External Email - Use Caution Hi Lea,
Thanks for the tips! I think I did something similar for a previous test without hipo segmentation (took nearly 3 to 4h). I will check the way I've got to set the number of cpu per tasks, just in case. Thanks Alex > Message: 20 > Date: Fri, 20 Apr 2018 09:19:12 +0000 > From: "Backhausen, Lea" <lea.backhau...@uniklinikum-dresden.de> > Subject: Re: [Freesurfer] SLURM - speed processing (Alexandre Obert) > To: "'freesurfer@nmr.mgh.harvard.edu'" > <freesurfer@nmr.mgh.harvard.edu> > Message-ID: > <1d0e7a9ed60d3e4399550c3a60c0badc39460...@g06edbn1.med.tu-dr > esden.de> > Content-Type: text/plain; charset="utf-8" > > External Email - Use Caution > > Hi Alex, > > I am also running FreeSurfer 6.0.0 on SLURM and recently did some tests on > how to parallelize it, how much ressources to ask for? This is what I > learned: > > 1) FreeSurfer 6.0.0 is able to use OpenMP parallelization (I guess > for the commands mri_em_register, mri_ca_register and mri_ca label used in > the steps Skull Stripping, EM registration, CA reg and Subcortical > registration). > 2) From Version 6.0.0 FreeSurfer is also able to process the two > hemispheres in parallel instead of sequentially (steps 16 ? 30). > > Taking advantage of these changes reduces processing time dramatically. If > I use 4 CPU per task on SLURM instead of 1 the processing time drops form > around 8 hours to around 4 or 4 ? hours. Increasing the CPU per task did > not improve processing time much though, so to save a bit CPU time now use > 4 CPU regularly. > I don?t know if you have to submit your jobs exactly the same way but a > typical job file for me looks like this: > > ------------------------------------------------------------ > ------------------------ > #!/bin/bash > #SBATCH --time=10:00:00 > #SBATCH --output=/your_working_directory/job-%j.out > #SBATCH --error=/your_working_directory/job-%j.err > #SBATCH --nodes=1 > #SBATCH --ntasks=1 > #SBATCH --tasks-per-node=1 > #SBATCH --cpus-per-task=4 > #SBATCH --partition=haswell > #SBATCH --mem-per-cpu=2500 > #SBATCH -A your_project_name > > module load modenv/eb > module load FreeSurfer > source $FREESURFER_HOME/SetUpFreeSurfer.sh > > export SUBJECTS_DIR=/your_subjects_directory > > recon-all -s your_subject_ID -all -parallel -openmp 4 > ------------------------------------------------------------ > -------------------------- > > > Of course you can just add the ?hippocampal-subfields-T1 tag flag your > command. > I found that asking for 2500 MB works just fine for 4CPU per task (as the > 2500 is multiplied times 4 in this case). The maximum RAM was about 7000 KB > for my jobs. > Just make sure you add the? -parallel -openmp 4? flag to your command line > AND ?#SBATCH --cpus-per-task=4? to your job file, otherwise the > parallelization will not work. > > > Hope this helps! Get back to me if you have any more questions! > > Best, > Lea > > ------------------------------ > Lea Backhausen > Research Assistant > > Department of Child and Adolescent Psychiatry, Faculty of Medicine of the > TU Dresden, Germany > http://www.uniklinikum-dresden.de > > > ------------------------------ > > Message: 5 > Date: Thu, 19 Apr 2018 17:05:46 +0200 > From: Alexandre Obert <obert.alexan...@gmail.com> > Subject: [Freesurfer] SLURM - speed processing > To: freesurfer@nmr.mgh.harvard.edu > Message-ID: > <CAGTEUh_XypWu4h+4ban62BfH8idf96HEquUL+OMMaWT_GEk4Cw@mail. > gmail.com> > Content-Type: text/plain; charset="utf-8" > > External Email - Use Caution > > Hi all, > > I'm definitively a noob with both freesurfer and SLURM processes and I > wonder if anyone could give me some advice. > I tried processing a subject (including hippocampal segmentation) using > the following command (freesurfer 6.0.0): > > recon-all -all -s s03 -hippocampal-subfields-T1 > > It took nearly 12h to process. > I then submit this job to a supercomputer (using slurm) and I asked for > nearly 30Go RAM It took nearly 7h to process. That seems good but I wonder > if it's possible to speed it up a little more? > > Regards, > > Alex > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachm > ents/20180419/cbcc829a/attachment-0001.html > > ------------------------------ > > Message: 6 > Date: Thu, 19 Apr 2018 11:57:45 -0400 > From: "Douglas N. Greve" <dgr...