Re: [Freesurfer] Freesurfer Template Creation
Dear experts, any suggestion about my question? (see below) Thank you in advance! Daniele \- Messaggio originale - \Da: "Daniele Orlandi" \A: freesurfer@nmr.mgh.harvard.edu \Inviato: Venerdì, 16 giugno 2017 18:01:59 \Oggetto: Freesurfer Template Creation \ \Dear experts, \ \I'm running the Fresurfer Longitudinal Stream and I didn't realize that creating the Template file, some time points were not in the right order: \ \ recon-all -base -tp -tp -tp -tp -all \ \instead of: \ \ recon-all -base -tp -tp -tp -tp -all \ \Does it affect the creation of the Template? \ \Thank you again! \ \Best \ \Daniele ___ 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] Freesurfer Template Creation
Dear experts,
I'm running the Fresurfer Longitudinal Stream and I didn't realize that
creating the Template file, some time points were not in the right order:
recon-all -base -tp -tp -tp -tp
-all
instead of:
recon-all -base -tp -tp -tp -tp
-all
Does it affect the creation of the Template?
Thank you again!
Best
Daniele
_____
Daniele Orlandi, PsyD
Laboratory of Alzheimer's Neuroimaging and Epidemiology
IRCCS Fatebenefratelli,Via Pilastroni 4,25125 Brescia - Italy
T: +39 030 35 01 563 - M: +39 346 50 90 531
daniele.orlandi@gmail.com
Skype: daniele.orlandi.skype
- Original Message -
From: freesurfer-requ...@nmr.mgh.harvard.edu
To: freesurfer@nmr.mgh.harvard.edu
Sent: Thursday, June 15, 2017 11:33:01 PM
Subject: Freesurfer Digest, Vol 160, Issue 27
Send Freesurfer mailing list submissions to
freesurfer@nmr.mgh.harvard.edu
To subscribe or unsubscribe via the World Wide Web, visit
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
or, via email, send a message with subject or body 'help' to
freesurfer-requ...@nmr.mgh.harvard.edu
You can reach the person managing the list at
freesurfer-ow...@nmr.mgh.harvard.edu
When replying, please edit your Subject line so it is more specific
than "Re: Contents of Freesurfer digest..."
Today's Topics:
1. Re: viewing 3D surfaces (Michael Davies)
2. Freesurfer parcelations of cortical regions in TrackVis
(Leyton Moscoso, Cristian Eduardo)
3. Re: viewing 3D surfaces (Bruce Fischl)
4. Re: mris_anatomical_stats and cortical thickness {Disarmed}
{Disarmed} (Hilton, Benjamin Taylor)
5. bvals and bvecs for tracula v6 (Marissa Pifer)
6. Re: bvals and bvecs for tracula v6 (Yendiki, Anastasia)
7. Re: viewing 3D surfaces (Michael Davies)
8. Re: viewing 3D surfaces (Bruce Fischl)
9. substract images (John Anderson)
10. Re: substract images (Bruce Fischl)
11. Re: substract images (John Anderson)
12. Re: viewing 3D surfaces (Michael Davies)
13. Re: substract images (Bruce Fischl)
14. Re: viewing 3D surfaces (Bruce Fischl)
15. Re: Freesurfer parcelations of cortical regions in TrackVis
(Lilla Zollei)
16. Re: substract images (John Anderson)
17. Re: substract images (Bruce Fischl)
18. Re: substract images (John Anderson)
19. Cropping of slices during recon-all (Jerry Jeyachandra)
20. When running mkcontrast-sess: A fatal error has been detected
by the Java Runtime Environment (???)
--
Message: 1
Date: Thu, 15 Jun 2017 16:01:58 +
From: Michael Davies
Subject: Re: [Freesurfer] viewing 3D surfaces
To: Freesurfer support list
Message-ID:
Content-Type: text/plain; charset="windows-1252"
That did it :) thank you so much for your help!!
Kind regards, Michael
From: freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of Ruopeng Wang
Sent: 15 June 2017 15:48:31
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] viewing 3D surfaces
Remove the '/' in front of "surf".
On 06/15/2017 11:45 AM, Michael Davies wrote:
Hi Bruce, i'm getting closer to opening it now. But the final command
/surf/lh.pial \ didnt work this time. Any further suggestions?
