote:
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Hello All,
I was wondering if the Right/Left-Cerebral-White-Matter in the
aparc+aseg.mgz contains WM hypointensities.
mri_segstats --seg aparc+aseg.mgz -i dti_fa.nii.gz --sum dti_fa.stats
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Hi Doug,
I ran
mri_glmfit \--table aseg.txt \--fsgd newCH_deblank3.fsgd dods \--C
groupdiff.mtx \--glmdir aseg.glmdir
this created a folder aseg.glmdir which contains another folder groupdiff,
where sig.ghm is,
I then tried to visualise results
How did you create the sig.mgh that you are trying to overlay?
On 5/28/2021 11:16 AM, Francisca Ferreira wrote:
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Dear Experts,
I have extracted subcortical vols corrected for intracranial vols
using asegstats2table and I ran mri_glmfit using the
No, you'll have to add it as a covariate. Or you can add --etiv when you run
mris_preproc and it will divide the maps by the eTIV
On 11/25/2020 3:23 PM, Sara Lyn wrote:
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Hi Freesurfer experts,
I'm doing a surface based volume analysis and wanted to know if
Try this instead
aparcstats2table --hemi lh --subjects subj10 --parc aparc.a2009s
--meas meancurv --tablefile /home/team33/ aparcstats.txt
On 11/3/2020 12:20 PM, saman fouladi wrote:
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hi
I run in linux command:
Hi Saman,
It looks like with the --subjects flag you are pointing Freesurfer to the stats
directory within a subject directory (where Freesurfer expects the subject
directory). aparcstats2table and asegstats2table assume a standard Freesurfer
directory configuration so try entering just the
Sorry, that is not a question for us but rather for your local sys admin
From: freesurfer-boun...@nmr.mgh.harvard.edu
On Behalf Of saman fouladi
Sent: Friday, October 23, 2020 6:52 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] (no subject)
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hi
Can you run recon-all again with -debug as the first argument? Send me
the command line and all the terminal output
On 7/9/2020 2:10 PM, Peka Savayan wrote:
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The file that I sent you is the recon-all.log file.
If copying file 'RB_all_2008-03-26.gca' from
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The file that I sent you is the recon-all.log file.
If copying file 'RB_all_2008-03-26.gca' from another FS version to
directory /freesurfer-7.1.0/average
will solve my problem?
On Thu, Jul 9, 2020 at 12:30 PM Douglas N. Greve
wrote:
> Can
Can you send the recon-all.log file?
On 7/9/2020 1:25 PM, Peka Savayan wrote:
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I can open it. Can you? No permission required to my knowledge.
On Thu, Jul 9, 2020 at 11:53 AM Douglas N. Greve
mailto:dgr...@mgh.harvard.edu>> wrote:
Do you have read
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I can open it. Can you? No permission required to my knowledge.
On Thu, Jul 9, 2020 at 11:53 AM Douglas N. Greve
wrote:
> Do you have read permission to it?
>
> On 7/8/2020 2:25 PM, Peka Savayan wrote:
>
> External Email - Use Caution
> Yes.
Do you have read permission to it?
On 7/8/2020 2:25 PM, Peka Savayan wrote:
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Yes.
On Wed, Jul 8, 2020 at 10:01 AM Douglas N. Greve
mailto:dgr...@mgh.harvard.edu>> wrote:
Does that file exist?
On 7/7/2020 8:59 AM, Peka Savayan wrote:
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Yes.
On Wed, Jul 8, 2020 at 10:01 AM Douglas N. Greve
wrote:
> Does that file exist?
>
> On 7/7/2020 8:59 AM, Peka Savayan wrote:
>
> External Email - Use Caution
> Dear experts,
>
> I try to run recon-all using FS 7.1.0 on a cluster with OS
Does that file exist?
On 7/7/2020 8:59 AM, Peka Savayan wrote:
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Dear experts,
I try to run recon-all using FS 7.1.0 on a cluster with OS CentOS6.
I got the recon-all.log error message:
ERROR: cannot find
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Thanks Bruce.
On 13/05/2020 15:41, Bruce Fischl wrote:
Hi Ian
we don't register to an individual subject - we register to a
probabilistic atlas compiled from many subjects. The fsaverage
subjects were also generated from that data so they are in
Hi Ian
we don't register to an individual subject - we register to a
probabilistic atlas compiled from many subjects. The fsaverage subjects
were also generated from that data so they are in register, but the actual
atlas is a .tif file that you can find as the target of mris_register in
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is there a way to visualize the changes in thickness, area, and volume between
the 2 timepoints (cortical and subcortical)? I was under the impression that
running mri_preproc would aloow me to visualize change in cortical thickness bt
the 2
For thickness, you can look at the difference (or percent difference).
