[Freesurfer] error mris_anatomicalstats
Dear Freesurfer experts, I have a question about trying to extract statistics from merged labels using mris_anatomical_stats. I have used the mri_annotation2label, and then the mri_merge label, however now when trying to do mris_anatomical stats, I get the error ; could not read input volume, eg Freesurfer cannot read the wm.mgz file. What step have I done wrong? Thank you very much, Kind Wishes, Linn ___ 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] error mris_anatomicalstats
Hi Linn can you send us the exact command line and screen output, and also what version and software/hardware environment you are running in? cheers Bruce On Mon, 25 Mar 2013, Linn Mittlestein wrote: Dear Freesurfer experts, I have a question about trying to extract statistics from merged labels using mris_anatomical_stats. I have used the mri_annotation2label, and then the mri_merge label, however now when trying to do mris_anatomical stats, I get the error ; could not read input volume, eg Freesurfer cannot read the wm.mgz file. What step have I done wrong? Thank you very much, Kind Wishes, Linn ___ 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] Which T1 data used for segmentations in fsaverage subject?
Hi freesurfites, The mri folder of the fsaverage subject contains the segmenation files, such as aparc+aseg.mgz, etc. and in the surf folder there the corresponding surface files (?h.pial. ?h.white, etc). Question: which T1 data was used for these segmentations? Cheers, Ed ___ 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] Which T1 data used for segmentations in fsaverage subject?
Hi Ed a combination of them (e.g. norm.mgz is used for the aseg.mz, but brain.finalsurfs.mgz for the white/pial) cheers Bruce On Mon, 25 Mar 2013, Ed Gronenschild wrote: Hi freesurfites, The mri folder of the fsaverage subject contains the segmenation files, such as aparc+aseg.mgz, etc. and in the surf folder there the corresponding surface files (?h.pial. ?h.white, etc). Question: which T1 data was used for these segmentations? Cheers, Ed ___ 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] Which T1 data used for segmentations in fsaverage subject?
Hi Bruce, I cannot find these files in the subjects-fsaverage folder (version v5.1.0). Ed On 25 Mar 2013, at 13:58, Bruce Fischl wrote: Hi Ed a combination of them (e.g. norm.mgz is used for the aseg.mz, but brain.finalsurfs.mgz for the white/pial) cheers Bruce On Mon, 25 Mar 2013, Ed Gronenschild wrote: Hi freesurfites, The mri folder of the fsaverage subject contains the segmenation files, such as aparc+aseg.mgz, etc. and in the surf folder there the corresponding surface files (?h.pial. ?h.white, etc). Question: which T1 data was used for these segmentations? Cheers, Ed ___ 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] Which T1 data used for segmentations in fsaverage subject?
oh, sorry Ed, I missed that part of your question. fsaverage is a special case. The surfaces don't correspond to any volume and really shouldn't be used for anything except visualization. The asegs and aparcs I think are generated by majority voting across subjects in the spherical and talairach.m3z coordinate systems. cheers Bruce On Mon, 25 Mar 2013, Ed Gronenschild wrote: Hi Bruce, I cannot find these files in the subjects-fsaverage folder (version v5.1.0). Ed On 25 Mar 2013, at 13:58, Bruce Fischl wrote: Hi Ed a combination of them (e.g. norm.mgz is used for the aseg.mz, but brain.finalsurfs.mgz for the white/pial) cheers Bruce On Mon, 25 Mar 2013, Ed Gronenschild wrote: Hi freesurfites, The mri folder of the fsaverage subject contains the segmenation files, such as aparc+aseg.mgz, etc. and in the surf folder there the corresponding surface files (?h.pial. ?h.white, etc). Question: which T1 data was used for these segmentations? Cheers, Ed ___ 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] Which T1 data used for segmentations in fsaverage subject?
It uses the 12 dof talairach.xfm. doug On 03/25/2013 09:04 AM, Bruce Fischl wrote: oh, sorry Ed, I missed that part of your question. fsaverage is a special case. The surfaces don't correspond to any volume and really shouldn't be used for anything except visualization. The asegs and aparcs I think are generated by majority voting across subjects in the spherical and talairach.m3z coordinate systems. cheers Bruce On Mon, 25 Mar 2013, Ed Gronenschild wrote: Hi Bruce, I cannot find these files in the subjects-fsaverage folder (version v5.1.0). Ed On 25 Mar 2013, at 13:58, Bruce Fischl wrote: Hi Ed a combination of them (e.g. norm.mgz is used for the aseg.mz, but brain.finalsurfs.mgz for the white/pial) cheers Bruce On Mon, 25 Mar 2013, Ed Gronenschild wrote: Hi freesurfites, The mri folder of the fsaverage subject contains the segmenation files, such as aparc+aseg.mgz, etc. and in the surf folder there the corresponding surface files (?h.pial. ?h.white, etc). Question: which T1 data was used for these segmentations? Cheers, Ed ___ 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 -- 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 Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Which T1 data used for segmentations in fsaverage subject?
