Re: [Freesurfer] mri_ca_register error
Glad to hear it Bruce On Jun 14, 2011, at 10:45 PM, Vanessa Lim wrote: > Hi Bruce, > > It was a RAM issue, I only had 1 G for the virtual machine, put it to it's > max which I think is 1.7 on a 4G machine. Worked! Thanks! > Cheers, > Vanessa > > -Original Message- > From: Bruce Fischl [mailto:fis...@nmr.mgh.harvard.edu] > Sent: Thursday, 2 June 2011 10:31 a.m. > To: Vanessa Lim > Cc: freesurfer@nmr.mgh.harvard.edu > Subject: Re: [Freesurfer] mri_ca_register error > > how much RAM do you have on your machine? For some reason gzip needs tons > of it > On Wed, 1 Jun 2011, Vanessa Lim wrote: > >> Hi, >> >> I got freesurfer to run with this command: >> >> mri_ca_register -align-after -nobigventricles -mask brainmask.mgz -T >> ~/Desktop/freeSurfer/CG/mri/transforms/talairach.lta >> ~/Desktop/freeSurfer/CG/mri/norm.mgz >> $FREESURFER_HOME/average/RB_all_2008-03-26.gca >> ~/Desktop/freeSurfer/CG/mri/transforms/talairach.m3z >> >> but now have this error after some hours... >> writing output transformation to >> /home/virtualuser/Desktop/freeSurfer/CG/mri/transforms/talairach.m3z... >> GCAMwrite(/home/virtualuser/Desktop/freeSurfer/CG/mri/transforms/talairach.m3z): >> gzip encountered error. >> mri_ca_register: >> GCAMwrite(/home/virtualuser/Desktop/freeSurfer/CG/mri/transforms/talairach.m3z) >> failed >> >> any ideas? I can write to the folder and it has space... >> Thanks, >> Vanessa >> >> >> >> >> Sent: Friday, 27 May 2011 11:44 a.m. >> To: freesurfer@nmr.mgh.harvard.edu >> Subject: mri_ca_register error >> >> >> Hi, >> >> >> >> I am getting the same error. I did set the environment to an external drive >> with LOTS of space. When I run it though I did notice it repeats the >> subject path which is the external drive but then says actual path >> ~/apps/freesurfer/subjects - this doesn't have much space cause it's a >> virtualbox and I don't know how to make it bigger. But the error below >> seems to be pointing to the right directory /home/...Desktop etc. >> >> >>> >>> GCAMwrite(transforms/talairach.m3z): gzip encountered error. >>> writing output transformation to transforms/talairach.m3z... >>> mri_ca_register: GCAMwrite(transforms/talairach.m3z) failed >>> ERROR: mri_ca_register with non-zero status 252 >>> but continuing despite the error >>> #-- >>> #@# CA Reg Inv Thu May 26 12:42:11 EDT 2011 >>> /home/virtualuser/Desktop/freeSurfer/CG2/mri >>> >>> mri_ca_register -invert-and-save transforms/talairach.m3z >>> >>> Loading, Inverting, Saving, Exiting ... >>> Reading transforms/talairach.m3z >>> ERROR: cannot find or read transforms/talairach.m3z >>> ERROR: mri_ca_register with non-zero status 0 >>> Linux FreeSurfer 2.6.28-11-generic #42-Ubuntu SMP Fri Apr 17 01:57:59 UTC >>> 2009 i686 GNU/Linux >>> >>> Cheers, >>> Vanessa >> > > > 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@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] mri_ca_register error
Hi Bruce, It was a RAM issue, I only had 1 G for the virtual machine, put it to it's max which I think is 1.7 on a 4G machine. Worked! Thanks! Cheers, Vanessa -Original Message- From: Bruce Fischl [mailto:fis...