Freesurfer

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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. > > > > >

1 0

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

4 6

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. > >> >> > > >> >> > >> >> > >> >> > >> >> > >> > >> > >> > >> > > > >

4 18

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. >>> >>>

2 1

Help：Freesurfer reg-feat2anat error
by 王志伟 21 Jun '13

21 Jun '13

Dear Sir or Madam, I am trying to apply FreeSurfer Tools to FSL fMRI Analysis (FEAT) as your tutorial. But there were many errors and I cannot figure them out. Could you help me deal with them? Thank you so much!The log files are attached. The details are as follows: the version of Linux: rhel6.2; the version of freesurfer: freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0 SUBJECTS_DIR: /usr/local/freesurfer/subjects working directory /usr/local/freesurfer/subjects/fbert-feat command: reg-feat2anat --feat fbert1.feat --subject bert there is no ERROR in anat2std.register.dat.fslregister.log the first ERROR in anat2exf.register.dat.fslregister.log is '' /usr/local/freesurfer/subjects/fbert-feat mri_convert ERROR: could not determine file for /usr/local/freesurfer/subjects/bert/mri/ERROR: fbert1.feat/reg/freesurfer/tmp/refvol.fslregister.nii mri_convert ERROR: could not determine file for /usr/local/freesurfer/subjects/bert/mri/ERROR: fbert1.feat/reg/freesurfer/tmp/refvol.fslregister.nii'' the reg-feat2anat.log is as follow: Wed Jun 19 20:41:16 CST 2013 /usr/local/freesurfer/subjects/fbert-feat /usr/local/freesurfer/bin/reg-feat2anat --feat fbert1.feat --subject bert Linux T7600-3 2.6.32-220.el6.x86_64 #1 SMP Wed Nov 9 08:03:13 EST 2011 x86_64 x86_64 x86_64 GNU/Linux example_func ras_good_flag 1 ------------------------------------------------------- Initializing exf2anat with header tkregister2_cmdl --targ /usr/local/freesurfer/subjects/bert/mri/brainmask.mgz --mov fbert1.feat/example_func.nii.gz --reg fbert1.feat/reg/freesurfer/anat2exf.register.dat.init --fslregout fbert1.feat/reg/freesurfer/exf2anat.init.fsl.mat --regheader --noedit tkregister_tcl /usr/local/freesurfer/tktools/tkregister2.tcl target volume /usr/local/freesurfer/subjects/bert/mri/brainmask.mgz movable volume fbert1.feat/example_func.nii.gz reg file fbert1.feat/reg/freesurfer/anat2exf.register.dat.init LoadVol 0 ZeroCRAS 0 $Id: tkregister2.c,v 1.121.2.1 2011/03/28 20:25:16 greve Exp $ Diagnostic Level -1 INFO: loading target /usr/local/freesurfer/subjects/bert/mri/brainmask.mgz Ttarg: -------------------- -1.000 0.000 0.000 128.000; 0.000 0.000 1.000 -128.000; 0.000 -1.000 0.000 128.000; 0.000 0.000 0.000 1.000; INFO: loading movable fbert1.feat/example_func.nii.gz Tmov: -------------------- -3.438 0.000 0.000 110.000; 0.000 0.000 4.000 -70.000; 0.000 -3.438 0.000 110.000; 0.000 0.000 0.000 1.000; mkheaderreg = 1, float2int = 0 Computing reg from header (and possibly input matrix) ---- Input registration matrix (computed) -------- 1.000 0.000 0.000 5.400; 0.000 0.000 1.000 0.000; 0.000 -1.000 0.000 -18.000; 0.000 0.000 0.000 1.000; --------------------------------------- ---- Input registration matrix -------- 1.000 0.000 0.000 5.400; 0.000 0.000 1.000 0.000; 0.000 -1.000 0.000 -18.000; 0.000 0.000 0.000 1.000; Determinant 1 subject = subject-unknown RegMat --------------------------- 1.000 0.000 0.000 5.400; 0.000 0.000 1.000 0.000; 0.000 -1.000 0.000 -18.000; 0.000 0.000 0.000 1.000; FSLOUTPUTTYPE NIFTI_GZ tkreg2FSL: mov det = -47.2656, ref det = -1 fslregister --s bert --reg fbert1.feat/reg/freesurfer/anat2exf.register.dat --mov fbert1.feat/example_func.nii.gz --dof 6 --bins 256 --cost corratio --fslmat