They were generated from the asegs of the input 40 subjects. They should not be used for much, certainly only for visualization purposes. doug On 03/25/2013 08:57 AM, Ed Gronenschild wrote: Hi freesurfites, The mri folder of the fsaverage subject contains the segmenation files, such as aparc+aseg.mgz, etc. and in the surf folder there the corresponding surface files (?h.pial. ?h.white, etc). Question: which T1 data was used for these segmentations? Cheers, Ed ___ 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 Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ___ 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] Xhemi stat questions
On 03/22/2013 06:45 AM, Gabriel Gonzalez Escamilla wrote: Dear Doug, I've seen that you restore the files to download, for the Xhemi registration. While I'm checking for the statistical process, I've seen that the one I have is: Date: 2012/12/06 16:06:52, Revision: 1.59.2.4, and the one that is on your ftp server is Date: 2012/12/06 16:06:17, Revision: 1.66, So mine is a lower version but recent hour, and the actual is newer version but seems that was created before the one I have. My question is, Which one should I keep? Can you send me a diff of the two files? If I change the mris_precproc version. Shall I re-run this step before statistical analyses, to create a new lh.lh-rh.thickness.sm00.mgh? On the other hand I have some doubts about the statistical procedure. It's supposed that if I apply the Xhemi registration, as result the left and right hemispheres are equals to each other on every subject, so: A) Where can I get the CT values after the Xhemi registration to FSaverage_sym for the left and right hemispheres? what are CT values? B) Given that I have two groups, Patients and Control, with two levels each, i.e male-female (Gp1male Gp1female Gp2male Gp2female Gp1maleVar1 Gp1femaleVar1 Grp2maleVar1 Grp2femaleVar1), and that I can set the contrasts and fsgd files as with a normal CT analisis, but only on my lh.lh-rh.thickness.smXX.mgh, wich is suppose to contain the left-right differences across subjects, right? Wich would be the right interpretation? of: The interpretation does not really change because it is a xhemi analysis 1) 5 .5 -.5 -.5 0 0 0 0 Is the L-R difference between Grp1 and Grp2 different than 0 (regressing out Var1 and gender) 2) 5 -.5 .5 -.5 0 0 0 0 Is the L-R difference between Males and Females different than 0 (regressing out Var1 and Group) 3) 0 0 0 0 .5 .5 -.5 -.5 Does the slope of the L-R difference with Var1 differ between Grp1 and Grp2(regressing out gender) 4) 0 0 0 0 5 -.5 .5 -.5 Does the slope of the L-R difference with Var1 differ between Male and Female(regressing out group) Many thanks in advanced. Gabriel. -- 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 Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ___ 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] cortical recontruction error
I was trying, but the administrator did reject that, because the file is too big. 2013/3/25 Claudia Dacquino claudia.dacqu...@gmail.com I was trying, but the administrator did reject that, because the file is too big. 2013/3/25 Claudia Dacquino claudia.dacqu...@gmail.com Hi Bruce, I'll try to upload dataset. Thanks, Claudia 2013/3/23 Bruce Fischl fis...@nmr.mgh.harvard.edu Hi Claudia hmmm, someone else mentioned that mri_cc hangs for them but we've never seen it. If you upload your dataset I'll see if we can replicate the problem Bruce On Fri, 22 Mar 2013, Claudia Dacquino wrote: Dear Freesurfers, I'm new and I'm starting using Freesurfer. I'm having a problem with one subject, during the cortical reconstruction (recon-all) the process stops at this stage: mri_cc -aseg aseg.auto_noCCseg.mgz -o aseg.auto.mgz subjid at this point: final transformation (x=128.0, yr=0.978, zr=0.153): 1.000 -0.003 0.017 -1.456; 0.003 1.000 0.000 8.654; -0.017 0.000 1.000 25.201; 0.000 0.000 0.000 1.000; without giving me any error message, it just stops. Do you have some ideas for why it happens? thanks to everyone, Claudia 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/**compliancelinehttp://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] cortical recontruction error
I'm sorry, I did mean the moderator of Freesurfer mailing list. 2013/3/25 Bruce Fischl fis...@nmr.mgh.harvard.edu you should be able to use our ftp site or file drop. Which administrator do you mean? On Mon, 25 Mar 2013, Claudia Dacquino wrote: I was trying, but the administrator did reject that, because the file is too big. 2013/3/25 Claudia Dacquino claudia.dacqu...@gmail.com Hi Bruce, I'll try to upload dataset. Thanks, Claudia 2013/3/23 Bruce Fischl fis...@nmr.mgh.harvard.edu Hi Claudia hmmm, someone else mentioned that mri_cc hangs for them but we've never seen it. If you upload your dataset I'll see if we can replicate the problem Bruce On Fri, 22 Mar 2013, Claudia Dacquino wrote: Dear Freesurfers, I'm new and I'm starting using Freesurfer. I'm having a problem with one subject, during the cortical reconstruction (recon-all) the process stops at this stage: mri_cc -aseg aseg.auto_noCCseg.mgz -o aseg.auto.mgz subjid at this point: final transformation (x=128.0, yr=0.978, zr=0.153): 1.000 -0.003 0.017 -1.456; 0.003 1.000 0.000 8.654; -0.017 0.000 1.000 25.201; 0.000 0.000 0.000 1.000; without giving me any error message, it just stops. Do you have some ideas for why it happens? thanks to everyone, Claudia 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/**compliancelinehttp://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] cortical recontruction error
yes, it will be too big to email. You can either use our ftp site or file drop cheers Bruce On Mon, 25 Mar 2013, Claudia Dacquino wrote: I'm sorry, I did mean the moderator of Freesurfer mailing list. 2013/3/25 Bruce Fischl fis...@nmr.mgh.harvard.edu you should be able to use our ftp site or file drop. Which administrator do you mean? On Mon, 25 Mar 2013, Claudia Dacquino wrote: I was trying, but the administrator did reject that, because the file is too big. 2013/3/25 Claudia Dacquino claudia.dacqu...@gmail.com Hi Bruce, I'll try to upload dataset. Thanks, Claudia 2013/3/23 Bruce Fischl fis...@nmr.mgh.harvard.edu Hi Claudia hmmm, someone else mentioned that mri_cc hangs for them but we've never seen it. If you upload your dataset I'll see if we can replicate the problem Bruce On Fri, 22 Mar 2013, Claudia Dacquino wrote: Dear Freesurfers, I'm new and I'm starting using Freesurfer. I'm having a problem with one subject, during the cortical reconstruction (recon-all) the process stops at this stage: mri_cc -aseg aseg.auto_noCCseg.mgz -o aseg.auto.mgz subjid at this point: final transformation (x=128.0, yr=0.978, zr=0.153): 1.000 -0.003 0.017 -1.456; 0.003 1.000 0.000 8.654; -0.017 0.000 1.000 25.201; 0.000 0.000 0.000 1.000; without giving me any error message, it just stops. Do you have some ideas for why it happens? thanks to everyone, Claudia 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] cortical recontruction error