@nmr.mgh.harvard.edu] Sent: Thursday, 2 June 2011 10:31 a.m. To: Vanessa Lim Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] mri_ca_register error how much RAM do you have on your machine? For some reason gzip needs tons of it On Wed, 1 Jun 2011, Vanessa Lim wrote: > Hi, > > I got freesurfer to run with this command: > > mri_ca_register -align-after -nobigventricles -mask brainmask.mgz -T > ~/Desktop/freeSurfer/CG/mri/transforms/talairach.lta > ~/Desktop/freeSurfer/CG/mri/norm.mgz > $FREESURFER_HOME/average/RB_all_2008-03-26.gca > ~/Desktop/freeSurfer/CG/mri/transforms/talairach.m3z > > but now have this error after some hours... > writing output transformation to > /home/virtualuser/Desktop/freeSurfer/CG/mri/transforms/talairach.m3z... > GCAMwrite(/home/virtualuser/Desktop/freeSurfer/CG/mri/transforms/talairach.m3z): > gzip encountered error. > mri_ca_register: > GCAMwrite(/home/virtualuser/Desktop/freeSurfer/CG/mri/transforms/talairach.m3z) > failed > > any ideas? I can write to the folder and it has space... > Thanks, > Vanessa > > > > > Sent: Friday, 27 May 2011 11:44 a.m. > To: freesurfer@nmr.mgh.harvard.edu > Subject: mri_ca_register error > > > Hi, > > > > I am getting the same error. I did set the environment to an external drive > with LOTS of space. When I run it though I did notice it repeats the subject > path which is the external drive but then says actual path > ~/apps/freesurfer/subjects - this doesn't have much space cause it's a > virtualbox and I don't know how to make it bigger. But the error below seems > to be pointing to the right directory /home/...Desktop etc. > > >> >> GCAMwrite(transforms/talairach.m3z): gzip encountered error. >> writing output transformation to transforms/talairach.m3z... >> mri_ca_register: GCAMwrite(transforms/talairach.m3z) failed >> ERROR: mri_ca_register with non-zero status 252 >> but continuing despite the error >> #-- >> #@# CA Reg Inv Thu May 26 12:42:11 EDT 2011 >> /home/virtualuser/Desktop/freeSurfer/CG2/mri >> >> mri_ca_register -invert-and-save transforms/talairach.m3z >> >> Loading, Inverting, Saving, Exiting ... >> Reading transforms/talairach.m3z >> ERROR: cannot find or read transforms/talairach.m3z >> ERROR: mri_ca_register with non-zero status 0 >> Linux FreeSurfer 2.6.28-11-generic #42-Ubuntu SMP Fri Apr 17 01:57:59 UTC >> 2009 i686 GNU/Linux >> >> Cheers, >> Vanessa > 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@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] Tracula - error in pre-proc
Hi, I do the pre-processing with the following command: trac-all -prep -c ./scripts/dmrirc_single_subject THe process exits with error when it comes to fslroi (attached pls find the log file). I try to re-run the fslroi command as follow: fslroi /autofs/space/guasha_001/users/phoebe/strab_func_chan4/strab_func_chan_diffrecons/040826_cst/dmri/dwi.nii. gz /autofs/space/guasha_001/users/phoebe/strab_func_chan4/strab_func_chan_diffrecons/040826_cst/dmri/lowb.nii.gz 0 25 It works and the lowb.nii.gz looks normal. In case if I have the same problem with another dataset, how can I incorporate the number of frames (25) in the trac-all command for the fslroi? Can I continue the remaining procedures of trac-all from this point? Thank you. Phoebe. -- ___ Phoebe Suk-tak Chan, Ph.D. Athinoula A. Martinos Center for Biomedical Imaging Massachusetts General Hospital Bldg. 149, 13th St., mailcode 149-2301 Charlestown, MA 02129 pho...@nmr.mgh.harvard.edu Tue Jun 14 21:05:37 EDT 2011 /autofs/space/guasha_001/users/phoebe/strab_func_chan4/strab_func_chan_diffrecons /usr/local/freesurfer/stable5_1_0/bin/trac-all -prep -c ./scripts/dmrirc_single_subject Subject 040826_cst SUBJECTS_DIR /autofs/space/guasha_001/users/phoebe/strab_func_chan4/strab_func_chan_inflated3 FREESURFER_HOME /usr/local/freesurfer/stable5_1_0 Actual FREESURFER_HOME /autofs/cluster/freesurfer/centos4.0_x86_64/stable5_1_0 build-stamp.txt: freesurfer-Linux-centos4_x86_64-stable-v5.1.0-20110514 phoebe deqi Linux deqi 2.6.18-194.32.1.el5 #1 SMP Wed Jan 5 17:52:25 EST 2011 x86_64 x86_64 x86_64 GNU/Linux cputime unlimited filesize unlimited datasize unlimited stacksize10240 kbytes coredumpsize 0 kbytes memoryuseunlimited vmemoryuse unlimited descriptors 