Kind regards, Michael
bash-4.1$ freesurfer_setup_freeview
freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c
Setting up environment for FreeSurfer/FS-FAST (and FSL)
FREESURFER_HOME /usr/local/freesurfer_v6.0.0
FSFAST_HOME /usr/local/freesurfer_v6.0.0/fsfast
FSF_OUTPUT_FORMAT nii.gz
SUBJECTS_DIR /usr/local/freesurfer_v6.0.0/subjects
MNI_DIR /usr/local/freesurfer_v6.0.0/mni
FSL_DIR /usr/local/fsl
bash-4.1$ cd /projects/pbic1030/Michael/subjects/Subj1/fsaverage
bash-4.1$ freeview -f \
> /surf/lh.pial:annot=aparc.annot:name=pial_aparc:visible=0 \
> /surf/lh.inflated:overlay=lh.thickness:overlay_threshold=0.1,3::name=inflated_thickness:visible=0
> \
> /surf/lh.inflated:visible=0 \
> /surf/lh.white:visible=0 \
> /surf/lh.pial \
> --viewport 3d
MRISread(/surf/lh.pial): could not open file
No such file or directory
MRISread failed
No such file or directory
ould not open file
bash-4.1$
From:
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
on behalf of Bruce Fischl
<mailto:fis...@nmr.mgh.harvard.edu>
Sent: 15 June 2017 15:19:21
To: Freesurfer support list
Subject: Re: [Freesurfer] viewing 3D surfaces
you are not calling freeview in this command. Try putting freeview at the
start
On Thu, 15 Jun 2017, Michael Davies wrote:
>
> Hi Bruce, i am still getting error messages. is there anything else i could
> try d
Re: [Freesurfer] Freesurfer Digest, Vol 153, Issue 8
Ciao Eugenio, I've just checked the presence of the file T1resampled.mgz and it doesn't show up in tmp/ folder as well as in other folders of the same subject. Morover, the T1resampled.mgz file is not present in ever subjects folder at every time point as well as for the base/template folder. Daniele Message: 11 Date: Mon, 7 Nov 2016 16:47:02 + From: "Iglesias Gonzalez, Eugenio" Subject: Re: [Freesurfer] FreeSurfer 6.0 (beta) Error in segmentSubjectT1_autoEstimateAlveusML (line 588) To: Freesurfer support list Message-ID: Content-Type: text/plain; charset="utf-8" Ciao Daniele, This is weird. Would you mind verifying that file T1resampled.mgz actually exists in the temporary directory of the subject? You can do that by CDing to $SUBJECT_DIR/[SUBJECT_NAME]/tmp and running the command: find . -name ?T1resampled.mgz? 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/ On 7 Nov 2016, at 16:39, Daniele Orlandi mailto:dorla...@fatebenefratelli.eu>> wrote: Dear experts, I've finished FSv5.3 longitudinal analysis and I'm now running FSv6.0(beta) for hippocampal subfield features extraction (always on Ubuntu 14.01 environment). After several trial I realized that before pipeline ends I've got the following error: /opt/FreeSurfer-6-Beta/bin//mri_mask -T 0.5 T1resampled.mgz hippoMaskResampledDilated.mgz T1resampled.mgz >/dev/null: Signal 127 Error using kvlGEMSMatlab /cluster/koen/eugenio/GEMS/itkMGHImageIO.cxx:216: itk::ERROR: MGHImageIO(0x7fe88bcda050): Can't find/open file: T1resampled.mgz Error in kvlReadCroppedImage (line 11) Error in segmentSubjectT1_autoEstimateAlveusML (line 588) Could you help me? Best Daniele PS: Even though one of the last row display " finished without error", no output is generated in the /mri/ folder. -- -- Daniele Orlandi, PsyD IRCCS Fatebenefratelli Via Pilastroni 4 25125 Brescia - Italy tel: +39 030 35 01 563 e-mail: dorla...@fatebenefratelli.eu<mailto:dorla...@fatebenefratelli.eu> ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu<mailto: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. -- next part -- An HTML attachment was scrubbed... URL: http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20161107/49274679/attachment-0001.html -- ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer End of Freesurfer Digest, Vol 153, Issue 8 ** ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] FreeSurfer 6.0 (beta) Error in segmentSubjectT1_autoEstimateAlveusML (line 588)
Dear experts, I've finished FSv5.3 longitudinal analysis and I'm now running FSv6.0(beta) for hippocampal subfield features extraction (always on Ubuntu 14.01 environment). After several trial I realized that before pipeline ends I've got the following error: /opt/FreeSurfer-6-Beta/bin//mri_mask -T 0.5 T1resampled.mgz hippoMaskResampledDilated.mgz T1resampled.mgz >/dev/null: Signal 127 Error using kvlGEMSMatlab /cluster/koen/eugenio/GEMS/itkMGHImageIO.cxx:216: itk::ERROR: MGHImageIO(0x7fe88bcda050): Can't find/open file: T1resampled.mgz Error in kvlReadCroppedImage (line 11) Error in segmentSubjectT1_autoEstimateAlveusML (line 588) Could you help me? Best Daniele PS: Even though one of the last row display " finished without error", no output is generated in the /mri/ folder. -- -- Daniele Orlandi, PsyD IRCCS Fatebenefratelli Via Pilastroni 4 25125 Brescia - Italy tel: +39 030 35 01 563 e-mail: dorla...@fatebenefratelli.eu ___ 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] -hippocampal-subfields-T1
dear all, I'm running analysis with the new FS-v6.0 using the flag -hippocampal-subfields-T1 and I get the following error: none Matrix: -3.3 0 0 0 0 -3.3 0 3.3 0 Offset: [-34.0783, 128.423, -71.9905] Center: [0, 0, 0] Translation: [-34.0783, 128.423, -71.9905] Inverse: -0.3 0 0 0 0 0.3 0 -0.3 0 Singular: 0 I am WriteImage and I'm running! Wrote image to file asmr2.mgz This file does not contain MRI parameters Error using zeros NaN and Inf not allowed. Error in segmentSubjectT1_autoEstimateAlveusML (line 1396) MATLAB:nonaninf How I can solve it? Best, Daniele ___ 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] subfields segmentation FS v6.0
Dear all I'm running the new pipleline for hippocampal subfields segmentation with FreeSurfer v6.0 on a T13D image. As results i can extract values for the Whole hippocampus and the following subfields: Hippocampal_tail, subiculum, CA1, hippocampal-fissure, presubiculum, parasubiculum, molecular_layer_HP, GC-ML-DG, CA3, CA4, fimbria, HATA but not for Alveus as reported in the paper of Iglesias, JE. et al. 2015. Was my computation wrong? Best, Daniele ___ 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.