p.s. the info on both is here: https://surfer.nmr.mgh.harvard.edu/fswiki On Mon, 25 Mar 2013, Bruce Fischl wrote: yes, it will be too big to email. You can either use our ftp site or file drop cheers Bruce On Mon, 25 Mar 2013, Claudia Dacquino wrote: I'm sorry, I did mean the moderator of Freesurfer mailing list. 2013/3/25 Bruce Fischl fis...@nmr.mgh.harvard.edu you should be able to use our ftp site or file drop. Which administrator do you mean? On Mon, 25 Mar 2013, Claudia Dacquino wrote: I was trying, but the administrator did reject that, because the file is too big. 2013/3/25 Claudia Dacquino claudia.dacqu...@gmail.com Hi Bruce, I'll try to upload dataset. Thanks, Claudia 2013/3/23 Bruce Fischl fis...@nmr.mgh.harvard.edu Hi Claudia hmmm, someone else mentioned that mri_cc hangs for them but we've never seen it. If you upload your dataset I'll see if we can replicate the problem Bruce On Fri, 22 Mar 2013, Claudia Dacquino wrote: Dear Freesurfers, I'm new and I'm starting using Freesurfer. I'm having a problem with one subject, during the cortical reconstruction (recon-all) the process stops at this stage: mri_cc -aseg aseg.auto_noCCseg.mgz -o aseg.auto.mgz subjid at this point: final transformation (x=128.0, yr=0.978, zr=0.153): 1.000 -0.003 0.017 -1.456; 0.003 1.000 0.000 8.654; -0.017 0.000 1.000 25.201; 0.000 0.000 0.000 1.000; without giving me any error message, it just stops. Do you have some ideas for why it happens? thanks to everyone, Claudia 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] problem with registration in preprocessing
Hi Maryam, I'm not sure what is wrong. Can you check the image in bold/018 to make sure that there is not something horribly wrong? Eg, it is not a localizer or only has one slice. And it is only the last run? The others are ok? doug On 03/22/2013 03:05 PM, Maryam Vaziri Pashkam wrote: Hi Doug, I am running fsfast preprocessing on my data and I am getting an error on one of the runs. This is the preprocessing code that I run: preproc-sess -s 130321_xu_Object4catmulti_01 -per-run -sliceorder siemens -fsd bold -fwhm 0 -mni305-2mm -surface self lhrh The error seems to happen during the fsl registration on the last run (out of 12 runs): /ncf/vcn/Maryam/mri-space/studies/Obj4catmulti/unpackdata/130321_xu_Object4catmulti_01 flirt.fsl -ref bold/018/tmp.bbregister.1228/fslregister/refvol.fslregister.nii -in bold/018/tmp.bbregister.1228/fslregister/movvol.fslregister.nii -bins 256 -cost corratio -dof 6 -searchrx -90 90 -searchry -90 90 -searchrz -90 90 -verbose 0 -omat bold/018/tmp.bbregister.1228/reg.init.dat.fsl.mat -init bold/018/tmp.bbregister.1228/fslregister/fslmat0.trans.mat -schedule /ncf/apps/freesurfer-5.1.0//bin/flirt.newdefault.20080811.sch terminate called after throwing an instance of 'NEWMAT::SingularException' Abort ERROR: flirt bellow is the register-sess log file. I have only included the section for the registration of the last run. I have looked at the raw data of this run and it does not look different from the other runs (all other runs are successfully registered). I am running freesurfer 5.1. Any idea how I can fix the error? Thanks, Maryam $Id: bbregister,v 1.49 2011/03/06 23:38:41 greve Exp $ Linux ncfws08.rc.fas.harvard.edu http://ncfws08.rc.fas.harvard.edu 2.6.18-274.17.1.el5 #1 SMP Tue Jan 10 17:25:58 EST 2012 x86_64 x86_64 x86_64 GNU/Linux FREESURFER_HOME /ncf/apps/freesurfer-5.1.0/ mri_convert bold/018/template.nii.gz bold/018/tmp.bbregister.1228/template.nii mri_convert bold/018/template.nii.gz bold/018/tmp.bbregister.1228/template.nii $Id: mri_convert.c,v 1.179.2.2 2011/05/16 20:53:47 greve Exp $ reading from bold/018/template.nii.gz... TR=2000.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-0.998239, -0.0522464, 0.0280991) j_ras = (0.0500393, -0.995986, -0.0742193) k_ras = (0.031864, -0.0726825, 0.996846) writing to bold/018/tmp.bbregister.1228/template.nii... fslregister --s blue_street_kcb --mov bold/018/tmp.bbregister.1228/template.nii --reg bold/018/tmp.bbregister.1228/reg.init.dat --niters 1 --maxangle 90 --nobetmov --tmp bold/018/tmp.bbregister.1228/fslregister --dof 6 Log file is bold/018/tmp.bbregister.1228/reg.init.dat.fslregister.log Fri Mar 22 14:42:18 EDT 2013 --s blue_street_kcb --mov bold/018/tmp.bbregister.1228/template.nii --reg bold/018/tmp.bbregister.1228/reg.init.dat --niters 1 --maxangle 90 --nobetmov --tmp bold/018/tmp.bbregister.1228/fslregister --dof 6 $Id: fslregister,v 1.34.2.1 2011/03/28 20:35:36 greve Exp $ ncfws08.rc.fas.harvard.edu http://ncfws08.rc.fas.harvard.edu Linux ncfws08.rc.fas.harvard.edu http://ncfws08.rc.fas.harvard.edu 2.6.18-274.17.1.el5 #1 SMP Tue Jan 10 17:25:58 EST 2012 x86_64 x86_64 x86_64 GNU/Linux nIters 1 -- /ncf/vcn/Maryam/mri-space/studies/Obj4catmulti/unpackdata/130321_xu_Object4catmulti_01 mri_convert /ncf/vcn/Maryam/mri-space/subjects/blue_street_kcb/mri/brainmask.mgz bold/018/tmp.bbregister.1228/fslregister/refvol.fslregister.nii mri_convert /ncf/vcn/Maryam/mri-space/subjects/blue_street_kcb/mri/brainmask.mgz bold/018/tmp.bbregister.1228/fslregister/refvol.fslregister.nii $Id: mri_convert.c,v 1.179.2.2 2011/05/16 20:53:47 greve Exp $ reading from /ncf/vcn/Maryam/mri-space/subjects/blue_street_kcb/mri/brainmask.mgz... TR=2530.00, TE=3.45, TI=1100.00, flip angle=7.00 i_ras = (-1, 4.47035e-08, -4.65661e-08) j_ras = (-5.58793e-08, -4.05125e-08, -1) k_ras = (-5.96046e-08, 1, 1.11759e-08) writing to bold/018/tmp.bbregister.1228/fslregister/refvol.fslregister.nii... -- /ncf/vcn/Maryam/mri-space/studies/Obj4catmulti/unpackdata/130321_xu_Object4catmulti_01 mri_convert bold/018/tmp.bbregister.1228/template.nii bold/018/tmp.bbregister.1228/fslregister/movvol.fslregister.nii --frame 0 mri_convert bold/018/tmp.bbregister.1228/template.nii bold/018/tmp.bbregister.1228/fslregister/movvol.fslregister.nii --frame 0 $Id: mri_convert.c,v 1.179.2.2 2011/05/16 20:53:47 greve Exp $ reading from bold/018/tmp.bbregister.1228/template.nii... TR=2000.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-0.998239, -0.0522464, 0.0280991) j_ras = (0.0500393, -0.995986, -0.0742193) k_ras = (0.031864, -0.0726825, 0.996846) keeping frame 0 writing to bold/018/tmp.bbregister.1228/fslregister/movvol.fslregister.nii... Mov determinant is 35.3062 Swapping dims for pos det WARNING:: Flipping Left/Right orientation (as det 0) tkregister_tcl
Re: [Freesurfer] advice in registering a binary mask to Freesurfer space.
