Freesurfer

freesurfer@nmr.mgh.harvard.edu

19 participants
30088 discussions

neuroimaging post-doc fellowship (fwd)
by Bruce Fischl 06 Mar '14

06 Mar '14

FYI ---------- Forwarded message ---------- Date: Thu, 6 Mar 2014 14:44:52 +0000 From: "Au, Rhoda" <rhodaau(a)bu.edu> To: Bruce Fischl <fischl(a)nmr.mgh.harvard.edu>, Ron KILLIANY <rkilliany(a)cajal-1.bu.edu>, "Palumbo, Carole Lee" <cpalumbo(a)bu.edu> Subject: neuroimaging post-doc fellowship Hi All: Angela Jefferson is looking for a neuroimaging post-doc – see attached description. If you know a soon-to-be- Ph.D. or new post-doc that is really sick of the winter weather, send them this! - Rhoda

1 0

Freesurfer 5.3 and CentOS 5.10
by Weiner, Michael 06 Mar '14

06 Mar '14

I have recently upgraded our server from v5.0.0 to v5.3.0 running on CentOS 5.10 and was a little surprised that there wasnt a version of Freesurfer built for this platform but rather 4 and 6. I guess my main question is, was the version for centos4 built with openmpi at all? THe server we are running Freesurfer on has 48 cores and we are trying to figure out how to make sure that while running Freesurfer we take advantage of all these cores. Is there any documentation that i can look at to help me in this endeavor or does anyone have any tips they can share? Thank you in advance Michael Weiner Lead Analyst/UNIX Systems Administrator Lerner Research Institute Computing Services Lerner Research Institute Cleveland Clinic =================================== Please consider the environment before printing this e-mail Cleveland Clinic is ranked as one of the top hospitals in America by U.S.News & World Report (2013). Visit us online at http://www.clevelandclinic.org for a complete listing of our services, staff and locations. Confidentiality Note: This message is intended for use only by the individual or entity to which it is addressed and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If the reader of this message is not the intended recipient or the employee or agent responsible for delivering the message to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please contact the sender immediately and destroy the material in its entirety, whether electronic or hard copy. Thank you.

2 4

Group comparisons
by Tudor Popescu 05 Mar '14

05 Mar '14

Hello, I have some questions on doing group comparisons with thickness, area and volume. Many thanks in advance for any help! 1) For a DOSS design with group and gender as categorical factors, I see that an interaction contrast ("Is there a group-gender interaction in the mean thickness?") still exists - but what does this contrast mean, given that DOSS by definition doesn't allow for interactions? 2) it makes sense that measures such as thickness are analysed vertex-wise in QDEC, however what does it mean when the dependent variable is area or volume - measures that do not make physical sense for a single vertex but only at the level of a region consisting of *several* vertices? 3) For values extracted from atlas regions with aparcstats2table, it seems that the product of the extracted CT and area is in the same order of magnitude as the extracted volume, but never really the same or even close - why, when the volume of a region should theoretically be the product of its surface area by its thickness? Tudor

2 1

Surface area in aparc stats
by 沈庄明 05 Mar '14

05 Mar '14

Hi all, I need to know how is the SurfArea in ?h.aparc.stats calculated by FreeSurfer? Since each cortical parcellation has its own thickness in 3D space, does the surface area computation consider both the exterior surface (i.e. the surface separating the gray matter and the background) and the interior surface (i.e. the surface separating the gray matter and the white matter)? Thanks! Zhuangming Shen

2 1

TkmEdit Scripting SetBrushInfo Error
by Joerg Pfannmoeller 05 Mar '14

05 Mar '14

Hi, I am getting tzhe following an error if I use the following command in a tcl-script: SetBrushInfo 3 1 2000 1 The error is: "Error: Parsing script file This error was encountered while running the script specified with the -tcl option. " What is wrong? Sincerely yours pfannmoe