fbert1.feat/reg/freesurfer/exf2anat.fsl.mat --fsvol brainmask --maxangle 90 --initfslmat fbert1.feat/reg/freesurfer/exf2anat.init.fsl.mat --tmp fbert1.feat/reg/freesurfer/tmp --out fbert1.feat/reg/freesurfer/tmp/exf-in-anat.nii.gz Log file is fbert1.feat/reg/freesurfer/anat2exf.register.dat.fslregister.log Wed Jun 19 20:41:18 CST 2013 --s bert --reg fbert1.feat/reg/freesurfer/anat2exf.register.dat --mov fbert1.feat/example_func.nii.gz --dof 6 --bins 256 --cost corratio --fslmat fbert1.feat/reg/freesurfer/exf2anat.fsl.mat --fsvol brainmask --maxangle 90 --initfslmat fbert1.feat/reg/freesurfer/exf2anat.init.fsl.mat --tmp fbert1.feat/reg/freesurfer/tmp --out fbert1.feat/reg/freesurfer/tmp/exf-in-anat.nii.gz $Id: fslregister,v 1.34.2.1 2011/03/28 20:35:36 greve Exp $ T7600-3 Linux T7600-3 2.6.32-220.el6.x86_64 #1 SMP Wed Nov 9 08:03:13 EST 2011 x86_64 x86_64 x86_64 GNU/Linux nIters 1 -------------------------------------- /usr/local/freesurfer/subjects/fbert-feat mri_convert ERROR: could not determine file for /usr/local/freesurfer/subjects/bert/mri/ERROR: fbert1.feat/reg/freesurfer/tmp/refvol.fslregister.nii mri_convert ERROR: could not determine file for /usr/local/freesurfer/subjects/bert/mri/ERROR: fbert1.feat/reg/freesurfer/tmp/refvol.fslregister.nii mri_convert: extra arguments ("not" and following) type mri_convert -u for usage -------------------------------------- /usr/local/freesurfer/subjects/fbert-feat mri_convert fbert1.feat/example_func.nii.gz fbert1.feat/reg/freesurfer/tmp/movvol.fslregister.nii --frame 0 mri_convert fbert1.feat/example_func.nii.gz fbert1.feat/reg/freesurfer/tmp/movvol.fslregister.nii --frame 0 $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from fbert1.feat/example_func.nii.gz... TR=3000.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (0, 1, 0) k_ras = (0, 0, 1) keeping frame 0 writing to fbert1.feat/reg/freesurfer/tmp/movvol.fslregister.nii... Mov determinant is -47.2656 Wed Jun 19 20:41:18 CST 2013 /usr/local/freesurfer/subjects/fbert-feat flirt.fsl -ref fbert1.feat/reg/freesurfer/tmp/refvol.fslregister.nii -in fbert1.feat/reg/freesurfer/tmp/movvol.fslregister.nii -bins 256 -cost corratio -dof 6 -searchrx -90 90 -searchry -90 90 -searchrz -90 90 -verbose 0 -omat fbert1.feat/reg/freesurfer/tmp/fslmat0.trans.mat -schedule /usr/local/fsl/etc/flirtsch/xyztrans.sch -init fbert1.feat/reg/freesurfer/exf2anat.init.fsl.mat ** ERROR (nifti_image_read): failed to find header file for 'fbert1.feat/reg/freesurfer/tmp/refvol.fslregister' ** ERROR: nifti_image_open(fbert1.feat/reg/freesurfer/tmp/refvol.fslregister): bad header info Error: failed to open file fbert1.feat/reg/freesurfer/tmp/refvol.fslregister ERROR: Could not open image fbert1.feat/reg/freesurfer/tmp/refvol.fslregister Image Exception : #22 :: Failed to read volume fbert1.feat/reg/freesurfer/tmp/refvol.fslregister.nii terminate called after throwing an instance of 'RBD_COMMON::BaseException' Abort (core dumped) Wed Jun 19 20:41:18 CST 2013 /usr/local/freesurfer/subjects/fbert-feat flirt.fsl -ref fbert1.feat/reg/freesurfer/tmp/refvol.fslregister.nii -in fbert1.feat/reg/freesurfer/tmp/movvol.fslregister.nii -bins 256 -cost corratio -dof 6 -searchrx -90 90 -searchry -90 90 -searchrz -90 90 -verbose 0 -omat fbert1.feat/reg/freesurfer/exf2anat.fsl.mat -init fbert1.feat/reg/freesurfer/tmp/fslmat0.trans.mat -schedule /usr/local/freesurfer/bin/flirt.newdefault.20080811.sch -o fbert1.feat/reg/freesurfer/tmp/outvol.fslregister.nii ** ERROR (nifti_image_read): failed to find header file for 'fbert1.feat/reg/freesurfer/tmp/refvol.fslregister' ** ERROR: nifti_image_open(fbert1.feat/reg/freesurfer/tmp/refvol.fslregister): bad header info Error: failed to open file