Can you compute the registration between the manually traced anat space and the FS conformed space? Eg, with BBR. If you can do that, then you can run mri_label2vol to convert the mask into FS conformed space (assuming that that is what you want to do). doug On 03/22/2013 04:43 PM, Joshua Lee wrote: Hi All, I wanted to get peoples advice on the best method of registration/interpolation to use on a manually traced segmentation (and its structural) that is not in the same space and orientation as the structurals I started Freesurfer with (although they both originally came from the same image. I want to maintain the integrity of the manual traced binary mask through this registration and reslice. For a number of reasons, I do not want to take Freesurfers output to the space of the manual segmentation. What do people think is a good technique? Flirt nearest neighbor interpolation? Something different from Freesurfer? ANTs? - Josh ___ 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 Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ___ 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] cortical recontruction error
he file is on martinos file drop. thanks claudia 2013/3/25 Bruce Fischl fis...@nmr.mgh.harvard.edu p.s. the info on both is here: https://surfer.nmr.mgh.**harvard.edu/fswikihttps://surfer.nmr.mgh.harvard.edu/fswiki On Mon, 25 Mar 2013, Bruce Fischl wrote: yes, it will be too big to email. You can either use our ftp site or file drop cheers Bruce On Mon, 25 Mar 2013, Claudia Dacquino wrote: I'm sorry, I did mean the moderator of Freesurfer mailing list. 2013/3/25 Bruce Fischl fis...@nmr.mgh.harvard.edu you should be able to use our ftp site or file drop. Which administrator do you mean? On Mon, 25 Mar 2013, Claudia Dacquino wrote: I was trying, but the administrator did reject that, because the file is too big. 2013/3/25 Claudia Dacquino claudia.dacqu...@gmail.com Hi Bruce, I'll try to upload dataset. Thanks, Claudia 2013/3/23 Bruce Fischl fis...@nmr.mgh.harvard.edu Hi Claudia hmmm, someone else mentioned that mri_cc hangs for them but we've never seen it. If you upload your dataset I'll see if we can replicate the problem Bruce On Fri, 22 Mar 2013, Claudia Dacquino wrote: Dear Freesurfers, I'm new and I'm starting using Freesurfer. I'm having a problem with one subject, during the cortical reconstruction (recon-all) the process stops at this stage: mri_cc -aseg aseg.auto_noCCseg.mgz -o aseg.auto.mgz subjid at this point: final transformation (x=128.0, yr=0.978, zr=0.153): 1.000 -0.003 0.017 -1.456; 0.003 1.000 0.000 8.654; -0.017 0.000 1.000 25.201; 0.000 0.000 0.000 1.000; without giving me any error message, it just stops. Do you have some ideas for why it happens? thanks to everyone, Claudia 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/**compliancelinehttp://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] Xhemi stat questions
Thanks a lot for your answer,I'm sending you attached the diff of the two mris_preproc.When I wrote CT, I was meaning cortical thickness, as normally this values are in surf/?h.thickness, But how do I know the Xhemi-registered thickness values of each subject for lh-rh, or area or any of those indices?Regards,GabrielEl 25/03/13, Douglas N Greve gr...@nmr.mgh.harvard.edu escribió:On 03/22/2013 06:45 AM, Gabriel Gonzalez Escamilla wrote: Dear Doug, I've seen that you restore the files to download, for the Xhemi registration. While I'm checking for the statistical process, I've seen that the one I have is: Date: 2012/12/06 16:06:52, Revision: 1.59.2.4, and the one that is on your ftp server is Date: 2012/12/06 16:06:17, Revision: 1.66, So mine is a lower version but recent hour, and the actual is newer version but seems that was created before the one I have. My question is, Which one should I keep?Can you send me a diff of the two files? If I change the mris_precproc version. Shall I re-run this step before statistical analyses, to create a new lh.lh-rh.thickness.sm00.mgh? On the other hand I have some doubts about the statistical procedure. It's supposed that if I apply the Xhemi registration, as result the left and right hemispheres are equals to each other on every subject, so: A) Where can I get the CT values after the Xhemi registration to FSaverage_sym for the left and right hemispheres?what are CT values? B) Given that I have two groups, Patients and Control, with two levels each, i.e male-female (Gp1male Gp1female Gp2male Gp2female Gp1maleVar1 Gp1femaleVar1 Grp2maleVar1 Grp2femaleVar1), and that I can set the contrasts and fsgd files as with a normal CT analisis, but only on my lh.lh-rh.thickness.smXX.mgh, wich is suppose to contain the left-right differences across subjects, right? Wich would be the right interpretation? of:The interpretation does not really change because it is a xhemi analysis 1) 5 .5 -.5 -.5 0 0 0 0Is the L-R difference between Grp1 and Grp2 different than 0 (regressing out Var1 and gender) 2) 5 -.5 .5 -.5 0 0 0 0Is the L-R difference between Males and Females different than 0 (regressing out Var1 and Group) 3) 0 0 0 0 .5 .5 -.5 -.5Does the slope of the L-R difference with Var1 differ between Grp1 and Grp2(regressing out gender) 4) 0 0 0 0 5 -.5 .5 -.5Does the slope of the L-R difference with Var1 differ between Male and Female(regressing out group) Many thanks in advanced. Gabriel.-- Douglas N. Greve, Ph.D.MGH-NMR Centergr...@nmr.mgh.harvard.eduPhone Number: 617-724-2358Fax: 617-726-7422Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReportingFileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.htmlOutgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/___Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurferThe information in this e-mail is intended only for the person to whom it isaddressed. If you believe this e-mail was sent to you in error and the e-mailcontains patient information, please contact the Partners Compliance HelpLine athttp://www.partners.org/complianceline . If the e-mail was sent to you in errorbut does not contain patient information, please contact the sender and properlydispose of the e-mail.-- --PhD. student Gabriel González-EscamillaLaboratory of Functional NeuroscienceDepartment of Physiology, Anatomy, and Cell BiologyUniversity Pablo de OlavideCtra. de Utrera, Km.141013 - Seville- Spain -Email: ggon...@upo.eshttp://www.upo.es/neuroaging/es/ /root/trabajo/freesurfer/bin/mris_preproc_old /root/trabajo/freesurfer/bin/mris_preproc 14,15c14,15 #$Date: 2012/12/06 16:06:52 $ #$Revision: 1.59.2.4 $ --- #$Date: 2012/12/06 16:06:17 $ #$Revision: 1.66 $ 32c32 set VERSION = '$Id: mris_preproc,v 1.59.2.4 2012/12/06 16:06:52 mreuter Exp $'; --- set VERSION = '$Id: mris_preproc,v 1.66 2012/12/06 16:06:17 mreuter Exp $'; 77a78 set DoXHemiOnly = 0; # do not include the non-xhemi 445a447,453 case --tal-xyz: if($#argv 1) goto arg1err; set svalsurf = $argv[1]; shift; set sval = tal-xyz set srcsurf = 1; breaksw 679a688,692 case --xhemi-only: set DoXHemi = 1; set DoXHemiOnly = 1; breaksw 923,924c936,941 if($srchemi == lh) set tmplist = ($tmplist $subj $subj/xhemi) if($srchemi == rh) set tmplist = ($tmplist $subj/xhemi $subj) --- if($DoXHemiOnly) then set tmplist = ($tmplist $subj/xhemi) else if($srchemi == lh) set tmplist = ($tmplist $subj $subj/xhemi) if($srchemi == rh) set tmplist = ($tmplist $subj/xhemi $subj) endif 1017a1035 echo --tal-xyz surfname : output xyz in mni305 for each subject 1109c1127 --area surfname --- --tal-xyz surfname ,1112c1129,1131 Extract vertex area from subject/surf/hemi.surfname to use as input. For use with --s, --fsgd, or --f.
