Freesurfer

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Possible to generate connectivity map using FS and Tracula
by Salil Soman 22 Jun '13

22 Jun '13

Dear Doug, Is there a way to use the Freesurfer and Tracula output to compute connectivity maps? Thanks! Sal

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check orientation
by Brigitte Dahmen 22 Jun '13

22 Jun '13

Dear Freesurfer experts, is there a command in Freesurfer to check for correct orientation (LAS vs. PSR) of T1 images (similar to "fslhd" in FSL)? Thank you very much! Brigitte

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retinotopic mapping selxavg3-sess error
by Bianca van Kemenade 21 Jun '13

21 Jun '13

Dear Freesurfers, I'm setting up freesurfer to do retinotopic mapping. I use a PC with Windows XP, so I installed Freesurfer using the VirtualBox (with Xubuntu). I managed to get through the initial steps for retinotopic mapping, but I get stuck at the actual analysis. The point where I get stuck is: selxavg3-sess -a rtopy.self.lh -s P2_BK It starts the analysis, but runs into problems at the stage "Using FSL's BET to extract brain" and gives the following error output: # ---------- Using FSL's BET to Extract Brain------------------ # /home/virtualuser/freesurfer/ shared/P2_BK/bold bet.fsl /tmp/mkbrainmask_4425/in.nii /tmp/mkbrainmask_4425/brain -m -f 0.1 /home/virtualuser/freesurfer/bin/bet.fsl: 150: /bin/remove_ext: not found /home/virtualuser/freesurfer/bin/bet.fsl: 151: /bin/remove_ext: not found /home/virtualuser/freesurfer/bin/bet.fsl: 158: /bin/imtest: not found [: 158: =: unexpected operator /home/virtualuser/freesurfer/bin/bet.fsl: 380: /bin/bet2: not found /bin/rm: cannot remove `_tmp*': Protocol error ERROR: bet failed I tried updating FSL in case that is the problem, but it is only available for Ubuntu 10.04 and up, whereas the Ubuntu system that is provided to install the Freesurfer virtual disk image is 9.04. If anyone has an idea how to proceed let me know, any help is much appreciated. Thanks, Bianca

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use mri_convert to flip A/P labels
by Ray, Siddharth 21 Jun '13

21 Jun '13

Hi, I have niftii files of some subjects where A/P labels are flipped. Is there anyway I can flip those labels using mri_convert, like mri_convert -left-right-reverse for flipping L/R labels. Thanks, -Siddharth

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Fwd: missing surfaces
by Deirdre O Shea 21 Jun '13

21 Jun '13

---------- Forwarded message ---------- From: Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> Date: Fri, Jun 21, 2013 at 11:33 AM Subject: Re: [Freesurfer] missing surfaces To: Deirdre O Shea <deirdreoshea84(a)gmail.com> Hi Deirdre can you cc the list so that others can answer? Bruce On Fri, 21 Jun 2013, Deirdre O Shea wrote: Hi Doug and Bruce, > > I have an error.logs file which shows only this message for one of the > subjects.. > > mrisReadTriangleFile(/share/**users/doshea/WHICAP_PET/** > W32714V2/3DT1/FreeSurfer/surf/**rh.pial): surface > doesn't match /share/users/doshes/WHICAP_**PET/w32714v2/3dt1/ > > > > > On Fri, Jun 21, 2013 at 9:57 AM, Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> > wrote: > Hi Deirdre > > can you send us the recon-all.log, or at least the last 100 lines of > it? > cheers > Bruce > > On Thu, 20 Jun 2013, Deirdre O Shea wrote: > > Dear FreeSurfers, > > I have been using FreeSurfer for editing for the past year now > and I have > recently come across an > issue that I have not seen before in a new dataset. The pial > surfaces are > missing in the right > hemisphere following the first run of Freesurfer (before any > edits). There > are also some without > white matter surfaces. However, not all my subjects have shown > this and are > just fine. Any > suggestions on how i can fix this? > > Thanks, > Deirdre > > > > > 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<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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Corrected thickness values?
by Jackie Lam 21 Jun '13

21 Jun '13

Hi there, I was wondering if the cortical thickness values of the ROIs in ?h.aparc.a2009s.stats or ?h.aparc.stats have been corrected based on the subject's whole brain volume or the template volume or if it is just the thickness measures without correction. Thanks, Jack

