Re: [Freesurfer] pial surface with FLAIR
Hi, Christopher!
Best of luck to you all in these difficult times!
Thank you very much for your advice. I'll try this as well.
Best wishes,
Veronica
-Original Message-
From: Watson, Christopher [mailto:christopher.wat...@childrens.harvard.edu]
Sent: Tuesday, 16 April, 2013 07:15
To: Bruce Fischl; Popescu, Veronica
Cc: 'freesurfer@nmr.mgh.harvard.edu'
Subject: RE: [Freesurfer] pial surface with FLAIR
Hi Veronica,
Did you try initially doing "recon-all -i $FLAIR -s $SUBJECT"?
And then, when you do the remaining recon-all steps:
recon-all -autorecon3 -s $SUBJECT -FLAIRpial
It has worked for me. (And worked very well! No edits necessary for the pial
surface!)
From: freesurfer-boun...@nmr.mgh.harvard.edu
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Bruce Fischl
[fis...@nmr.mgh.harvard.edu]
Sent: Monday, April 15, 2013 12:31 PM
To: Popescu, Veronica
Cc: 'freesurfer@nmr.mgh.harvard.edu'
Subject: Re: [Freesurfer] pial surface with FLAIR
Hi Veronica,
we haven't seen that before. Can you upload your subject including the FLAIR
and we'll take a look?
thanks
Bruce
On Mon, 15 Apr 2013, Popescu, Veronica wrote:
>
> Dear all,
>
> I have already run the FreeSurfer 5.2 -all, and I would like to
> improve the pial surface recongition using the FLAIR. From the
> $SUBJECTS_DIR (where I have also placed the FLAIR file) I use the following
> syntax:
>
> recon-all -autorecon3 -subjid ${SUBJ_ID} -FLAIR $FLAIRFILE -FLAIRpial
>
> It starts running but then it hangs, I never get an output. The FLAIR
> file is in nifti format.
>
> I am not sure what I am doing wrong: it is the syntax? Should I first
> convert the FLAIR file to .mgz?
>
> Thank you in advance for the help!
>
> Veronica Popescu, MD, MSc
> Department of Radiology & Nuclear Medicine VU University Medical
> Center Amsterdam, The Netherlands
>
>
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Re: [Freesurfer] recon-all for multiple subjects using "for" loop
Hello, In our lab, we create a txt file with all the subject names (as they appear on their respective folders). Name that txt file whatever you want (like "* subs.txt*") and save it somewhere in one of the paths (we use /Users/* Home_User*). Then in terminal, after setting the environments for Freesurfer and the subjects directory, insert the following: for SubjectName in `cat *subs.txt*` do recon-all -s $SubjectName -all -qcache done Make sure you have the ` (not ') on either side of the "cat" command or it won't work. This works for us and we have 200 subjects. Good luck, -David Vazquez, M. A. Graduate Student, University of California Riverside NSF Graduate Student Fellow dvazq...@ucr.edu 951-827-5243 Dept. Office 951-827-3985 Dept. Fax On Mon, Apr 15, 2013 at 10:10 PM, Anupa AV wrote: > Dear FS experts, > > I'd like to know about the for loop command for running recon-all for > multiple subjects. > > I went thru this link, > https://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/2006-November/004083.html > But didn't get much info. > > Can anyone please tell me how to run recon-all for multiple subjects? > Thanks in advance. > > > ___ > 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.
Re: [Freesurfer] pial surface with FLAIR
Hi Veronica,
Did you try initially doing "recon-all -i $FLAIR -s $SUBJECT"?
And then, when you do the remaining recon-all steps:
recon-all -autorecon3 -s $SUBJECT -FLAIRpial
It has worked for me. (And worked very well! No edits necessary for the pial
surface!)
From: freesurfer-boun...@nmr.mgh.harvard.edu
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Bruce Fischl
[fis...@nmr.mgh.harvard.edu]
Sent: Monday, April 15, 2013 12:31 PM
To: Popescu, Veronica
Cc: 'freesurfer@nmr.mgh.harvard.edu'
Subject: Re: [Freesurfer] pial surface with FLAIR
Hi Veronica,
we haven't seen that before. Can you upload your subject including the
FLAIR and we'll take a look?
thanks
Bruce
On Mon, 15 Apr 2013, Popescu, Veronica wrote:
>
> Dear all,
>
> I have already run the FreeSurfer 5.2 -all, and I would like to improve the
> pial surface recongition using the FLAIR. From the $SUBJECTS_DIR (where I
> have also placed the FLAIR file) I use the following syntax:
>
> recon-all -autorecon3 -subjid ${SUBJ_ID} -FLAIR $FLAIRFILE -FLAIRpial
>
> It starts running but then it hangs, I never get an output. The FLAIR file
> is in nifti format.
>
> I am not sure what I am doing wrong: it is the syntax? Should I first
> convert the FLAIR file to .mgz?
>
> Thank you in advance for the help!