Re: [Freesurfer] Xhemi stat questions
On 03/25/2013 10:52 AM, Gabriel Gonzalez Escamilla wrote: Thanks a lot for your answer, I'm sending you attached the diff of the two mris_preproc. Those differences are just added features and won't change your results. When I wrote CT, I was meaning cortical thickness, as normally this values are in surf/?h.thickness, But how do I know the Xhemi-registered thickness values of each subject for lh-rh, or area or any of those indices? I'm not sure what you mean. When you run mris_preproc, you specify whether you want thickness, etc. doug Regards, Gabriel El 25/03/13, *Douglas N Greve * gr...@nmr.mgh.harvard.edu escribió: On 03/22/2013 06:45 AM, Gabriel Gonzalez Escamilla wrote: Dear Doug, I've seen that you restore the files to download, for the Xhemi registration. While I'm checking for the statistical process, I've seen that the one I have is: Date: 2012/12/06 16:06:52, Revision: 1.59.2.4, and the one that is on your ftp server is Date: 2012/12/06 16:06:17, Revision: 1.66, So mine is a lower version but recent hour, and the actual is newer version but seems that was created before the one I have. My question is, Which one should I keep? Can you send me a diff of the two files? If I change the mris_precproc version. Shall I re-run this step before statistical analyses, to create a new lh.lh-rh.thickness.sm00.mgh? On the other hand I have some doubts about the statistical procedure. It's supposed that if I apply the Xhemi registration, as result the left and right hemispheres are equals to each other on every subject, so: A) Where can I get the CT values after the Xhemi registration to FSaverage_sym for the left and right hemispheres? what are CT values? B) Given that I have two groups, Patients and Control, with two levels each, i.e male-female (Gp1male Gp1female Gp2male Gp2female Gp1maleVar1 Gp1femaleVar1 Grp2maleVar1 Grp2femaleVar1), and that I can set the contrasts and fsgd files as with a normal CT analisis, but only on my lh.lh-rh.thickness.smXX.mgh, wich is suppose to contain the left-right differences across subjects, right? Wich would be the right interpretation? of: The interpretation does not really change because it is a xhemi analysis 1) 5 .5 -.5 -.5 0 0 0 0 Is the L-R difference between Grp1 and Grp2 different than 0 (regressing out Var1 and gender) 2) 5 -.5 .5 -.5 0 0 0 0 Is the L-R difference between Males and Females different than 0 (regressing out Var1 and Group) 3) 0 0 0 0 .5 .5 -.5 -.5 Does the slope of the L-R difference with Var1 differ between Grp1 and Grp2(regressing out gender) 4) 0 0 0 0 5 -.5 .5 -.5 Does the slope of the L-R difference with Var1 differ between Male and Female(regressing out group) Many thanks in advanced. Gabriel. -- 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 Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ___ 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. -- -- PhD. student Gabriel González-Escamilla Laboratory of Functional Neuroscience Department of Physiology, Anatomy, and Cell Biology University Pablo de Olavide Ctra. de Utrera, Km.1 41013 - Seville - Spain - Email: ggon...@upo.es http://www.upo.es/neuroaging/es/ -- 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 Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Talairach manual correction
Hi Andreia, you don't need a separate flag. It will automatically see that you have manually edited the talairach.xfm and not overwrite it. doug On 03/22/2013 11:48 AM, _andre...@sapo.pt wrote: Hello! After completing the talairach correction in tkregister2 (saving the changes with the SAVEREG button), I am running recon-all -all -s subj. But now I'm wondering if by doing it this way the changes will be incorporated or the process will start from the beggining leaving everything as before the manual corrections... Is there any flag needed? Thank you, Andreia ___ 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 Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ___ 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] Xhemi stat questions
Thank you, so I'm keeping the one I had.Sorry for my bad explanation. When I do a normal cortical thickness study, I know the average thickness for a label, e.g. cortex, and the values at each vertex of each hemisphere are stored in $subject/surf/?l.thickness. I would like to know if it is possible to obtain the same cortical thickness measure from the lh-rh registered hemispheres of each subject.Regards,GabrielEl 25/03/13, Douglas N Greve gr...@nmr.mgh.harvard.edu escribió:On 03/25/2013 10:52 AM, Gabriel Gonzalez Escamilla wrote:Thanks a lot for your answer,I'm sending you attached the diff of the two mris_preproc.Those differences are just added features and won't change your results.When I wrote CT, I was meaning cortical thickness, as normally this values are in surf/?h.thickness, But how do I know the Xhemi-registered thickness values of each subject for lh-rh, or area or any of those indices?I'm not sure what you mean. When you run mris_preproc, you specify whether you want thickness, etc.dougRegards,GabrielEl 25/03/13, *Douglas N Greve * gr...@nmr.mgh.harvard.edu escribió:On 03/22/2013 06:45 AM, Gabriel Gonzalez Escamilla wrote: Dear Doug, I've seen that you restore the files to download, for the Xhemi registration. While I'm checking for the statistical process, I've seen that the one I have is: Date: 2012/12/06 16:06:52, Revision: 1.59.2.4, and the one that is on your ftp server is Date: 2012/12/06 16:06:17, Revision: 1.66, So mine is a lower version but recent hour, and the actual is newer version but seems that was created before the one I have. My question is, Which one should I keep?Can you send me a diff of the two files? If I change the mris_precproc version. Shall I re-run this step before statistical analyses, to create a new lh.lh-rh.thickness.sm00.mgh? On the other hand I have some doubts about the statistical procedure. It's supposed that if I apply the Xhemi registration, as result the left and right hemispheres are equals to each other on every subject, so: A) Where can I get the CT values after the Xhemi registration to FSaverage_sym for the left and right hemispheres?what are CT values? B) Given that I have two groups, Patients and Control, with two levels each, i.e male-female (Gp1male Gp1female Gp2male Gp2female Gp1maleVar1 Gp1femaleVar1 Grp2maleVar1 Grp2femaleVar1), and that I can set the contrasts and fsgd files as with a normal CT analisis, but only on my lh.lh-rh.thickness.smXX.mgh, wich is suppose to contain the left-right differences across subjects, right? Wich would be the right interpretation? of:The interpretation does not really change because it is a xhemi analysis 1) 5 .5 -.5 -.5 0 0 0 0Is the L-R difference between Grp1 and Grp2 different than 0 (regressingout Var1 and gender) 2) 5 -.5 .5 -.5 0 0 0 0Is the L-R difference between Males and Females different than 0(regressing out Var1 and Group) 3) 0 0 0 0 .5 .5 -.5 -.5Does the slope of the L-R difference with Var1 differ between Grp1 andGrp2(regressing out gender) 4) 0 0 0 0 5 -.5 .5 -.5Does the slope of the L-R difference with Var1 differ between Male andFemale(regressing out group) Many thanks in advanced. Gabriel.