2 1

missing surfaces
by Deirdre O Shea 21 Jun '13

21 Jun '13

Dear FreeSurfers, I have been using FreeSurfer for editing for the past year now and I have recently come across an issue that I have not seen before in a new dataset. The pial surfaces are missing in the right hemisphere following the first run of Freesurfer (before any edits). There are also some without white matter surfaces. However, not all my subjects have shown this and are just fine. Any suggestions on how i can fix this? Thanks, Deirdre

3 2

problem bbregister onto longitudinal pipeline
by Daniel Garcia 21 Jun '13

21 Jun '13

Dear Freesurfer Users, I'm having a problem to register my PET images into the longitudinal pipeline of freesurfer (version 5.1). I have use bbregister without any problem to put the PET image into the crossectional images but it fails to register to the long version of it. Someone can tell me if I'm doing something wrong? bbregister -s P09_TA --mov pet_09.nii --init-fsl --reg matrix.mat --o pet2free.mgz This last command works perfectly, but bbregister -s P09_TA.long.P09 --mov pet_09.nii --init-fsl --reg matrix.mat --o pet2free.mgz Fails completely. My objective is to project my pet cortex into the surface in longitudinal that is why I'm interested in this processing. Maybe you can tell my another way of doing this. Thank you very much. Daniel

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Re: [Freesurfer] SPM ROI to Cortical Thickness
by Bruce Fischl 21 Jun '13

21 Jun '13

please cc the list so others can answer. Do you mean get cortical thickness? If so, then you need to run recon-all on the structural image On Mon, 17 Jun 2013, xiangbo_2010 wrote: > I have obtained the mask from xjview (.img), I want to obtain the CT from > the mask, thanks! > Bo > > > > > > At 2013-06-17 22:40:43,"Bruce Fischl" <fischl(a)nmr.mgh.harvard.edu> wrote: > >what are you trying to map to the surface? > >On Mon, 17 Jun 2013, xiangbo_2010 > >wrote: > > > >> > >> Hi Bruce > >> Thank you for my help, when I use the bbregister, do not know how to choo > se > >> data for --mov, thanks! > >> > >> Bo > >> > >> > >> > >> > >> At 2013-06-17 20:34:39,"Bruce Fischl" <fischl(a)nmr.mgh.harvard.edu> wrote: > >> >Hi Bo, > >> > > >> >tksurfer doesn't take a path to a file. Read the help on it - you need t > o > >> >reconstrcut the subject with recon-all then give it the subject id. To > >> >project a volumetric map onto the surface use mri_vol2surf, with the > >> >registration typically computed by bbregister. > >> > > >> >cheers > >> >Bruce > >> > > >> > > >> >On Mon, 17 Jun 2013, xiangbo_2010 wrote: > >> > > >> >> Hi dougThank you for giving this information, I used the > >> >command: "/tksurfer fsaverage lh inflated -aparc -mni152reg -overlay /pa > thn > >> ame/to/s > >> >> pm/roi/yourfile.img/", but do not have results for me, and do not know > ho > >> w > >> >> to do next? thanks! > >> >> > >> >> > >> >> Bo > >> >> > >> >> > >> >> > >> >> > >> >> > >> >> At 2013-06-06 23:04:30,"Douglas N Greve" <greve(a)nmr.mgh.harvard.edu> w > rot > >> e: > >> >> >Hi Stephanie, I don't know which recommendation you are referring to. > We > >> > >> >> >get a lot of emails, and I can't remember each one. Can you repost wi > th > >> >> >the full thread? > >> >> >doug > >> >> > > >> >> > > >> >> >On 06/06/2013 10:40 AM, McMains, Stephanie wrote: > >> >> >> I am wondering why you didn't tell them to go through fsvarege spac > e? > >> >> >> I thought that was an easy way to go from SPM MNI to freesurfer la > nd. > >> >> >> > >> >> >>> /tksurfer fsaverage lh inflated -aparc -mni152reg -overlay /pathna > me/ > >> to/ > >> >> spm/roi/yourfile.img/ > >> >> >> > >> >> >> > >> >> >> I am wondering because when I look at the segmentation for fsaverag > e, > >> >> >> it seems like it is missing a lot of the gray matter, particularly > in > >> >> >> the big sulci, most likely from the 'smoothing' that comes with > >> >> >> averaging subjects together. And therefore I wonder if this is the > > >> >> >> best thing to use as an intermediate step. Are you instead suggest > ing > >> > >> >> >> (as it seemed like in this thread), to put the SPM roi into individ > ual > >> > >> >> >> subject space and then somehow project it to the surface in free su > rfe > >> r? > >> >> >> > >> >> >> Thanks, > >> >> >> Stephanie > >> >> >> > >> >> >> > >> >> >> +++++++++++++++++++++++++ > >> >> >> > >> >> >> Stephanie McMains > >> >> >> Neuroimaging Staff Scientist > >> >> >> Center for Brain Science > >> >> >> Harvard University > >> >> >> 52 Oxford Street > >> >> >> Cambridge, MA 02138 > >> >> >> > >> >> >> +++++++++++++++++++++++++ > >> >> >> For answers to frequently asked questions: > >> >> >> http://cbs.fas.harvard.edu/science/core-facilities/neuroimaging/inf > orm > >> ati > >> >> on-investigators/faq > >> >> >> > >> >> >> > >> >> >> > >> >> >> > >> >> >> > >> >> >> > >> >> >> > >> >> >> > >> >> >> > >> >> >> _______________________________________________ > >> >> >> Freesurfer mailing list > >> >> >> Freesurfer(a)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/gre > ve/ > >> >> > > >> >> >_______________________________________________ > >> >> >Freesurfer mailing list > >> >> >Freesurfer(a)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 who > m i > >> t i > >> >> s > >> >> >addressed. If you believe this e-mail was sent to you in error and th > e e > >> -ma > >> >> il > >> >> >contains patient information, please contact the Partners Compliance > Hel > >> pLi > >> >> ne at > >> >> >http://www.partners.org/complianceline . If the e-mail was sent to yo > u i > >> n e > >> >> rror > >> >> >but does not contain patient information, please contact the sender a > nd > >> pro > >> >> perly > >> >> >dispose of the e-mail. > >> >> > > >> >> > >> >> > >> >> > >> >> > >> > >> > >> > >> > > > >