>
> Veronica Popescu, MD, MSc
> Department of Radiology & Nuclear Medicine
> VU University Medical Center
> Amsterdam, The Netherlands
>
>
___
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] recon-all for multiple subjects using "for" loop
Dear FS experts, I'd like to know about the for loop command for running recon-all for multiple subjects. I went thru this link, https://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/2006-November/004083.html But didn't get much info. Can anyone please tell me how to run recon-all for multiple subjects? Thanks in advance.___ 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] recon-all problems [solved]
Marcos, Can you give this version of tkmedit a try on your Fedora 18 system? ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/misc/linux-centos6_x86_64/ you will need to copy tkmedit.bin to your freesurfer/tktools directory (not the freesurfer/bin directory). you may need to type this to make it executable: chmod a+x tkmedit.bin it contains a potential fix to the problem (but i dont have a way to replicate the error to test it). Nick On Mon, 2013-04-15 at 18:02 -0400, Nick Schmansky wrote: > Marcos, > > Thanks for looking into this. We dont have a Fedora 18 system to > replicate the problem on, but we're looking at the section of code > described in bugzilla report. We may need your help to test any fixes > we devise. > > Nick > > > On Mon, 2013-04-15 at 17:59 -0300, Marcos Martins da Silva wrote: > > > > I had several problems testing freesurfer 5.2 installation, as > > previously posted. Now it is all OK and I would like to share what I > > could learn: > > > > 1- It does not work on Fedora 18 (segfaults with all tests with > > tkmedit, tksurfer and recon-all) that is due to a restriction imposed > > by glibc (only newest version). Only freeview works under Fedora 18 > > but, even here, I got a misalignment problem among surfaces and > > volumes. More details at > > https://bugzilla.redhat.com/show_bug.cgi?id=905638 > > 2- I got partial functionality using VirtualBox (4.2.8 and 4.2.10). I > > cannot say about previous versions and the latest one (4.2.12 was > > released on Apriil, 12th). But I had problems with both virtual > > machines I tried: CentOS6 (fresh install) and the Xubuntu + FreeSurfer > > 5.1 vdi file I downloaded from FreeSurfer website. Tkmedit, tksurfer > > and freeview all worked but recon-all failed all time. > > 3- Fedora 17 and CentOS 6 work flawlessly out of box if you do not use > > virtualbox. Probably, other distros will work too, except if they are > > using the latest glibc (2.16-30). So my final setup is a dual boot > > machine: Fedora 18 (day-by-day tasks) and CentOS6 (freesurfer tasks). > > You can do it with only one disk but it is a lot easier with two. > > > > I hope it can help people with similar problems. > > ___ > > 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 > > ___ 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] recon-all problems [solved]
Marcos, Thanks for looking into this. We dont have a Fedora 18 system to replicate the problem on, but we're looking at the section of code described in bugzilla report. We may need your help to test any fixes we devise. Nick On Mon, 2013-04-15 at 17:59 -0300, Marcos Martins da Silva wrote: > > I had several problems testing freesurfer 5.2 installation, as > previously posted. Now it is all OK and I would like to share what I > could learn: > > 1- It does not work on Fedora 18 (segfaults with all tests with > tkmedit, tksurfer and recon-all) that is due to a restriction imposed > by glibc (only newest version). Only freeview works under Fedora 18 > but, even here, I got a misalignment problem among surfaces and > volumes. More details at > https://bugzilla.redhat.com/show_bug.cgi?id=905638 > 2- I got partial functionality using VirtualBox (4.2.8 and 4.2.10). I > cannot say about previous versions and the latest one (4.2.12 was > released on Apriil, 12th). But I had problems with both virtual > machines I tried: CentOS6 (fresh install) and the Xubuntu + FreeSurfer > 5.1 vdi file I downloaded from FreeSurfer website. Tkmedit, tksurfer > and freeview all worked but recon-all failed all time. > 3- Fedora 17 and CentOS 6 work flawlessly out of box if you do not use > virtualbox. Probably, other distros will work too, except if they are > using the latest glibc (2.16-30). So my final setup is a dual boot > machine: Fedora 18 (day-by-day tasks) and CentOS6 (freesurfer tasks). > You can do it with only one disk but it is a lot easier with two. > > I hope it can help people with similar problems. > ___ > 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.
Re: [Freesurfer] QDEC questions
Tudor, In the recon-all.log, it has this line: ERROR: writing lh.jacobian_white.fwhm15.fsaverage.mgh but earlier in the log it saved lh.jacobian_white.fwhm10.fsaverage.mgh correctly, so this indicates to me that it might have run out of disk space. is that the case? to answer the others: 2. not sure 3. you can select discrete can a regular variate along with your main variate. 'nuisance' variates are like any other. 4. depends on the expected 'blob' size 5. the selection of fwhm in qdec corresponds directly with the values selected by qcache (they are one-to-one related, ie the 10mm fwhm values created by qcache are used by the 10mm fwhm selection in qdec). Nick On Mon, 2013-04-15 at 18:38 +0200, Tudor Popescu wrote: > Dear experts, > > Upgrading to 5.2.0 stopped QDEC (specifically, mri_concat) from > misbehaving, and so after running a first whole-brain group cortical > thickness analysis on my structural data, I have some questions: > > 1. After running recon-all with the –qcache flag (i.e. presmoothing), > files of the type lh.thickness.*.mgh were created for all 38 subjects > (19 in each group), however files of the type rh.thickness.*.mgh were > not created for 5 out of the 19 subjects of the first group. Log files > recon-all-status.log and recon-all.log (attached, for one of those 5 > subjects) both mention that the process ran on Mar22nd ended with > errors, although I can't quite see what that was > > > > 2. When I take age as a continuous factor (covariate), the list of > clusters in my results look dramatically different from the clusters > that I get for the same contrast ran without the covariate. Why is > that, given that normally adding a covariate very rarely changes the > results by a great deal? Also in my case, I had quite a narrow (and > well-balanced between the groups) age range! > > > > 3. I know that discrete factors cannot be taken as nuisance factors, > but it seems they also can't be taken as covariates. How does one, > then, control for the effects of e.g. gender in a group comparison? > > > 4. When should values other than 10 be used for the FWHM parameter of > the smoothing? > > > 5. How come QDEC allows you to set the FWHM parameter, when in fact it > is also set in the qcache stage of recon-all, which precedes QDEC? > > > Many thanks in advance!! > > Tudor > ___ > 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.
[Freesurfer] recon-all problems [solved]
I had several problems testing freesurfer 5.2 installation, as previously posted. Now it is all OK and I would like to share what I could learn: 1- It does not work on Fedora 18 (segfaults with all tests with tkmedit, tksurfer and recon-all) that is due to a restriction imposed by glibc (only newest version). Only freeview works under Fedora 18 but, even here, I got a misalignment problem among surfaces and volumes. More details at https://bugzilla.redhat.com/show_bug.cgi?id=905638 2- I got partial functionality using VirtualBox (4.2.8 and 4.2.10). I cannot say about previous versions and the latest one (4.2.12 was released on Apriil, 12th). But I had problems with both virtual machines I tried: CentOS6 (fresh install) and the Xubuntu + FreeSurfer 5.1 vdi file I downloaded from FreeSurfer website. Tkmedit, tksurfer and freeview all worked but recon-all failed all time. 3- Fedora 17 and CentOS 6 work flawlessly out of box if you do not use virtualbox. Probably, other distros will work too, except if they are using the latest glibc (2.16-30). So my final setup is a dual boot machine: Fedora 18 (day-by-day tasks) and CentOS6 (freesurfer tasks). You can do it with only one disk but it is a lot easier with two. I hope it can help people with similar problems. ___ 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] Use our own training subjects?