1024 memorylocked 32 kbytes maxproc 407552 total used free sharedbuffers cached Mem: 49444976 28266052 21178924 01082748 20974188 -/+ buffers/cache:6209116 43235860 Swap: 16787904252 16787652 Program versions: $Id: trac-all,v 1.22.2.6 2011/05/24 06:49:09 ayendiki Exp $ mri_convert --all-info ProgramName: mri_convert ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2011/06/15-01:05:37-GMT BuildTimeStamp: May 14 2011 05:56:56 CVS: $Id: mri_convert.c,v 1.179.2.1 2011/03/22 16:37:02 nicks Exp $ User: phoebe Machine: deqi Platform: Linux PlatformVersion: 2.6.18-194.32.1.el5 CompilerName: GCC CompilerVersion: 30400 FLIRT version 5.5 $Id: bbregister,v 1.49 2011/03/06 23:38:41 greve Exp $ $Id: mri_cvs_register,v 1.15.2.5 2011/05/13 23:40:25 lzollei Exp $ ProgramName: dmri_train ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2011/06/15-01:05:38-GMT BuildTimeStamp: May 24 2011 05:40:10 CVS: User: phoebe Machine: deqi Platform: Linux PlatformVersion: 2.6.18-194.32.1.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: dmri_paths ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2011/06/15-01:05:38-GMT BuildTimeStamp: May 24 2011 05:40:10 CVS: User: phoebe Machine: deqi Platform: Linux PlatformVersion: 2.6.18-194.32.1.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: dmri_pathstats ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2011/06/15-01:05:38-GMT BuildTimeStamp: May 24 2011 05:40:10 CVS: User: phoebe Machine: deqi Platform: Linux PlatformVersion: 2.6.18-194.32.1.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: dmri_mergepaths ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2011/06/15-01:05:38-GMT BuildTimeStamp: May 24 2011 05:40:10 CVS: User: phoebe Machine: deqi Platform: Linux PlatformVersion: 2.6.18-194.32.1.el5 CompilerName: GCC CompilerVersion: 30400 New invocation of trac-preproc phoebe deqi Linux deqi 2.6.18-194.32.1.el5 #1 SMP Wed Jan 5 17:52:25 EST 2011 x86_64 x86_64 x86_64 GNU/Linux cputime unlimited filesize unlimited datasize unlimited stacksize10240 kbytes coredumpsize 0 kbytes memoryuseunlimited vmemoryuse unlimited descriptors 1024 memorylocked 32 kbytes maxproc 407552 total used free sharedbuffers cached Mem: 49444976 28267092 21177884 01082748 20974188 -/+ buffers/cache:6210156 43234820 Swap: 16787904252 16787652 #- /usr/local/freesurfer/stable5_1_0/bin/trac-preproc #- #@# Image corrections Tue Jun 14 21:05:38 EDT 2011 mri_convert /autofs/space/guasha_001/users/phoebe/strab_func_chan4/strab_func_chan_diffrecons/dcm/040826_cst/040826_cst_009_1.dcm /autofs/space/guasha_001/users/phoebe/strab_func_chan4/strab_func_chan_diffrecons/040826_cst/dmri/dwi_orig.nii.gz mri_convert /autofs/space/guasha_001/users/phoebe/
Re: [Freesurfer] error in *recon-all -all -s* and *qdec*
what version of freesurfer is being run? that error is from an old version (prior to v4.5 i think). i suggest updating to v5.1. n. On Wed, 2011-06-15 at 08:52 +0800, Sophy Zhu wrote: > Hello, Freesurfers, > > When I use *recon-all -all -s ...* > there exists the error *mris_volmask.bin: error while loading shared > libraries: /usr/local/freesurfer//lib/vtk/lib/vtk-5.2/libvtkRendering.so.5.2: > cannot restore segment prot after reloc: Permission denied* > > Would you please tell me how to solve it? > > Another problem is that I cannot use the *qdec*, does this error come > from my installation of freesurfer? > > Thanks a lot > > Sophy > ___ > 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] Resampling from MNI 152 to MNI 305 - Problem with orientation
You should be able to use the reg and mni305.2mm.nii.gz in 4.5
doug
On 6/14/11 12:25 PM, Balaji Goparaju wrote:
Thanks for the response! I seem to be getting better results.