You would use freeview (or tksurferfv, which is a frontend for
freeview). When you run mris_preproc, you can specify that you want it
to compute the (percent) difference, or you can do it with the
multi-frame output of
Oh, right. You only have one data point (the difference) and you are
computing one parameter (the mean), so you have 0 DOF. If you only have
one data point, there are not statistical tests you can do
On 5/1/2020 3:34 AM, KennethSPrice wrote:
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In the FSGD
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In the FSGD file I have one subject pair (timepoint 1 and timepoint 2), and it
is the only group. However, I removed --fsgd and replaced it with --osgm upon
your reccomendation, and am still getting the error.
I am also having an issue visualizing
how many subjects are there in your fsgd? How many groups in your fsgd
file? Also, you should not use --osgm and --fsgd
On 4/30/2020 1:09 PM, KennethSPrice wrote:
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Hello Freesurfer friends!
I'm going through the "paired analysis" tutorial and am running
eve the minimal compiled
> distribution is less than 2GB.
>
> Andrew
>
>
>
> *From: * on behalf of Ерохин
> Александр
> *Reply-To: *Ерохин Александр , FS Help <
> freesurfer@nmr.mgh.harvard.edu>
> *Date: *Wednesday, April 22, 2020 at 12:35 PM
> *To: *FS He
I don’t have an exact number, but I believe the minimal compiled distribution
is less than 2GB.
Andrew
From: on behalf of Ерохин Александр
Reply-To: Ерохин Александр , FS Help
Date: Wednesday, April 22, 2020 at 12:35 PM
To: FS Help
Subject: Re: [Freesurfer] (no subject)
External
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Hi Andrew,
Alright, many thanks for the hint! I started experimenting myself with file
exclusion, but is seems I've excluded too much and recon-all is not able to
complete successfully anymore.
Regarding this MINIMAL flag option — could you
Hi Aleksandr,
Yes, this is an unfortunate limitation, but we are working towards making
freesurfer more modular in the future. There’s no single straightforward
solution to cutting down the distribution, but you do have a couple of options.
The BIDS group has created a minimal FS6 docker
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Thank you so much. I shall modify my other scripts then.
Peng
On Mon, 6 Apr 2020 at 16:59, Ruopeng Wang
wrote:
> I don’t think look up table works with negative indices. It was mainly
> designed for label volumes.
>
> Ruopeng
>
> On Apr 6, 2020,
I don’t think look up table works with negative indices. It was mainly designed
for label volumes.
Ruopeng
> On Apr 6, 2020, at 10:35 AM, Peng Liu wrote:
>
> External Email - Use Caution
>
>
> Hi Ruopeng,
>
> Thank you for your reply.
>
> I have also tried NIH and JET,
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Hi Ruopeng,
Thank you for your reply.
I have also tried NIH and JET, but with negative scale, the entire image
will turn into one same color as if there is some error.
Meanwhile the reason of me trying to create .lut map is because I want five
Hi Peng,
Your lookup table only contains indices between 0 to 6. In any case I would not
use look up table to display negative scales. Have you tried any other color
maps like JET or NIH which has more colors?
Best,
Ruopeng
> On Apr 6, 2020, at 6:30 AM, Peng Liu wrote:
>
> External
: [Freesurfer] within-subject contrast between runs
On 3/6/2020 11:15 AM, Milde, Christopher wrote:
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Dear Freesurfer Experts,
I have a very basic questions about creating subject-wise contrasts
between runs
*
*
*Background*
Study with two runs per subject where
wishes
Chris
Von: freesurfer-boun...@nmr.mgh.harvard.edu
im Auftrag von Douglas N. Greve
Gesendet: Freitag, 6. März 2020 17:54:16
An: freesurfer@nmr.mgh.harvard.edu
Betreff: Re: [Freesurfer] within-subject contrast between runs
On 3/6/2020 11:15 AM, Milde
On 3/6/2020 11:15 AM, Milde, Christopher wrote:
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Dear Freesurfer Experts,
I have a very basic questions about creating subject-wise contrasts
between runs
*
*
*Background*
Study with two runs per subject where each run corresponds two a
different
It is is really bright there, try putting a few control points in WM
(make sure they are in WM)
On 3/3/20 12:30 PM, Laboratorio de Neurociencia Funcional wrote:
>
> External Email - Use Caution
>
> Dear Freesurfeer experts,
> After running the recon-all in one of my subjets, part of the
I'm guessing that the fragments might cause problems later either in gtmseg as
a hard failure or in gtmpvc as an ill-conditioned matrix. But you can try it
out:)
On 1/11/2020 6:04 PM, Boris Rauchmann wrote:
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Thanks, that solution seems to work finally. I
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That's it! Thank you Doug!