Re: [Freesurfer] visualizing paths stats by voxel
;> Hi Anastasia, > >>>>>> > >>>>>> yes, I am. But it looks similar in the distributed version :( > >>>>>> > >>>>>> Thanks, > >>>>>> > >>>>>> Janosch > >>>>>> > >>>>>>> Am 08.08.2015 um 00:48 schrieb Anastasia Yendiki < > ayend...@nmr.mgh.harvard.edu>: > >>>>>>> > >>>>>>> > >>>>>>> Hi Janosch - Are you by any chance using the dev version of > freeview? > >>>>>>> > >>>>>>> a.y > >>>>>>> > >>>>>>> On Fri, 7 Aug 2015, Janosch Linkersdörfer wrote: > >>>>>>> > >>>>>>>> Hi Anastasia and list, > >>>>>>>> > >>>>>>>> I'm trying to do analyses along the tract with the > path_stats_byvoxel files. > >>>>>>>> > >>>>>>>> When I am visualizing the points using the waypoint functionality > of Freeview, it looks a little strange, i.e., the points are not equally > spaces on the tract, but clumped together at some parts and spread out on > others, see: > >>>>>>>> > >>>>>>>> > >>>>>>>> > >>>>>>>> this looks different to your slides: > >>>>>>>> > >>>>>>>> > >>>>>>>> > >>>>>>>> Also, the most posterior points seem to be strangely located (in > the other hemisphere). What could be the reason for this strange behavior? > >>>>>>>> > >>>>>>>> Thanks, > >>>>>>>> > >>>>>>>> Janosch > >>>>>>> > >>>>>>> > >>>>>>> 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. > > -- ___ Daniele Orlandi, PsyD, Research Assistant Laboratory of Epidemiology, Neuroimaging Alzheimer IRCCS Centro San Giovanni di Dio, Fatebenefratelli Via Pilastroni 4 25125 Brescia - Italy tel:+39 030/3501563 cell: +39 3495119685 <%2B39%20030%2F3501563> email: dorla...@fatebenefratelli.it; daniele.orlandi@gmail.com (http://www.centroalzheimer.org/sito/chi_staff_e.php) ___ 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] -hippocampal-subfields-T1T2
Dear All, I'm trying to run the flag -hippocampal-subfields-T1T2 with the new FS v6.0 but I get the following error: >Fitting mesh to synthetic image from ASEG took 217.8633 seconds >Transforming points >Transforming points >ltaReadFile(/media/orlandi/Ub4_Shared_HD/orlandi/PharmaCog-Volontari/CARTELLE-avg+base+long+T2/out_v5.3_35-MRIT1-VO-003-T01-avg.long.base_v5.3_35-MRIT1-VO-003/mri/transforms/T1_to_T1+T2.v10.lta): can't open file >No such file or directory >ERROR: Reading transform from file /media/orlandi/Ub4_Shared_HD/orlandi/PharmaCog-Volontari/CARTELLE-avg+base+long+T2/out_v5.3_35-MRIT1-VO-003-T01-avg.long.base_v5.3_35-MRIT1-VO-003/mri/transforms/T1_to_T1+T2.v10.lta Do you have any suggestion? thank you all for your collaboration Daniele ___________ Daniele Orlandi, PsyD, Research Assistant Laboratory of Epidemiology, Neuroimaging Alzheimer IRCCS Centro San Giovanni di Dio, Fatebenefratelli Via Pilastroni 4 25125 Brescia - Italy tel:+39 030/3501563 cell: +39 3495119685 <%2B39%20030%2F3501563> email: dorla...@fatebenefratelli.it; daniele.orlandi@gmail.com (http://www.centroalzheimer.org/sito/chi_staff_e.php) ___ 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.