Hi Anastasia, We were viewing the arcuate fasiculus tract created by TRACULA, and noticed that the tract did not reach Broca's area. While there exists literature that now challenges this neuroanatomical convention, I would like to investigate the possibility of creating and inputting on our own training subjects as priors. Do you know if we can try this? Thank you! -- Susie Kuo Mediocrity knows nothing higher than itself, but talent instantly recognizes genius. - Sir Arthur Conan Doyle,* Sherlock Holmes- Valley of Fear* ___ 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] setting thresholds in qdec
Thanks Nick -- that fixed it. -MH -- Michael Harms, Ph.D. --- Conte Center for the Neuroscience of Mental Disorders Washington University School of Medicine Department of Psychiatry, Box 8134 660 South Euclid Ave. Tel: 314-747-6173 St. Louis, MO 63110Email: mha...@wustl.edu On 4/14/13 4:18 PM, "Nick Schmansky" wrote: >Mike, > >We dont have a RHEL 5.9 system to replicate the issue. However, I did >find a bug in qdec where the 'Min' value in the Threshold settings would >not update the display when a value was entered. This bug was >introduced when the 'Mid' value was removed (which is why I think the >v5.1 qdec works). > >A fixed version of qdec.bin for linux is available here: >ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/misc/linux-centos4_x8 >6_64/ > >Nick > > >On Fri, 2013-04-12 at 12:20 -0500, Michael Harms wrote: >> >> >> I just transferred all the data to a different system running CentOS >> 5.5 and I'm able to set the display thresholds in qdec on that >> system. It also uses a different FS version (5.1) but I think it is >> an OS issue, and not a FS version issue, since I have the same problem >> on the original RHEL 5.9 system using the qdec in FS 5.1 as well. >> >> >> So, must be something about the libraries qdec uses not quite playing >> nice in RHEL 5.9 ? >> >> >> thanks, >> -MH >> >> >> -- >> Michael Harms, Ph.D. >> --- >> Conte Center for the Neuroscience of Mental Disorders >> Washington University School of Medicine >> Department of Psychiatry, Box 8134 >> 660 South Euclid Ave. Tel: 314-747-6173 >> St. Louis, MO 63110 Email: mha...@wustl.edu >> >> >> From: Michael Harms >> Date: Friday, April 12, 2013 11:32 AM >> To: "freesurfer@nmr.mgh.harvard.edu" >> Subject: [Freesurfer] setting thresholds in qdec >> >> >> >> >> >> Hello, >> Is it no longer possible to set the Min, Mid, and Max thresholds >> directly on the Qdec display tab? >> The only way I seem to be able to change them is via the sliders in >> the histogram at the bottom, which I don't recall previously being the >> case. >> This is Qdec 1.4 (FS 5.2) on a RHEL 5.9 system using >> freesurfer-Linux-centos4_x86_64-stable-pub-v5.2.0 distribution. >> >> >> I can't change the FDR "Rate" either. >> >> >> thanks, >> -MH >> >> >> -- >> Michael Harms, Ph.D. >> --- >> Conte Center for the Neuroscience of Mental Disorders >> Washington University School of Medicine >> Department of Psychiatry, Box 8134 >> 660 South Euclid Ave. Tel: 314-747-6173 >> St. Louis, MO 63110 Email: mha...@wustl.edu >> ___ 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 > > >___ >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
Re: [Freesurfer] pial surface with FLAIR
Veronica,
Hi, can you copy me on the subject data upload? You can upload data
here:
https://www.nmr.mgh.harvard.edu/facility/filedrop/index.html
Nick
On Mon, 2013-04-15 at 12:30 -0400, Bruce Fischl wrote:
> Hi Veronica,
>
> we haven't seen that before. Can you upload your subject including the
> FLAIR and we'll take a look?
>
> thanks
> Bruce
>
> On Mon, 15 Apr 2013, Popescu, Veronica wrote:
>
> >
> > Dear all,
> >
> > I have already run the FreeSurfer 5.2 -all, and I would like to improve the
> > pial surface recongition using the FLAIR. From the $SUBJECTS_DIR (where I
> > have also placed the FLAIR file) I use the following syntax:
> >
> > recon-all -autorecon3 -subjid ${SUBJ_ID} -FLAIR $FLAIRFILE -FLAIRpial
> >
> > It starts running but then it hangs, I never get an output. The FLAIR file
> > is in nifti format.
> >
> > I am not sure what I am doing wrong: it is the syntax? Should I first
> > convert the FLAIR file to .mgz?
> >
> > Thank you in advance for the help!
> >
> > Veronica Popescu, MD, MSc
> > Department of Radiology & Nuclear Medicine
> > VU University Medical Center
> > Amsterdam, The Netherlands
> >
> >
> ___ 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.
Re: [Freesurfer] unit of corpus callosum segmentation
Hi Marie, But division by 5 would give the average area of the 5 mid slices. Maybe that is even more meaningful (reliable) than just a single slice. Best, Martin On 04/14/2013 09:05 AM, Bruce Fischl wrote: > Hi Marie, > > no, that won't account for variability across slices in the l/r > direction. Try rerunning mri_cc with -t 0 (thickness) and see if it > generates a cc in just the midsagittal plane > > cheers > Bruce > > > On Sun, 14 Apr 2013, Marie Schaer wrote: > >> Hi Bruce, >> >> Thanks for your response. Then I assume that I can divide these values by 5 >> and present them as area of the CC on the midline section, right? >> >> Have a nice week-end, >> >> Marie >> >> On Apr 13, 2013, at 5:18 AM, Bruce Fischl >> wrote: >> >>Hi Marie >> It is mm^3 of I believe a 5 mm thick cc. We don't measure the >> thickness by default >> Cheers >> Bruce >> >> >> >> On Apr 13, 2013, at 2:18 AM, Marie Schaer >> wrote: >> >> >>Hi Bruce, >> >>Thanks for your response. My question was indeed: what is >>the unit of the CC_* output in the aseg.stats? E.g. in the >>attached file, the last 5 rows depict CC segmentation >>measurements (between ~400+ and 900+), and I was wondering >>what was the unit of these measurements. The other values >>are clearly mm^3, but what about the CC? From what I >>understood from Diana Rosas' paper, the CC was measured as >>the thickness / distance from the medial axis of the CC to >>the superior and inferior boundaries, but I may have >>wrongly understood. >> >>Thanks for the clarification, >> >>Marie >> >> >> >> >> >> >> On Apr 12, 2013, at 8:07 PM, Bruce Fischl >> wrote: >> >>> Hi Marie, >>> 400 or 900 what? Not mm. How are you calculating thickness? I >> think in Diana's paper it was the radius of the inscribed circle >> on the medial axis, wasn't it? >>> Bruce >>> >>> >>> On Apr 12, 2013, at 10:44 PM, Marie Schaer >> wrote: Hi all, I have a quick question related to the corpus callosum >> segmentation: I read in previous posts that the reference >> explaining more about the CC subdivision in 5 segments was the >> one by Rosas et al, Neuroimage 2010. But in this publication, >> you show thickness of the corpus callosum as the main outcome >> variable, with average values ranging from ~4 to 9 mm. And when >> I extract the values from the aseg.stats, in my dataset I rather >> get average values that are ranging between ~400 and 900 >> depending on the segment. Do these values correspond to >> thickness in mm/100, or to area, or to something else? Is that a >> thickness measurement, or a surface area measurement? Many thanks in advance for your reply, Marie ___ 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 > > -- Dr. Martin Reuter Assistant in Neuroscience - Massachusetts General Hospital Instructor in Neurology - Harvard Medical School MGH / HMS / MIT A.A.Martinos Center for Biomedical Imaging 149 Thirteenth Street, Suite 2301 Charlestown, MA 02129 Phone: +1-617-724-5652 Email: mreu...@nmr.mgh.harvard.edu reu...@mit.edu Web : http://reuter.mit.edu ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] using volume label mask in mri_vol2surf
Hey
I wrote out to .w since I couldn't write to curv. (And I'm old fashioned!)