Best wishes,
Marina.
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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Thanks, that solution seems to work finally. I just ignored the remaining
voxels labeled according to the standard aseg scheme and proceeded with the the
PET analysis and the combined LUT.
I will ignore the remaining fragment labels from the original
On 1/8/2020 10:17 AM, Boris Rauchmann wrote:
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Ok. i figured it out. The problem was just that you can not specify the file
type - so .mgz in BN_Atlas_subcotex.mgz was actually the problem.
Ah, ok. This is actually fixed in our development version.
Now I
when you make the average subject, just use --ico 5
On 1/9/2020 11:15 AM, Marina Fernández wrote:
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Dear Freesurfer experts,
Now, I would like to downsample the average subject of a dataset (that is a 7th
order icosahedron tesselation) to have surfaces with
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Ok. i figured it out. The problem was just that you can not specify the
file type - so .mgz in BN_Atlas_subcotex.mgz was actually the problem.
Now I run in a new issue:
gtmseg --head BN_apas+head.mgz --s 1122_test --o NEU_BN.gtmseg.mgz
--ctx-annot
Are you sure you have permission to view that file?
On 1/6/20 5:01 PM, Boris Rauchmann wrote:
> External Email - Use Caution
>
> I’m sure just double checked it. I don’t know what’s wrong here.
>
> Von meinem iPhone gesendet
>
>>> Am 06.01.2020 um 18:35 schrieb Greve, Douglas N.,Ph.D.
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I’m sure just double checked it. I don’t know what’s wrong here.
Von meinem iPhone gesendet
>> Am 06.01.2020 um 18:35 schrieb Greve, Douglas N.,Ph.D.
>> :
> This is not making any sense to me. Are you sure you are in
> $SUBJECTS_DIR/1122/mri when
This is not making any sense to me. Are you sure you are in
$SUBJECTS_DIR/1122/mri when you run mri_aparc2aseg and are you sure that
BN_Atlas_subcotex.mgz is in the same folder?
On 1/3/20 3:07 PM, Boris Rauchmann wrote:
>
> External Email - Use Caution
>
> Thank you for testing it. As
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Thank you for testing it. As before I get the same error message.
Do you know what I´m doing wrong here?
Best,
Boris
MacBook-Pro:mri boris$ mri_aparc2aseg --s 1122 --volmask --aseg
BN_Atlas_subcotex.mgz --o aparc+BN_Atlas_subcotex.mgz
SUBJECTS_DIR
OK, using the data you sent I was able to get mri_aparc2aseg to run. Can you
try this command again?
On 12/12/2019 11:57 AM, Boris Rauchmann wrote:
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My-Computer:~ boris$ mri_aparc2aseg --s 1122 --volmask --aseg
BN_Atlas_subcotex.mgz --o
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Dear Douglas,
I uploaded two files: 1122.tar.gz is the sample subject and
BN_Atlas_freesurfer.tar.gz this is the Atlas I want use for the cortical and
subcortical parcellation/segmentation.
Thank you so much,
Boris
> Am 02.01.2020 um 17:06
Can you send me the subject data following these steps?
From the linux command line,
Create the file you want to upload, eg,
cd $SUBJECTS_DIR
tar cvfz subject.tar.gz ./subject
Now log into our anonymous FTP site:
ftp surfer.nmr.mgh.harvard.edu
It will ask you for a user name: use "anonymous" (no
OK, I'm still at a loss. The one suspicious thing is that it only took a few
min to run. So you have never looked at that volume? What is in the atlas?
