Hi Eugenio,
The folder scripts/ does not contain T1.log for hippocampal subfields. It only
has the log files I sent earlier.
Thanks
Theo
________________________________
From: freesurfer-boun...@nmr.mgh.harvard.edu
<freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of
freesurfer-requ...@nmr.mgh.harvard.edu <freesurfer-requ...@nmr.mgh.harvard.edu>
Sent: 27 February 2018 17:00:01
To: freesurfer@nmr.mgh.harvard.edu
Subject: Freesurfer Digest, Vol 168, Issue 54
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When replying, please edit your Subject line so it is more specific
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Today's Topics:
1. Re: Hippocampal Subfield Error (Iglesias Gonzalez, Eugenio)
2. Re: Invalid MEX file - FS dev-version error? (Hoopes, Andrew)
3. Re: Creating ROI on the functional map (Sarah Cole)
4. Freeview update on Mac (Sarah Cole)
5. Re: Invalid MEX file - FS dev-version error? (Fereshte)
6. Re: Antwort: Re: Quality issues when running recon-all
(Bruce Fischl)
----------------------------------------------------------------------
Message: 1
Date: Tue, 27 Feb 2018 16:13:30 +0000
From: "Iglesias Gonzalez, Eugenio" <e.igles...@ucl.ac.uk>
Subject: Re: [Freesurfer] Hippocampal Subfield Error
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Message-ID: <cd18a07c-5fc8-4ec4-be83-d282314ff...@ucl.ac.uk>
Content-Type: text/plain; charset="utf-8"
Hi Theo,
Sorry for not being more clear; I meant hippocampal-subfields-T1.log, which
should be in the directory ?scripts?.
Cheers,
/Eugenio
--
Juan Eugenio Iglesias
ERC Senior Research Fellow
Translational Imaging Group
University College London
http://www.jeiglesias.com
http://cmictig.cs.ucl.ac.uk/
From: <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of "AKUDJEDU,
THEOPHILUS" <t.akudje...@nuigalway.ie>
Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Date: Tuesday, 27 February 2018 at 15:31
To: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu>
Subject: [Freesurfer] Hippocampal Subfield Error
Dear Eugenio,
Attached as requested.
Thanks
Theo
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Message: 2
Date: Tue, 27 Feb 2018 16:23:36 +0000
From: "Hoopes, Andrew" <ahoo...@mgh.harvard.edu>
Subject: Re: [Freesurfer] Invalid MEX file - FS dev-version error?
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>,
"Reetta-Liina Armio" <rls...@utu.fi>
Message-ID: <etpan.5a958607.6e9d99d4....@mgh.harvard.edu>
Content-Type: text/plain; charset="utf-8"
Hi Reetta, can you source freesurfer, run the ?bugr? command, and send the
given buildstamp?
thanks
Andrew
On February 27, 2018 at 5:42:14 AM, Reetta-Liina Armio
(rls...@utu.fi<mailto:rls...@utu.fi>) wrote:
Dear Freesurfer developers,
I have run basic segmentation (and hippocampal segmentation) with Freesurfer
6.0. I have now tried to run amygdala segmentation with dev-version (downloaded
from the FS-site today).
I have run the same amygdalasegmentation with same platform etc in October 2017
and was able to get the volumes. I?m now trying to repeat the run with newer
dev-version.
I get this Error
?invalid MEX file.?
So there is something wrong with the path?
Could you kindly help me with this?
Thank you in advance!
See log-file and Matlab-version attached.
Best,
Reetta-Liina Armio
L?hetetty iPhonesta
[cid:399A78D3-2E7E-4165-AFF6-773C57D612D7]
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Message: 3
Date: Tue, 27 Feb 2018 10:23:30 -0600
From: Sarah Cole <coleashle...@gmail.com>
Subject: Re: [Freesurfer] Creating ROI on the functional map
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Message-ID:
<cajwstc22mc84bj-rfh2d32awhd3w7hfesgtsh+_one2qvqa...@mail.gmail.com>
Content-Type: text/plain; charset="utf-8"
I apologize. I was wrong.
Thanks,
S
On Mon, Feb 26, 2018 at 5:16 PM, Sarah Cole <coleashle...@gmail.com> wrote:
> It doesn't work on tksurfer. But it's ok.
>
> So Doug, is this the latest tutorial: https://surfer.nmr.mgh.
> harvard.edu/fswiki/FsTutorial/MultiModalFmriIndividual_freeview for
> FS-FAST and creating functional ROI?
>
> More specifically, do I need to use "mri_vol2surf" to get the activation
> on the surface?