1 1

Fwd: AW: different thickness after converting wm.mgz in nifti and back
by Koschutnig, Karl (karl.koschutnig＠uni-graz.at) 05 Mar '14

05 Mar '14

Betreff: Re: AW: [Freesurfer] different thickness after converting wm.mgz in nifti and back can you cc the list so that others can help? On Wed, 5 Mar 2014, Koschutnig, Karl (karl.koschutnig(a)uni-graz.at<mailto:karl.koschutnig@uni-graz.at>) wrote: Hi Bruce, thanks for the fast answer! 1) convert from mgz to nii mri_convert wm.mgz wm.nii $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from wm.mgz... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, -1.86265e-08, -5.40167e-08) j_ras = (7.82311e-08, 1.52504e-08, -1) k_ras = (2.23517e-08, 1, -1.59052e-08) writing to wm.nii... 2) and back to mgz mri_convert wm.nii wm.mgz $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from wm.nii... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, -1.86265e-08, -5.40167e-08) j_ras = (7.82311e-08, 1.52504e-08, -1) k_ras = (2.23517e-08, 1, -1.59052e-08) writing to wm.mgz... 3) the difference between the original wm and the converted one mri_diff wm.mgz wm_orig.mgz Volumes differ in geometry row=1 col=1 diff=0.000000 (5.96046e-08) ... for more details: mri_diff FREESURFER_HOME /usr/local/freesurfer cwd /media/Data/FREESURFER/Fage_P026a/mri cmdline mri_diff wm.mgz wm_orig.mgz --log diff timestamp 2014/03/05-15:26:19-GMT sysname Linux hostname fMRI-04 machine x86_64 user fmri v1 wm.mgz v2 wm_orig.mgz pixthresh 0.000000 checkres 1 checkacq 1 checkpix 1 checkgeo 1 checkori 1 checkprec 1 absdiff 1 diffabs 0 diffpct 0 rss 0 ssd 0 rms 0 logfile diff v1 vox2ras ---------- -1.000 0.000 0.000 130.238; -0.000 0.000 1.000 -128.800; -0.000 -1.000 -0.000 121.348; 0.000 0.000 0.000 1.000; v2 vox2ras --------- -1.000 0.000 0.000 130.238; -0.000 0.000 1.000 -128.800; -0.000 -1.000 -0.000 121.348; 0.000 0.000 0.000 1.000; Volumes differ in geometry vox2ras r=1 c=1 0.000000 best Karl ________________________________________ Von: Bruce Fischl [fischl(a)nmr.mgh.harvard.edu<mailto:fischl@nmr.mgh.harvard.edu>] Gesendet: Mittwoch, 5. März 2014 16:00 An: Koschutnig, Karl (karl.koschutnig(a)uni-graz.at<mailto:karl.koschutnig@uni-graz.at>) Cc: freesurfer(a)nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu> Betreff: Re: [Freesurfer] different thickness after converting wm.mgz in nifti and back Hi Karl why is there any difference in either geometry or pixel values after converting back and forth? Can you send us your mri_convert command lines and screen output? cheers Bruce On Wed, 5 Mar 2014, Koschutnig, Karl (karl.koschutnig(a)uni-graz.at<mailto:karl.koschutnig@uni-graz.at>) wrote: Dear experts, our group decided to make all the white matter edits in brainvoyager (don't ask me why;-). So we converted the wm.mgz into nii and then into the brainvoyager format vmr, made the edits and the same way back into freesurfer. We started the recon-all -autorecon2-wm … and found massive reduction in the thickness. So far so bad. To figure out the problem we started at the beginning of the conversion-mess and converted the wm.mgz into wm.nii and back into wm.mgz and found nearly the same reduction in the thickness. Finally, here comes my question. Is it possible that due to interpolation errors in the mri_convert routine this reduction can be explained? PS: here is the output from mri_diff for the wm_orig.mgz and the converted one: Volumes differ in geometry row=1 col=1 diff=0.000000 (5.96046e-08) Please fin attached the reconstructed white matter surface (red = original, yellow = after converting the wm from nii in mgz and back) thank you so much best Karl 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.