fbert1.feat/reg/freesurfer/tmp/refvol.fslregister ERROR: Could not open image fbert1.feat/reg/freesurfer/tmp/refvol.fslregister Image Exception : #22 :: Failed to read volume fbert1.feat/reg/freesurfer/tmp/refvol.fslregister.nii terminate called after throwing an instance of 'RBD_COMMON::BaseException' Abort (core dumped) Wed Jun 19 20:41:18 CST 2013 /usr/local/freesurfer/subjects/fbert-feat mri_convert fbert1.feat/reg/freesurfer/tmp/outvol.fslregister.nii fbert1.feat/reg/freesurfer/tmp/exf-in-anat.nii.gz mri_convert fbert1.feat/reg/freesurfer/tmp/outvol.fslregister.nii fbert1.feat/reg/freesurfer/tmp/exf-in-anat.nii.gz niiRead(): error opening file fbert1.feat/reg/freesurfer/tmp/outvol.fslregister.nii $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from fbert1.feat/reg/freesurfer/tmp/outvol.fslregister.nii... tkregister2_cmdl --s bert --mov fbert1.feat/example_func.nii.gz --reg fbert1.feat/reg/freesurfer/anat2exf.register.dat --fslreg fbert1.feat/reg/freesurfer/exf2anat.fsl.mat --noedit tkregister_tcl /usr/local/freesurfer/tktools/tkregister2.tcl ERROR: cannot open fbert1.feat/reg/freesurfer/exf2anat.fsl.mat Started at Wed Jun 19 20:41:18 CST 2013 Ended at Wed Jun 19 20:41:18 CST 2013 fslregister Done To check results, run: tkregister2 --mov fbert1.feat/example_func.nii.gz --reg fbert1.feat/reg/freesurfer/anat2exf.register.dat --surf orig bbregister --mov fbert1.feat/example_func.nii.gz --bold --6 --init-reg fbert1.feat/reg/freesurfer/anat2exf.register.dat --reg fbert1.feat/reg/freesurfer/anat2exf.register.dat ERROR: cannot find fbert1.feat/reg/freesurfer/anat2exf.register.dat fslregister --mov fbert1.feat/reg/standard.nii.gz --s bert --reg fbert1.feat/reg/freesurfer/anat2std.register.dat --dof 12 Log file is fbert1.feat/reg/freesurfer/anat2std.register.dat.fslregister.log Wed Jun 19 20:41:18 CST 2013 --mov fbert1.feat/reg/standard.nii.gz --s bert --reg fbert1.feat/reg/freesurfer/anat2std.register.dat --dof 12 $Id: fslregister,v 1.34.2.1 2011/03/28 20:35:36 greve Exp $ T7600-3 Linux T7600-3 2.6.32-220.el6.x86_64 #1 SMP Wed Nov 9 08:03:13 EST 2011 x86_64 x86_64 x86_64 GNU/Linux nIters 1 -------------------------------------- /usr/local/freesurfer/subjects/fbert-feat mri_convert /usr/local/freesurfer/subjects/bert/mri/brainmask.mgz fbert1.feat/reg/tmp.fslregister.17828/refvol.fslregister.nii mri_convert /usr/local/freesurfer/subjects/bert/mri/brainmask.mgz fbert1.feat/reg/tmp.fslregister.17828/refvol.fslregister.nii $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from /usr/local/freesurfer/subjects/bert/mri/brainmask.mgz... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (0, 0, -1) k_ras = (0, 1, 0) writing to fbert1.feat/reg/tmp.fslregister.17828/refvol.fslregister.nii... -------------------------------------- /usr/local/freesurfer/subjects/fbert-feat mri_convert fbert1.feat/reg/standard.nii.gz fbert1.feat/reg/tmp.fslregister.17828/movvol.fslregister.nii --frame 0 mri_convert fbert1.feat/reg/standard.nii.gz fbert1.feat/reg/tmp.fslregister.17828/movvol.fslregister.nii --frame 0 $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from fbert1.feat/reg/standard.nii.gz... TR=1000.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (0, 1, 0) k_ras = (0, 0, 1) keeping frame 0 writing to fbert1.feat/reg/tmp.fslregister.17828/movvol.fslregister.nii... Mov determinant is -8 /usr/local/freesurfer/subjects/fbert-feat tkregister2_cmdl --mov fbert1.feat/reg/tmp.fslregister.17828/movvol.fslregister.nii --reg fbert1.feat/reg/tmp.fslregister.17828/reg0.17828.dat --regheader --fslregout fbert1.feat/reg/freesurfer/anat2std.register.dat.fsl.mat0 --s bert --noedit tkregister_tcl /usr/local/freesurfer/tktools/tkregister2.tcl INFO: no target volume