>
> This was not in the other tutorial: http://surfer.nmr.mgh.harvard.
> edu/fswiki/FsFastTutorialV6.0/FsFastFirstLevel
>
>
> Thanks
>
> On Mon, Feb 26, 2018 at 3:28 PM, Douglas N Greve <
> gr...@nmr.mgh.harvard.edu> wrote:
>
>> I think it should work; We are not using tksurfer any more (freeview
>> instead), but I think it should still work
>>
>>
>> On 02/23/2018 05:16 PM, Sarah Cole wrote:
>> > Hi,
>> >
>> > I was wondering if this method is still applicable in version 6
>> > https://surfer.nmr.mgh.harvard.edu/fswiki/CreatingROIs
>> >
>> >
>> > I cannot seem to find any of the options for creating an ROI.
>> >
>> > Thank you,
>> >
>> > S
>> >
>> >
>> > _______________________________________________
>> > Freesurfer mailing list
>> > Freesurfer@nmr.mgh.harvard.edu
>> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>
>> --
>> Douglas N. Greve, Ph.D.
>> MGH-NMR Center
>> gr...@nmr.mgh.harvard.edu
>> Phone Number: 617-724-2358
>> Fax: 617-726-7422
>>
>> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
>> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
>> www.nmr.mgh.harvard.edu/facility/filedrop/index.html<http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html>
>> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
>>
>> _______________________________________________
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu
>> 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, please contact the Partners Compliance
>> HelpLine at
>> http://www.partners.org/complianceline . If the e-mail was sent to you
>> in error
>> but does not contain patient information, please contact the sender and
>> properly
>> dispose of the e-mail.
>>
>>
>
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------------------------------
Message: 4
Date: Tue, 27 Feb 2018 10:37:08 -0600
From: Sarah Cole <coleashle...@gmail.com>
Subject: [Freesurfer] Freeview update on Mac
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Message-ID:
<cajwstc3+sg4fg41k11djhmmzctw6ryp55-bbifdhvh_kp6_...@mail.gmail.com>
Content-Type: text/plain; charset="utf-8"
Hi Doug/Zeke,
Could you please update the page for freeview update on Mac- if it is
available.
https://surfer.nmr.mgh.harvard.edu/fswiki/UpdateFreeview
Thanks,
S
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Message: 5
Date: Tue, 27 Feb 2018 16:43:55 +0000
From: Fereshte <fereshte.ramez...@gmail.com>
Subject: Re: [Freesurfer] Invalid MEX file - FS dev-version error?
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Message-ID:
<caadxbzp83unnqkzzetdt39_cbzocu7avyaw3vwhru4s2cpj...@mail.gmail.com>
Content-Type: text/plain; charset="utf-8"
I?m not sure about MATLAB 2014b but you need to have installed Microsoft
Visual c++ ( 2008 works fine with R2014a) and Fortran to compile MEX files;
that may be the problem.
Cheers
On Tue, Feb 27, 2018 at 3:42 PM Reetta-Liina Armio <rls...@utu.fi> wrote:
> Thank you, but what exactly should I do?
>
> -Reetta-Liina Armio
>
> L?hetetty iPhonesta
>
> Fereshte <fereshte.ramez...@gmail.com> kirjoitti 27.2.2018 kello 13.00:
>
> Dear Reetta
> Check if you?ve got the right compiler for the MEX files.
> Regards,
> Fereshte
> On Tue, Feb 27, 2018 at 2:10 PM Reetta-Liina Armio <rls...@utu.fi> wrote:
>
>> Dear Freesurfer developers,
>>
>> I have run basic segmentation (and hippocampal segmentation) with
>> Freesurfer 6.0. I have now tried to run amygdala segmentation with
>> dev-version (downloaded from the FS-site today).
>>
>> I have run the same amygdalasegmentation with same platform etc in
>> October 2017 and was able to get the volumes. I?m now trying to repeat the
>> run with newer dev-version.
>>
>> I get this Error
>> ?invalid MEX file.?
>>
>> So there is something wrong with the path?
>>
>> Could you kindly help me with this?
>>
>> Thank you in advance!
>>
>> See log-file and Matlab-version attached.
>>
>> Best,
>> Reetta-Liina Armio
>>
>> L?hetetty iPhonesta
>>
>>
>>
>> _______________________________________________
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu
>> 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, please contact the Partners Compliance
>> HelpLine at
>> http://www.partners.org/complianceline . If the e-mail was sent to you
>> in error
>> but does not contain patient information, please contact the sender and
>> properly
>> dispose of the e-mail.
