Dear Free Surfer experts,
I am having problems with my FS installation. I am working with
Linux/Ubuntu version 11.10...I have followed the indications of the FS wiki
and it seems that it is installed but it does not work...it does not run in
the terminal and I do not know why and how can I do:
os
Dear Free Surfer experts,
Sorry for posting this again...but I have been trying this all the day and
nothing seems to change the situation.
I am having problems with my FS installation. I am working with
Linux/Ubuntu version 11.10...I have followed the indications of the FS wiki
and it seems that
Dear FreeSurfer list,
My name is Rosalia and this is the first time I post an email on your list.
I have never run FreeSurfer before and I have a doubt regarding the
converting process.
For every T1 folder, I have 192.ima files. I do not know how to pass from
this point to .mgz. It seems that in
Hello FreeSurfer Developers,
I am attempting to compute autorecon1 in a subject to see how it works
recon-all in a stepwise as described in the tutorial.
Sorry if this is a very naive question but it is the first time I am trying
to run an analysis with FreeSurfer.
After running: *r*
*econ-all
GNU/Linux
4. Recon-all.log: see attached
2017-11-12 18:50 GMT+01:00 Rosalia Dacosta Aguayo :
> Hello FreeSurfer Developers,
>
> I am attempting to compute autorecon1 in a subject to see how it works
> recon-all in a stepwise as described in the tutorial.
> Sorry if this
Dear FreeSurfer Developers,
I have run recon-all-qcache after reviewing the recon-all...-all
outputs in freeview.
I have been looking into:
https://surfer.nmr.mgh.harvard.edu/fswiki/mris_preproc
Now it seems that I could have omitted the -qcache...and I am a bit lost
with the examples sh
files? I mean, in order to do
not overload the mail list...
Kind regards,
Rosalia
2017-11-21 18:09 GMT+01:00 Bruce Fischl :
> hmmm, that is odd looking. Can you upload that subject so we can see if
> it is just a display bug or not?
> On Tue, 21 Nov 2017, Rosalia Dacosta Aguayo
> wrote
Sorry Bruce,
I have sent it to your email directly...in order to avoid the process of
uploading the data...because I am not familiar with it.
Kind regards,
Rosalia
2017-11-21 18:25 GMT+01:00 Rosalia Dacosta Aguayo :
> Sorry Bruce,
>
> I prefer sending it to your email directly, th
Dear Bruce,
I am using FileDropv2.0...
I hope you and all the members of the list can access into this subject.
Thank you for your help in advance,
Rosalia
2017-11-21 18:35 GMT+01:00 Rosalia Dacosta Aguayo :
> Sorry Bruce,
>
> Here is the problem I wanted to avoid:
>
>
Dear FreeSurfer Developers,
I am having problems with FtpFileExchange. I am trying to upload a
compressed file Bruce asked me to upload and it seems I am missing
something in the last point of the instructions:
https://surfer.nmr.mgh.harvard.edu/fswiki/FtpFileExchange
*What I have done till now*:
Congratulations!!
El 5 dic. 2017 22:47, "Bruce Fischl" escribió:
> Hi All
>
> we just published a paper on 3D microscopic imaging of connectivity and
> architecture:
>
> https://www.sciencedirect.com/science/article/pii/S105381191730825X
>
> if you are interested.
>
> cheers
> Bruce
>
>
Dear FreeSurfer team,
I have run recon-all and I have done smoothing in a sample of 24
participants which are divided into 3 groups.
Now that I know which smoothing I would like to use, I am a bit lost
regarding which of the files generated should I use and how I should
concatenate them. It is my
Another issue is that the T1 images they have provided me have been
preprocessed with AFNI, and I have to work with FSL format. So, I have to
go back with a function called 3dAFNItoNIFT but I have not never done this
beforecould you help me?
2017-12-23 22:01 GMT+01:00 Rosalia Dacosta Aguayo
And finally, I have a dual-task but I do not know anything about the
design...the only way to see how has been set is by opening one of the
files with i-prime and I do not have it and I have not ever worked with
this before...
2017-12-23 22:03 GMT+01:00 Rosalia Dacosta Aguayo :
> Another is
Dear FreeSurfer team,
Sorry for double posting, but I have realized that in my previous email I
posted some ideas that were not intended for any list...