@mgh.harvard.edu> > Subject: Re: [Freesurfer] LGI for the lobar annotation > To: "Fernanda Hansen P. de Moraes" <fernandahmor...@gmail.com> > Cc: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu> > Message-ID: <9822cb24-192a-2713-0418-b215da87d...@mgh.harvard.edu> > Content-Type: text/plain; charset="utf-8"; format=flowed > > yes > > > On 04/19/2018 07:17 AM, Fernanda Hansen P. de Moraes wrote: > > Douglas, thank you very much again. > > So I can assume it is the lGI for the area (in this case the lobe)? > > > > Thank you again! > > > > On Wed, Apr 18, 2018 at 11:48 PM Douglas Greve <dgr...@mgh.harvard.edu > > <mailto:dgr...@mgh.harvard.edu>> wrote: > > > > The "intensity" is the mean value of the input (lh.pial_lgi in > > this case) averaged over vertices. If? you wan the total number, > > multiply it by the number of vertices or re-run with --accumulate. > > The area is the surface area of the entire lobe. > > > > > > On 4/18/18 3:23 PM, Fernanda Hansen P. de Moraes wrote: > >> Sorry, my mistake. > >> > >> mri_segstats --annot DA011 lh lobesStrict --i > >> DA011/surf/lh.pial_lgi --sum lh.lobesStrict.annot.pial_lgi.stats > >> > >> On Wed, Apr 18, 2018 at 4:13 PM Douglas N. Greve > >> <dgr...@mgh.harvard.edu <mailto:dgr...@mgh.harvard.edu>> wrote: > >> > >> What is your command line? Also, please remember to post to > >> the list > >> > >> > >> On 04/18/2018 02:10 PM, Fernanda Hansen P. de Moraes wrote: > >> > Dear Douglas, > >> > > >> > thank you. > >> > > >> > ?The code worked, but I didn't understand the result very > >> well. What > >> > means intensity? The area, is the ara from the piall_lgi > >> surface > >> > (outer surface)? > >> > > >> > Thank you again > >> > > >> > On Tue, Apr 17, 2018 at 1:07 PM Douglas Greve > >> <dgr...@mgh.harvard.edu <mailto:dgr...@mgh.harvard.edu> > >> > <mailto:dgr...@mgh.harvard.edu > >> <mailto:dgr...@mgh.harvard.edu>>> wrote: > >> > > >> >? ? ?If you run it with --help you will see an example > >> > > >> > > >> >? ? ?On 4/16/18 7:16 AM, Fernanda Hansen P. de Moraes wrote: > >> >>? ? ?Thank you, Douglas, > >> >> > >> >>? ? ?do you have any suggestions?on how to make you work? > >> >> > >> >>? ? ?Fernanda > >> >> > >> >> > >> >> > >> >>? ? ?On Fri, Apr 13, 2018 at 5:56 PM Douglas Greve > >> >>? ? ?<dgr...@mgh.harvard.edu > >> <mailto:dgr...@mgh.harvard.edu> > >> <mailto:dgr...@mgh.harvard.edu > >> <mailto:dgr...@mgh.harvard.edu>>> wrote: > >> >> > >> >>? ? ? ? ?that should work, except the command line is not > >> quite right > >> >> > >> >> > >> >>? ? ? ? ?On 4/13/18 4:22 PM, Fernanda Hansen P. de Moraes > >> wrote: > >> >>>? ? ? ? ?Good night, > >> >>> > >> >>>? ? ? ? ?does anyone know if it is possible to calculate > >> the lGI for > >> >>>? ? ? ? ?the ?h.lobesStrict.annot? And if it yes, how can > >> I do it? > >> >>> > >> >>>? ? ? ? ?I've already tried to use: > >> >>> > >> >>>? ? ? ? ?/mri_segstats --annot > >> subjxx/label/lh.lobesStrict.annot --i > >> >>> ?$SUBJECTS_DIR/subjxx/surf/lh.pial_lgi --sum > >> >>> ?lh.lobesStrict.annot.pial_lgi.stats/ > >> >>> > >> >>>? ? ? ? ?Thank you! > >> >>>? ? ? ? ?-- > >> >>>? ? ? ? ?Fernanda Hansen P. de Moraes > >> >>>? ? ? ? ?F?sica M?dica | Instituto D'Or de Pesquisa e > >> Ensino?| Rede > >> >>>? ? ? ? ?D'Or S?o Luiz > >> >>> > >> >>> > >> >>> ?_______________________________________________ > >> >>>? ? ? ? ?Freesurfer mailing list > >> >>> Freesurfer@nmr.mgh.harvard.edu > >> <mailto:Freesurfer@nmr.mgh.harvard.edu> > >> >>>? ? ? ? ?<mailto:Freesurfer@nmr.mgh.harvard.edu > >> <mailto:Freesurfer@nmr.mgh.harvard.edu>> > >> >>> https://mail.nmr.mgh.harvard.e > du/mailman/listinfo/freesurfer > >> >> > >> >> ?_______________________________________________ > >> >>? ? ? ? ?Freesurfer mailing list > >> >> Freesurfer@nmr.mgh.harvard.edu > >> <mailto:Freesurfer@nmr.mgh.harvard.edu> > >> >>? ? ? ? ?<mailto: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. > >> >> > >> >>? ? ?-- > >> >>? ? ?Fernanda Hansen P. de Moraes > >> >>? ? ?F?sica M?dica | Instituto D'Or de Pesquisa e Ensino?| > >> Rede D'Or > >> >>? ? ?S?o Luiz > >> >> > >> >> > >> >> ?_______________________________________________ > >> >>? ? ?Freesurfer mailing list > >> >> Freesurfer@nmr.mgh.harvard.edu > >> <mailto:Freesurfer@nmr.mgh.harvard.edu> > >> >>? ? ?