[Freesurfer] fmri pipeline
Hi, I am getting a bit confused from the mailing archive on how to properly map volume fmri data into surface fsaverage5. 1. Should I map the volume fmri into individual surface first and then to fsaverage, or I won't loose data if I map it directly to fsaverage5? 2. Should I smooth the data when mapping into the individual surface or from individual surface to fasaverage5? Thanks Adonay ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] Fwd: Tkregister2 error, moveable not present just white screen
> > Hi Doug and all, > I just resend this email in case it did not reach, any help will be appreciated. > > Thanks for your help. I was using the preprocessed thinking that after > motion correction it would be more accurate and --init-header because they > where acquired in the same session. I changed to a raw moveable and the > results did not change for the following: > > With -init-fsl the moveable is now showing, but about 40% of the subjects > the registration has fail, in many cases the moveable is rotated with > respect to the target. I tried to use -init-spm but then the moveable and > target don't even overlay. > > I also tried to use a successful registration .dat from another subject > using the command --init-reg $SUBJECTS_DIR/subj2/mri/register.dat but > the registration is not accurate. > > In many cases there is the WARNING: initial G-W contrast was negative, but > expected positive. If the mov data has a T1 contrast, re-run with --T1. if > I run the same command changing --bold to --T1 the results aren't good, as > well as if I try -int $SUBJECTS_DIR/subj//T1.mgz. > > Is there anything else to try rather than manual registration? I just have > the T1 and the fmri. Would you recommend another registration method? > > Thanks > Adonay > > > On Mon, Sep 12, 2016 at 12:37 PM, Douglas N Greve < > gr...@nmr.mgh.harvard.edu> wrote: > >> I think the problem is the initialization. I noticed you used >> --init-header. This should only be used if the two volumes were acquired >> during the same session and the direction cosines (ie, geometry) info is >> accurate for both. Is this the case? I noticed that the input has >> "preproc" in the name, so I'm a bit suspicious. You can try --init-fsl >> instead >> >> >> On 09/12/2016 01:36 PM, A Nunes wrote: >> > Hi Doug >> > >> > I can't see any errors in the log file, and with other datasets I did >> > not have this issue. My register.dat is: >> > >> > 50664 >> > 3.00 >> > 4.50 >> > 0.15 >> > 9.996076822280884e-01 -2.117119915783405e-02 -1.833262108266354e-02 >> > 3.139470825195312e+02 >> > 1.872027479112148e-02 1.825972087681293e-02 9.996579289436340e-01 >> > 2.150849456787109e+02 >> > -2.082921005785465e-02 -9.996089935302734e-01 1.864889077842236e-02 >> > 4.339286499023438e+02 >> > 0 0 0 1 >> > round >> > >> > and my register.dat.log is: >> > >> > setenv SUBJECTS_DIR /Users/adonay/Desktop/data/freesurfer/5 >> > cd /Users/adonay/Desktop/data/prepo_cpac >> > /Applications/freesurfer/bin/bbregister --s 50664 --mov >> > 50664_preprocessed.nii.gz --init-header --reg >> > /Users/adonay/Desktop/data/freesurfer/5/50664/mri/register.dat --bold >> > >> > $Id: bbregister,v 1.49.2.3 2013/03/25 18:04:53 greve Exp $ >> > Darwin sc-155014 15.6.0 Darwin Kernel Version 15.6.0: Mon Aug 29 >> > 20:21:34 PDT 2016; root:xnu-3248.60.11~1/RELEASE_X86_64 x86_64 >> > FREESURFER_HOME /Applications/freesurfer >> > mri_convert 50664_preprocessed.nii.gz >> > /Users/adonay/Desktop/data/freesurfer/5/50664/mri/tmp.bbregi >> ster.14726/template.nii >> > mri_convert 50664_preprocessed.nii.gz >> > /Users/adonay/Desktop/data/freesurfer/5/50664/mri/tmp.bbregi >> ster.14726/template.nii >> > >> > $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ >> > reading from 50664_preprocessed.nii.gz... >> > TR=2000.00, 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) >> > writing to >> > /Users/adonay/Desktop/data/freesurfer/5/50664/mri/tmp.bbregi >> ster.14726/template.nii... >> > tkregister2_cmdl --s 50664 --mov >> > /Users/adonay/Desktop/data/freesurfer/5/50664/mri/tmp.bbregi >> ster.14726/template.nii >> > --regheader --reg >> > /Users/adonay/Desktop/data/freesurfer/5/50664/mri/tmp.bbregi >> ster.14726/reg.init.dat >> > --noedit >> > tkregister_tcl /Applications/freesurfer/tktools/tkregister2.tcl >> > INFO: no target volume specified, assuming FreeSurfer orig volume. >> > target volume orig >> > movable volume >> > /Users/adonay/Desktop/data/freesurfer/5/50664/mri/tmp.bbregi >> ster.14726/template.nii >> > reg file >> > /Users/adonay/Desktop/data/freesurfer/5/50664/mri/tmp.bbregi >> ster.14726/reg.init.dat >> > LoadVol0 >> > ZeroCRAS 0 >> > $Id: tkregister2.c,v 1.121.2
Re: [Freesurfer] Fwd: Tkregister2 error, moveable not present just white screen
Hi Dough, Thanks for your help. I was using the preprocessed thinking that after motion correction it would be more accurate and --init-header because they where acquired in the same session. I changed to a raw moveable and the results did not change for the following: With -init-fsl the moveable is now showing, but about 40% of the subjects the registration has fail, in many cases the moveable is rotated with respect to the target. I tried to use -init-spm but then the moveable and target don't even overlay. I also tried to use a successful registration .dat from another subject using the command --init-reg $SUBJECTS_DIR/subj2/mri/register.dat but the registration is not accurate. In many cases there is the WARNING: initial G-W contrast was negative, but expected positive. If the mov data has a T1 contrast, re-run with --T1. if I run the same command changing --bold to --T1 the results aren't good, as well as if I try -int $SUBJECTS_DIR/subj//T1.mgz. Is there anything else to try rather than manual registration? I just have the T1 and the fmri. Would you recommend another registration method? Thanks Adonay On Mon, Sep 12, 2016 at 12:37 PM, Douglas N Greve <gr...@nmr.mgh.harvard.edu > wrote: > I think the problem is the initialization. I noticed you used > --init-header. This should only be used if the two volumes were acquired > during the same session and the direction cosines (ie, geometry) info is > accurate for both. Is this the case? I noticed that the input has > "preproc" in the name, so I'm a bit suspicious. You can try --init-fsl > instead > > > On 09/12/2016 01:36 PM, A Nunes wrote: > > Hi Doug > > > > I can't see any errors in the log file, and with other datasets I did > > not have this issue. My register.dat is: > > > > 50664 > > 3.00 > > 4.50 > > 0.15 > > 9.996076822280884e-01 -2.117119915783405e-02 -1.833262108266354e-02 > > 3.139470825195312e+02 > > 1.872027479112148e-02 1.825972087681293e-02 9.996579289436340e-01 > > 2.150849456787109e+02 > > -2.082921005785465e-02 -9.996089935302734e-01 1.864889077842236e-02 > > 4.339286499023438e+02 > > 0 0 0 1 > > round > > > > and my register.dat.log is: > > > > setenv SUBJECTS_DIR /Users/adonay/Desktop/data/freesurfer/5 > > cd /Users/adonay/Desktop/data/prepo_cpac > > /Applications/freesurfer/bin/bbregister --s 50664 --mov > > 50664_preprocessed.nii.gz --init-header --reg > > /Users/adonay/Desktop/data/freesurfer/5/50664/mri/register.dat --bold > > > > $Id: bbregister,v 1.49.2.3 2013/03/25 18:04:53 greve Exp $ > > Darwin sc-155014 15.6.0 Darwin Kernel Version 15.6.0: Mon Aug 29 > > 20:21:34 PDT 2016; root:xnu-3248.60.11~1/RELEASE_X86_64 x86_64 > > FREESURFER_HOME /Applications/freesurfer > > mri_convert 50664_preprocessed.nii.gz > > /Users/adonay/Desktop/data/freesurfer/5/50664/mri/tmp. > bbregister.14726/template.nii > > mri_convert 50664_preprocessed.nii.gz > > /Users/adonay/Desktop/data/freesurfer/5/50664/mri/tmp. > bbregister.14726/template.nii > > > > $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ > > reading from 50664_preprocessed.nii.gz... > > TR=2000.00, 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) > > writing to > > /Users/adonay/Desktop/data/freesurfer/5/50664/mri/tmp. > bbregister.14726/template.nii... > > tkregister2_cmdl --s 50664 --mov > > /Users/adonay/Desktop/data/freesurfer/5/50664/mri/tmp. > bbregister.14726/template.nii > > --regheader --reg > > /Users/adonay/Desktop/data/freesurfer/5/50664/mri/tmp. > bbregister.14726/reg.init.dat > > --noedit > > tkregister_tcl /Applications/freesurfer/tktools/tkregister2.tcl > > INFO: no target volume specified, assuming FreeSurfer orig volume. > > target volume orig > > movable volume > > /Users/adonay/Desktop/data/freesurfer/5/50664/mri/tmp. > bbregister.14726/template.nii > > reg file > > /Users/adonay/Desktop/data/freesurfer/5/50664/mri/tmp. > bbregister.14726/reg.init.dat > > LoadVol0 > > ZeroCRAS 0 > > $Id: tkregister2.c,v 1.121.2.1 2011/03/28 20:25:16 greve Exp $ > > Diagnostic Level -1 > > INFO: loading target > > /Users/adonay/Desktop/data/freesurfer/5/50664/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 > > /Users/adonay/Desktop/data/freesurfer/5/50664/mri/tmp. > bbregister.14726/template.nii
[Freesurfer] Fwd: Tkregister2 error, moveable not present just white screen
/Users/adonay/Desktop/data/freesurfer/5/50664/mri/register.dat UseMask 0 UseLH 1 UseRH 1 nsubsamp 1 PenaltySign -1 PenaltySlope 0.50 PenaltyCenter 0.00 surfname white GMProjFrac 0.50 WMProjAbs 2.00 lhcostfile (null) rhcostfile (null) interp trilinear (1) frame 0 TolPowell 0.00 nMaxItersPowell 36 n1dmin 3 Profile 0 Gdiag_no -1 AddNoise 0 (0) SynthSeed 1474349903 TransRandMax 0.00 RotRandMax 0.00 Translations 0.00 0.00 0.00 Rotations 0.00 0.00 0.00 Input reg 0.999 0.024 0.025 301.214; -0.024 -0.025 0.999 218.039; 0.024 -0.999 -0.024 435.913; 0.000 0.000 0.000 1.000; Loading mov Extracting frame 0 Projecting LH Surfs Loading lh.white surf Loading lh.thickness for GM GM Proj: 1 0.50 2.00 WM Proj: 0 0.50 2.00 Projecting RH Surfs Loading rh.white surf Loading rh.thickness Projecting RH Surfs Computing relative cost 0 -25.0 -25.0 -25.0 10.00 1 -25.0 -25.0 25.0 10.00 2 -25.0 25.0 -25.0 10.00 3 -25.0 25.0 25.0 10.00 4 25.0 -25.0 -25.0 10.00 5 25.0 -25.0 25.0 10.00 6 25.0 25.0 -25.0 10.00 7 25.0 25.0 25.0 10.00 REL: 8 10.00 80.00 10.00 rel = 1 Initial costs Number of surface hits 0 WM Intensitynan +/- nan Ctx Intensitynan +/- nan Pct Contrast nan +/- nan Cost 10. RelCost 1. Brute force preopt -0.1 0.1 0.1, n = 729 0 -0.1000 -0.1000 -0.1000 -0.1000 -0.1000 -0.1000 10. 10. 