eliminate the message and any attachments it carries
from your account.
El mar, 15 abr 2025, 19:22, Douglas N. Greve
escribió:
> First of all, can you confirm that that file exists and is readable by
> you?
>
> On 3/28/2025 2:31 PM, Rosalia Dacosta Aguayo wrote:
>
> Ex
eliminate the message and any attachments it carries
from your account.
On Fri, Mar 28, 2025 at 7:13 PM Rosalia Dacosta Aguayo
wrote:
> Dear Freesurfer team,
>
> I am having a trouble with aparcstats2table I have never seen before and I
> do not know how to solve it.
>
>
External Email - Use Caution
Dear Freesurfer team,
I am having a trouble with aparcstats2table I have never seen before and I
do not know how to solve it.
I have run it with --help and still I don't quite understand it.
Any help would be appreciated.
Kind regards,
Rosie
ros
External Email - Use Caution
Dear Freesurfer subjects,
After saving my control.dat file into the tmp folder and running the
command line recon-all -autorecon2-cp -autorecon3 -s
It does not seem to parse the control.dat file correctly and find the
control points.
This is what
different so I changed the values and then it appeared as always.
Thank you for your time!
Kind regards,
Rosie
On Thu, May 4, 2023 at 7:55 PM Rosalia Dacosta Aguayo
wrote:
> Why is the brain white?
>
> I have been changing the thresholds and nothing seems to work...
>
> Kind r
gt;
> On 5/4/2023 1:34 PM, Rosalia Dacosta Aguayo wrote:
>
> External Email - Use Caution
> Dear Freesurfer's experts,
>
> Why is this happening?
>
> Kind regards,
> Rosie
>
>
>
> ___
> Freesurfer
External Email - Use Caution
Thank you for the clarification, Douglas.
Kind regards,
Rosie
On Thu, Jan 5, 2023 at 3:21 PM Douglas N. Greve
wrote:
> no, it is not
>
> On 1/4/2023 9:20 AM, Rosalia Dacosta Aguayo wrote:
>
> External Email - Use
External Email - Use Caution
Dear Freesurfer team,
I have found a warning about not using amygdala, hippocampus and brainstem
volumes from asegstats file.
I wonder if that is true.
Best wishes,
Rosie
___
Freesurfer mailing list
Freesu
External Email - Use Caution
I do not get the cingulate, for example...
On Wed, Dec 21, 2022 at 4:35 PM Rosalia Dacosta Aguayo
wrote:
> Hi Douglas,
>
> I am only getting the main volumes like putamen right and left, amygdala,
> right and left...just gross anatom
10:11 AM, Rosalia Dacosta Aguayo wrote:
>
> External Email - Use Caution
> Maybe is -qcache ?
>
>
>
>
> On Wed, Dec 21, 2022 at 4:10 PM Rosalia Dacosta Aguayo <
> rdacos...@gmail.com> wrote:
>
>> Dear Freesurfer group,
>>
>> Could y
External Email - Use Caution
Maybe is -qcache ?
On Wed, Dec 21, 2022 at 4:10 PM Rosalia Dacosta Aguayo
wrote:
> Dear Freesurfer group,
>
> Could you tell me which is the flag I need to use to get all the brain
> parcellation when I run recon-all? It seems I am
External Email - Use Caution
Dear Freesurfer group,
Could you tell me which is the flag I need to use to get all the brain
parcellation when I run recon-all? It seems I am getting the tables with
few volumes and I guess there is something wrong.
Best wishes and Merry Christmas,
; voxels don't change). Also note that you only need to change the wm.mgz if
> the surfaces are not following the gray white boundary. It is not used for
> anything else.
>
> On 1/27/2022 8:41 AM, Rosalia Dacosta Aguayo wrote:
>
> External Email - Use Caution
> Dear Fr
External Email - Use Caution
FYI!!
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
ut from an analysis standpoint those are the two big differences
>
> Bruce
>
>
>
> *From:* freesurfer-boun...@nmr.mgh.harvard.edu <
> freesurfer-boun...@nmr.mgh.harvard.edu> *On Behalf Of *Rosalia Dacosta
> Aguayo
> *Sent:* Sunday, November 21, 2021 1:42 PM
> *To:*
External Email - Use Caution
Dear Freesurfer team,
I know this is a basic question, but I would like to be sure before
proceeding. Are those statements below right?
For cortical thickness, I should covariate for age and sex
For volume, I should covariate only for TBV
Thank you
n I do in this
> case?
>
> Thank you and best regards,
>
> Rubina
> --
> *From:* freesurfer-boun...@nmr.mgh.harvard.edu <
> freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Rosalia Dacosta
> Aguayo
> *Sent:* Monday, September 13, 2021
k> wrote:
> External Email - Use Caution
>
> Hi Rosie,
>
> I used MRIcroGL to convert DICOMs to Niftis.
>
> Kind regards,
>
> Rubina
> --
> *From:* freesurfer-boun...@nmr.mgh.harvard.edu <
> freesurfer-boun...@nmr.mgh.
External Email - Use Caution
Hi Rubina,
How did you gzip your data? Which software did you use?