2 1

(no subject)
by Hugh Pemberton 05 Mar '14

05 Mar '14

Hi guys, just wondering what you'd say is the best measure for whole brain volume? Cortex volume.. Cortical white matter volume.. Total gray volume.. Intracranial volume.. etc. Cheers! Hugh

2 1

Re: [Freesurfer] Problematic dilated ventricles
by Douglas N Greve 05 Mar '14

05 Mar '14

It contains the volumes of the white matter parcellation. You can make a table with asegstats2table and specifying --stats=wmparc.stats doug On 03/05/2014 11:16 AM, Victor Kovac wrote: > So, I assume the aseg.mgz contains the values represented in the > asegstats2table, but what values does the wmparc.mgz contain? Is this > where the output for the aparcstats2table comes from? > > Thanks! > Victor > > > On Tue, Mar 4, 2014 at 9:43 AM, Douglas N Greve > <greve(a)nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> wrote: > > > The wmparc is off because the surfaces are incorrect. The aseg > does not > have to follow the surfaces, but wmparc does > doug > > > On 03/03/2014 03:10 PM, Victor Kovac wrote: > > Hi Bruce and Doug, > > > > "cp aseg.auto.mgz aseg.mgz" was my last step before running > > -autorecon2-cp -autorecon3, as suggested by Bruce before, so I > am not > > sure what the problem could be. Since there seem to be problems > > re-creating the pial/wm surfaces this way, would it be possible for > > you to send the entire subject folder to me via GoogleDrive or some > > other method? > > > > I also have another question: I have loaded a subject with tkmedit, > > but the segmentation looks drastically improved when the > -segmentation > > is aseg.auto_noCCseg.mgz instead of -wmparc.mgz (images attached), > > though the pial surface does not reflect this. > > > > Could you tell me why this is? And is it possible to get the pial/wm > > surfaces to follow along the lines of the aseg.auto_noCCseg.mgz > > segmentation? I am sorry if this is a naive question. > > > > Also: the images are from the original aseg.auto_noCCseg.mgz of this > > subject (MPS2002-3), not the updated one you sent me, Bruce. > > > > Thank you! > > Victor > > > > > > On Mon, Mar 3, 2014 at 10:53 AM, Douglas N Greve > > <greve(a)nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu>>> wrote: > > > > > > I think that it should. To be safe, I would "cp aseg.auto.mgz > > aseg.mgz" > > otherwise aseg.mgz will not change (any differences will be > > interpreted > > as manual changes) > > doug > > > > > > On 03/02/2014 10:07 AM, Bruce Fischl wrote: > > > Hi Victor > > > > > > hmmm, I'm not sure why that didn't work. Perhaps someone > else can > > > comment? Doug or Nick: if the aseg.mgz is recreated and you > > start with > > > -autorecon2-cp shouldn't it propagate the effects of the > new aseg > > > forward? > > > > > > cheers > > > Bruce > > > > > > > > > On Thu, 27 Feb 2014, Victor Kovac wrote: > > > > > >> Dear Bruce, > > >> Have you had any time to try to analyze our subject > MPS2002-3? I > > >> believe you > > >> mentioned you would give it a shot in your free time a > couple of > > >> months ago. > > >> > > >> Also, you were kind enough to analyze a subject for me, > MPS1036-1, > > >> and sent > > >> me aseg.auto_noCCseg.new.mgz. I replaced the original > file and > > >> removed thee > > >> "new" within the title, and then, to re-create the pial > and wm > > >> surfaces, I > > >> ran: > > >> > > >> set mdir=$SUBJECTS_DIR/MPS1036-1/mri > > >> mri_cc -aseg aseg.auto_noCCseg.mgz -o aseg.auto.mgz \ > > >> -lta $mdir/transforms/cc_up.lta MPS1036-1 > > >> cp aseg.auto.mgz aseg.mgz > > >> > > >> and then: recon-all -autorecon2-cp -autorecon3, which I > believe > > >> starts the > > >> recon-all pipeline at normalization2, as you suggested. > > However, this > > >> has > > >> yielded no effect that I can see when I visualize the > subject with > > >> > > >> tkmedit $proc brainmask.mgz lh.white -aux T1.mgz -aux-surface > > rh.white > > >> -segmentation