-- Douglas N. Greve, Ph.D.MGH-NMR Centergr...@nmr.mgh.harvard.eduPhone Number: 617-724-2358Fax: 617-726-7422Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReportingFileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.htmlOutgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/___Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurferThe information in this e-mail is intended only for the person to whom it isaddressed. If you believe this e-mail was sent to you in error and the e-mailcontains patient information, please contact the Partners Compliance HelpLine athttp://www.partners.org/complianceline . If the e-mail was sent to you in errorbut does not contain patient information, please contact the sender and properlydispose of the e-mail.-- --PhD. student Gabriel González-EscamillaLaboratory of Functional NeuroscienceDepartment of Physiology, Anatomy, and Cell BiologyUniversity Pablo de OlavideCtra. de Utrera, Km.141013 - Seville- Spain -Email: ggon...@upo.eshttp://www.upo.es/neuroaging/es/ -- Douglas N. Greve, Ph.D.MGH-NMR Centergr...@nmr.mgh.harvard.eduPhone Number: 617-724-2358Fax: 617-726-7422Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReportingFileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.htmlOutgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/-- --PhD. student Gabriel González-EscamillaLaboratory of Functional NeuroscienceDepartment of Physiology, Anatomy, and Cell BiologyUniversity Pablo de OlavideCtra. de Utrera, Km.141013 - Seville- Spain -Email: ggon...@upo.eshttp://www.upo.es/neuroaging/es/ ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu
Re: [Freesurfer] Merging PArcellation labels
it sounds like you want a different parcellation of the lateral prefrontal cortex than what is offered by the default atlas (aparc, AKA the desikan atlas) - I suggest you load in ?h.aparc.a2009s.annot (aka the destrieux atlas) as your annotation in tksurfer and select the annotations of the PFC that you want from there and save as labels. The aparc.a2009 annotation offers a more fine grained parcellation of the PFC - e.g. you can get the DLPFC by merging the middle frontal gyrus middle frontal sulcus parcellations. On Mon, Mar 25, 2013 at 3:19 AM, Anupa AV av.an...@yahoo.com wrote: Dear Laura, Thank you so much. It worked well. Do you know how to make cuts on the merged label, for eg. if I need to seperate DLPFC from premotor cortex. -- *From:* Laura M. Tully tully.la...@googlemail.com *To:* Anupa AV av.an...@yahoo.com *Cc:* freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu *Sent:* Sunday, March 24, 2013 12:20 AM *Subject:* Re: [Freesurfer] Merging PArcellation labels First save each parcellation that you want as its own separate label by selecting it in tksurfer (simply click on it with your mouse and its boarder will be highlighted in yellow) and then file - label - save selected label... Then you can merge these separate labels into one label at the command line using mri_mergelabels -i [labelfile1] -i [labelfile2] -o [newlabelfile.label] If doing glms from the command line you can then feed mri_glmfit the label with the --label option. This will conduct the glm in the region specified in the label only (i.e. an roi analysis) There is also a quick way to turn all of the desikan parcellations into individual label files at the command line using mri_annotation2label I think, but I can't remember precisely. This is a lot faster than using tksurfer as it simply dumps *all* the individual parcellations into a specified output directory. But I don't know if you can do it with the Destrieux atlas parcellations (if you were interested in doing that.) Laura. On Sat, Mar 23, 2013 at 2:36 AM, Anupa AV av.an...@yahoo.com wrote: Dear All, Can anyone tell me how to merge the parcellation labels using tksurfer.? For eg. How can I merge, Superior frontal gyrus, middle frontal gyrus and caudal middle frontal gyrus. ___ 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. -- -- Laura M. Tully, MA Social Neuroscience Psychopathology, Harvard University Center for the Assessment and Prevention of Prodromal States, UCLA Semel Institute of Neuroscience ltu...@mednet.ucla.edu ltu...@fas.harvard.edu 310-267-0170 -- My musings as a young clinical scientist: http://theclinicalbrain.blogspot.com/ Follow me on Twitter: @tully_laura ___ 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. -- -- Laura M. Tully, MA Social Neuroscience Psychopathology, Harvard University Center for the Assessment and Prevention of Prodromal States, UCLA Semel Institute of Neuroscience ltu...@mednet.ucla.edu ltu...@fas.harvard.edu 310-267-0170 -- My musings as a young clinical scientist: http://theclinicalbrain.blogspot.com/ Follow me on Twitter: @tully_laura ___ 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] [Fwd: Segmentation Brush Info]
Ursprüngliche Nachricht Betreff: Segmentation Brush Info Von: Stefanie Scheuchenstuhl scheuchen...@zedat.fu-berlin.de Datum: Mo, März 25, 2013 16:53 An: freesur...@nmr.mgh.harvard.ed -- Dear Freesurfer experts, i have question regarding the segmentation tools. I am currently checking the Hippocampus-Segmentation by using tkmedit and found out that irrespective of what brain area i choose in the Segmentation Brush Info, the corrected area is always labeled Right-Cerebral-WM-unknown. Which was also the first label used when i started. So i ask my self (and you) is this label important for further analysis or not? And if so, how can this error be corrected? Thanks so much! Best, Stefanie ___ 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] Problem with tracula: incomplete or lacking tracts