<mailto:Freesurfer@nmr.mgh.harvard.edu > >> <mailto:Freesurfer@nmr.mgh.harvard.edu>> > >> >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > >> > > >> > -- > >> > Fernanda Hansen P. de Moraes > >> > F?sica M?dica | Instituto D'Or de Pesquisa e Ensino?| Rede > >> D'Or S?o Luiz > >> > >> -- > >> Fernanda Hansen P. de Moraes > >> F?sica M?dica | Instituto D'Or de Pesquisa e Ensino?| Rede D'Or > >> S?o Luiz > > > > -- > > Fernanda Hansen P. de Moraes > > F?sica M?dica | Instituto D'Or de Pesquisa e Ensino?| Rede D'Or S?o > > Luiz > > > > ------------------------------ > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > End of Freesurfer Digest, Vol 170, Issue 31 > ******************************************* > > > > ------------------------------ > > Message: 21 > Date: Fri, 20 Apr 2018 11:19:27 +0100 > From: "C.P.E. Rollins" <cp...@cam.ac.uk> > Subject: Re: [Freesurfer] FSGD design for multi-centre study > To: Freesurfer <freesurfer@nmr.mgh.harvard.edu> > Message-ID: <b262bd397c7854132bad39678373b...@cam.ac.uk> > Content-Type: text/plain; charset=US-ASCII; format=flowed > > External Email - Use Caution > > Thanks a lot for the explanation. The issue is that I don't think > Freesurfer will run a design for which there are no subjects for a given > class. So if I keep the classes (24 classes since 6 centres x 2 gender x > 2 groups (patient vs. control), and have the contrast with 12 (-1) and > 12 (1), > -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 1 1 1 1 1 1 1 1 1 1 1 1 0 > I get the error: > -------------------------------- > ERROR: matrix is ill-conditioned or badly scaled, condno = 1e+08 > -------------------------------- > Possible problem with experimental design: > Check for duplicate entries and/or lack of range of > continuous variables within a class. > > I'm assuming this is because there are no participants in, for example, > patient_centre2_female > Is there any way to get around this issue, or should I remove those > centres from my analysis (since I can't only remove > "patient_centre2_female", as this would make the contrast unbalanced > (positives and negatives would not add to the same number). I hope this > was clear but please let me know if it was not. > > Thanks again, > Colleen > > > > > ------------------------------ > > Message: 22 > Date: Fri, 20 Apr 2018 12:20:10 +0200 > From: Daniel Margulies <daniel.margul...@gmail.com> > Subject: [Freesurfer] 8th Annual Brain-Art Competition @ OHBM open for > submissions! > To: freesurfer@nmr.mgh.harvard.edu > Message-ID: > <CAA9bqVrA9+TO3pmKrVYOXRYM2nuECZP=2syDwqccKjwmBsvDFg@mail. > gmail.com> > Content-Type: text/plain; charset="utf-8" > > External Email - Use Caution > > In order to recognize the beauty and creativity of artistic renderings > emerging from the neuroimaging community, we are launching the eighth > annual Brain-Art Competition. > > Countless hours are devoted to the creation of informative visualizations > for communicating neuroscientific findings. The Brain-Art Competition aims > to recognize this often unappreciated aspect of the publication process, > and highlight the artistic creativity of our community. > > We are inviting researchers to submit their favorite unpublished works for > entry. Both team and single-person entries are welcomed. The competition > will have six award categories: > > 1. Best Representation of the Human Connectome > 2. Best Abstract Brain Illustration > 3. Best Humorous Brain Illustration > 4. Best Video Illustration of the Brain > 5. Updating classics > 6. Special Topic: Comparative neuroanatomy > > The last two categories are new additions for the 2018 competition: > > "Updating classics" invites submissions that bring fresh ideas, data, and > visualization techniques to famous illustrations from the neuroscience > canon. > > With the increasing availability of non-human brain data, the special topic > in "comparative neuroanatomy" invites submissions that address the > visualization challenge of translating findings across species. How can > cross-species information be more effectively be presented? > > Submission Deadline: 11:59PM CDT, Wednesday, June 6th, 2018 > > Award Notification: Monday, June 18th, 2018 > > For more information, check out the competition details: > http://www.neurobureau.org/brainart/ > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachm > ents/20180420/dd235644/attachment-0001.html > > ------------------------------ > > Message: 23 > Date: Fri, 20 Apr 2018 12:13:11 +0000 > From: "Boggess, Matthew Jozsef" <mbogg...