I was wondering if there was any way the same resampling can be
achieved using Freesurfer 4.5 since a
lot of analysis (including analysis with other tasks) has already been
done in it, or if it is okay to use JUST the reg.2mm.mni152.dat file
from Freesurfer 5.1 and keep the rest of the analysis the same as before?
Thank you once again for this help!
Regards,
Balaji Goparaju
On Tue, Jun 14, 2011 at 11:46 AM, Douglas N Greve
mailto:gr...@nmr.mgh.harvard.edu>> wrote:
To go from mni152 to the MNI305 2mm space, use
mri_vol2vol --mov mni305.2mm.nii.gz \
--targ $FSLDIR/data/standard/MNI152_T1_2mm.nii.gz \
--reg
$FREESURFER_HOME/subjects/fsaverage/mri.2mm/reg.2mm.mni152.dat \
--inv --o output.mni305.2mm.nii.gz
This will resample MNI152_T1_2mm.nii.gz (or anything in that
space) to the mni305 2mm space.
For your application, add --interp nearest, or use
mri_label2vol --seg BA_mask.mni152.nii \
--reg $FREESURFER_HOME/subjects/fsaverage/mri.2mm/reg.2mm.mni152.dat \
--invertmtx --o outfile.nii
doug
Balaji Goparaju wrote:
Hello Freesurfers,
I have Brodmann Area binary masks in the ICBM MNI 152 space,
that I acquired using WFU_PickAtlas toolbox in SPM. These
masks are .nii files, and have a RAS orientation.
I am trying to resample these masks into the fsaverage MNI 305
space, specifically with the dimensions matching the
"mni305.cor.subfov2.mgz"
file found in the $FREESURFER_HOME/average file. This file is
in the LIA orientation.
However, the mni152.register.dat file seems to be transforming
volumes from the MNI 305 space to the MNI 152 Space in LAS
orientation (MNI152_T1_2mm.nii in FSL).
Should I transform my Brodmann Area masks from the RAS
orientation to a LAS orientation? If so, how can I achieve
this? The RAS orientation is correct, so I know using
mri_convert --out_dimension is out of the question.
I have tried to use
*mri_label2vol --seg {BA_mask} --temp
{$FREESURFER_HOME/average/mni305.cor.subfov2.mgz} --o
{output_file} --reg mni152.register.dat --invertmtx*
Also, I have tried to use the inverted matrix from
mni152.register.dat and use it with
*mri_vol2vol -mov {BA_mask} --reg
{inverted_mni152.register.dat} --o {output_file} --tal --talres 2*
However, the output files had interchanged posterior (P) and
anterior (A), and superior (S) and interior (I) orientations.
What is the best way to achieve the resampling? Any guidance
is really appreciated!
Regards,
Balaji Goparaju
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--
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MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html
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
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but does not contain patient information, please contact the
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dispose of the e-mail.
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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] error in *recon-all -all -s* and *qdec*
Hello, Freesurfers, When I use *recon-all -all -s ...* there exists the error *mris_volmask.bin: error while loading shared libraries: /usr/local/freesurfer//lib/vtk/lib/vtk-5.2/libvtkRendering.so.5.2: cannot restore segment prot after reloc: Permission denied* Would you please tell me how to solve it? Another problem is that I cannot use the *qdec*, does this error come from my installation of freesurfer? Thanks a lot Sophy ___ 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] Talairach Transformation failed on Freesurfer 5.1
Thank you, Nick This is much appreciated !! It works now and the talairach.xfm is: 1.08349275588989 -0.0557942688465118 -0.0535474419593811 3.1632091999054 0.0642405077815056 1.0216326713562 0.235359072685242 -13.4880638122559 0.0452854037284851 -0.281521290540695 1.20965027809143 16.3635120391846 Yi-Yu From: Nick Schmansky [ni...