Problem: I do not know how to concatenate the different files generated in
order to perform a cortical thickness analysis. Any help on this issu
Thank you very much Douglas for answering. I will do it.
Happy New Year :)
Rosalia
El 31 dic. 2017 23:24, "Douglas Greve" escribió:
> Use preproc-sess to do the concatnation. If that does not work, you can do
> it by hand with mri_concat
>
> On 12/26/17 7:49 PM, Rosali
Hi Douglas,
Could you please tell me which of the generated files I should take into
account for the concatenation process and if I should generate two
concatenated files: one for tge right and another for the left hemisphere?
Thank you,
Rosalia
El 31 dic. 2017 23:35, "Rosalia Dacosta A
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Dear Experts,
I would like to run statistical analyses with the output of cortical
thickness. The problem is that I would like to do it with FSL as I have
more experience.
Any one of you could tell me which are the two outputs (right and left
hemispher
External Email - Use Caution
Hi Douglas,
I wonder why anybody has answered to my question about the outputs of
cortical thickness with FreeSurfer. I am not familiarized with them and I
would just to do statistical comparisons. Could you help me with this,
please?
Best regards,
Ro
by mris_preproc and
> use that as input, but you won't be able to do clusterwise correction
> for multiple comparisons
>
>
> On 05/21/2018 02:20 PM, Rosalia Dacosta Aguayo wrote:
> >
> >
> > Dear Experts,
> >
> > I would like to run statistical analyses with
External Email - Use Caution
Dear Free Surfer's team,
I have a doubt. I have a sample of patients in which I already have done
the skull stripping using specific options with bet, so the skull stripping
has been successful. I wonder if I could feed autorecon1 with the skull
stripp
).
>
>
>
> Best,
>
> Falk
>
>
>
> *Von:* freesurfer-boun...@nmr.mgh.harvard.edu [mailto:
> freesurfer-boun...@nmr.mgh.harvard.edu] *Im Auftrag von *Rosalia Dacosta
> Aguayo
> *Gesendet:* Donnerstag, 18. Oktober 2018 06:30
> *An:* Freesurfer support list
&
External Email - Use Caution
Dear Free Surfer team,
Surely this is a basic question but I am having a trouble setting the
subjects_dir in my terminal and, as a result, any of the commands work.
This is how I have my Free Surfer configurated in my computer:
freesurfer-Li
mri/orig subdir. Note you can
> also specify SUBJECTS_DIR explicitly on the recon-all command line with
> -sd
> if you don't want to put it in the environment.
>
> That is, try this:
>
> recon-all -s 001 -autorecon1 -sd ~/Desktop/subjects
>
> cheers
> Bru
; can you send us the full command line, screen output and recon-all.log?
> In the arrangement you show below it would be:
>
> recon-all -sd ~/Desktop/MS_STUDY/subjects -s 001 -i
> -all
>
> cheers
> Bruce
> On Thu, 18 Oct 2018, Rosalia
> Dacosta Aguayo wrote:
>
>
correct (e.g. mprage) series.
> cheers
> Bruce
> On Thu, 18 Oct 2018, Rosalia
> Dacosta Aguayo wrote:
>
> >
> > External Email - Use Caution
> >
> > Hi Bruce,
> >
> > There is not recon-all.log.
> >
> > The full command line is:
>
all through the skill stripping,
> then replace the brainmask.mgz with yours generated by bet, we should
> detect that and retain it for further processing
>
> cheers
> Bruce
> On Thu, 18 Oct 2018,
> Rosalia Dacosta Aguayo wrote:
>
> >
> > External Email - Us
External Email - Use Caution
Dear FreeSurfer team,
I am experiencing an error when trying to run a subject from a different
group but with the same number.
I would much appreciate your helping here.
Regards,
Rosalia
rosalia@rosalia-Lenovo-Y520-15IKBN
~/Desktop/MS_STUDY/subjects_c
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Dear FreeSurfer team,
I am trying to run recon -all -autorecon2 using the following command
line: *recon-all -sd ~/Desktop/MS_STUDY/subjects -s 001 -i
/home/rosalia/Desktop/MS_STUDY/subjects/001 -autorecon2*
It is the same command I used yesterday t
External Email - Use Caution
Dear Free Surfer team,
I keep trying to run -autorecon2 but it seems that I should have run recon
-all -all instead as I am having problems with the names of my subjects and
the same error appears once and again and I do not know how I should do it
so
ue processing your data, as this flag tells
> FreeSurfer to create a new subject folder (which already exists and
> therefore give an error).