@mgh.harvard.edu> > Subject: Re: [Freesurfer] fmriprep to fsfast interface > To: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu> > Message-ID: > <CY1PR04MB19274A32BF93228DEDE20EF993B70@CY1PR04MB1927.namprd > 04.prod.outlook.com> > > Content-Type: text/plain; charset="iso-8859-1" > > Thank you for the response! > > > I'm interested primarily in tal space, but potentially native as well. For > tal space, is there no easy way to just directly transform the data into > tal space or provide an identity matrix for the registration? > > ________________________________ > From: freesurfer-boun...@nmr.mgh.harvard.edu < > freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Douglas Greve < > dgr...@mgh.harvard.edu> > Sent: Tuesday, April 17, 2018 12:01:46 PM > To: freesurfer@nmr.mgh.harvard.edu > Subject: Re: [Freesurfer] fmriprep to fsfast interface > > > sorry for the delay, see below > > On 4/14/18 10:00 AM, Boggess, Matthew Jozsef wrote: > > Hello, > > > I just wanted to follow up to see if anyone could help with any of my > questions, particularly # 1. > > > Thank you! > > Matt Boggess > > ________________________________ > From: freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-bou > n...@nmr.mgh.harvard.edu> <freesurfer-boun...@nmr.mgh.harvard.edu><mailto: > freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Boggess, Matthew > Jozsef <mbogg...@mgh.harvard.edu><mailto:mbogg...@mgh.harvard.edu> > Sent: Thursday, April 5, 2018 8:02:07 AM > To: freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu> > Subject: [Freesurfer] fmriprep to fsfast interface > > Hello, > > I've been working on taking the outputs of the fmriprep BOLD preprocessing > tool (https://fmriprep.readthedocs.io/en/latest/index.html) and coercing > them into the fsfast structure so that first levels can be run with > mkanalysis-sess and selxavg3b-sess. It's been a bit trickier than > anticipated and I was hoping to get some help verifying my current approach > (attached to this email). > > Question 1: > > fmriprep outputs the preprocessed BOLD data in the T1 space (mni305 is not > an option). However, the typical spatial normalization workflow uses a > registration matrix from the bold to T1 to transform to talairach. Is there > a way to do this transformation without having to specify a registration > matrix given the functional data is already in the T1 space? My current > approach is to use mri_convert with the --apply_transform flag pointing to > the talairach.xfm registration matrix in the subject's recon folder, but I > am not sure if this is a reasonable workaround. > Do you want to analyze it in the native T1 space or in talairach space? If > native, then when you run mkanalysis-sess you can bypass the preprocessing > by directly specifying the stem of the functional data you want to process > (-funcstem). If tal space, then I think it should work out of the box (it > would recalc the registration, but that should be ok). > > Question 2: > > fsfast normally calculates the global mean value of the raw data to be > used for intensity normalization. However, with fmriprep I only have access > to the preprocessed data in T1 space. Would extracting the global mean > value for intensity normalization from the preprocessed BOLD in T1 space be > valid? > Yes > > Question 3: > > Is there a way to do first levels in the native subcortical space? If so, > what is the filename structure expected (maybe mni305.2mm gets replaced > with the subject name as with the surface data)? I've only seen examples > transforming to mni305 space, but ideally an option would be to just > transfer the preprocessed BOLD in T1 space and run first levels staying in > the native T1 space. > See above. > > Thanks for your help! > > Matt > > > > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachm > ents/20180420/74554851/attachment-0001.html > > ------------------------------ > > Message: 24 > Date: Fri, 20 Apr 2018 15:15:06 +0300 > From: Zohar Berman <zork...