@nmr.mgh.harvard.edu] Sent: Tuesday, June 14, 2011 11:14 AM To: Bruce Fischl Cc: Yiyu Chou; freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Talairach Transformation failed on Freesurfer 5.1 a change in 5.1 over 5.0 is that in 5.1 the talairach stage takes orig.mgz as input, whereas in 5.0 and prior, it used nu.mgz as input. (this was done so that the nu correction stage could make use of the talairach.xfm). you can either: - add the flag -use-mritotal to the end of recon-all to have it use an alternate tal registration program that sometimes works better on some images. or - use tkregister2 --s subjid --fstalto check the registration. either manually adjust it, or if it looks good, add -notalcheck to the end of recon-all to have it skip the tal checking step. n. On Tue, 2011-06-14 at 13:30 -0400, Bruce Fischl wrote: > is this the talairach.xfm? > On Tue, 14 Jun 2011, Yiyu Chou wrote: > > > Dear Freesurfer users, > > > > I got different transformation matrices (shown below) when running ver 5.0 > > and ver 5.1 on the same subject > > - ver 5.0 was doing great but ver 5.1 failed: > > I would appreciate it if you can give me some advice. > > Yi-Yu Chou > > - > > ver 5.0 > > 1.09499812 -0.07903829 -0.058642763.68856287 > > -0.005314621.045850040.30695227 -12.39152050 > > 0.05851136 -0.390315741.20183659 13.30094814 > > ver 5.1 > > 1.128152 -0.008014 -0.149835 2.440697 > > 1.389055 4.761067 -3.739542 -67.997681 > > -0.828629 -2.725178 3.870089 46.025513 > > > ___ > 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 mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Talairach Transformation failed on Freesurfer 5.1
a change in 5.1 over 5.0 is that in 5.1 the talairach stage takes orig.mgz as input, whereas in 5.0 and prior, it used nu.mgz as input. (this was done so that the nu correction stage could make use of the talairach.xfm). you can either: - add the flag -use-mritotal to the end of recon-all to have it use an alternate tal registration program that sometimes works better on some images. or - use tkregister2 --s subjid --fstalto check the registration. either manually adjust it, or if it looks good, add -notalcheck to the end of recon-all to have it skip the tal checking step. n. On Tue, 2011-06-14 at 13:30 -0400, Bruce Fischl wrote: > is this the talairach.xfm? > On Tue, 14 Jun 2011, Yiyu Chou wrote: > > > Dear Freesurfer users, > > > > I got different transformation matrices (shown below) when running ver 5.0 > > and ver 5.1 on the same subject > > - ver 5.0 was doing great but ver 5.1 failed: > > I would appreciate it if you can give me some advice. > > Yi-Yu Chou > > - > > ver 5.0 > > 1.09499812 -0.07903829 -0.058642763.68856287 > > -0.005314621.045850040.30695227 -12.39152050 > > 0.05851136 -0.390315741.20183659 13.30094814 > > ver 5.1 > > 1.128152 -0.008014 -0.149835 2.440697 > > 1.389055 4.761067 -3.739542 -67.997681 > > -0.828629 -2.725178 3.870089 46.025513 > > > ___ > 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] Talairach Transformation failed on Freesurfer 5.1
is this the talairach.xfm? On Tue, 14 Jun 2011, Yiyu Chou wrote: > Dear Freesurfer users, > > I got different transformation matrices (shown below) when running ver 5.0 > and ver 5.1 on the same subject > - ver 5.0 was doing great but ver 5.1 failed: > I would appreciate it if you can give me some advice. > Yi-Yu Chou > - > ver 5.0 > 1.09499812 -0.07903829 -0.058642763.68856287 > -0.005314621.045850040.30695227 -12.39152050 > 0.05851136 -0.390315741.20183659 13.30094814 > ver 5.1 > 1.128152 -0.008014 -0.149835 2.440697 > 1.389055 4.761067 -3.739542 -67.997681 > -0.828629 -2.725178 3.870089 46.025513 > ___ 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] Resampling from MNI 152 to MNI 305 - Problem with orientation
Thanks for the response! I seem to be getting better results.
I was wondering if there was any way the same resampling can be achieved
using Freesurfer 4.5 since a
lot of analysis (including analysis with other tasks) has already been done
in it, or if it is okay to use JUST the reg.2mm.mni152.dat file from
Freesurfer 5.1 and keep the rest of the analysis the same as before?
Thank you once again for this help!
Regards,
Balaji Goparaju
On Tue, Jun 14, 2011 at 11:46 AM, Douglas N Greve wrote:
> To go from mni152 to the MNI305 2mm space, use
>
> mri_vol2vol --mov mni305.2mm.nii.gz \
> --targ $FSLDIR/data/standard/MNI152_T1_2mm.nii.gz \
> --reg $FREESURFER_HOME/subjects/fsaverage/mri.2mm/reg.2mm.mni152.dat \
> --inv --o output.mni305.2mm.nii.gz
>
> This will resample MNI152_T1_2mm.nii.gz (or anything in that space) to the
> mni305 2mm space.