specified, assuming FreeSurfer orig volume. target volume orig movable volume fbert1.feat/reg/tmp.fslregister.17828/movvol.fslregister.nii reg file fbert1.feat/reg/tmp.fslregister.17828/reg0.17828.dat LoadVol 0 ZeroCRAS 0 $Id: tkregister2.c,v 1.121.2.1 2011/03/28 20:25:16 greve Exp $ Diagnostic Level -1 INFO: loading target /usr/local/freesurfer/subjects/bert/mri/orig.mgz Ttarg: -------------------- -1.000 0.000 0.000 128.000; 0.000 0.000 1.000 -128.000; 0.000 -1.000 0.000 128.000; 0.000 0.000 0.000 1.000; INFO: loading movable fbert1.feat/reg/tmp.fslregister.17828/movvol.fslregister.nii Tmov: -------------------- -2.000 0.000 0.000 91.000; 0.000 0.000 2.000 -91.000; 0.000 -2.000 0.000 109.000; 0.000 0.000 0.000 1.000; mkheaderreg = 1, float2int = 0 Computing reg from header (and possibly input matrix) ---- Input registration matrix (computed) -------- 1.000 0.000 0.000 6.400; 0.000 0.000 1.000 -19.000; 0.000 -1.000 0.000 -35.000; 0.000 0.000 0.000 1.000; --------------------------------------- ---- Input registration matrix -------- 1.000 0.000 0.000 6.400; 0.000 0.000 1.000 -19.000; 0.000 -1.000 0.000 -35.000; 0.000 0.000 0.000 1.000; Determinant 1 subject = bert RegMat --------------------------- 1.000 0.000 0.000 6.400; 0.000 0.000 1.000 -19.000; 0.000 -1.000 0.000 -35.000; 0.000 0.000 0.000 1.000; FSLOUTPUTTYPE NIFTI tkreg2FSL: mov det = -8, ref det = -1 Wed Jun 19 20:41:20 CST 2013 /usr/local/freesurfer/subjects/fbert-feat flirt.fsl -ref fbert1.feat/reg/tmp.fslregister.17828/refvol.fslregister.nii -in fbert1.feat/reg/tmp.fslregister.17828/movvol.fslregister.nii -bins 256 -cost corratio -dof 12 -searchrx -90 90 -searchry -90 90 -searchrz -90 90 -verbose 0 -omat fbert1.feat/reg/tmp.fslregister.17828/fslmat0.trans.mat -schedule /usr/local/fsl/etc/flirtsch/xyztrans.sch -init fbert1.feat/reg/freesurfer/anat2std.register.dat.fsl.mat0 Wed Jun 19 20:41:27 CST 2013 /usr/local/freesurfer/subjects/fbert-feat flirt.fsl -ref fbert1.feat/reg/tmp.fslregister.17828/refvol.fslregister.nii -in fbert1.feat/reg/tmp.fslregister.17828/movvol.fslregister.nii -bins 256 -cost corratio -dof 12 -searchrx -90 90 -searchry -90 90 -searchrz -90 90 -verbose 0 -omat fbert1.feat/reg/freesurfer/anat2std.register.dat.fsl.mat -init fbert1.feat/reg/tmp.fslregister.17828/fslmat0.trans.mat -schedule /usr/local/freesurfer/bin/flirt.newdefault.20080811.sch tkregister2_cmdl --s bert --mov fbert1.feat/reg/standard.nii.gz --reg fbert1.feat/reg/freesurfer/anat2std.register.dat --fslreg fbert1.feat/reg/freesurfer/anat2std.register.dat.fsl.mat --noedit tkregister_tcl /usr/local/freesurfer/tktools/tkregister2.tcl ---- FSL registration matrix -------- 0.905 0.003 0.033 43.546; 0.039 -0.091 -0.903 197.762; 0.008 1.050 -0.080 4.971; 0.000 0.000 0.000 1.000; --------------------------------------- INFO: no target volume specified, assuming FreeSurfer orig volume. target volume orig movable volume fbert1.feat/reg/standard.nii.gz reg file fbert1.feat/reg/freesurfer/anat2std.register.dat LoadVol 0 ZeroCRAS 0 $Id: tkregister2.c,v 1.121.2.1 2011/03/28 20:25:16 greve Exp $ Diagnostic Level -1 INFO: loading target /usr/local/freesurfer/subjects/bert/mri/orig.mgz Ttarg: -------------------- -1.000 0.000 0.000 128.000; 0.000 0.000 1.000 -128.000; 0.000 -1.000 0.000 128.000; 0.000 0.000 0.000 1.000; INFO: loading movable fbert1.feat/reg/standard.nii.gz Tmov: -------------------- -2.000 0.000 0.000 91.000; 0.000 0.000 2.000 -91.000; 0.000 -2.000 0.000 109.000; 0.000 0.000 0.000 1.000; mkheaderreg = 0, float2int = 0 FSLOUTPUTTYPE NIFTI fsl2TkReg: mov det = -8, ref det = -1 ---- Input registration matrix (computed) -------- 1.103 -0.001 0.040 0.610; -0.048 -0.095 1.097 -22.130; -0.005 -0.945 -0.084 -12.686; 