But actually it's because I am really behind the times and forgot that .mgh was
also used for surface data. And yup, this worked fine.
So in answer to my question 'Bug or stupidity' - the latter!
Thanks Doug,
Fred
On 15 Apr 2013, at 17:58, Douglas Greve wrote:
> Hi Fred, why do you want to save it as a wfile? We're trying to phase wfiles
> out. Can you use mgh format?
> doug
>
>
> On 4/15/13 12:56 PM, Fred Dick wrote:
>> Hey again
>>
>> sorry, I seem not to be able to accomplish this very simple thing!
>>
>> First wrote out mask as .w file using vol2surf, but mri_cor2label couldn't
>> read ('mri_read(): couldn't determine type of file ./rh.R2MaskBrain.w').
>>
>> Then tried writing out as curv using the following command:
>>
>> mri_vol2surf --mov R2MaskBrain.nii.gz --reg register.dat --hemi $hemi
>> --interp nearest --o ./$hemi.R2MaskBrain --out_type curv --projfrac 0.5
>>
>> and got this error,
>>
>>
>> Writing to ./lh.R2MaskBrain
>> Dim: 152308 1 1
>> MRIwriteType(): code inconsistency (file type recognized but not caught)
>> ERROR: saving ./lh.R2MaskBrain
>> #
>>
>> Bug, or user stupidity???
>>
>> cheers,
>> Fred
>>
>>
>> On 14 Apr 2013, at 22:56, Douglas Greve wrote:
>>
>>>
>>> Oh, the label should be a surface label. mri_cor2label creates a volume
>>> label (basically it just means that each label point corresponds to a 1mm3
>>> cube instead of a verex -- the vertex numbers should all be -1). Try
>>> running vol2surf on the mask (using nearest interp) to create a surface
>>> mask. Then create a surface label with mri_cor2label using the --surf
>>> option.
>>> doug
>>>
>>>
>>>
>>>
>>> On 4/14/13 5:01 PM, Fred Dick wrote:
Hi Doug
I've actually tried both inclusive and exclusive and have failed - just
checked again in tkmedit that the label was coming up correctly and it
was.
Just to double-check - the label should be in the space of the --mov,
right?
Thanks!
Fred
Hi Fred, that mask is an inclusive mask, not an exclusive mask. Try
inverting you mask.
doug
On 4/14/13 4:31 PM, Fred Dick wrote:
Dear all
I am painting some higher-res anatomical data from a volume to a surface,
and want to use a mask that excludes the vessels. (The same data but 1x1x1
conformed were used to create the surface).
I've created a binary label in the same space
>> mri_cor2label --i ./R2Mask.nii.gz --l ./R2s.label --id 1
made sure that it looks ok when I read in hi-res to tkmedit and display
label,
then ran mri_vol2surf
>> mri_vol2surf --mov ./sPQ07082012-0009-1-000208-01_R1.nii
>> --regregister.dat --surf-fwhm 4 --hemi $hemi --projfrac $frac --interp
>> trilinear --out_type w --mask R2s.label --o ./dancar-0.5-lh.w
And got the output (pasted below), showing that the output is all zero.
Output is fine without label, or with -cortex.
I've also tried this with a conformed version of the label (also verified
in tkmedit) and have had the same thing. (I thought maybe it was applying
it to orig vol, which I admit would be strange).(I noticed someone had a
similar issue a couple of years ago, but it involved a surface rather than
volume label, and looked like it had been resolved).
Am running current stable version on Mountain Lion.
Thanks for any pointers,
best,
Fred
##
masking output with label R2s.label
INFO: output format is paint
srcvol = ./sPQ07082012-0009-1-000208-01_R1.nii
srcreg = register.dat
srcregold = 0
srcwarp unspecified
surf = white
hemi = lh
ProjFrac = 0.5
thickness = thickness
reshape = 0
interp = trilinear
float2int = round
GetProjMax = 0
INFO: float2int code = 0
Done loading volume
Loading label R2s.label
Reading surface
/Applications/freesurfer/subjects/dancar-synth-handnorm/surf/lh.white
Done reading source surface
Reading thickness
/Applications/freesurfer/subjects/dancar-synth-handnorm/surf/lh.thickness
Done
Mapping Source Volume onto Source Subject Surface
1 0.5 0.5 0.5
using old
Done mapping volume to surface
Number of source voxels hit = 108676
Surface smoothing by fwhm = 4 (n=10)
Masking with R2s.label
Warning: all vertex values are zero
>>>
>>>
>>> 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.
Re: [Freesurfer] using volume label mask in mri_vol2surf
Hi Fred, why do you want to save it as a wfile? We're trying to phase
wfiles out. Can you use mgh format?
doug
On 4/15/13 12:56 PM, Fred Dick wrote:
Hey again
sorry, I seem not to be able to accomplish this very simple thing!
First wrote out mask as .w file using vol2surf, but mri_cor2label
couldn't read ('mri_read(): couldn't determine type of file
./rh.R2MaskBrain.w').