>
>
>
> Best,
>
> Falk
>
>
>
>
>
> *Von:* freesurfer-boun...@nmr.mgh.harvard.edu [mailto:
> freesurfer-boun...@nm
t; 3. Run ‘recon-all -autorecon2 -autorecon3 -s
> -qcache -openmp 8’
>
>
>
>
>
> Best,
>
> Falk
>
>
>
>
>
>
>
> *Von:* freesurfer-boun...@nmr.mgh.harvard.edu [mailto:
> freesurfer-boun...@nmr.mgh.harvard.edu] *Im Auftrag von *Rosalia Dacosta
T1.mgz and name the output brainmask.mgz
>
> 3. Run ‘recon-all -autorecon2 -autorecon3 -s
> -qcache -openmp 8’
>
>
>
>
>
> Best,
>
> Falk
>
>
>
>
>
>
>
> *Von:* freesurfer-boun...@nmr.mgh.harvard.edu [mailto:
> freesurfer-bou
External Email - Use Caution
Dear FreeSurfer team,
I Have run -autorecon1 in my sample and the report.log was "finished
without errors"
Now, running recon-all -all I have seen that a participant is stuck in
CORRECTING DEFECT 0 (vertices=31977, convex hull=5359, v0=0) for more than
weeks). Examine the ?h.orig.nofix and ?h.inflated.nofix surfaces and see if
> there is some big problem like skull or cerebellum attached to the surface.
> >
> > cheers
> > Bruce
> >
> >
> > On Mon, 22 Oct 2018, Rosalia Dacosta Aguayo wrote:
> >
>
vertices,
> which is about 1/4 of
> > the total surface more or less, something is dramatically wrong
> and it is not worth
> > waiting for it to finish (it might take days or weeks). Examine
> the ?h.orig.nofix and
> > ?h.inflated.nofix surfaces and see if t
External Email - Use Caution
Dear Free Surfer team,
I am visually checking for errors in every step of the recon-all process.
In the skull stripping stage, some participants have left skull behind, but
the grey matter (gm) and white matter (wm) separation is right.
Should I edit
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Dear Free Surfer team,
I wonder how I could pass from .nii.gz format to .mgz format in order to
change the brainmask.mgz generated by FreeSurfer for my bet image from FSL.
I have noticed that lot of brainmask images have optic radiations and part
of th
External Email - Use Caution
Dear FreeSurfer team,
In order to improve the skull stripping for some of the participants of the
sample, I replaced the brainmask.mgz generated in FreeSurfer by the betted
image generated from FSL, and I run recon-all again. The problem is that,
again
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Dear Free Surfer team,
Sorry for double posting but I would like to explain well so it will be
easier to understand what I am looking for.
1. I have run recon-all -all in a participant
2. The skull stripped image has skull and dura behind.
3. I can m
7:42 PM Bruce Fischl
wrote:
> Hi Rosalia
>
> yes, editing and rerunning recon-all should work. Or update the
> brainmask.mgz with your own version if you want. We should detect that and
> retain it.
>
> cheers
> Bruce
>
> On Wed, 14 Nov 2018,
's
> dir and it gets overwritten? That shouldn't happen
>
> thanks
> Bruce
> On Thu, 15 Nov 2018,
> Rosalia Dacosta Aguayo wrote:
>
> >
> > External Email - Use Caution
> >
> > HI Bruce,
> >
> > I have to run recon-
External Email - Use Caution
Hi Bruce,
Sorry for my intromission.
I am replacing the brainmask because dura mater or skull were left behind
with independence of the WM and GM segmemtation. Does this is useless?
Regards,
Rosalia
El dom., 18 nov. 2018 16:16, Bruce Fischl
escribió
t; the aseg)
> cheers
> Bruce
>
> On Sun, 18 Nov 2018, Rosalia Dacosta Aguayo wrote:
>
> >
> > External Email - Use Caution
> >
> > Hi Bruce,
> > Sorry for my intromission.