Kind regards,
Rosie
On Mon, Sep 13, 2021 at 5:59 PM Rubina Chandnani <
rubinachandn...@hotmail.co.uk> wrote:
> External Email - Use Caution
>
> Hi there,
>
> I'm getting i
; Bruce
>
>
>
> *From:* freesurfer-boun...@nmr.mgh.harvard.edu <
> freesurfer-boun...@nmr.mgh.harvard.edu> *On Behalf Of *Rosalia Dacosta
> Aguayo
> *Sent:* Wednesday, July 21, 2021 5:10 AM
> *To:* Freesurfer support list
> *Subject:* [Freesurfer] Control points and
External Email - Use Caution
Dear Freesurfer team,
Sorry for this basic question.
I wonder if once I have edited the white matter (topological defects), I
can run control points without deleting what I have done to white matter
segmentation.
Kind regards,
Rosie
_
External Email - Use Caution
Hi Paul,
Not sure what command I should run when I edit the brainmask because the
pial got too much.
Kind regards,
Rosie
On Thu, Jul 8, 2021 at 6:13 PM Paul Wighton wrote:
> External Email - Use Caution
>
> Hi Rosie,
>
>
>> It is my firs
External Email - Use Caution
Thank you!
Rosie
On Thu, Jul 8, 2021 at 6:13 PM Paul Wighton wrote:
> External Email - Use Caution
>
> Hi Rosie,
>
>
>> It is my first time editing wm segmentation (white matter segmentation
>> errors + topological errors).
>>
>> I wonder
External Email - Use Caution
Dear Freesurfer team,
It is my first time editing wm segmentation (white matter segmentation
errors + topological errors).
I wonder if there is a good tutorial on which I could rely.
Also, I have read there is an example of segmentation that comes wi
recon-all -s sub-002_ses-BSL -hippocampal-subfields-T1
>
> -Paul
>
> On Wed, Jul 7, 2021 at 3:21 PM Rosalia Dacosta Aguayo
> wrote:
>
>> External Email - Use Caution
>>
>> Hi Paul,
>>
>> Thank you.
>>
>> The think is that I a
fswiki%2FHippocampalSubfields>
>
> Otherwise, if you upgrade to the latest version (v7.1.1) you can use
> the segmentHA_T1.sh script.
>
> -Paul
>
> On Wed, Jul 7, 2021 at 2:29 PM Rosalia Dacosta Aguayo
> wrote:
>
>> External Email - Use Caution
>&
> What version of FreeSurfer is installed at /usr/local/freesurfer? Can you
> run the following command and copy the output
>
> cat $FREESURFER_HOME/build-stamp.txt
>
> -Paul
>
> On Wed, Jul 7, 2021 at 1:58 PM Rosalia Dacosta Aguayo
> wrote:
>
>> Extern
ork that way.
>
> Thanks and Regards
> Nayan Wadhwani
>
>
> On Wed, Jul 7, 2021 at 10:27 PM Rosalia Dacosta Aguayo <
> rdacos...@gmail.com> wrote:
>
>> External Email - Use Caution
>>
>> Hi Paul,
>>
>> I did it:
>>
>&g
`segmentHA_T1.sh` again.
>
> -Paul
>
>
> On Wed, Jul 7, 2021 at 12:39 PM Rosalia Dacosta Aguayo <
> rdacos...@gmail.com> wrote:
>
>> External Email - Use Caution
>>
>> Hi Paul,
>>
>> Thank you very much for answering my question. I set
en I run the command, it gives me this error:
>>
>> rosalia@rosalia-Lenovo-Y520-15IKBN ~/Desktop/CAN_RUTI $ segmentHA_T1.sh
>> sub-002_ses-BSL
>> segmentHA_T1.sh: command not found
>> rosalia@rosalia-Lenovo-Y520-15IKBN ~/Desktop/CAN_RUTI $
>>
>>
>> Any idea what
$ 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
External Email - Use Caution
Dear Freesurfer team,
Following this link:
https://secure-web.cisco.com/1JQvIqqm3-q4IvkVi2SEZWuHP3qoo3qga0SfN71vLNIZ9qj4cNFwxFqvjroWv9feMAvJHN9UgN0BkjDoYeCHTilHRlhYVCx9NC7MYk-9O0bZVNfhvJz8OO5I1ewNoWK_GpUl2x9NzWTare9e3GblcaHIpBuMhXHYKv_uZ0aA0f7RFNcL2xlX
External Email - Use Caution
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
External Email - Use Caution
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
External Email - Use Caution
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
___
External Email - Use Caution
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
External Email - Use Caution
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
External Email - Use Caution
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
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 -
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
External Email - Use Caution
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 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
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
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
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:*
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
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 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
External Email - Use Caution
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 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
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:
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
External Email - Use Caution
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
__
External Email - Use Caution
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
External Email - Use Caution
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
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
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
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
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,
>
> /
; 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
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
>
External Email - Use Caution
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,
>
External Email - Use Caution
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
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
External Email - Use Caution
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
External Email - Use Caution
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
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
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
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
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,
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,
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
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
> >
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
> 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
External Email - Use Caution
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 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
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
>
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
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
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 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
External Email - Use Caution
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
External Email - Use Caution
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
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
, 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
> >
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
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
'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-
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,
External Email - Use Caution
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
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
External Email - Use Caution
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 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
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
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:
> >
>
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
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
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
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
1 - 100 of 130 matches
Mail list logo