@gmail.com> > Subject: Re: [Freesurfer] Calculation of surface area > To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu> > Message-ID: > <CAOu_4t3Do224twg+CtmWns0SS4USEESjPU2Lvhi6jr-dBO33DA@mail. > gmail.com> > Content-Type: text/plain; charset="utf-8" > > External Email - Use Caution > > Dear Douglas, > > Thank you for your quick answer! > The thing is, we don't have access to the original surface area files which > were created by FreeSurfer anymore. Thus, we were wondering if we can > calculate a region's surface area if we have its volume & cortical > thickness values. > Is that possible? > > Thank you very much! > Zoi > > > > On 20 April 2018 at 00:04, Douglas N. Greve <dgr...@mgh.harvard.edu> > wrote: > > > We output surface area separately both as a map and as statistics > > > > > > On 04/19/2018 04:47 PM, Zohar Berman wrote: > > > Dear FreeSurfer experts, > > > > > > Can one use the volume and cortical thickness of a region to calculate > > > the surface area of this region? > > > > > > Thanks a lot in advance! > > > Best, > > > Zoi > > > > > > > > > > > > _______________________________________________ > > > Freesurfer mailing list > > > Freesurfer@nmr.mgh.harvard.edu > > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > _______________________________________________ > > 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. > > > > > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachm > ents/20180420/91079426/attachment-0001.html > > ------------------------------ > > Message: 25 > Date: Fri, 20 Apr 2018 12:46:17 +0000 > From: "Alexopoulos, Dimitrios" <dimitriosalexopou...@wustl.edu> > Subject: Re: [Freesurfer] using T2 for hippo subfields > To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu> > Message-ID: > <cy1pr0201mb1914cd281130fcbaa1ece228d6...@cy1pr0201mb1914.na > mprd02.prod.outlook.com> > > Content-Type: text/plain; charset="windows-1252" > > External Email - Use Caution > > Ok. Can you run -hippocampal-subfields-T1 without the -hires flag using a > submillimeter T1? > > Jim > ________________________________ > From: freesurfer-boun...@nmr.mgh.harvard.edu < > freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Iglesias Gonzalez, > Eugenio <e.igles...@ucl.ac.uk> > Sent: Friday, April 20, 2018 2:24:59 AM > To: Freesurfer support list > Subject: Re: [Freesurfer] using T2 for hippo subfields > > > External Email - Use Caution > > Sorry, I?m not sure I follow. But, if you run recon-all with the hires > flag, then you can just run ?hippo-subfields-T1 and it?ll take advantage of > the high resolution. > > > > -- > > 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 "Alexopoulos, > Dimitrios" <dimitriosalexopou...@wustl.edu> > Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu> > Date: Friday, 20 April 2018 at 01:34 > To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu> > Subject: Re: [Freesurfer] using T2 for hippo subfields > > > > External Email - Use Caution > > Yes the output appears ok. > I was under the impression there would be benefits from using the -hires > flag with submillimeter T1s as input. > > If you suggest not having to use the -hires flag in our case (because of > little benefit from 0.8mm input compared to 1mm), I presume I can still use > the -hippocampal-subfields-T1 option in the traditional recon-all -all > stream? > > Jim > > ________________________________ > > From: freesurfer-boun...@nmr.mgh.harvard.edu < > freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Iglesias Gonzalez, > Eugenio <e.igles...@ucl.ac.uk> > Sent: Thursday, April 19, 2018 1:57:18 PM > To: Freesurfer support list > Subject: Re: [Freesurfer] using T2 for hippo subfields > > > > External Email - Use Caution > > Hi Jim, > >From my experience .8 isotropic is on the edge. Did you take a look at > the output? You can always send us the data if you want us to take a look. > 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 19/04/2018, 19:55, "freesurfer-boun...@nmr.mgh.harvard.edu on behalf > of Alexopoulos, Dimitrios" <freesurfer-boun...@nmr.mgh.harvard.edu on > behalf of dimitriosalexopou...@wustl.edu> wrote: > > External Email - Use Caution > > Thanks. I ran several subjects that were native 0.82 x 0.82 x 0.85mm > through the standard recon-all -all stream, with the -hires flag (but with > no experts file). The volumes and surafces look good. Is there any need to > be concerened with the output since I did not use an experts file? > > Jim > > -----Original Message----- > From: freesurfer-boun...