> > I am replacing the brainmask because dura mater or skull
, 18 Nov
> 2018, Rosalia Dacosta Aguayo wrote:
>
> >
> > External Email - Use Caution
> >
> > Hi Bruce,
> > Thank you a lot for your reply. How could I inspect if affects the
> surfaces?
> >
> > Yours sincerely,
> > Rosalia
> >
External Email - Use Caution
Hi Maedeh,
You can. But you will to name them different and change the .bahsrc file
every time you use one or the other.
Hope this helps,
Rosalia
El dom., 18 nov. 2018 17:51, Maedeh Khalilian
escribió:
> External Email - Use Caution
>
> Dea
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Dear Free Surfer experts,
I am trying to load my brainmask and the T1 to make editions but I have a
problem I do not know how to solve.
I would much appreciate your helping here.
Best regards,
Rosalia
*Problem: *
ms_naroa@neuroimagen1:~/Escritorio/sub
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Dear Free Surfer team,
I have edited the pial surface and I am running: -autorecon-pial. This
process is taking its time.
Then I will look for intensity normalization and control points. Then I
will have to run recon-all -autorecon2-cp -autorecon3.
I
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Dear Free Surfer experts,
I am experiencing a problem with 4 participants. Whrn I open the brainmask
with freeview, it appears white (binarized). I was editing this brainmask
and at sone point I switched something and it changed to white. I deleted
alk
ed out, so as long as it more-or-less outlines the brain v nonbrain
> boundary you should be fine.
>
> cheers
> Bruce
>
>
>
> On Fri, 23 Nov 2018, Rosalia Dacosta Aguayo wrote:
>
> >
> > External Email - Use Caution
> >
> > Dear Free Surfer
External Email - Use Caution
Dear Free Surfer experts,
I have run recon-all for all my participants and I am editing the brainmask
and making control points. I have seen that for two participants, Free
Surfer were not run. I run those two participant again and I saw that they
were
s
> Bruce
>
>
> On
> Tue, 27 Nov
> 2018, Rosalia Dacosta Aguayo wrote:
>
> >
> > External Email - Use Caution
> >
> > Dear Free Surfer experts,
> >
> > I have run recon-all for all my participants and I am editing the
> brainmask
gt; https://surfer.nmr.mgh.harvard.edu/fswiki/FtpFileExchange
>
> On Tue, 27 Nov
> 2018, Rosalia Dacosta Aguayo wrote:
>
> >
> > External Email - Use Caution
> >
> > Hi Bruce,
> > Could you send me a link to upload one subject? I have never done this
>
:
> you don't need a password. Just use anonymous as your user name and your
> email as the password I think
> On Fri, 30 Nov 2018, Rosalia Dacosta Aguayo
> wrote:
>
> >
> > External Email - Use Caution
> >
> > HI Bruce,
> >
> > I wo
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Dear Bruce and Bram,
After improving the pial surface for my participants, I have seen that some
of them do not need control points. My question is: for those ones, should
I run -autorecon2 and -autorecon3 or only -autorecon3.
Hi Bruce and Bram, I wil
> you always have to run autorecon3 every time autorecon2 is run
>
> cheers
> Bruce
>
>
> On Mon, 3 Dec 2018, Rosalia
> Dacosta Aguayo wrote:
>
> >
> > External Email - Use Caution
> >
> > Dear Bruce and Bram,
> >
> > After impr
ftp> two_different_problems.txt
?Invalid command
ftp>
On Mon, Dec 3, 2018 at 4:06 PM Rosalia Dacosta Aguayo
wrote:
> Hi Bruce,
>
> Thank you for your reply.
> I am having problems when trying to upload the two files with FTP, it
> seems the problem is with the directory.
> rosalia
file, I provided the name of the file.txt
Thank you,
Rosalia
On Mon, Dec 3, 2018 at 4:51 PM Bruce Fischl
wrote:
> is that the right directory/path on your end?