wmparc.mgz > $FREESURFER_HOME/FreeSurferColorLUT.txt > > >> > > >> Any advice would be greatly appreciated! Attached is the > > >> recon-all.log for > > >> this subject. Let me know if I should cc the group. > > >> > > >> Thank you. > > >> Victor > > >> > > >> > > >> On Tue, Jan 7, 2014 at 11:19 AM, Bruce Fischl > > >> <fischl(a)nmr.mgh.harvard.edu > <mailto:fischl@nmr.mgh.harvard.edu> > <mailto:fischl@nmr.mgh.harvard.edu > <mailto:fischl@nmr.mgh.harvard.edu>>> > > >> wrote: > > >> Hi Victor > > >> > > >> for each subject I think you want to run: > > >> > > >> > > >> set mdir=$SUBJECTS_DIR/$subject/mri > > >> mri_cc -aseg aseg.auto_noCCseg.mgz -o aseg.auto.mgz \ > > >> -lta $mdir/transforms/cc_up.lta $subject > > >> cp aseg.auto.mgz aseg.mgz > > >> > > >> > > >> then run recon-all from normalization2 forward > (check the > > >> recon-all -help for these steps) > > >> > > >> cheers > > >> Bruce > > >> > > >> On Tue, 7 Jan 2014, Victor Kovac wrote: > > >> > > >> Hi Bruce, > > >> > > >> I ran recon-all -autorecon2-cp -autorecon3 -s > > >> MPS1036-1 but, again, this did > > >> not affect the pial or wm surfaces. I have > attached > > >> the recon-all.log in > > >> case that would be helpful in diagnosing the > issue. > > >> > > >> Any advise would be greatly appreciated. > > >> > > >> Thanks! > > >> Victor > > >> > > >> > > >> On Thu, Jan 2, 2014 at 12:12 PM, Bruce Fischl > > >> <fischl(a)nmr.mgh.harvard.edu > <mailto:fischl@nmr.mgh.harvard.edu> > > <mailto:fischl@nmr.mgh.harvard.edu > <mailto:fischl@nmr.mgh.harvard.edu>>> > > >> wrote: > > >> Hi Victor > > >> > > >> you can look in the recon-all -help and run > > >> the stages that are > > >> after mri_ca_label. Not sure why -make all > > >> didn't work, perhaps > > >> Zeke and/or Nick can comment? > > >> Bruce > > >> > > >> > > >> On Thu, 2 Jan 2014, Victor Kovac wrote: > > >> > > >> Dear Bruce, > > >> > > >> A few weeks ago you made code mods to > > >> mri_em_register and got recon-all to > > >> process a subject of mine, MPS1036-1. > > >> You sent me > > >> the new > > >> aseg.auto_noCCseg.mgz and told me to run > > >> recon-all > > >> -make all -s MPS1036-1. > > >> > > >> I did this but I get the message > > >> make: Nothing to be done for 'all' > > >> and when I visualize the segmentation > > >> with tkmedit, > > >> there appears to be no > > >> change to the pial or wm surfaces. > > >> > > >> Could you please advise? > > >> > > >> Thank you. > > >> Victor > > >> > > >> > > >> On Mon, Dec 9, 2013 at 2:11 PM, Bruce > > >> Fischl > > >> <fischl(a)nmr.mgh.harvard.edu > <mailto:fischl@nmr.mgh.harvard.edu> > > <mailto:fischl@nmr.mgh.harvard.edu > <mailto:fischl@nmr.mgh.harvard.edu>>> > > >> wrote: > > >> if you rename > > >> aseg.auto_noCCseg.new.mgz to be > > >> aseg.auto_noCCseg.mgz > > >> > > >> then run: > > >> > > >> recon-all -make all -s MPS1036-1 > > >> > > >> you should be all set > > >> > > >> Bruce > > >> > > >> > > >> On Mon, 9 Dec 2013, Victor > Kovac > > >> wrote: > > >> > > >> I was hoping to > MPS1036-1. I > > >> only got > > >> aseg.auto_noCCseg.new.mgz. > > >> Thank you > > >> for looking into MPS2002-3 > > >> -- it is > > >> quite the brain. > > >> And somehow, with all > > >> those morphological > > >> abnormalities, this > > >> subject has > > >> an IQ of 130. Very > > >> strange. > > >> Thanks, > > >> Victor > > >> > > >> > > >> On Mon, Dec 9, 2013 > at 2:03 > > >> PM, Bruce > > >> Fischl > > >> <fischl(a)nmr.mgh.harvard.edu > <mailto:fischl@nmr.mgh.harvard.edu> > <mailto:fischl@nmr.mgh.harvard.edu > <mailto:fischl@nmr.mgh.harvard.edu>>> > > >> wrote: > > >> which one? I'm still > > >> messing with > > >> MPS2002-3 in > > >> my spare time > > >> On Mon, 9 Dec 2013, > > >> Victor Kovac > > >> wrote: > > >> > > >> Hi Bruce, > > >> Is there a way > > >> for you to > > >> send the > > >> subject(s) you > > >> analyzed to me? > > >> I know > > >> it's too big for > > >> email, but > > >> could you > > >> possibly > > >> upload it to > > >> GoogleDrive? > > >> > > >> Thanks! > > >> Victor > > >> > > >> > > >> On Wed, Dec 4, > > >> 2013 at 3:40 > > >> PM, Bruce > > >> Fischl > > >> > > >> <fischl(a)nmr.mgh.harvard.edu > <mailto:fischl@nmr.mgh.harvard.edu> > > <mailto:fischl@nmr.mgh.harvard.edu > <mailto:fischl@nmr.mgh.harvard.edu>>> > > >> wrote: > > >> p.s. the > > >> other thing I > > >> did was run > > >> the graph > > >> cut skull > > >> stripping, > > >> which > > >> removed a bunch > > >> of extraneous > > >> stuff > > >> On Wed, 4 > > >> Dec 2013, > > >> kovac081(a)umn.edu <mailto:kovac081@umn.edu> > <mailto:kovac081@umn.edu <mailto:kovac081@umn.edu>> wrote: > > >> > > >> Hey! > > >> > > >> Victor > > >> Kovac > > >> (kovac081(a)umn.edu > <mailto:kovac081@umn.edu> > > <mailto:kovac081@umn.edu <mailto:kovac081@umn.edu>>) > > >> has uploaded > > >> some files > > >> for you at > > >> the > > >> Martinos Center > > >> FileDrop: > > >> > > >> -> MPS2002-3.zip > > >> (292.12 > > >> MiB) > > >> > > >> > > >> > > >> > > > <http://gate.nmr.mgh.harvard.edu/filedrop2/?u=8mo9zg0isep&f=55xjt9pflsi> > > >> -> MPS2017-1.zip > > >> (264.15 > > >> MiB) > > >> > > >> > > >> > > >> > > > <http://gate.nmr.mgh.harvard.edu/filedrop2/?u=8mo9zg0isep&f=ak4v31bzu4p> > > >> > > >> Also, they left > > >> this message > > >> for you: > > >> Hi Bruce, > > >> > > >> Here are the two > > >> subjects > > >> with > > >> ventriculomegaly that > > >> are causing > > >> the worst > > >> issues. The worst > > >> segmentation > > >> in > > >> MPS2002-3 is in > > >> the > > >> superior frontal > > >> (slices > > >> 150-180) and > > >> parietal > > >> (slices 50-95) > > >> cortical areas; > > >> this may be > > >> due to the > > >> numerous > > >> dilated > > >> Virchow-Robin > > >> spaces in his > > >> brain, which > > >> is another > > >> > > >> neuropathological feature of > > >> this > > >> disease. > > >> > > >> Thanks! > > >> Victor > > >> > > >> Please be aware, > > >> your upload > > >> will expire > > >> on December > > >> 31st. If > > >> you'd like to > > >> download these > > >> files, feel > > >> free to use > > >> the link > > >> below: > > >> > > >> > > >> > > >> > > >> http://gate.nmr.mgh.harvard.edu/filedrop2/?u=8mo9zg0isep > > >> > > >> Cheers, > > >> The NMR Team > > >> > > >> > > >> > > >> > > >> > > >> 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(a)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. > > >> > > >> > > >> > > >> > > > > > > > > > _______________________________________________ > > > Freesurfer mailing list > > > Freesurfer(a)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 > > > > -- > > Douglas N. Greve, Ph.D. > > MGH-NMR Center > > greve(a)nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> > <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> > > Phone Number: 617-724-2358 <tel:617-724-2358> > <tel:617-724-2358 <tel:617-724-2358>> > > Fax: 617-726-7422 <tel:617-726-7422> <tel:617-726-7422 > <tel:617-726-7422>> > > > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > > FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 > > www.nmr.mgh.harvard.edu/facility/filedrop/index.html > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > > Outgoing: > > ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer(a)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 > > > > > > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > greve(a)nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> > Phone Number: 617-724-2358 <tel:617-724-2358> > Fax: 617-726-7422 <tel:617-726-7422> > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 > www.nmr.mgh.harvard.edu/facility/filedrop/index.html > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > Outgoing: > ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > -- Douglas N. Greve, Ph.D. MGH-NMR Center greve(a)nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