Then tried writing out as curv using the following command:
mri_vol2surf --mov R2MaskBrain.nii.gz --reg register.dat --hemi $hemi
--interp nearest --o ./$hemi.R2MaskBrain --out_type curv --projfrac 0.5
and got this error,
Writing to ./lh.R2MaskBrain
Dim: 152308 1 1
MRIwriteType(): code inconsistency (file type recognized but not caught)
ERROR: saving ./lh.R2MaskBrain
#
Bug, or user stupidity???
cheers,
Fred
On 14 Apr 2013, at 22:56, Douglas Greve > wrote:
Oh, the label should be a surface label. mri_cor2label creates a
volume label (basically it just means that each label point
corresponds to a 1mm3 cube instead of a verex -- the vertex numbers
should all be -1). Try running vol2surf on the mask (using nearest
interp) to create a surface mask. Then create a surface label with
mri_cor2label using the --surf option.
doug
On 4/14/13 5:01 PM, Fred Dick wrote:
Hi Doug
I've actually tried both inclusive and exclusive and have failed -
just checked again in tkmedit that the label was coming up correctly
and it was.
Just to double-check - the label should be in the space of the
--mov, right?
Thanks!
Fred
Hi Fred, that mask is an inclusive mask, not an exclusive mask. Try
inverting you mask.
doug
On 4/14/13 4:31 PM, Fred Dick wrote:
Dear all
I am painting some higher-res anatomical data from a volume to a
surface, and want to use a mask that excludes the vessels. (The
same data but 1x1x1 conformed were used to create the surface).
I've created a binary label in the same space
>> mri_cor2label --i ./R2Mask.nii.gz --l ./R2s.label --id 1
made sure that it looks ok when I read in hi-res to tkmedit and
display label,
then ran mri_vol2surf
>> mri_vol2surf --mov ./sPQ07082012-0009-1-000208-01_R1.nii
--regregister.dat --surf-fwhm 4 --hemi $hemi --projfrac $frac
--interp trilinear --out_type w --mask R2s.label --o
./dancar-0.5-lh.w
And got the output (pasted below), showing that the output is all zero.
Output is fine without label, or with -cortex.
I've also tried this with a conformed version of the label (also
verified in tkmedit) and have had the same thing. (I thought
maybe it was applying it to orig vol, which I admit would be
strange).(I noticed someone had a similar issue a couple of
years ago, but it involved a surface rather than volume label,
and looked like it had been resolved).
Am running current stable version on Mountain Lion.
Thanks for any pointers,
best,
Fred
##
masking output with label R2s.label
INFO: output format is paint
srcvol = ./sPQ07082012-0009-1-000208-01_R1.nii
srcreg = register.dat
srcregold = 0
srcwarp unspecified
surf = white
hemi = lh
ProjFrac = 0.5
thickness = thickness
reshape = 0
interp = trilinear
float2int = round
GetProjMax = 0
INFO: float2int code = 0
Done loading volume
Loading label R2s.label
Reading surface
/Applications/freesurfer/subjects/dancar-synth-handnorm/surf/lh.white
Done reading source surface
Reading thickness
/Applications/freesurfer/subjects/dancar-synth-handnorm/surf/lh.thickness
Done
Mapping Source Volume onto Source Subject Surface
1 0.5 0.5 0.5
using old
Done mapping volume to surface
Number of source voxels hit = 108676
Surface smoothing by fwhm = 4 (n=10)
Masking with R2s.label
Warning: all vertex values are zero
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
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but does not contain patient information, please contact the sender
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Re: [Freesurfer] using volume label mask in mri_vol2surf
Hey again
sorry, I seem not to be able to accomplish this very simple thing!
First wrote out mask as .w file using vol2surf, but mri_cor2label couldn't read
('mri_read(): couldn't determine type of file ./rh.R2MaskBrain.w').
Then tried writing out as curv using the following command:
mri_vol2surf --mov R2MaskBrain.nii.gz --reg register.dat --hemi $hemi --interp
nearest --o ./$hemi.R2MaskBrain --out_type curv --projfrac 0.5
and got this error,
Writing to ./lh.R2MaskBrain
Dim: 152308 1 1
MRIwriteType(): code inconsistency (file type recognized but not caught)
ERROR: saving ./lh.R2MaskBrain
#
Bug, or user stupidity???
cheers,
Fred
On 14 Apr 2013, at 22:56, Douglas Greve wrote:
>
> Oh, the label should be a surface label. mri_cor2label creates a volume label
> (basically it just means that each label point corresponds to a 1mm3 cube
> instead of a verex -- the vertex numbers should all be -1). Try running
> vol2surf on the mask (using nearest interp) to create a surface mask. Then
> create a surface label with mri_cor2label using the --surf option.
> doug
>
>
>
>
> On 4/14/13 5:01 PM, Fred Dick wrote:
>> Hi Doug
>>
>> I've actually tried both inclusive and exclusive and have failed - just
>> checked again in tkmedit that the label was coming up correctly and it was.
>>
>> Just to double-check - the label should be in the space of the --mov, right?
>>
>> Thanks!
>>
>> Fred
>>
>>
>>
>> Hi Fred, that mask is an inclusive mask, not an exclusive mask. Try
>> inverting you mask.
>> doug
>> On 4/14/13 4:31 PM, Fred Dick wrote:
>> Dear all
>>
>> I am painting some higher-res anatomical data from a volume to a surface,
>> and want to use a mask that excludes the vessels. (The same data but 1x1x1
>> conformed were used to create the surface).
>> I've created a binary label in the same space
>>
>> >> mri_cor2label --i ./R2Mask.nii.gz --l ./R2s.label --id 1
>>
>> made sure that it looks ok when I read in hi-res to tkmedit and display
>> label,
>> then ran mri_vol2surf
>>
>> >> mri_vol2surf --mov ./sPQ07082012-0009-1-000208-01_R1.nii
>> >> --regregister.dat --surf-fwhm 4 --hemi $hemi --projfrac $frac --interp
>> >> trilinear --out_type w --mask R2s.label --o ./dancar-0.5-lh.w
>> And got the output (pasted below), showing that the output is all zero.
>>
>> Output is fine without label, or with -cortex.
>>
>> I've also tried this with a conformed version of the label (also verified in
>> tkmedit) and have had the same thing. (I thought maybe it was applying it to
>> orig vol, which I admit would be strange).(I noticed someone had a similar
>> issue a couple of years ago, but it involved a surface rather than volume
>> label, and looked like it had been resolved).
>> Am running current stable version on Mountain Lion.