>
> On Mon, 3 Dec 2018, Rosalia Dacosta
> Aguayo wrote:
>
> >
> > External Email - Use Caution
> >
tal
> 149 13th Street
> Charlestown, MA 02129
> (p): 617-726-6598
>
> ----------
> *From:* freesurfer-boun...@nmr.mgh.harvard.edu <
> freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Rosalia Dacosta
> Aguayo
> *Sent:* Monday, December 3, 2018 10:5
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Dear Free Surfer team,
I am checking my group of HCs. I have seen that GM and WM segmentation is
nearly perfect (for now) but, there are some point in which I can see more
pial, but pial has not been considered in the segmentation. I have the
believe,
you send some images to show what you
> mean?
> Bruce
> On Fri, 7 Dec 2018, Rosalia Dacosta Aguayo wrote:
>
> >
> > External Email - Use Caution
> >
> > Dear Free Surfer team,
> >
> > I am checking my group of HCs. I have seen that GM and WM
External Email - Use Caution
Dear Free Surfer team and Bruce,
I have been doing well editing the skull stripping, and using control
points to improve white matter segmentation. Furthermore, the few
participants I had problems with due to large ventricles were solved using
the flag
ue, 11 Dec 2018, Rosalia Dacosta Aguayo wrote:
>
> >
> > External Email - Use Caution
> >
> > Dear Free Surfer team and Bruce,
> >
> > I have been doing well editing the skull stripping, and using control
> points
> > to improve white matter seg
Dec 12, 2018 at 1:39 PM Rosalia Dacosta Aguayo
wrote:
> Hi Bruce,
>
> Thank you for your reply.
> I am sending now a file called 013.tar.gz via ftp. And this is not the
> worst...there are other with more regions that have not been considered in
> the segmentation process. I would
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Dear FreeSufer team,
I have been working with MS patients using T1 lesion filled images. I
corrected pial surface and I did control points for white matter. However,
I have not found how to edit gray matter segmentation.
I would much appreciate if you
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Dear Free Surfer team,
Sorry for double posting but I need your help on this (see below).
Best regards,
Rosalia
-- Forwarded message -
From: Rosalia Dacosta Aguayo
Date: jue., 10 ene. 2019 17:10
Subject: How to make grey matter
a month ago so you could give a quick look to the
problem.
Thank you,
Rosalia
El vie., 11 ene. 2019 12:30, Bruce Fischl
escribió:
> Hi Rosalia
>
> do you mean cortical or subcortical? Aseg or surfaces?
>
> cheers
> Bruce
> On Fri, 11 Jan 2019,
> Rosa
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Dear Free Surfer team,
I few days ago I sent you personally the dicom files as well as the mask of
the lesion you asked me for as I am having problems with GM segmentation.
I would greatly appreciate if you could help me with this issue and tell me
how
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Hi Olamide,
How to check your line errors without the bash script you are using?
Could you at least send the .sh script?
Best regards,
Rosalia
On Thu, Oct 10, 2019 at 8:29 PM Olamide Abiose wrote:
> External Email - Use Caution
>
> Hello,
>
ommand line argument, because I'm only testing one
> subject. Are you asking for the segmentHA_T1.sh script?
> --
> *From:* freesurfer-boun...@nmr.mgh.harvard.edu <
> freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Rosalia Dacosta
> Aguayo
>
; echo "" |& tee -a $HSFLOG
> echo "For more details, see the log file $HSFLOG"
> echo ""
> rm -f $IsRunningFile
> exit 1;
> endif
> end
>
> # Convert the txt files into a stats file so that asegstats2table can
> # be
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You are really the boss Dr. Iglesias!!
Happy to know Ola is in expert hands :)
Rosalia
El jue., 10 oct. 2019 15:35, Iglesias Gonzalez, Juan E. <
jiglesiasgonza...@mgh.harvard.edu> escribió:
> Bummer!
>
> Andrew, any ideas on this?
>
> Cheers,
>
> /
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Hi Andrew,
For some reason you do not have the following library:
/usr/X11/lib/libGLU.1.dylib
You need to get this library.
Hope this helps,
Best,
Rosie
Do not bother just to be better than your contemporaries or predecessors.
Try to be better than
External Email - Use Caution
Thank you very much, Bruce.
Rosalia
Do not bother just to be better than your contemporaries or predecessors.
Try to be better than yourself.