0.000 0.000 0.000 1.000; --------------------------------------- ---- Input registration matrix -------- 1.103 -0.001 0.040 0.610; -0.048 -0.095 1.097 -22.130; -0.005 -0.945 -0.084 -12.686; 0.000 0.000 0.000 1.000; Determinant 1.15433 subject = bert RegMat --------------------------- 1.103 -0.001 0.040 0.610; -0.048 -0.095 1.097 -22.130; -0.005 -0.945 -0.084 -12.686; 0.000 0.000 0.000 1.000; Cleaning up Started at Wed Jun 19 20:41:18 CST 2013 Ended at Wed Jun 19 20:41:48 CST 2013 fslregister Done To check results, run: tkregister2 --mov fbert1.feat/reg/standard.nii.gz --reg fbert1.feat/reg/freesurfer/anat2std.register.dat --surf orig mri_matrix_multiply -im fbert1.feat/reg/freesurfer/anat2exf.register.dat -iim fbert1.feat/reg/freesurfer/anat2std.register.dat -om fbert1.feat/reg/freesurfer/exf2std.register.dat tkregister2_cmdl --targ fbert1.feat/reg/standard.nii.gz --mov fbert1.feat/example_func.nii.gz --reg fbert1.feat/reg/freesurfer/exf2std.register.dat --fslregout fbert1.feat/reg/freesurfer/example_func2standard.mat --noedit tkregister_tcl /usr/local/freesurfer/tktools/tkregister2.tcl target volume fbert1.feat/reg/standard.nii.gz movable volume fbert1.feat/example_func.nii.gz reg file fbert1.feat/reg/freesurfer/exf2std.register.dat LoadVol 0 ZeroCRAS 0 $Id: tkregister2.c,v 1.121.2.1 2011/03/28 20:25:16 greve Exp $ Diagnostic Level -1 ERROR: reading fbert1.feat/reg/freesurfer/exf2std.register.dat mri_matrix_multiply -im fbert1.feat/reg/freesurfer/anat2std.register.dat -iim fbert1.feat/reg/freesurfer/anat2exf.register.dat -om fbert1.feat/reg/freesurfer/std2exf.register.dat ------------------------------------------------------- tkregister2_cmdl --s bert --targ /usr/local/freesurfer/subjects/bert/mri/brainmask.mgz --mov fbert1.feat/reg/standard.nii.gz --reg fbert1.feat/reg/freesurfer/anat2std.register.dat --fslregout fbert1.feat/reg/freesurfer/std2anat.fsl.mat --noedit tkregister_tcl /usr/local/freesurfer/tktools/tkregister2.tcl target volume /usr/local/freesurfer/subjects/bert/mri/brainmask.mgz movable volume fbert1.feat/reg/standard.nii.gz reg file fbert1.feat/reg/freesurfer/anat2std.register.dat LoadVol 0 ZeroCRAS 0 $Id: tkregister2.c,v 1.121.2.1 2011/03/28 20:25:16 greve Exp $ Diagnostic Level -1 ---- Input registration matrix -------- 1.103 -0.001 0.040 0.610; -0.048 -0.095 1.097 -22.130; -0.005 -0.945 -0.084 -12.686; 0.000 0.000 0.000 1.000; float2int = 0 --------------------------------------- INFO: loading target /usr/local/freesurfer/subjects/bert/mri/brainmask.mgz Ttarg: -------------------- -1.000 0.000 0.000 128.000; 0.000 0.000 1.000 -128.000; 0.000 -1.000 0.000 128.000; 0.000 0.000 0.000 1.000; INFO: loading movable fbert1.feat/reg/standard.nii.gz Tmov: -------------------- -2.000 0.000 0.000 91.000; 0.000 0.000 2.000 -91.000; 0.000 -2.000 0.000 109.000; 0.000 0.000 0.000 1.000; mkheaderreg = 0, float2int = 0 ---- Input registration matrix -------- 1.103 -0.001 0.040 0.610; -0.048 -0.095 1.097 -22.130; -0.005 -0.945 -0.084 -12.686; 0.000 0.000 0.000 1.000; Determinant 1.15433 subject = bert RegMat --------------------------- 1.103 -0.001 0.040 0.610; -0.048 -0.095 1.097 -22.130; -0.005 -0.945 -0.084 -12.686; 0.000 0.000 0.000 1.000; FSLOUTPUTTYPE NIFTI_GZ tkreg2FSL: mov det = -8, ref det = -1 To visually check your results, run: tkregister2 --s bert --mov fbert1.feat/example_func.nii.gz --reg fbert1.feat/reg/freesurfer/anat2exf.register.dat --fslreg fbert1.feat/reg/freesurfer/exf2anat.fsl.mat --surf orig --tag Wed Jun 19 20:41:50 CST 2013 reg-feat2anat done -- Zhiwei Wang（王志伟）, Graduate Student Laboratory of Brain Imaging Institute of Neuroscience Chinese Academy of Sciences 320 Yue-Yang Road， ION Building 313 Shanghai 200031,China