>
> For your application, add --interp nearest, or use
>
> mri_label2vol --seg BA_mask.mni152.nii \
> --reg $FREESURFER_HOME/subjects/fsaverage/mri.2mm/reg.2mm.mni152.dat \
> --invertmtx --o outfile.nii
>
> doug
>
>
> Balaji Goparaju wrote:
>
>> Hello Freesurfers,
>>
>> I have Brodmann Area binary masks in the ICBM MNI 152 space, that I
>> acquired using WFU_PickAtlas toolbox in SPM. These
>> masks are .nii files, and have a RAS orientation.
>>
>> I am trying to resample these masks into the fsaverage MNI 305 space,
>> specifically with the dimensions matching the "mni305.cor.subfov2.mgz"
>> file found in the $FREESURFER_HOME/average file. This file is in the LIA
>> orientation.
>>
>> However, the mni152.register.dat file seems to be transforming volumes
>> from the MNI 305 space to the MNI 152 Space in LAS orientation
>> (MNI152_T1_2mm.nii in FSL).
>>
>> Should I transform my Brodmann Area masks from the RAS orientation to a
>> LAS orientation? If so, how can I achieve this? The RAS orientation is
>> correct, so I know using mri_convert --out_dimension is out of the question.
>>
>> I have tried to use
>> *mri_label2vol --seg {BA_mask} --temp
>> {$FREESURFER_HOME/average/mni305.cor.subfov2.mgz} --o {output_file} --reg
>> mni152.register.dat --invertmtx*
>>
>> Also, I have tried to use the inverted matrix from mni152.register.dat and
>> use it with
>> *mri_vol2vol -mov {BA_mask} --reg {inverted_mni152.register.dat} --o
>> {output_file} --tal --talres 2*
>> However, the output files had interchanged posterior (P) and anterior (A),
>> and superior (S) and interior (I) orientations.
>>
>> What is the best way to achieve the resampling? Any guidance is really
>> appreciated!
>>
>> Regards,
>>
>> Balaji Goparaju
>>
>>
>> ___
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>
>
> --
> Douglas N. Greve, Ph.D.
> MGH-NMR Center
> gr...@nmr.mgh.harvard.edu
> Phone Number: 617-724-2358 Fax: 617-726-7422
>
> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
> FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html
>
>
>
> 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@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] trac-all - bedp errors
Hi Deryk , Thanks for checking...As Anastasia mentioned, If FSL's bedpostx runs well then that should work as well...I'm not exactly sure about why the error is coming up and I can't replicate it on my computer either. Can you check one more thing in your terminal? In your dmri.bedpostX directory there will be a commands.txt file which contains commandline arguments for each of the slices seperately...It should be something like this: /usr/pubsw/packages/fsl/current/bin/bedpostx_single_slice.sh /autofs/cluster/freesurfer/subjects/diffusion_tutorial/Diff001/dmri 2 1 1000 1250 25 1 0 If you copy paste one of these lines, does it give you the same error? If not we can take a look at it if you upload the data to see if we can replicate the error. Thanks, Priti > Hi Priti > > In addition, if I run bedpostx from the command line as follows: > > bedpostx /usr/local/freesurfer/subjects/C001/dmri > > it works just fine without errors. > > Deryk > > Deryk S. Beal, Ph.D., CCC-SLP, S-LP(C), Reg. CASLPO > Speech-Language Pathologist > C.I.H.R. Post Doctoral Research Fellow > Department of Cognitive and Neural Systems Speech Laboratory > Boston University, 677 Beacon Street, Boston, MA 02215 > dsb...@bu.edu > http://blogs.bu.edu/dsbeal/about/ > * This email may contain confidential and/or privileged information for the > sole use of the intended recipient. Any review or distribution by others is > strictly prohibited. If you have received this email in error, please contact the sender and delete all copies. Opinions, conclusions or other information expressed or contained in this email are not given or endorsed > by the sender unless otherwise affirmed independently by the sender. > > > On Mon, Jun 13, 2011 at 1:51 PM, Deryk S. Beal, Ph.D. wrote: > >> Hi Priti >> Thank you for your quick replay. The following files / folders are listed >> in