--Faulkner
On Mon, Jun 8, 2020 at 9:21 AM Tim Schäfer wrote:
> External Email - Use Caution
>
>
External Email - Use Caution
Dear FreeSurfer forum,
Sorry for the cross posting.
We are looking to cover a position for a* pre-doc* student working in the
field of life sciences (medical doctor, biologist, psychologist) to work on
a project about arteriopathies and atherosclerosi
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The Institut d’Investigació en Atenció Primària Jordi Gol i Gurina is
looking to cover *a Ph.D. position *for the Grenssap Group (led by Dra.
Concepció Violán). This is a multidisciplinary team formed by medical
doctors, nurses, statisticians, pharmacis
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Dear all,
I would like to parcellate the brain and calculate the volumes, but I am
unsure about the command lines I should use.
I thought about first doing this: recon-all -subject subjectname -i
/path//Artico1.nii.gz -all. Should I need any othe
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Dear Freesurfer community,
I would like to include the T2 image in the recon-all command to improve
segmentation.
Any idea how I should do this in the following command?
recon-all -s Artico1 -i subj01_anat.nii.gz -all -qcache -3T
Regards,
Rosalia
__
UsingT2orFLAIRdatatoimprovepialsurfaces>
> on our wiki.
>
>
>
> Bill Ammon
>
>
>
> *From: * on behalf of Rosalia
> Dacosta Aguayo
> *Reply-To: *Freesurfer support list
> *Date: *Wednesday, March 3, 2021 at 7:36 AM
> *To: *Freesurfer support list
> *Su
essage, I think you should just add -T2 /path/to/T2_volume -T2pial.
>
>
>
> Hope this helps,
>
> Bill Ammon
>
>
>
> *From: * on behalf of Rosalia
> Dacosta Aguayo
> *Reply-To: *Freesurfer support list
> *Date: *Wednesday, March 3, 2021 at 1:18 PM
> *To:
External Email - Use Caution
Dear Freesurfer's experts,
I run FreeSurfer and I got the following stats:
rosalia@rosalia-Lenovo-Y520-15IKBN
/media/rosalia/Nuevo_vol/ARTICO/derivatives/freesurfer/sub-003/stats $ ls
aseg.stats lh.BA_exvivo.thresh.stats rh.aparc.stats
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Dear Freesurfer's experts,
I have run recon-all all to one subject with fmriprep.
The work finished without errors. However, after inspecting the results, I
have seen that there are some *grey regions* (mainly frontal and temporal
ones) that have not
External Email - Use Caution
Dear Freesurfer's team,
I am trying to run FreeSurfer recon-all -all in a folder placed *on my
Desktop* and I am having some trouble.
rosalia@rosalia-Lenovo-Y520-15IKBN ~/Desktop $ recon-all -subject
sub-003_ses-BSL_T1w.nii -i
/home/rosalia/Desktop/AR
CI6Mn0%253D%257C1000%26sdata%3DwkpejqTmmo%252Fe4JA9QIaA6Z3%252BzipbFY%252FCEmRXC9UvKJs%253D%26reserved%3D0>
>
>
>
> *Feladó:* freesurfer-boun...@nmr.mgh.harvard.edu <
> freesurfer-boun...@nmr.mgh.harvard.edu> *E személy nevében: *Rosalia
> Dacosta Aguayo
> *Küldve:* 19 June 2021 12:36
&
External Email - Use Caution
Dear Freesurfer's experts
I am trying to run recon-all -all in a subject and it seems there is a
problem I do not know how to solve.
rosalia@rosalia-Lenovo-Y520-15IKBN ~/Desktop $ recon-all -s sub-001_ses-BSL
-i /home/rosalia/Desktop/ARTICO/sub-001_se
ICO/sub-001_ses-BSL_T1w exist? Shouldn’t it
> have an extension like .nii.gz or .mgz?