>>
>> Thanks for any pointers,
>>
>> best,
>> Fred
>>
>> ##
>> masking output with label R2s.label
>> INFO: output format is paint
>> srcvol = ./sPQ07082012-0009-1-000208-01_R1.nii
>> srcreg = register.dat
>> srcregold = 0
>> srcwarp unspecified
>> surf = white
>> hemi = lh
>> ProjFrac = 0.5
>> thickness = thickness
>> reshape = 0
>> interp = trilinear
>> float2int = round
>> GetProjMax = 0
>> INFO: float2int code = 0
>> Done loading volume
>> Loading label R2s.label
>> Reading surface
>> /Applications/freesurfer/subjects/dancar-synth-handnorm/surf/lh.white
>> Done reading source surface
>> Reading thickness
>> /Applications/freesurfer/subjects/dancar-synth-handnorm/surf/lh.thickness
>> Done
>> Mapping Source Volume onto Source Subject Surface
>> 1 0.5 0.5 0.5
>> using old
>> Done mapping volume to surface
>> Number of source voxels hit = 108676
>> Surface smoothing by fwhm = 4 (n=10)
>> Masking with R2s.label
>> Warning: all vertex values are zero
>>
>>
>>
>
>
> 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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but does not contain patient information, please contact the sender and properly
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Re: [Freesurfer] pial surface with FLAIR
Hi Veronica,
we haven't seen that before. Can you upload your subject including the
FLAIR and we'll take a look?
thanks
Bruce
On Mon, 15 Apr 2013, Popescu, Veronica wrote:
Dear all,
I have already run the FreeSurfer 5.2 -all, and I would like to improve the
pial surface recongition using the FLAIR. From the $SUBJECTS_DIR (where I
have also placed the FLAIR file) I use the following syntax:
recon-all -autorecon3 -subjid ${SUBJ_ID} -FLAIR $FLAIRFILE -FLAIRpial
It starts running but then it hangs, I never get an output. The FLAIR file
is in nifti format.
I am not sure what I am doing wrong: it is the syntax? Should I first
convert the FLAIR file to .mgz?
Thank you in advance for the help!
Veronica Popescu, MD, MSc
Department of Radiology & Nuclear Medicine
VU University Medical Center
Amsterdam, The Netherlands
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[Freesurfer] Job: Postdoc in Cognitive Neuroscience at Haskins Laboratories
Postdoctoral position in Cognitive Neuroscience at Haskins Laboratories Applications are solicited for a postdoctoral fellowship in Cognitive Neuroscience at Haskins Laboratories. Applicants should have a Ph.D. in psychology, linguistics, cognitive neuroscience, or a related field. The selected candidate will contribute to multiple funded NIH studies of speech perception, reading, word acquisition, and language processing. Prior experience in research using MRI/fMRI is required. Responsibilities will include assistance with design and execution of fMRI and behavioral experiments; fMRI data analysis; formulating and participating in writing of scientific papers as part of the research team; participating in grant writing towards the eventual goal of independent funding; and developing independent projects in the areas of speech, reading, and language. Position requirements include: - Experience with MRI/fMRI data acquisition and analysis - Strong analytical and statistical skills - Strong computer and data management skills Additional desirable qualifications include: - Experience with MRI/fMRI data analysis using AFNI and/or FreeSurfer - Experience with EEG/ERP analysis - Experience with modeling, broadly construed - Programming skills, e.g., Python, R, Matlab The successful applicant will join Haskins Laboratories (www.haskins.yale.edu), a private, non-profit research institute located in downtown New Haven, CT. Founded in 1935, our primary focus is on speech, language, reading, and their biological bases. Haskins Laboratories has long-standing, formal affiliations with the University of Connecticut and Yale University. We are also actively engaged in research collaborations and partnerships with institutions, groups, and individuals around the world. We house facilities for conducting eye tracking, including 3 Eyelink 1000 eye-trackers, EEG/ERP (both Biosemi and EGI systems), ultrasound and NIRS technology, and a mock fMRI scanner, which replicates the 3T scanner used for fMRI research at Yale University. Interested applicants should direct application materials to Dr. W. Einar Mencl, Director of Neuroimaging Research (ei...@haskins.yale.edu) including cover letter, statement of research interests, CV, and three letters of recommendation. Please reference Job Posting #5001. This position is initially for a one-year duration, with potential of an additional 1-2 years contingent on performance and continued funding. Applications should be submitted by 15 May 2013; the application process will continue until the position is filled. International applicants are welcome. Haskins Laboratories is an Equal Opportunity Employer. ___ 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] pial surface with FLAIR
Dear all,
I have already run the FreeSurfer 5.2 -all, and I would like to improve the
pial surface recongition using the FLAIR. From the $SUBJECTS_DIR (where I have
also placed the FLAIR file) I use the following syntax:
recon-all -autorecon3 -subjid ${SUBJ_ID} -FLAIR $FLAIRFILE -FLAIRpial
It starts running but then it hangs, I never get an output. The FLAIR file is
in nifti format.
I am not sure what I am doing wrong: it is the syntax? Should I first convert
the FLAIR file to .mgz?
Thank you in advance for the help!
