al lobe is WM or GM. Try putting some
> control points in regions where the intensity is in say [95, 110) and see
> if that helps
>
> cheers
> Bruce
>
>
> On Sat, 28 Apr 2018, Miguel Ángel Rivas Fernández wrote:
>
>
>> External Email - Use Caution
>
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
> The information in this e-mail is intended only for the person to whom it
> is
> addressed. If you believe this e-mail was sent to you in error and the
> e-mail
> contains patient information, p
our ftp
> site and we will take a look
> cheers
> Bruce
>
> On Tue, 1 May 2018, Miguel Ángel Rivas Fernández wrote:
>
>
>> External Email - Use Caution
>>
>>
>> Hi Bruce,
>>
>>
>> The problem is that the reconstruction of the pial s
t, you need to run the T1 through recon-all normally, as you have
> already done. Next, you run the subfield module with the highres T2 as
> input - no recon-all on the T2 required, as it's used in a different way.
>
> Cheers
>
> Eugenio
>
> Sent from my phone, p
Eugenio Iglesias
>
> ERC Senior Research Fellow
>
> Translational Imaging Group
>
> University College London
>
> http://www.jeiglesias.com
>
> http://cmictig.cs.ucl.ac.uk/
>
>
>
>
>
> *From: * on behalf of Miguel
> Ángel Rivas Fernández
> *Reply-To: *Freesu
,
Cheers,
--
*Miguel Ángel Rivas Fernández*
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addressed
,
El vie., 4 may. 2018 1:02, Miguel Ángel Rivas Fernández <
miguelrivasf...@gmail.com> escribió:
> Hi Bruce,
>
>
> I tried to upload the whole subject dir in the ftp site but i didn´t
> works. I send you the file in 7zip format trough a google drive link . I
> would k
,
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The information in this e-mail is intended only for the person to whom it is
addressed. If you believe
;
> Centre for Medical Image Computing (CMIC)
>
> University College London
>
> http://www.jeiglesias.com
>
> http://cmictig.cs.ucl.ac.uk/
>
>
>
>
>
> *From: * on behalf of Miguel
> Ángel Rivas Fernández
> *Reply-To: *Freesurfer support list
> *Date: *Tuesd
>
> ERC Senior Research Fellow
>
> Centre for Medical Image Computing (CMIC)
>
> University College London
>
> http://www.jeiglesias.com
>
> http://cmictig.cs.ucl.ac.uk/
>
>
>
>
>
> *From: * on behalf of Miguel
> Ángel Rivas Fernández
> *Reply-T
gt; Juan Eugenio Iglesias
>
> ERC Senior Research Fellow
>
> Centre for Medical Image Computing (CMIC)
>
> University College London
>
> http://www.jeiglesias.com
>
> http://cmictig.cs.ucl.ac.uk/
>
>
>
>
>
> *From: * on behalf of Miguel
> Ángel Riva
specific analysis?
Thanks in advance.
Best,
--
*Miguel Ángel Rivas Fernández*
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The information in this e-mail is intended only for the
numerical
transformation on the eTIV values before including it as a covariate in the
statistical analysis (for example, a logarithmic transformation).
Best,
--
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Hello Freesurfer developers,
Did hoy have chance to read this question?.
Thank you very much for your help!
Best regards,
-- Forwarded message -
From: Miguel Ángel Rivas Fernández
Date: mar., 4 sept. 2018 20:37
Subject: strange
ever, when I use the command that segment only the hippocampal subfields
(recon-all -s -hippocampal-subfields-T2 ) I don´t have any problem.
What would be the reason?
Thanks in advance.
Best,
--
*Miguel Ángel Rivas Fernández*
___
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--
> *From:* freesurfer-boun...@nmr.mgh.harvard.edu <
> freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Miguel Ángel Rivas
> Fernández
> *Sent:* Tuesday, September 11, 2018 12:20:55 PM
> *To:* Freesurfer support list
> *Subject:* [Freesurfer] Amygdala subfields segm
you give more info on how you arrived at those numbers? Eg, are those
> the numbers after you imported into SPSS? If you look in an individual's
> aseg.stats file, do you see the same value?