2 1

OptSeq nullmax
by A a 21 Jun '13

21 Jun '13

Hi all, Is there a rule that let me avoid having the error message could not force null max? -- ntp 200 --tr 2.5 --psdwin 0 20 2.5 --ev 1 3 15 -ev 2 3 15 -ev 3 3 15 --ev 4 3 15 ---ev 5 3 15--tnullmin 2 --tnullmax 4.5 .. Thanks AS

2 1

Tutorial data <Adding control points>
by ye tian 20 Jun '13

20 Jun '13

Dear FreeSurfers, It seems that the tutorial sample data <cp_before> needs correction for skull strip, too. I am just curious why it only serves a sample for control points. Thank you very much! Sincerely, Ye

1 0

recon-all -localGI results in "ERROR:: Too many arguments."
by Tudor Popescu 20 Jun '13

20 Jun '13

Dear Freesurfer & localGI experts, I want to compare local GI (gyrification index) between my two groups. Following the help <https://surfer.nmr.mgh.harvard.edu/fswiki/LGI>, I ran this command for one of my subjects: recon-all -s M01 -localGI but it resulted in the error: make_outer_surface('/media/math/all38subj/M01/surf/tmp-mris_compute_lgi-lh.pial/lh.pial.filled.mgz',15,'/media/math/all38subj/M01/surf/tmp-mris_compute_lgi-lh.pial/lh.pial-outer'); exit ================= ERROR:: Too many arguments. Someone previously<http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg23414.html>received this error due to a space in their path, but I don't specify any path in the above command, and my $SUBJECTS_DIR path doesn't have any spaces or any other dodgy characters. I'm running FreeSurfer v5.2 from inside Virtualbux/Ubuntu, so Matlab is not included in there, although it exists separately on my Windows partition. I could run recon through FSL, but I don't see any matlab folder there either. Could Matlab be the problem? Also, which files/folders will I need to delete after I'll have fixed the problem, before re-running the recon for all subjects? Or will it just overwrite any left-overs? Many thanks in advance for any help! Tudor

3 8

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