On 12/16/2019 3:42 PM, Boris Rauchmann wrote:
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This is the log when I´m creating this file:
sorry, my fault. That was for someone else
On Mon, 16 Dec 2019, Boris
Rauchmann wrote:
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This is the log when I´m creating this file:
Boriss-MacBook-Pro:BN_Atlas_freesurfer boris$ mri_ca_label
$SUBJECTS_DIR/1122/mri/brain.mgz
to summarize, I want a warp that:
foreach subject
compute warp based on curvature
apply warp to a functional overlay
add that functional overlay to avg
return (tf.reduce_mean(tf.square(avg)))
make sense? So maximizing the mean squared average acivation
On Mon, 16 Dec 2019, Boris
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This is the log when I´m creating this file:
Boriss-MacBook-Pro:BN_Atlas_freesurfer boris$ mri_ca_label
$SUBJECTS_DIR/1122/mri/brain.mgz
$SUBJECTS_DIR/1122/mri/transforms/talairach.m3z
$SUBJECTS_DIR/BN_Atlas_subcortex.gca
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Thanks, it was created using:
mri_ca_label $SUBJECTS_DIR/1122/mri/brain.mgz
$SUBJECTS_DIR/1122/mri/transforms/talairach.m3z
$SUBJECTS_DIR/BN_Atlas_subcortex.gca
$SUBJECTS_DIR/1122/mri/BN_Atlas_subcotex.mgz
Best,
Boris
> Am 16.12.2019 um 21:12
There is something weird about that file. How was it created?
doug
ps. Please include previous correspondence in the email
On 12/16/19 1:12 PM, Boris Rauchmann wrote:
>
> External Email - Use Caution
>
> Boriss-MacBook-Pro:mri boris$ mri_info N_Atlas_subcotex.mgz
>
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Boriss-MacBook-Pro:mri boris$ mri_info N_Atlas_subcotex.mgz
mghRead(/Users/boris/Desktop/MirLIND_test/1122/mri/N_Atlas_subcotex.mgz, -1):
could not open file
> Am 16.12.2019 um 19:08 schrieb Greve, Douglas N.,Ph.D.
> :
>
> mri_info
OK, now I'm really confused. Try this
mri_info N_Atlas_subcotex.mgz
On 12/14/19 3:04 AM, Boris Rauchmann wrote:
>
> External Email - Use Caution
>
> Here the results:
>
>
> pwd:
> /Users/boris/Desktop/MirLIND_test/1122/mri
>
> ls -l BN_Atlas_subcotex.mgz:
> -rwxrwxrwx 1 boris staff
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Here the results:
pwd:
/Users/boris/Desktop/MirLIND_test/1122/mri
ls -l BN_Atlas_subcotex.mgz:
-rwxrwxrwx 1 boris staff 37013 13 Aug 23:30 BN_Atlas_subcotex.mgz
Best,
Boris
> Am 13.12.2019 um 23:53 schrieb Greve, Douglas N.,Ph.D.
> :
>
> pwd
ok, this is very strange to me. Can you send the result of these two commands
pwd
and
ls -l BN_Atlas_subcotex.mgz
On 12/13/2019 2:22 AM, Boris Rauchmann wrote:
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yes to both. I always get the error ERROR: cannot find aseg...
On Fri, Dec 13, 2019 at 12:58
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yes to both. I always get the error ERROR: cannot find aseg...
On Fri, Dec 13, 2019 at 12:58 AM Greve, Douglas N.,Ph.D. <
dgr...@mgh.harvard.edu> wrote:
> Are you running this from 1122/mri and is BN_Atlas_subcotex.mgz in that
> folder?
>
> On
Are you running this from 1122/mri and is BN_Atlas_subcotex.mgz in that
folder?
On 12/12/19 12:57 PM, Boris Rauchmann wrote:
>
> External Email - Use Caution
>
> My-Computer:~ boris$ mri_aparc2aseg --s 1122 --volmask --aseg
> BN_Atlas_subcotex.mgz --o aparc+BN_Atlas_subcotex.mgz
>
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My-Computer:~ boris$ mri_aparc2aseg --s 1122 --volmask --aseg
BN_Atlas_subcotex.mgz --o aparc+BN_Atlas_subcotex.mgz
SUBJECTS_DIR /Users/boris/Desktop/mydir
subject 1122
outvol aparc+BN_Atlas_subcotex.mgz
useribbon 0
baseoffset 0
RipUnknown 0
Reading
Hi Boris
can you send us the full command line and screen output of the commands
that are failing?
cheers
Bruce
On Thu, 12 Dec
2019, Boris Rauchmann wrote:
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Thanks. unfortunately I get an error message when I use the --aseg flag for
External Email - Use Caution
Thanks. unfortunately I get an error message when I use the --aseg flag for
BN_Atlas_subcotex.mgz but even, if I'm using the original aseg.mgz I get:
ERROR: cannot find aseg .../fs_all_subjects/xyz/mri/aseg.mgz
The file BN_Atlas_subcotex.mgz was
What is in BN_Atlas_subcotex.mgz ? Is it like aseg.mgz but with your
subcortical ROIs added? If so, you can try merging it with the aparc, eg,
mri_aparc2aseg --s subject --volmask --aseg BN_Atlas_subcotex.mgz --o
aparc+BN_Atlas_subcotex.mgz
Then use aparc+BN_Atlas_subcotex.mgz as input to
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In this example tried it with only the subcortical segmentations from my
atlas. Please find the logfile attached. It gives me back: "tissue type is
not set" but I set it to 2 in the LUT.txt
In principle look the following commands right to you?