>
> On 09/06/2018 12:41 PM, Miguel Ángel Rivas Fernández wrote:
> >
> >
Best wishes,
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The information in this e-mail is intended only for the person to whom it is
address
> <http://rmnlab1.inv.usc.es> 17.4.0 Darwin Kernel Version 17.4.0: Sun Dec 17
> 09:19:54 PST 2017; root:xnu-4570.41.2~1/RELEASE_X86_64 x86_64 T2
> hippocampal subfields exited with ERRORS at jueves, 13 de septiembre de
> 2018, 21:37:33 CEST*
>
>
>
>
>
>
>
> What would be
t;
> http://www.jeiglesias.com
>
> http://cmictig.cs.ucl.ac.uk/
>
>
>
>
>
> *From: * on behalf of Miguel
> Ángel Rivas Fernández
> *Reply-To: *Freesurfer support list
> *Date: *Sunday, 16 September 2018 at 15:52
> *To: *Freesurfer support list
> *Subjec
.
Best,
--
*Miguel Ángel Rivas Fernández*
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The information in this e-mail is intended only for the person to whom it is
addressed
-
>>
>> Juan Eugenio Iglesias
>>
>> ERC Senior Research Fellow
>>
>> Centre for Medical Image Computing (CMIC)
>>
>> University College London
>>
>> http://www.jeiglesias.com
>>
>> http://cmictig.cs.ucl.ac.uk/
>>
>>
>>
&g
could be the problem? The Freesurfer version that I am using at this
moment is freesurfer-Darwin-OSX-stable-pub-v6.0.0-2beb96c
Thanks in advance,
Best,
--
*Miguel Ángel Rivas Fernández*
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018, at 1:35 PM, Miguel Ángel Rivas Fernández <
> miguelrivasf...@gmail.com> wrote:
>
> External Email - Use Caution
>
>
> Hi Freesurfer devs,
>
>
> I tried to re run the recon -all after put some control points in the
> brainmask and I get the fol
-- Forwarded message -
From: Iglesias Gonzalez, Eugenio
Date: mié., 10 oct. 2018 a las 11:53
Subject: Re: [Freesurfer] Hippocampal-Amygdala subfields error
To: Miguel Ángel Rivas Fernández
Cc: Hoopes, Andrew
Hi again, MA.
I totally forgot to attach the binary.
The thing is that I don’t have
other information of a sensitive nature. If you
> are not the intended recipient, be advised that any unauthorized use,
> disclosure, copying or the taking of any action in reliance on the contents
> of this information is strictly prohibited. If you have received this email
> in error, please immediately notify the sender via teleph
it using separate commands?
Thanks in advance,
Cheers
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ed
> something not in those files?
> cheers
> Bruce
> On Thu, 1 Nov 2018, Miguel Ángel Rivas
> Fernández wrote:
>
> >
> > External Email - Use Caution
> >
> >
> > Hi Freesurfer devs,
> >
> > Is there any way to export all the stat
External Email - Use Caution
Hi Freesurfer devs,
How can I create a qdec.table.dat file? I tried using a txt file but it
doesn´t works. I attached the qdec.table.dat file that I have created.
Sorry for this absurd question and thanks in advance.
Cheers,
--
*Miguel Ángel Rivas
the lookup table used in the freeview.
Cheers,
--
*Miguel Ángel Rivas Fernández*
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in advance.
Cheers,
--
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smoothing of the images using a FWHM filter of 5,10,12.
Thanks in advance,
Cheers,
--
*Miguel Ángel Rivas Fernández*
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ó:
> Hi Miguel,
>
> not sure exactly where you mean, but the big chunk of gray that is
> missing from the surfaces is probably hippocampus (so not a problem, since
> it is not neocortex)
>
> cheers
> Bruce
>
>
> On Thu, 29 Nov 2018, Miguel Ángel Rivas Fernández
> wr
External Email - Use Caution
Hi Freesurfer devs,
I saw that Freesurfer export measures of hypointensities. I was wondering
if it´s possible to know where are located this brain lesions using as
reference some neuroanatomical atlas.
Best,
--
*Miguel Ángel Rivas Fernández
me neuroanatomical atlas.
>
>
> Best,
>
> --
> *Miguel Ángel Rivas Fernández*
>
> ___
> Freesurfer mailing
> listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
> ___
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Hi Douglas,
have you had occasion to review this matter? I was thinking that we also
have FLAIR and T2 images...
Thanks in advance for your help.
Best,
El vie., 8 feb. 2019 a las 18:36, Miguel Ángel Rivas Fernández (<
miguelrivasf...@gmail.
?. Any help would be appreciated.
Thanks in advance.
Best,
--
*Miguel Ángel Rivas Fernández*
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Dear Freesurfer devs,
Have you had occasion to review this error?. Could it be due to the gcc
version?
Thank you very much for your help.