my dmri.bedpostx directory: >> ** >> /usr/local/freesurfer/subjects/C001/dmri.bedpostX$ ls >> commands.txt diff_slices logs monitor xfms >> ** >> I am able to call bedpostx from the command line without error. It is worth >> noting that I am running Ubuntu 10.10 and the Neurodebian distro of FSL4.1. >> However, FSL and bedpostx appear to be sourced properly: >> ** :/usr/local/freesurfer/subjects/C001/dmri.bedpostX$ bedpostx >> Usage: bedpostx [options] >> expects to find bvals and bvecs in subject directory >> expects to find data and nodif_brain_mask in subject directory >> options: >> -n (number of fibres per voxel, default 2) >> -w (ARD weight, more weight means less secondary fibres per voxel, default >> 1) >> -b (burnin period, default 1000) >> -j (number of jumps, default 1250) >> -s (sample every, default 25) >> Deryk S. Beal, Ph.D., CCC-SLP, S-LP(C), Reg. CASLPO >> Speech-Language Pathologist >> C.I.H.R. Post Doctoral Research Fellow >> Department of Cognitive and Neural Systems Speech Laboratory >> Boston University, 677 Beacon Street, Boston, MA 02215 >> dsb...@bu.edu >> http://blogs.bu.edu/dsbeal/about/ >> * This email may contain confidential and/or privileged information for the >> sole use of the intended recipient. Any review or distribution by others >> is >> strictly prohibited. If you have received this email in error, please contact the sender and delete all copies. Opinions, conclusions or other >> information expressed or contained in this email are not given or endorsed >> by the sender unless otherwise affirmed independently by the sender. On Mon, Jun 13, 2011 at 1:25 PM, wrote: >>> Hi Deryk, >>> Is bedpostx properly installed in your computer? Can you just type bedpostx in your terminal to see if it gives this message? >>> Usage: bedpostx [options] >>> expects to find bvals and bvecs in subject directory >>> expects to find data and nodif_brain_mask in subject directory options: >>> -n (number of fibres per voxel, default 2) >>> -w (ARD weight, more weight means less secondary fibres per voxel, default >>> 1) >>> -b (burnin period, default 1000) >>> -j (number of jumps, default 1250) >>> -s (sample every, default 25) >>> Also can you let us know if any files are created after this error in /usr/local/freesurfer/subjects/C001/dmri.bedpostx directory ? >>> This looks like an error with the bedpostx itself...I've used the trac-all >>> -bedp on my local machine (instead of a cluster) and it seems to work fine. >>> Priti >>> > Dear Tracula Users >>> > >>> > I completed trac-all -prep -c without difficulty or e
Re: [Freesurfer] Resampling from MNI 152 to MNI 305 - Problem with orientation
To go from mni152 to the MNI305 2mm space, use
mri_vol2vol --mov mni305.2mm.nii.gz \
--targ $FSLDIR/data/standard/MNI152_T1_2mm.nii.gz \
--reg $FREESURFER_HOME/subjects/fsaverage/mri.2mm/reg.2mm.mni152.dat \
--inv --o output.mni305.2mm.nii.gz
This will resample MNI152_T1_2mm.nii.gz (or anything in that space) to
the mni305 2mm space.
For your application, add --interp nearest, or use
mri_label2vol --seg BA_mask.mni152.nii \
--reg $FREESURFER_HOME/subjects/fsaverage/mri.2mm/reg.2mm.mni152.dat \
--invertmtx --o outfile.nii
doug
Balaji Goparaju wrote:
> Hello Freesurfers,
>
> I have Brodmann Area binary masks in the ICBM MNI 152 space, that I
> acquired using WFU_PickAtlas toolbox in SPM. These
> masks are .nii files, and have a RAS orientation.
>
> I am trying to resample these masks into the fsaverage MNI 305 space,
> specifically with the dimensions matching the "mni305.cor.subfov2.mgz"
> file found in the $FREESURFER_HOME/average file. This file is in the
> LIA orientation.
>
> However, the mni152.register.dat file seems to be transforming volumes
> from the MNI 305 space to the MNI 152 Space in LAS orientation
> (MNI152_T1_2mm.nii in FSL).
>
> Should I transform my Brodmann Area masks from the RAS orientation to
> a LAS orientation? If so, how can I achieve this? The RAS orientation
> is correct, so I know using mri_convert --out_dimension is out of the
> question.