Hi Anastasia, I ran again trac-all, after checking all bvecs. Some tract are incomplete. Is possible that it depends from an error in my configuration file? I'm using to create bvecs file DTI TABLE CREATOR. Do you advice mi another one? Thanks, Stefano On Fri, 22 Mar 2013, std...@virgilio.it wrote: Thank you Anastasia. I'm checking bvecs/bvals. I obtain it by DTI table creator (http://godzilla.kennedykrieger.org/~jfarrell/OTHERphilips/GUI.html) bvecs/bvals should be done. Gradients can be the unique responsable? Stefano Messaggio originale Da: ayend...@nmr.mgh.harvard.edu Data: 22-mar-2013 17.07 A: std...@virgilio.it Cc: freesurfer@nmr.mgh.harvard.edu Ogg: Re: [Freesurfer] R: Re: R: Re: R: Re: R: R: Re: Problem with tracula: incomplete or lacking tracts Your gradient table is wrong. See where I've marked the corpus callosum in your screenshot. The eigenvectors are not pointing along the corpus callosum, but perpendicular to it. So they're off by 90 degrees, which means the same is true about the vectors in your gradient table. On Fri, 22 Mar 2013, std...@virgilio.it wrote: Hi Anastasia - I attacked the screenshots. Thanks, Stefano Messaggio originale Da: ayend...@nmr.mgh.harvard.edu Data: 22-mar-2013 1.39 A: std...@virgilio.it Cc: freesurfer@nmr.mgh.harvard.edu Ogg: Re: [Freesurfer] R: Re: R: Re: R: R: Re: Problem with tracula: incomplete or lacking tracts Hi Stefano - There's nothing in these screenshots that tells you that the eigenvectors are correct. These are vectors, so the way to check them is to display them as lines. You display dtifit_V1 as lines, overlaid on dtifit_FA. Then you see if the lines point in the right direction. a.y On Fri, 22 Mar 2013, std...@virgilio.it wrote: Here they are attacked. Thanks, Stefano Messaggio originale Da: ayend...@nmr.mgh.harvard.edu Data: 21-mar-2013 21.50 A: std...@virgilio.it Cc: freesurfer@nmr.mgh.harvard.edu Ogg: Re: R: Re: [Freesurfer] R: R: Re: Problem with tracula: incomplete or lacking tracts Can you send a screenshot that shows dtifit_V1 and dtifit_FA? On Thu, 21 Mar 2013, std...@virgilio.it wrote: I have checked the gradient directions. How can I resolve the brain mask problem. Can I send you my files of this subject? Stefano Messaggio originale Da: ayend...@nmr.mgh.harvard.edu Data: 20-mar-2013 22.46 A: std...@virgilio.it Cc: freesurfer@nmr.mgh.harvard.edu Ogg: Re: [Freesurfer] R: R: Re: Problem with tracula: incomplete or lacking tracts There are chunks of the brain missing from the brain mask. This may cause some tracts to be incomplete or missing. But you should still check that the gradient directions are correct, so you know if you have multiple problems or just one. The FA map can't tell you if the gradient table was correct, you have to check the eigenvectors in dtifit_V1 for that. On Wed, 20 Mar 2013, std...@virgilio.it wrote: File attacked Messaggio originale Da: std...@virgilio.it Data: 20-mar-2013 22.34 A: ayend...@nmr.mgh.harvard.edu Cc: freesurfer@nmr.mgh.harvard.edu Ogg: [Freesurfer] R: Re: Problem with tracula: incomplete or lacking tracts Thank you Anastasia. I'm checking gradient table but I would like underline that I'm noting some holes in dti_FA.nii.gz and not in dwi.nii.gz (I have attacked the relative images). Stefano Messaggio originale Da: ayend...@nmr.mgh.harvard.edu Data: 20-mar-2013 16.40 A: std...@virgilio.it Cc: freesurfer@nmr.mgh.harvard.edu Ogg: Re: [Freesurfer] Problem with tracula: incomplete or lacking tracts Hi Stefano - Have you checked that your gradient table is correct by looking at the output of the tensor fit? a.y On Wed, 20 Mar 2013, std...@virgilio.it wrote: Hi list and Anastasia, if you remember the last week I had same problems with tracula output: the final tract are lacking or incomplete for same subjects. Some of these are less wrong (only forceps major), other have more evident error (you can see this in picture that I have attacked). To resolve this issue I have: 1-checked the correct overlap of dwi and dwi_mask 2-rerun data with new version 5.2 3-rerun new registration using bbregister (fsl/spm option): for example, in the subject of the picture attacked, the .mincost file now contains as first value 0.87 (previous it was 1.1) Please, give me an advise Thanks Stefano Messaggio originale Da: std...@virgilio.it
Re: [Freesurfer] problem with registration in preprocessing
The raw images of the last run seems fine. And it is only the last run out of 12. M On Mar 25, 2013, at 10:36 AM, Douglas N Greve gr...@nmr.mgh.harvard.edu wrote: Hi Maryam, I'm not sure what is wrong. Can you check the image in bold/018 to make sure that there is not something horribly wrong? Eg, it is not a localizer or only has one slice. And it is only the last run? The others are ok? doug On 03/22/2013 03:05 PM, Maryam Vaziri Pashkam wrote: Hi Doug, I am running fsfast preprocessing on my data and I am getting an error on one of the runs. This is the preprocessing code that I run: preproc-sess -s 130321_xu_Object4catmulti_01 -per-run -sliceorder siemens -fsd bold -fwhm 0 -mni305-2mm -surface self lhrh The error seems to happen during the fsl registration on the last run (out of 12 runs): /ncf/vcn/Maryam/mri-space/studies/Obj4catmulti/unpackdata/130321_xu_Object4catmulti_01 flirt.fsl -ref bold/018/tmp.bbregister.1228/fslregister/refvol.fslregister.nii -in bold/018/tmp.bbregister.1228/fslregister/movvol.fslregister.nii -bins 256 -cost corratio -dof 6 -searchrx -90 90 -searchry -90 90 -searchrz -90 90 -verbose 0 -omat bold/018/tmp.bbregister.1228/reg.init.dat.fsl.mat -init bold/018/tmp.bbregister.1228/fslregister/fslmat0.trans.mat -schedule /ncf/apps/freesurfer-5.1.0//bin/flirt.newdefault.20080811.sch terminate called after throwing an instance of 'NEWMAT::SingularException' Abort ERROR: flirt bellow is the register-sess log file. I have only included the section for the registration of the last run. I have looked at the raw data of this run and it does not look different from the other runs (all other runs are successfully registered). I am running freesurfer 5.1. Any idea how I can fix the error? Thanks, Maryam $Id: bbregister,v 1.49 2011/03/06 23:38:41 greve Exp $ Linux ncfws08.rc.fas.harvard.edu http://ncfws08.rc.fas.harvard.edu 2.6.18-274.17.1.el5 #1 SMP Tue Jan 10 17:25:58 EST 2012 x86_64 x86_64 x86_64 GNU/Linux FREESURFER_HOME /ncf/apps/freesurfer-5.1.0/ mri_convert bold/018/template.nii.gz bold/018/tmp.bbregister.1228/template.nii mri_convert bold/018/template.nii.gz bold/018/tmp.bbregister.1228/template.nii $Id: mri_convert.c,v 1.179.2.2 2011/05/16 20:53:47 greve Exp $ reading from bold/018/template.nii.gz... TR=2000.