Best regards,
El mié., 13 mar. 2019 a las 16:09, Miguel Ángel Rivas Fernández (<
miguelrivasf...@gmail.
Thank you very much for your help.
> >
> >
> > Best regards,
> >
> > El mié., 13 mar. 2019 a las 16:09, Miguel Ángel Rivas Fernández
> > (mailto:miguelrivasf...@gmail.com>>)
> escribió:
> >
> >
> > Dear Freesurfer experts,
> >
/Applications/freesurfer/subjects/10018/label/lh.aparc.annot: Signal 124
ans =
252
Best,
El jue., 14 mar. 2019 a las 18:59, Miguel Ángel Rivas Fernández (<
miguelrivasf...@gmail.com>) escribió:
>
> Hello Douglas,
>
> Yes it works
>
> El jue., 14 mar. 2019 a las 18:51
/001.mgz -rt nearest cerebellum_brainstem_mask.mgz
cerebellum_brainstem_mask.nii
Any help would be appreciated. Thanks in advance.
Best regards,
--
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https
ince they may change the
> topology of the cortex). If you upload the subject we will take a look, or
> you can try manually filling in the lesion in the wm.mgz (or marking it as
> lesion in the aseg.mgz) and seeing if that helps
>
> cheers
> Bruce
> On Wed, 26 Jun 2019, Miguel
External Email - Use Caution
Dear Freesurfer devs,
Is possible to change the image orientation of the t1.nii images? In that
case, what command should be used?. I would like to change them from a LPI
orientation to a RAI orientation.
Best regards,
--
*Miguel Ángel Rivas
spital
> 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 Miguel Ángel Rivas
> Fernández
> Sent: Wednesday, June 26, 2019
version that is installed in a Ubuntu 18.04 virtual machine. It is very
strange because few weeks ago everything it was working correctly.
Thanks in advance.
Best regards,
--
*Miguel Ángel Rivas Fernández*
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Freesurfer
available commands.
Best regards,
El lun., 16 sept. 2019 a las 22:58, Ruopeng Wang (<
rpw...@nmr.mgh.harvard.edu>) escribió:
> If you run:
>
> ls /usr/local/freesurfer/subjects/4227/mri/brainmask.mgz
>
> What does it show?
>
> Ruopeng
> On 9/16/19 4:2
sept. 2019 a las 1:56, Ruopeng Wang ()
escribió:
> Can you run the command in the command window that you start freeview?
>
> Ruopeng
>
> On Sep 16, 2019, at 5:11 PM, Miguel Ángel Rivas Fernández <
> miguelrivasf...@gmail.com> wrote:
>
> External Email - Use C
diciembre de 2019,
20:55:31 CET
For more details, see the log file
/Applications/freesurfer_dev/freesurfer/subjects/4001/scripts/thalamic-nuclei-BBREGISTER_MODE.log
Is the command right? I think that I have followed correctly the
instructions of the website.
Best regards,
--
*Miguel Ángel Rivas
22:53:14 PDT 2018; root:xnu-4570.71.2~1/RELEASE_X86_64 x86_64
trac-preproc exited with ERRORS at Mon Dec 9 22:00:14 CET 2019
You can find the configuration file and the trac-all.log file in attached.
Best regards,
--
*Miguel Ángel Rivas Fernández*
trac-all.log
Description: Binary data
.1.dylib
Expected in: /usr/lib/libSystem.B.dylib
I tried to fix this error disabling the SIP but this did not work. Maybe
could be due to the gcc compiler?
Any help would be appreciated
Thanks in advance
Best regards,
--
*Miguel Ángel Rivas Fernández
x27;
*PIR*
Thanks in advance,
Best regards,
--
*Miguel Ángel Rivas Fernández*
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r
> sourcing freesurfer. Also, are you using 6.0?
>
> Best,
> Andrew
>
>
> From: freesurfer-boun...@nmr.mgh.harvard.edu <
> freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Miguel Ángel Rivas
> Fernández
> Sent: Friday, February 7, 2020 6:17 AM
> To: Freesurf
is it not truly in PIR) or do
> you want to change the orientation? doing a left-right swap is more than
> changing the orientation
>
> On 2/11/2020 4:06 PM, Miguel Ángel Rivas Fernández wrote:
>
> External Email - Use Caution
> Dear Freesurfer experts,
>
> Which co
gards,
>
> El vie., 14 feb. 2020 a las 16:01, Douglas N. Greve (<
> dgr...@mgh.harvard.edu>) escribió:
>
>> Is the image in the wrong orientation (ie, is it not truly in PIR) or do
>> you want to change the orientation? doing a left-right swap is more than
>> changing t
External Email - Use Caution
Dear freesurfer experts,
Before running group analysis in qdec is necessary run the qcache command
over all subjects but, does this command change some segmentation file (eg.
rh/lh Pial or white surface) or other importants file?