>
> Cheers
>
> Bruce
>
>
>
> *From:* freesurfer-boun...@nmr.mgh.harvard.edu <
> freesurfer-boun...@nmr.mgh.harvard.edu> *On Behalf Of *Rosalia Dacosta
> Aguayo
> *Sent:*
jun. 2021 17:10, Douglas N. Greve
escribió:
> It looks like the data are fairly low quality. This will require some
> manual intervention (control points, fixing topologogical errors, etc). See
> our wiki on manual interventions
>
> On 6/15/2021 10:52 AM, Rosalia Dacos
all
>
> On 6/24/2021 12:00 PM, Rosalia Dacosta Aguayo wrote:
>
> External Email - Use Caution
> Hi Douglas,
>
> Whay do you exactly mean by low quality data? As far as I have been told,
> is high. I would like to know so I cam discuss it further with the
> e
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Dear Freesurfer team,
Sorry for posting this question but I have been trying different things and
nothing seems to work.
rosalia@rosalia-Lenovo-Y520-15IKBN ~/Desktop $ recon-all -s sub-001_ses-BSL
-i sub-001_ses-BSL_T1w.nii -T2 sub-001_ses-BSL_T2w.nii
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I noticed the error and I fixed.
Thank you,
Rosie
On Fri, Jun 25, 2021 at 8:45 PM Rosalia Dacosta Aguayo
wrote:
> Dear Freesurfer team,
>
> Sorry for posting this question but I have been trying different things
> and nothing s
External Email - Use Caution
Dear Freesurfer experts,
I have noticed I have both topological and control point erros in my image.
What would you recommend me to do first, topological or the control points?
Kind regards,
Rosie
___
Frees
vard.edu <
> freesurfer-boun...@nmr.mgh.harvard.edu> *On Behalf Of *Rosalia Dacosta
> Aguayo
> *Sent:* Saturday, June 26, 2021 11:39 AM
> *To:* Freesurfer support list
> *Subject:* [Freesurfer] Topological and control point errors
>
>
>
> *External Email -
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Dear Freesurfer team,
I am inspecting the different participants I have run recon-all -all and I
have found different errors I would like to discuss with you before
proceeding as I am new with this software.
1. I have found dura at some regions of the
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Dear Freesurfer team,
I was wondering if there is any way to improve GM segmentation with
FreeSurfer in cases like this, when all they GM has not been included by
FreeSurfer:
https://secure-web.cisco.com/1Vs511OuC3LYOAyRmiyTn4sfCMK9fVD-cPX8iYOmw7fzgPT
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Also,
When part of the ventricle is being considered as GM...
On Thu, Jul 1, 2021 at 9:53 AM Rosalia Dacosta Aguayo
wrote:
> Dear Freesurfer team,
>
> I was wondering if there is any way to improve GM segmentation with
> FreeSurfer i
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Dear Freesurfer's experts,
I wonder if there is any chance to correct the pial surface when it does
not cover entirely certain regions of GM, such for example, orbital frontal
cortex
Kind regards,
Rosie
___
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Dear Freesurfer team,
I am having the following error message when I try to run the stats table:
rosalia@rosalia-Lenovo-Y520-15IKBN ~/Desktop/CAN_RUTI/FREESURFER_CAN_RUTI $
asegstats2table --subjects sub-002_ses-BSL sub-003_ses-BSL sub-004_ses-BSL
sub
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Dear Freesurfer team,
I already found the error.
Kind regards,
Rosie
On Mon, Jul 5, 2021 at 3:31 PM Rosalia Dacosta Aguayo
wrote:
> Dear Freesurfer team,
>
> I am having the following error message when I try to run the stats table:
&g
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Dear Freesurfer team,
Following this link:
https://secure-web.cisco.com/1JQvIqqm3-q4IvkVi2SEZWuHP3qoo3qga0SfN71vLNIZ9qj4cNFwxFqvjroWv9feMAvJHN9UgN0BkjDoYeCHTilHRlhYVCx9NC7MYk-9O0bZVNfhvJz8OO5I1ewNoWK_GpUl2x9NzWTare9e3GblcaHIpBuMhXHYKv_uZ0aA0f7RFNcL2xlX
$ segmentHA_T1.sh
sub-002_ses-BSL
segmentHA_T1.sh: command not found
rosalia@rosalia-Lenovo-Y520-15IKBN ~/Desktop/CAN_RUTI $
Any idea what I am doing wrong?
Kind regards,
Rosie
On Tue, Jul 6, 2021 at 5:32 PM Rosalia Dacosta Aguayo
wrote:
> Dear Freesurfer team,
>
> Following this link:
> ht
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