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Fwd: problem downloading Xhemi files
by amirhossein manzouri 21 Jun '13

21 Jun '13

Dear Doug, I just installed 5.3 version and now I have the Xhemi. I need to study asymmetry of the brains -processed with FS 5.1- comparing right and left hemispheres for each subject individually and between male and female groups including 40 subjects each. Would you please let me know the procedure with Xhemi. BR-Amir On Wed, Jun 19, 2013 at 9:18 AM, amirhossein manzouri < a.h.manzouri(a)gmail.com> wrote: > I use curl to download in MAC with the links you mentioned and it is not > there! > amir% curl -O > ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/surfreg > % Total % Received % Xferd Average Speed Time Time Time > Current > Dload Upload Total Spent Left > Speed > 0 0 0 0 0 0 0 0 --:--:-- 0:00:01 --:--:-- > 0 > curl: (78) RETR response: 550 > > > > On Wed, Jun 19, 2013 at 8:42 AM, Douglas Greve <greve(a)nmr.mgh.harvard.edu>wrote: > >> try now >> >> >> On 6/18/13 9:37 PM, amirhossein manzouri wrote: >> >> I have version 5.1 so please recreate the links! >> BR >> >> >> On Tue, Jun 18, 2013 at 8:43 AM, Douglas Greve <greve(a)nmr.mgh.harvard.edu >> > wrote: >> >>> >>> Hi Amir, if you are using 5.2 or 5.3, then you should already have it. >>> If not, I'll have to recreate the links. let me know >>> doug >>> >>> >>> On 6/17/13 6:52 AM, amirhossein manzouri wrote: >>> >>> Dear Doug, >>> I can not download the files needed for Xhemi in mentioned link. Would >>> you please advise how to download them? >>> >>> -- >>> Best regards, >>> Amir >>> >>> >>> >>> >>> >>> >>> _______________________________________________ >>> Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>> >>> >>> >>> _______________________________________________ >>> Freesurfer mailing list >>> Freesurfer(a)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. >>> >>>

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