0.0 Brute Force -- Min cost was 10.00 Number of iterations 729 Search time 0.976000 sec Parameters at best (transmm, rotdeg) -0.100 -0.100 -0.100 -0.100 -0.100 -0.100 Starting Powell Minimization Init Powel Params dof = 6 0 -0.1 1 -0.1 2 -0.1 3 -0.1 4 -0.1 5 -0.1 Powell done niters = 0 Computing relative cost 0 -25.0 -25.0 -25.0 10.00 1 -25.0 -25.0 25.0 10.00 2 -25.0 25.0 -25.0 10.00 3 -25.0 25.0 25.0 10.00 4 25.0 -25.0 -25.0 10.00 5 25.0 -25.0 25.0 10.00 6 25.0 25.0 -25.0 10.00 7 25.0 25.0 25.0 10.00 REL: 8 10.00 80.00 10.00 rel = 1 Number of iterations 0 Min cost was 10.00 Number of FunctionCalls 109 TolPowell 0.00 nMaxItersPowell 36 OptimizationTime 3.303000 sec Parameters at optimum (transmm) 2.51611 2.51611 2.51611 Parameters at optimum (rotdeg) 2.51611 2.51611 2.51611 Final costs Number of surface hits 0 WM Intensitynan +/- nan Ctx Intensitynan +/- nan Pct Contrast nan +/- nan Cost 10. RelCost 1. Reg at min cost was 1.000 -0.021 -0.018 313.947; 0.019 0.018 1.000 215.085; -0.021 -1.000 0.019 433.929; 0.000 0.000 0.000 1.000; Writing optimal reg to /Users/adonay/Desktop/data/freesurfer/5/50664/mri/register.dat, type = 14 Original Reg 0.999 0.024 0.025 301.214; -0.024 -0.025 0.999 218.039; 0.024 -0.999 -0.024 435.913; 0.000 0.000 0.000 1.000; Original Reg - Optimal Reg -0.000 0.045 0.043 -12.733; -0.043 -0.043 -0.000 2.954; 0.045 0.000 -0.043 1.985; 0.000 0.000 0.000 0.000; Computing change in lh position LH rmsDiffMean 13.402319 Computing change in rh position Surface RMS Diff (mm) 13.076895 18.900088 mri_segreg done Cleaning up Started at Thu Sep 8 19:09:02 PDT 2016 Ended at Thu Sep 8 19:09:28 PDT 2016 BBR-Run-Time-Sec 26 bbregister Done To check results, run: tkregister2 --mov 50664_preprocessed.nii.gz --reg /Users/adonay/Desktop/data/freesurfer/5/50664/mri/register.dat --surf Thanks, Adonay Douglas Greve <http://www.mail-archive.com/search?l=freesurfer@nmr.mgh.harvard.edu=from:%22Douglas+Greve%22> Sun, 11 Sep 2016 19:14:45 -0700 <http://www.mail-archive.com/search?l=freesurfer@nmr.mgh.harvard.edu=date:20160911> What is your command line and log file? Sounds like the initial registration failed. -- Forwarded message ------ From: A Nunes <adonay.s.nu...@gmail.com> Date: Sun, Sep 11, 2016 at 7:04 PM Subject: Tkregister2 error, moveable not present just white screen To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu> Hi, After doing a bbregistration I visualized the results with tkregister2. The target is alright, however, the moveable is not present, it is just a white screen. What steps could I take to solve this issue? Thanks Adonay ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at
[Freesurfer] Tkregister2 error, moveable not present just white screen
Hi, After doing a bbregistration I visualized the results with tkregister2. The target is alright, however, the moveable is not present, it is just a white screen. What steps could I take to solve this issue? Thanks Adonay ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] Subject: Re: Zero cortical thickness
I mean the area of an ROI On Tue, Aug 16, 2016 at 6:59 AM, Douglas N Greve <gr...@nmr.mgh.harvard.edu> wrote: > please include previous correspondence. Do you mean the area of a vertex > or the area of an ROI? > > On 08/15/2016 06:06 PM, A Nunes wrote: >> Hi Douglas, >> >> I meant a surface area extracted from a surface based atlas. >> >> Thanks >> Adonay >> ___ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> Hi I looked at the distribution areas with almost zero thickness and when I saw they were on one hemisphere, I checked my bash script and found out that for the left cortex it was calling the right hemisphere areas. However, I still have a few subjects which have zero thickness in some areas of my parcelled atlas. This zero thickness is it caused by a segmentation or a sphere reconstruction error/imperfection (in which case the value should be NaN), or is it capturing a brain structural characteristic worth to account for? Thanks Adonay >>>> Date: Mon, 15 Aug 2016 16:27:24 -0400 From: Douglas Greve <gr...