>>
> _______________________________________________
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> 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, please contact the Partners Compliance
> HelpLine at
> http://www.partners.org/complianceline . If the e-mail was sent to you in
> error
> but does not contain patient information, please contact the sender and
> properly
> dispose of the e-mail.
>
> _______________________________________________
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> 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, please contact the Partners Compliance
> HelpLine at
> http://www.partners.org/complianceline . If the e-mail was sent to you in
> error
> but does not contain patient information, please contact the sender and
> properly
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>
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------------------------------
Message: 6
Date: Tue, 27 Feb 2018 11:45:03 -0500 (EST)
From: Bruce Fischl <fis...@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] Antwort: Re: Quality issues when running
recon-all
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Message-ID:
<alpine.lrh.2.21.1802271144120.49...@tiamat.nmr.mgh.harvard.edu>
Content-Type: text/plain; charset="utf-8"
no worries. That is a pretty short TR and a pretty long TE for a typical
T1-weighted scan. Do you know what kind of scan it was? That is, the name
of the sequence (e.g. FLASH, MPRAGE, SPGR, etc...)
cheers
Bruce
On Tue, 27 Feb 2018, adriancarl.stei...@uzh.ch wrote:
> Hi Bruce
> Thank you very much for your swift response. Our image was?
> T1-weighted, with a resolution of 240 x 240 x 160 and a field
> intensity of 3 Tesla. The Sequence was TR/TE 10.66/6.04 ms.
> I have attached the recon-all.log file to this?mail. Sorry for?
> not having supplied the required information
> the first time, as I said it is my first try with freesurfer.
>
> Cheers?
>
> Adrian
>
> -----freesurfer-boun...@nmr.mgh.harvard.edu schrieb: -----An: Freesurfer
> support list <freesurfer@nmr.mgh.harvard.edu>
> Von: Bruce Fischl
> Gesendet von: freesurfer-boun...@nmr.mgh.harvard.edu
> Datum: 27.02.2018 16:05
> Kopie: Fedele Tommaso <tommaso.fed...@usz.ch>
> Betreff: Re: [Freesurfer] Quality issues when running recon-all
>
> Hi Adrian
>
> it's impossible for us to diagnose without more information. What was the
> acquisition (field strength, resolution, sequence type, etc...) and at
> least send us the contents of the recon-all.log file.
>
> cheers
> Bruce
> On Tue, 27 Feb 2018,
> adriancarl.stei...@uzh.ch wrote:
>
> > Dear Freesurfer community,
> >
> > I am at my first experience with Freesurfer. Following the tutorial,
> > I ran Freesurfer on MR images for my Master Thesis.
> >
> > When running Freesurfer's 'recon-all' command on a Mac Pro to
> > process a .nii MRI file, I was able to complete all calculations
> > in approximately 10 hours as estimated, and obtained a message
> > that all operations were completed without Errors or bugs.
> >
> > However, the image I was able to retrieve from the lh.pial file
> > seems to be of greatly inferior quality compared to the ones we
> > obtained from a test run using tutorial data. Attached to this mail,
> > you will find screenshots of the MR and?the lh.pial output from
> > Freesurfer.
> >
> > This is the code I entered into Terminal to set up recon-all:
> >
> > export FREESURFER_HOME=/Volumes/LaCie/freesurfer
> >
> > source $FREESURFER_HOME/SetUpFreeSurfer.sh
> >
> > mri_convert -c -oc 0 0 0 /Volumes/LACIE-SHARE/Adrian/Patient data
> > .nii/IA/IA_MRpre
> > .nii/T1_3D_TFE_DBS.nii
> > /Volumes/LaCie/freesurfer/buckner_data/tutorial_subjs/multimodal/fmri/fbirn-101/template.nii
> >
> > ?
> >
> > S_NAME=IA
> >
> > DATA_PATH=/Volumes/LaCie/freesurfer/buckner_data/tutorial_subjs/multimodal/fmri/fbirn-101/template.
> > nii
> >
> > ?
> >
> > recon-all -i $DATA_PATH -subject $S_NAME -all
> >
> > ?
> > Given the good quality of the MR, I expected a better quality in
> > the Freesurfer Output. Could you please help me understand how I
> > can improve my results?
> >
> > Thank you in advance for your Support
> >
> > Adrian Steiner
> >
> >
> _______________________________________________
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> 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, please contact the Partners Compliance HelpLine
> at
> http://www.partners.org/complianceline?. If the e-mail was sent to you in
> error
> but does not contain patient information, please contact the sender and
> properly
> dispose of the e-mail.
>
>
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