Freesurfer March 2014

freesurfer@nmr.mgh.harvard.edu

147 participants
247 discussions

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.

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(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

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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/

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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/

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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

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Qdec failed
by Yinfei Li 05 Mar '14

05 Mar '14

Dear experts, I have Freesurfer running quite well on Ubuntu for some time. But today when I tried to run the command ‘qdec’, I got the following error: Qdec.bin: error while loading shared libraries: libXss.so.1: cannot open shared object file: No such file or directory How do I fix this? Thank you. Yinfei

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

05 Mar '14

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

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Is there a better direction for acquiring T1 structural scan? sagittal or axial
by Tartaglia, Carmela 05 Mar '14

05 Mar '14

I am wondering if there is a preferred direction for acquiring T1 structural scan? sagittal or axial? and what is the rational? Thanks Carmela This e-mail may contain confidential and/or privileged information for the sole use of the intended recipient. Any review or distribution by anyone other than the person for whom it was originally intended is strictly prohibited. If you have received this e-mail in error, please contact the sender and delete all copies. Opinions, conclusions or other information contained in this e-mail may not be that of the organization.

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Combining sagittal and axial T1 for volumetric analysis
by Tartaglia, Carmela 05 Mar '14

05 Mar '14

I have patients and controls scanned on the same scanner but their data was acquired in different orientations. One group is sagittal and the other is axial. The sizes are 1X1X1 vs 1X1X1.2. Is it possible to combine these images for freesurfer analysis? Thanks carmela This e-mail may contain confidential and/or privileged information for the sole use of the intended recipient. Any review or distribution by anyone other than the person for whom it was originally intended is strictly prohibited. If you have received this e-mail in error, please contact the sender and delete all copies. Opinions, conclusions or other information contained in this e-mail may not be that of the organization.

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comparing models
by Eric Cunningham 04 Mar '14

04 Mar '14

Hello Freesurfer experts, I have a question about how to determine if a covariate is important in a mixed effects model for example: Y1 = B1 + B2(time) + B3(rand_effect1) + B4(rand_effect*time) + B5(covariate_1) +B6(covariate_2) Y2 = B1 + B2(time) + B3(rand_effect1) + B4(rand_effect*time) + B5(covariate_1) Would it be appropriate to use the lme_mass_LR script? (the script says it is for comparing models with q and q+1 random effects). Thanks, -E

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