Veronica Popescu, MD, MSc
Department of Radiology & Nuclear Medicine
VU University Medical Center
Amsterdam, The Netherlands
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Re: [Freesurfer] creating new curv/thick/area files using tweaked white/pial
Hey, thanks Bruce. I will let you know what happens with -n 0. Area not a big deal for this. cheers, Fred On 15 Apr 2013, at 14:32, Bruce Fischl wrote: > Hi Fred > > mris_thickness will make thickness. Not sure we have anything to make area. I > guess you could try setting -n 0 in mris_make_surfaces to it runs for 0 > iterations. Or we can put something together to create area - it should be > trivial > > cheers > Bruce > On Mon, 15 Apr 2013, Fred Dick wrote: > >> Hi there >> >> [Doug/Bruce, sorry for storm of enquiries!] >> >> V quick question: I've fixed up some small defects in white and pial surfs >> (using reposition), and need to regenerate area/thickness/curv etc without >> changing them. Is there a straightforward way to do this with >> mris_make_surfaces, or should one use mris_thickness and mris_curvature? >> (Not sure which binary makes area). >> >> Is there a straightforward way to use mris_make_surfaces to create these >> without altering the pial & white? (Maybe with --white NOWRITE --pial >> NOWRITE?) >> >> cheers, >> Fred >> >> >> ___ >> 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
Re: [Freesurfer] Very different results between 5.1.0 and 5.2.0
Daniel, Unfortunately, since I run all the individuals again with FreeSurfer 5.2, I just saved from the 5.1 the info I was using for comparison between version - the aseg stats. I don't have cortical thickness information for 5.1 unless we run all the cases again in 5.1 - Pedro Paulo de Magalhães Oliveira Junior Netfilter & SpeedComm Telecom -- www.netfilter.com.br -- For mobile: http://itunes.apple.com/br/artist/netfilter/id365306441 On Thu, Apr 11, 2013 at 2:47 PM, Yang, Daniel wrote: > Hi PPJ and all, > > I found that the 5.2 – 5.1 difference is primarily seen in the cortical > thickness, and much less so in the aseg.volume. > > Here, I picked right-amygdala volume as an example of aseg.volume and > rh_bankssts_thickness as an example of rh.aparc.thickness. > > While the correlation between the two versions of right-amygdala is r = > .92 (n = 161), that of the rh_bankssts_thickness is r = .45. > > Presumably I believe the correlation should be > .90 for a strong > continuity between the two versions? > > Do you have anything in the cortical thickness? > > Daniel > > -- > Yung-Jui "Daniel" Yang, PhD > Postdoctoral Researcher > Yale Child Study Center > New Haven, CT > (203) 737-5454 > > From: Pedro Paulo de Magalhães Oliveira Junior > Date: Wednesday, April 10, 2013 11:07 AM > To: Daniel Yang > Cc: Bruce Fischl , " > freesurfer@nmr.mgh.harvard.edu" > > Subject: Re: [Freesurfer] Very different results between 5.1.0 and 5.2.0 > > Ok, I'll try to put together a stat from aparc too. > > - > Pedro Paulo de Magalhães Oliveira Junior > Netfilter & SpeedComm Telecom > -- www.netfilter.com.br > -- For mobile: http://itunes.apple.com/br/artist/netfilter/id365306441 > > > > On Wed, Apr 10, 2013 at 12:04 PM, Yang, Daniel wrote: > >> Hi PPJ, >> >> Thanks! It looks interesting. I also found FS 5.2 is faster. Is there >> any chance you could also provide the cortical thickness of the 2009 atlas >> (e.g., rh)? >> >> I will take a look into the aseg.volume in my data too. >> >> Best, >> Daniel >> >> >> -- >> Yung-Jui "Daniel" Yang, PhD >> Postdoctoral Researcher >> Yale Child Study Center >> New Haven, CT >> (203) 737-5454 >> >> From: Pedro Paulo de Magalhães Oliveira Junior >> Date: Wednesday, April 10, 2013 10:49 AM >> To: Bruce Fischl >> Cc: Daniel Yang , "freesurfer@nmr.mgh.harvard.edu" >> >> Subject: Re: [Freesurfer] Very different results between 5.1.0 and 5.2.0 >> >> You'll find attached some preliminary data of the comparison we did >> among versions. >> >> - >> Pedro Paulo de Magalhães Oliveira Junior >> Netfilter & SpeedComm Telecom >> -- www.netfilter.com.br >> -- For mobile: http://itunes.apple.com/br/artist/netfilter/id365306441 >> >> >> >> On Wed, Apr 10, 2013 at 10:42 AM, Bruce Fischl < >> fis...@nmr.mgh.harvard.edu> wrote: >> >>> Hi PPJ >>> That's exactly what we are doing. Good to hear its stable for you >>> Bruce >>> >>> >>> >>> On Apr 10, 2013, at 8:38 AM, Pedro Paulo de Magalhães Oliveira Junior< >>> p...@netfilter.com.br> wrote: >>> >>> I have processed more that 600 brains with both versions in the last >>> weeks and the only difference I'm seeing between version 5.2.0 and 5.1, >>> besides the obvious new features, is processing time. >>> >>> Version 5.2 is 10% faster than 5.1 in an Amazon EC2 instance. >>> >>> Besides that there's no visible difference in terms of cortical >>> thickness, volumes, etc. >>> >>> If you have access to computer resources to spare you can run >>> recon-all of both versions in some well known database of images and do a >>> more formal test. >>> >>> >>> >>> >>> >>> >>> - >>> Pedro Paulo de Magalhães Oliveira Junior >>> Netfilter & SpeedComm Telecom >>> -- www.netfilter.com.br >>> -- For mobile: http://itunes.apple.com/br/artist/netfilter/id365306441 >>> >>> >>> >>> On Wed, Apr 10, 2013 at 8:11 AM, Yang, Daniel wrote: >>> Dear FreeSurfer Experts and Users, Did anyone find similar things using FS 5.2 (please see my previous post below)? That is, FS 5.2 is including more non-cortical "black spaces" within pial surfaces, compared to FS 5.1? I'm not interested in nitpicking but I feel this is a rather serious issue, so I would like to raise it again before it's completely forgotten. At the meantime I keep receiving Emails from people asking me this issue. Thanks! Daniel -- Yung-Jui "Daniel" Yang, PhD Postdoctoral Researcher Yale Child Study Center New Haven, CT (203) 737-5454 On 3/19/13 7:07 AM, "Yang, Daniel" wrote: > >Posting one of the brains. > >https://yalesurvey.qualtrics.com/SE/?SID=SV_ddw
Re: [Freesurfer] creating new curv/thick/area files using tweaked white/pial
Hi Fred mris_thickness will make thickness. Not sure we have anything to make area. I guess you could try setting -n 0 in mris_make_surfaces to it runs for 0 iterations. Or we can put something together to create area - it should be trivial cheers Bruce On Mon, 15 Apr 2013, Fred Dick wrote: > Hi there > > [Doug/Bruce, sorry for storm of enquiries!] > > V quick question: I've fixed up some small defects in white and pial surfs > (using reposition), and need to regenerate area/thickness/curv etc without > changing them. Is there a straightforward way to do this with > mris_make_surfaces, or should one use mris_thickness and mris_curvature? (Not > sure which binary makes area). > > Is there a straightforward way to use mris_make_surfaces to create these > without altering the pial & white? (Maybe with --white NOWRITE --pial > NOWRITE?) > > cheers, > Fred > > > ___ > 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.