Can you send the log file for each of the gtmseg runs?
On 11/26/2019 1:09 PM, Boris Rauchmann wrote:
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Thank you! I have a gca for subcortical and two gcs (lh/rh) for cortical
structures.
I created an annot (rh/lh) and a mgz using mris_ca_label and
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Thank you! I have a gca for subcortical and two gcs (lh/rh) for cortical
structures.
I created an annot (rh/lh) and a mgz using mris_ca_label and mri_ca_label
for parcellation/segmentation stats.
For the PET analysis I have the following problem:
If
It gets the subcortical from apas+head.mgz which gets created along the
way by xcerebralseg. You can create your own with xcerebralseg by
specifying your volume as the mergevol. I think this will work, but I'm
not sure. I'm assuming you've used the GCA to create your own
subcortical seg for
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I just realized that the above mentioned command (gtmseg --s XYZ --o
BN.gtmseg.mgz --ctx-annot BN_Atlas.annot --ctab
'/media/XYZ/BN_Atlas_freesurfer/BN_Atlas_246_LUT.txt' --no-xcerseg) gives
me only the cortical segmentation. Is there any way to also
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Thanks alot lilla.
Nader
On Tue, 29 Oct 2019, 19:37 Lilla Zollei
> Our default setting to run mrri_cvs_register on our cluster is to use
> 35gb.
> Lilla
>
> On Tue, 29 Oct 2019, Nader Razmara wrote:
>
> >
> > Hi expertsI use freesurfer vm 5.3 on
Our default setting to run mrri_cvs_register on our cluster is to use
35gb.
Lilla
On Tue, 29 Oct 2019, Nader Razmara wrote:
Hi expertsI use freesurfer vm 5.3 on oracle vb 6 with 8 GB ram.
When i use mri_cvs_register as:
mri_cvs_register --mov subjid --mni or
mri_cvs_register --mov subjid
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Alright, thanks!
On Tue, Aug 13, 2019 at 5:10 PM Greve, Douglas N.,Ph.D. <
dgr...@mgh.harvard.edu> wrote:
> There is no cut off for the minimum size. As it gets smaller, the PVC
> noise amplification will become bigger (it also depends on the shape
There is no cut off for the minimum size. As it gets smaller, the PVC
noise amplification will become bigger (it also depends on the shape as
well).
I think the --no-xcerseg is the right way to go now
On 8/13/19 11:00 AM, Boris Rauchmann wrote:
>
> External Email - Use Caution
>
>
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Thank you for your prompt answer - the command worked. This is the atlas
mentioned: http://atlas.brainnetome.org/brainnetome.html
What is approximately the smallest possible segment when using PVC?
Also, does the exclusion of extracerebral structures
I don't know what the Brainnetome is, but it looks like you have it in
annotation form. I think that command should work. Why are you using
--no-xcerseg? This will cause it to not include extracerebral
structures. Also note that you cannot use arbitrarily small segments
when doing PVC.
On
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I understand.
Thanks for your response, Feifei!
Bruce Fischl 于2019年7月16日周二 下午10:09写道：
> Hi Feifei
>
> we don't compute thickness using the method introudced by (MacDonald et
> al.2000). For that you can look at either our 1999 NeuroImage pair of
>
Hi Feifei
we don't compute thickness using the method introudced by (MacDonald et
al.2000). For that you can look at either our 1999 NeuroImage pair of
papers or the 2000 PNAS paper.
Essentially surface area is just the average area of the triangles that the
vertex is attached to, and then
I don't know. There is no way for me to answer that. It depends on the
signal-to-noise of each of the modalities. You'll probably have to experiment a
bit
On 6/22/2019 8:08 AM, Matthieu Vanhoutte wrote:
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I effectively smoothed both modalities the same
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I effectively smoothed both modalities the same amount.
The question is whether I should or not smooth before calculating
within-subject correlation?