@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] Zero cortical thickness To: freesurfer@nmr.mgh.harvard.edu Message-ID: <8c1593aa-77fc-333e-e7d7-1901f9a39...@nmr.mgh.harvard.edu> Content-Type: text/plain; charset=windows-1252; format=flowed what do you mean by "area"? do you mean one of the cortical ROIs or do you mean a general location? On 8/15/16 4:13 PM, A Nunes wrote: > Hi, > > I have read in the mailing list about zero cortical thickness, but I > still have some doubts. > > I am calculating the average cortical thickness of some areas, and > there are a few that almost all the subjects' thickness is zero, > others only some subjects score zero. For the ones that almost all > subjects is zero, I would guess is not considered cortical, however, > all my areas are cortical. > > - If I compute a ttest against two groups, should I set the zeros as > NaNs? or are the zero thickness meaningful (a genuine measure or a > segmentation artifact)? > > -Should I use the -l ?h.cortex.label to avoid having zero thickness in > some areas? If so, at which point? the commands used are: > > mri_surf2surf --srcsubject fsaverage --trgsubject subjid --hemi ?h > --sval-annot fsaverage/label/?h.areas.annot --tval > $SUBJECTS_DIR/subjid/label/?h.areas.annot > > mris_anatomical_stats -a > $SUBJECTS_DIR/subjid/label/?h.areas.annot$SUBJECTS_DIR/subjid/label/?h.areas.annot > -f $SUBJECTS_DIR/subjid/stats/?h.areas.stats -b subjid ?h > > > Thanks > Adonay > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] Subject: Re: Zero cortical thickness
Hi I looked at the distribution areas with almost zero thickness and when I saw they were on one hemisphere, I checked my bash script and found out that for the left cortex it was calling the right hemisphere areas. However, I still have a few subjects which have zero thickness in some areas of my parcelled atlas. This zero thickness is it caused by a segmentation or a sphere reconstruction error/imperfection (in which case the value should be NaN), or is it capturing a brain structural characteristic worth to account for? Thanks Adonay On Mon, Aug 15, 2016 at 3:06 PM, A Nunes <adonay.s.nu...@gmail.com> wrote: > Hi Douglas, > > I meant a surface area extracted from a surface based atlas. > > Thanks > Adonay ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] Subject: Re: Zero cortical thickness
Hi Douglas, I meant a surface area extracted from a surface based atlas. Thanks Adonay ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] Zero cortical thickness
Hi, I have read in the mailing list about zero cortical thickness, but I still have some doubts. I am calculating the average cortical thickness of some areas, and there are a few that almost all the subjects' thickness is zero, others only some subjects score zero. For the ones that almost all subjects is zero, I would guess is not considered cortical, however, all my areas are cortical. - If I compute a ttest against two groups, should I set the zeros as NaNs? or are the zero thickness meaningful (a genuine measure or a segmentation artifact)? -Should I use the -l ?h.cortex.label to avoid having zero thickness in some areas? If so, at which point? the commands used are: mri_surf2surf --srcsubject fsaverage --trgsubject subjid --hemi ?h --sval-annot fsaverage/label/?h.areas.annot --tval $SUBJECTS_DIR/subjid/label/?h.areas.annot mris_anatomical_stats -a $SUBJECTS_DIR/subjid/label/?h.areas.annot$SUBJECTS_DIR/subjid/label/?h.areas.annot -f $SUBJECTS_DIR/subjid/stats/?h.areas.stats -b subjid ?h Thanks Adonay ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