1 0

Re: [Freesurfer] Freesurfer for rodents
by Douglas N Greve 05 Mar '14

05 Mar '14

Hi Claudia, I don't know of anyone using it for rodents. In general, it is highly tuned to the parameters of the primate (mostly human) brain, and I think it would be quite difficult to adapt it to rodents. I'm cc'ing the FS list in case someone else has anything to add. doug On 03/05/2014 03:09 AM, Falfan-Melgoza, Claudia wrote: > Dear Dr. Greve, > > I work at the Central Institute of Mental Health in Mannheim, Germany > and I am quite sure you have heard this question to no end but I would > like to ask you how viable would it be to use Freesurfer for rats and > mice?, I have read that providing an atlas of the rodent brain would > be the first step but as a first timer attempting to use Freesurfer I > am not quite sure that would cut it, or if the next steps in the > pipeline would need also a good amount of modification. And one last > question, do you know of other software that in your opinion could be > more suitable for rodents? > > I appreciate greatly your time and thank you very much in advance, > > Claudia Falfan-Melgoza > > > > > > Central Institute of Mental Health > J5- 68159 > Mannheim, Germany -- Douglas N. Greve, Ph.D. MGH-NMR Center greve(a)nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

1 0

LGI in Qdec
by krista kelly 05 Mar '14

05 Mar '14

Hello, I followed instructions on how to incorporate the lgi_pial measure into QDec, however, it's not coming up when I go to choose this as a measure. I ran recon-all -s my_subject_id -qcache -measure pial_lgi and created a Qdecrc file in my $SUBJECTS_DIR directory. Does anyone have any insight as to why this may be occurring? Thanks, Krista

2 8

Jump to page:

2026

2025

2024

2023

2022

2021

2020

2019

2018

2017

2016

2015

2014

2013

2012

2011

2010

2009

2008

2007

2006

2005

2004

Freesurfer