Best,
Matthieu
Le sam. 22 juin 2019 à 02:14, Greve, Douglas N.,Ph.D. <
dgr...@mgh.harvard.edu> a
I'm not sure that this is a question we can answer. If you do smooth, then you
should smooth both modalities the same amount.
On 6/18/2019 10:12 PM, Matthieu Vanhoutte wrote:
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Dear FS experts,
I would like to compute within-subject correlation between two
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Alright, thanks I confused that. I already found a better way for my purposes.
Im just running mri_gtmpvc using the flags —psf=0 and —no-tfe to get the non
PVC subcortical SUVs.
> Am 17.05.2019 um 17:28 schrieb Greve, Douglas N.,Ph.D.
> :
>
> In
In mri_segstats, use --seg $SUBJECTS_DIR/xyz/mri/aparc+aseg.mgz --ctab-default
...
when you use --annot, you are saying that the input is on the surface.
On 5/17/2019 9:07 AM, Boris Rauchmann wrote:
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Dear Freesurfer community,
I am trying to extract SUV
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Yes, the theshold was the solution. Thanks again for your precious help!
On Fri, Mar 29, 2019 at 3:50 PM Greve, Douglas N.,Ph.D. <
dgr...@mgh.harvard.edu> wrote:
> What threshold are you using in tksurfer? It should be the same as
> -log10(cwp),
What threshold are you using in tksurfer? It should be the same as -log10(cwp),
where cwp is the --cwp threshold you used in mri_glmfit-sim. If it is
different, then it might not show all the cluster
On 3/29/19 6:48 AM, Giuliana Klencklen wrote:
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Hi FS
do you mean the section in the left hemi temporal lobe (the lower right
portion of your image)? That does not look like real white matter to me as
it is adjacent to csf. Did you accidentally put some control points in gray
matter (or csf)?
On Mon, 25 Mar 2019, Erika Portera wrote:
yes, because the differences in their morphology don't change the average
very much. You can try it both ways to verify this is true for your
subjects.
cheers
Bruce
On Tue, 19 Feb 2019,
Laboratorio de Neurociencia Funcional wrote:
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Thank,
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Thank, Bruce. So the final message is that I should use the same average
subject to display results of cortical thickness even when samples to be
compared have highly different brain morphology. Is that correct?
El lun., 18 feb. 2019 a las 23:37,
Hi Jose
usually we don't need multiple averages (or study specific ones), which
simplifies things considerably. Is there a reason you think you need one?
We intentially use the gray/white boundary for this reason, which is
insensitive to any possible cortical atrophy.
cheers
Bruce
On Mon,
_
From: freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of Bruce
Fischl
Sent: Monday, February 4, 2019 12:27:48 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] (no subject)
Hi Jorgan
do you have read permission
list
Subject: Re: [Freesurfer] (no subject)
Hi Jorgan
do you have read permission for that file/directory? It looks like not
cheers
Bruce
On Mon, 4 Feb 2019, Jordan Fowler wrote:
>
> External Email - Use Caution
>
> Here is the message displayed:
>
>
> S
Hi Jorgan
do you have read permission for that file/directory? It looks like not
cheers
Bruce
On Mon, 4 Feb 2019, Jordan Fowler wrote:
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Here is the message displayed:
Setting up environment for FreeSurfer/FS-FAST (and FSL)
FREESURFER_HOME
Hi Sofia
what would that mean? Do you want to normalize the volumes? The volumes
themselves are independent of any coordinate system, except for scaling.
Normalizing usually isn't very useful since the goal of it would be to have
them all be the same.
cheers
Bruce
On
Wed, 30 Jan 2019,
tart because it could not find or load the Qt
platform plugin "xcb"
in "".
Reinstalling the application may fix this problem.
Abort
<<
Any advice on how to solve this problem?
With best regards,
Emil
Date: Mon, 7 Jan 2019 17:52:39 +0100
> From: "Larissa Bec
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Hi Ruopeng,
Thank you very much for your quick answer and advice. So I am going to update
freeview!
Thanks!
Larissa
Gesendet mit der WEB.DE Mail App
Am 07.01.19 um 17:35 schrieb Ruopeng Wang
> Hi Larissa,
>
> The latest development version of
Hi Larissa,
The latest development version of freeview supports drawing labels on
surface. You can take a look here on how to update freeview:
https://surfer.nmr.mgh.harvard.edu/fswiki/UpdateFreeview
In the latest version, you can draw paths on surface and use custom fill
to create/edit
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