We would also like to
left hemisphere and my subject have
the lesion in the right hemisphere. After the lesion estimation I need to
flip the left-right orientation.
Thank you very much for your time and attention.
Best regards,
El vie., 14 feb. 2020 a las 17:34, Miguel Ángel Rivas Fernández (<
miguelrivasf...@gmail.
subject?
Thanks for your time.
Best regards,
--
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Dear Freesurfer experts,
it is possible to export the stats of subjects reconstructed with
freesurfer v.6 using the HCP Multi Modal parcellation? (Glasser et al.,
2016).
Thank you in advance.
Best regards,
--
*Miguel Ángel Rivas Fernández
External Email - Use Caution
>
> What stats are you looking for?
>
> Matt.
>
>
>
> *From: * on behalf of Miguel
> Ángel Rivas Fernández
> *Reply-To: *Freesurfer support list
> *Date: *Wednesday, March 31, 2021 at 4:36 AM
> *To: *Freesurfer support list
>
4166 --meas thickness --parc
aparc.a2009s --tablefile thickness.txt
Usage: python [options]
python: error: no such option: --hemi
Could you give me some suggestions to solve this problem?
Thank you very much in advance.
Best regards,
--
*Miguel Ángel Rivas Fernández
External Email - Use Caution
Hi Douglas,
I would going from freesurfer 6 to freesurfer 5.3, not from FS 5.3 to FS 6.
Best,
El vie., 12 nov. 2021 15:51, Douglas N. Greve
escribió:
> If you are going from 5.3 to 6, you should just be able to run recon-all
> -all on the 5.3 fold
External Email - Use Caution
I am in the same situation as Steve. Is there a particular flag to rerun
subjects in freesurfer 5.3.
Best regards,
El vie., 12 nov. 2021 16:45, Miguel Ángel Rivas Fernández <
miguelrivasf...@gmail.com> escribió:
> Hi Douglas,
>
> I w
External Email - Use Caution
Dear Tim,
Thank you for your reply. I used these two commands and now it seems that
everything worked fine:
1) cd glmdir/contrast fscalc gamma.mgh div ../rstd.mgh -o cohensd.mgh
2) mri_segstats --i cohensd.mgh --seg cluster.sig.ocn.mgh --exclude 0
External Email - Use Caution
Sorry, I wrote this previous email from a different adress because I did
not receive emails from the freesurfer's support list 😅
Thank you!
El sáb., 25 dic. 2021 17:01, Miguel Ángel Rivas Fernández <
miguelrivasf...@gmail.com> escribió:
Py5tUIN1R8yNE0z6inFNO03qNg_rCEc4nZdI21ovpgphwZ_vGSDjElx46DXOl8-gN7QUoGJaNWa3gw2dNN6OFJf1PfG2BzwyfC1lpluweNf2UEC34tF23X4Cg_hk07mv_ah3X1EKDkAyhZPMGMr1Oqt09ot3g8Rv/http%3A%2F%2Fwww.jeiglesias.com
>
>
>
> *From: *freesurfer-boun...@nmr.mgh.harvard.edu <
> freesurfer-boun...@nmr.mgh.harvard.edu>
your time.
Best,
--
*Miguel Ángel Rivas Fernández*
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addressed
sub-NDARINVEMZZZWB9 --threads 1 --o apas+head.mgz
ERROR: cannot find
/input/Freesurfer_outputs//sub-NDARINVEMZZZWB9/mri/transforms/talairach.m3z
ERROR: xcerebralseg --s sub-NDARINVEMZZZWB9 --threads 1 --o apas+head.mgz
gtmseg exited with errors
Thank you very much
Best
--
*Miguel Ángel Rivas
External Email - Use Caution
Dear Eugenio,
My name is Miguel. I am currently processing data of the ABCD Study using
FreeSurfer. In our pipeline, we also include the specific FreeSurfer
segmentations for the hippocampus and amygdala. As an additional step, we
would like to use the
this step? If so, could you please specify the correct flag to use in
order to run recon-all properly?
Thank you very much for your assistance.
Best
--
*Miguel Ángel Rivas Fernández*
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