>
> I have tried to use
> *mri_label2vol --seg {BA_mask} --temp
> {$FREESURFER_HOME/average/mni305.cor.subfov2.mgz} --o {output_file}
> --reg mni152.register.dat --invertmtx*
>
> Also, I have tried to use the inverted matrix from mni152.register.dat
> and use it with
> *mri_vol2vol -mov {BA_mask} --reg {inverted_mni152.register.dat} --o
> {output_file} --tal --talres 2*
> However, the output files had interchanged posterior (P) and anterior
> (A), and superior (S) and interior (I) orientations.
>
> What is the best way to achieve the resampling? Any guidance is really
> appreciated!
>
> Regards,
>
> Balaji Goparaju
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
--
Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html
___
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] make_average_subject error in T1.mgz and t1.mgz
that's weird. I'm not sure what to do. The log says that it is creating T1.mgz and not t1.mgz. Can you try this: cd $SUBJECTS_DIR/subject/mri mri_normalize -g 1 nu.mgz T1.mgz this should create T1.mgz and not t1.mgz doug tulu wrote: > Dear FS experts and Prof. Douglas N Greve, > Here is log file. I work on other machine under CentOS 5 and FS 4.5 version > but I copy the result from this machine to other machine and find it only > have t1.mgz rather than T1.mgz. > I guess is the language system problem ? > Finally I use a short matlab script to change t1.mgz name as T1.mgz. > > Thanks in advance > Best > JLH > > -Original Message- > From: Douglas N Greve [mailto:gr...@nmr.mgh.harvard.edu] > Sent: Monday, June 13, 2011 11:01 PM > To: t...@ms36.hinet.net > Cc: freesurfer > Subject: Re: [Freesurfer] make_average_subject error in T1.mgz and t1.mgz > > Do you mean your individual subject after running through FS has a file > called t1.mgz and not T1.mgz? Something is definitely wrong there. Can > you send the log file? > doug > > t...@ms36.hinet.net wrote: > >> Dear FS experts, >> I use FS5.1 and previous data run on other machine. When I try to >> make_average_subjects program, I get error message that it can not get >> T1.mgz data from subject folder. When I check my dataset, actually it >> has t1.mgz rather than T1.mgz. how could I change the setting from >> T1.mgz to t1.mgz >> thanks help >> JLH >> >> >> >> ___ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> > > -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html ___ 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] Talairach Transformation failed on Freesurfer 5.1
Dear Freesurfer users, I got different transformation matrices (shown below) when running ver 5.0 and ver 5.1 on the same subject - ver 5.0 was doing great but ver 5.1 failed: I would appreciate it if you can give me some advice. Yi-Yu Chou - ver 5.0 1.09499812 -0.07903829 -0.058642763.68856287 -0.005314621.045850040.30695227 -12.39152050 0.05851136 -0.390315741.20183659 13.30094814 ver 5.1 1.128152 -0.008014 -0.149835 2.440697 1.389055 4.761067 -3.739542 -67.997681 -0.828629 -2.725178 3.870089 46.025513 ___ 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] Adding a new measure to the design tab
Hi Jeanette, Which version of FreeSurfer are you running. Also, can you try renaming the qdec.Qdecrc to .Qdecrc and try again. Here's more info on editing the .Qdecrc file with the new measures. https://surfer.nmr.mgh.harvard.edu/fswiki/.Qdecrc Sita. On Mon, 13 Jun 2011, Jeanette Berberich wrote: > Hi, > > So I'm trying to add new measures, after having run recon-all -qcache, to my > design tab drop-down menu and it doesn't seem to be working. I was a little > confused about the .Qdecrc file. I put a file named qdec.Qdecrc file inside > my $SUBJECTS_DIR/qdec/ and i also have a qdec.fsgd file in the same place. > I'm not sure what else to do to get my new measurements to show up. > > Thank you so much, > > > Jeanette > ___ > 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] Resampling from MNI 152 to MNI 305 - Problem with orientation
Hi Balaji, fslswapdim (a command line program which comes as part of fsl) should solve your orientation problems. If you have fsl installed (which you should do!) then typing fslswapdim input_volume_name -x output_volume_name into the terminal should swap RAS to LAS and vice versa. Or you can just type in fslswapdim into the terminal to get help. Best of luck! Sean ___ 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.