@nmr.mgh.harvard.edu [mailto: > freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Bruce Fischl > Sent: Wednesday, April 04, 2018 7:52 AM > To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu> > Subject: Re: [Freesurfer] using T2 for hippo subfields > > no it is not required > > cheers > Bruce > On Wed, 4 Apr 2018, Alexopoulos, Dimitrios wrote: > > > Per an earlier post below, is an 'expert_file' always required when > using the -hires option? > > > > Jim > > > > ____________________________________________________________ > __________ > > ______________________________ > > From: freesurfer-boun...@nmr.mgh.harvard.edu > > <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Alexopoulos, > > Dimitrios <dimitriosalexopou...@wustl.edu> > > Sent: Sunday, March 25, 2018 9:47:07 PM > > To: Freesurfer support list > > Subject: Re: [Freesurfer] using T2 for hippo subfields > > > > Thanks for the input. I processed a few subjects (T1-mprage, 0.8mm > > isotropic) using the -hires flag, with no expert file, which > generated nice surfaces. > > > > Is an 'expert_file' required ?? > > > > > > Jim > > > > ____________________________________________________________ > __________ > > ______________________________ > > From: freesurfer-boun...@nmr.mgh.harvard.edu > > <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Iglesias > > Gonzalez, Eugenio <e.igles...@ucl.ac.uk> > > Sent: Friday, March 23, 2018 11:02:00 AM > > To: Freesurfer support list > > Subject: Re: [Freesurfer] using T2 for hippo subfields > > > > Hi Jim, > > > > In the end it's an empirical question, but my gut feeling is that the > > T1 with hi-res flag will be best. > > > > Cheers, > > > > /E > > > > > > > > -- > > > > 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 > "Alexopoulos, Dimitrios" > > <dimitriosalexopou...@wustl.edu> > > Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu> > > Date: Friday, 23 March 2018 at 16:00 > > To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu> > > Subject: [Freesurfer] using T2 for hippo subfields > > > > > > > > Hi. We are acquiring sequences on a pediatric cohort that include a > > T1-mprage (0.8mm isotropic) and a T2-space (1mm isotropic), and I'd > > like to run the hippocampal subfields module on the subjects using > FS 6.0. > > > > > > > > Is it recommended/useful to run the multispectral segmentation mode > > with the additional lower resolution T2 sequence? > > > > I read that you really only benefit if the T2 is of similar or > better resolution than the T1. > > > > > > > > If that's the case, would it be best to just run with the single T1 > > but with the hi-res flag in the recon-all command? > > > > > > Thanks. > > > > Jim > > > > > > > > > > > > > > > > > > > > > > > > > > ____________________________________________________________ > __________ > > ______________________________ > > > > > > The materials in this message are private and may contain Protected > > Healthcare Information or 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 > telephone or return mail. > > > > > > > > > > ____________________________________________________________ > __________ > > ______________________________ > > > > > > The materials in this message are private and may contain Protected > > Healthcare Information or 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 > telephone or return mail. > > > > > > > > > > ____________________________________________________________ > __________ > > ______________________________ > > > > > > The materials in this message are private and may contain Protected > > Healthcare Information or 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 > telephone or return mail. > > > > > > > > ________________________________ > The materials in this message are private and may contain Protected > Healthcare Information or other information of a sensitive nature. 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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 materials in this message are private and may contain Protected > Healthcare Information or 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. 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