[Freesurfer] convert MNI152 mask to label file
Hi all, I want to convert a mask I made in MNI152 space using the Harvard-Oxford Atlas into a (subcortical) label file so that I can run an ROI analysis using func2roi-sess. Does anyone know what commands I would need to do so? Thanks! Emily___ 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] creating new curv/thick/area files using tweaked white/pial
Hi there [Doug/Bruce, sorry for storm of enquiries!] V quick question: I've fixed up some small defects in white and pial surfs (using reposition), and need to regenerate area/thickness/curv etc without changing them. Is there a straightforward way to do this with mris_make_surfaces, or should one use mris_thickness and mris_curvature? (Not sure which binary makes area). Is there a straightforward way to use mris_make_surfaces to create these without altering the pial & white? (Maybe with --white NOWRITE --pial NOWRITE?) cheers, Fred ___ 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] Very different results between 5.1.0 and 5.2.0
The 5.2 image has been smoothed, by a small degree, relative to 5.1. Either prior to FS processing or by FS, it would seem. On Mon, Apr 15, 2013 at 3:29 AM, Christopher Bell < christopherbell2...@gmail.com> wrote: > Looking at the image posted previously. > > https://yalesurvey.qualtrics.com/SE/?SID=SV_ddwW7I9yMQuCtPn > > I think it is pretty clear the 5.1 picture has better gray/white contrast. > It is a very subtle difference, but you can see it if you look at some > pieces of > wm that were "missed" by 5.2 in this image. > > > > > On Thu, Apr 11, 2013 at 12:33 PM, Yang, Daniel wrote: > >> Thanks Nick! I have uploaded the relevant files to you. >> >> Thanks, >> Daniel >> >> -- >> Yung-Jui "Daniel" Yang, PhD >> Postdoctoral Researcher >> Yale Child Study Center >> New Haven, CT >> (203) 737-5454 >> >> >> >> >> >> >> On 4/10/13 1:19 PM, "Nick Schmansky" wrote: >> >> >Daniel, >> > >> >We're repeating our paired-analysis of thickness measures between 5.1 >> >and 5.2. In the meantime, to check for correctness, open the >> >brain.finalsurfs.mgz file with the surfaces overlayed, and check the >> >intensity value of the voxels which appear to be non-cortical 'black >> >spaces', relative to neighboring gm voxels. ignore the aseg.mgz gm >> >voxels, as those are not accurate (ie, dont load aseg.mgz when >> >inspecting surfaces, or at least turn if off when inspecting gm >> >regionsits still handy to see where hippocampus sits). >> > >> >Nick >> > >> > >> >On Wed, 2013-04-10 at 11:11 +, Yang, Daniel wrote: >> >> Dear FreeSurfer Experts and Users, >> >> >> >> Did anyone find similar things using FS 5.2 (please see my previous >> post >> >> below)? That is, FS 5.2 is including more non-cortical "black spaces" >> >> within pial surfaces, compared to FS 5.1? >> >> >> >> I'm not interested in nitpicking but I feel this is a rather serious >> >> issue, so I would like to raise it again before it's completely >> >>forgotten. >> >> >> >> At the meantime I keep receiving Emails from people asking me this >> >>issue. >> >> >> >> Thanks! >> >> Daniel >> >> >> > >> > >> > >> > >> >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 >> > > ___ 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] 32 bit ubuntu in a 64 bit workstation- Problem
Dear All, I'm working with a system, where 32 bit ubuntu is loaded on to a 64 bit computer. Previously there were graphics problem (Screen gets stuck-- So I restarts it and 'll log in again). Now I'm facing a problem where I cannot enter into ubuntu. Any solutions for this problem will be greatly appreciated.___ 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] Very different results between 5.1.0 and 5.2.0
Looking at the image posted previously. https://yalesurvey.qualtrics.com/SE/?SID=SV_ddwW7I9yMQuCtPn I think it is pretty clear the 5.1 picture has better gray/white contrast. It is a very subtle difference, but you can see it if you look at some pieces of wm that were "missed" by 5.2 in this image. On Thu, Apr 11, 2013 at 12:33 PM, Yang, Daniel wrote: > Thanks Nick! I have uploaded the relevant files to you. > > Thanks, > Daniel > > -- > Yung-Jui "Daniel" Yang, PhD > Postdoctoral Researcher > Yale Child Study Center > New Haven, CT > (203) 737-5454 > > > > > > > On 4/10/13 1:19 PM, "Nick Schmansky" wrote: > > >Daniel, > > > >We're repeating our paired-analysis of thickness measures between 5.1 > >and 5.2. In the meantime, to check for correctness, open the > >brain.finalsurfs.mgz file with the surfaces overlayed, and check the > >intensity value of the voxels which appear to be non-cortical 'black > >spaces', relative to neighboring gm voxels. ignore the aseg.mgz gm > >voxels, as those are not accurate (ie, dont load aseg.mgz when > >inspecting surfaces, or at least turn if off when inspecting gm > >regionsits still handy to see where hippocampus sits). > > > >Nick > > > > > >On Wed, 2013-04-10 at 11:11 +, Yang, Daniel wrote: > >> Dear FreeSurfer Experts and Users, > >> > >> Did anyone find similar things using FS 5.2 (please see my previous post > >> below)? That is, FS 5.2 is including more non-cortical "black spaces" > >> within pial surfaces, compared to FS 5.1? > >> > >> I'm not interested in nitpicking but I feel this is a rather serious > >> issue, so I would like to raise it again before it's completely > >>forgotten. > >> > >> At the meantime I keep receiving Emails from people asking me this > >>issue. > >> > >> Thanks! > >> Daniel > >> > > > > > > > > > >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 > ___ 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] How to calcutate Brain volume?
Dear Cedric, Thanks a bunch. I'll try with mri_label2label. From: "Koolschijn, Cédric" To: Anupa AV Sent: Monday, April 15, 2013 1:07 PM Subject: Re: [Freesurfer] How to calcutate Brain volume? Dear Anupa, The DLPFC is not a standard label in FS. So you need to create it yourself by merging the following labels: DLPFC: middle frontal gyrus, and inferior and middle frontal sulci See also: https://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/2009-February/009600.html Best, Cédric P.C.M.P. Koolschijn (Cédric), PhD Dutch Autism & ADHD Research Center Brain and Cognition Weesperplein 4; Room 3.07 1018 XA Amsterdam The Netherlands E p.c.m.p.koolsch...@uva.nl W http://www.dutcharc.nl// On 4/15/13 7:34 AM, "Anupa AV" wrote: Dear FreeSurfer Experts, > > >I'd like to know how to measure the volume of a brain region using freesurfer. >I know to obtain the volumes after runnin recon-all command. But I don't find >the brain volume of my interest which is DLPFC. >How can I get the brain volume of my interest.? > > > > >Thanks for your response in advance. > > > > > ___ 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.