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-0.998239, -0.0522464, 0.0280991) j_ras = (0.0500393, -0.995986, -0.0742193) k_ras = (0.031864, -0.0726825, 0.996846) writing to bold/018/tmp.bbregister.1228/template.nii... fslregister --s blue_street_kcb --mov bold/018/tmp.bbregister.1228/template.nii --reg bold/018/tmp.bbregister.1228/reg.init.dat --niters 1 --maxangle 90 --nobetmov --tmp bold/018/tmp.bbregister.1228/fslregister --dof 6 Log file is bold/018/tmp.bbregister.1228/reg.init.dat.fslregister.log Fri Mar 22 14:42:18 EDT 2013 --s blue_street_kcb --mov bold/018/tmp.bbregister.1228/template.nii --reg bold/018/tmp.bbregister.1228/reg.init.dat --niters 1 --maxangle 90 --nobetmov --tmp bold/018/tmp.bbregister.1228/fslregister --dof 6 $Id: fslregister,v 1.34.2.1 2011/03/28 20:35:36 greve Exp $ ncfws08.rc.fas.harvard.edu http://ncfws08.rc.fas.harvard.edu Linux ncfws08.rc.fas.harvard.edu http://ncfws08.rc.fas.harvard.edu 2.6.18-274.17.1.el5 #1 SMP Tue Jan 10 17:25:58 EST 2012 x86_64 x86_64 x86_64 GNU/Linux nIters 1 -- /ncf/vcn/Maryam/mri-space/studies/Obj4catmulti/unpackdata/130321_xu_Object4catmulti_01 mri_convert /ncf/vcn/Maryam/mri-space/subjects/blue_street_kcb/mri/brainmask.mgz bold/018/tmp.bbregister.1228/fslregister/refvol.fslregister.nii mri_convert /ncf/vcn/Maryam/mri-space/subjects/blue_street_kcb/mri/brainmask.mgz bold/018/tmp.bbregister.1228/fslregister/refvol.fslregister.nii $Id: mri_convert.c,v 1.179.2.2 2011/05/16 20:53:47 greve Exp $ reading from /ncf/vcn/Maryam/mri-space/subjects/blue_street_kcb/mri/brainmask.mgz... TR=2530.00, TE=3.45, TI=1100.00, flip angle=7.00 i_ras = (-1, 4.47035e-08, -4.65661e-08) j_ras = (-5.58793e-08, -4.05125e-08, -1) k_ras = (-5.96046e-08, 1, 1.11759e-08) writing to bold/018/tmp.bbregister.1228/fslregister/refvol.fslregister.nii... -- /ncf/vcn/Maryam/mri-space/studies/Obj4catmulti/unpackdata/130321_xu_Object4catmulti_01 mri_convert bold/018/tmp.bbregister.1228/template.nii bold/018/tmp.bbregister.1228/fslregister/movvol.fslregister.nii --frame 0 mri_convert bold/018/tmp.bbregister.1228/template.nii bold/018/tmp.bbregister.1228/fslregister/movvol.fslregister.nii --frame 0 $Id: mri_convert.c,v 1.179.2.2 2011/05/16 20:53:47 greve Exp $ reading from bold/018/tmp.bbregister.1228/template.nii... TR=2000.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-0.998239, -0.0522464, 0.0280991) j_ras = (0.0500393, -0.995986, -0.0742193) k_ras = (0.031864, -0.0726825, 0.996846) keeping frame 0 writing to
Re: [Freesurfer] Xhemi stat questions
Do you mean you want the right hemi thicknesses on the left hemisphere of a given subject or on the fsaverage_sym? doug On 03/25/2013 11:25 AM, Gabriel Gonzalez Escamilla wrote: Thank you, so I'm keeping the one I had. Sorry for my bad explanation. When I do a normal cortical thickness study, I know the average thickness for a label, e.g. cortex, and the values at each vertex of each hemisphere are stored in $subject/surf/?l.thickness. I would like to know if it is possible to obtain the same cortical thickness measure from the lh-rh registered hemispheres of each subject. Regards, Gabriel El 25/03/13, *Douglas N Greve * gr...@nmr.mgh.harvard.edu escribió: On 03/25/2013 10:52 AM, Gabriel Gonzalez Escamilla wrote: Thanks a lot for your answer, I'm sending you attached the diff of the two mris_preproc. Those differences are just added features and won't change your results. When I wrote CT, I was meaning cortical thickness, as normally this values are in surf/?h.thickness, But how do I know the Xhemi-registered thickness values of each subject for lh-rh, or area or any of those indices? I'm not sure what you mean. When you run mris_preproc, you specify whether you want thickness, etc. doug Regards, Gabriel El 25/03/13, *Douglas N Greve * gr...@nmr.mgh.harvard.edu escribió: On 03/22/2013 06:45 AM, Gabriel Gonzalez Escamilla wrote: Dear Doug, I've seen that you restore the files to download, for the Xhemi registration. While I'm checking for the statistical process, I've seen that the one I have is: Date: 2012/12/06 16:06:52, Revision: 1.59.2.4, and the one that is on your ftp server is Date: 2012/12/06 16:06:17, Revision: 1.66, So mine is a lower version but recent hour, and the actual is newer version but seems that was created before the one I have. My question is, Which one should I keep? Can you send me a diff of the two files? If I change the mris_precproc version. Shall I re-run this step before statistical analyses, to create a new lh.lh-rh.thickness.sm00.mgh? On the other hand I have some doubts about the statistical procedure. It's supposed that if I apply the Xhemi registration, as result the left and right hemispheres are equals to each other on every subject, so: A) Where can I get the CT values after the Xhemi registration to FSaverage_sym for the left and right hemispheres? what are CT values? B) Given that I have two groups, Patients and Control, with two levels each, i.e male-female (Gp1male Gp1female Gp2male Gp2female Gp1maleVar1 Gp1femaleVar1 Grp2maleVar1 Grp2femaleVar1), and that I can set the contrasts and fsgd files as with a normal CT analisis, but only on my lh.lh-rh.thickness.smXX.mgh, wich is suppose to contain the left-right differences across subjects, right? Wich would be the right interpretation? of: The interpretation does not really change because it is a xhemi analysis 1) 5 .5 -.5 -.5 0 0 0 0 Is the L-R difference between Grp1 and Grp2 different than 0 (regressing out Var1 and gender) 2) 5 -.5 .5 -.5 0 0 0 0 Is the L-R difference between Males and Females different than 0 (regressing out Var1 and Group) 3) 0 0 0 0 .5 .5 -.5 -.5 Does the slope of the L-R difference with Var1 differ between Grp1 and Grp2(regressing out gender) 4) 0 0 0 0 5 -.5 .5 -.5 Does the slope of the L-R difference with Var1 differ between Male and Female(regressing out group) Many thanks in advanced. Gabriel. -- 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 Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ___ 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. -- -- PhD. student Gabriel González-Escamilla Laboratory of Functional Neuroscience Department of Physiology, Anatomy, and Cell Biology University Pablo de Olavide Ctra. de Utrera, Km.1 41013 - Seville - Spain - Email: ggon...@upo.es http://www.upo.es/neuroaging/es/ -- 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:
Re: [Freesurfer] problem with registration in preprocessing
Can you tar up the subject and the last run and drop it to me on our file drop system? doug On 03/25/2013 12:07 PM, Maryam wrote: The raw images of the last run seems fine. And it is only the last run out of 12. M On Mar 25, 2013, at 10:36 AM, Douglas N Greve gr...@nmr.mgh.harvard.edu wrote: Hi Maryam, I'm not sure what is wrong. Can you check the image in bold/018 to make sure that there is not something horribly wrong? Eg, it is not a localizer or only has one slice. And it is only the last run? The others are ok? doug On 03/22/2013 03:05 PM, Maryam Vaziri Pashkam wrote: Hi Doug, I am running fsfast preprocessing on my data and I am getting an error on one of the runs. This is the preprocessing code that I run: preproc-sess -s 130321_xu_Object4catmulti_01 -per-run -sliceorder siemens -fsd bold -fwhm 0 -mni305-2mm -surface self lhrh The error seems to happen during the fsl registration on the last run (out of 12 runs): /ncf/vcn/Maryam/mri-space/studies/Obj4catmulti/unpackdata/130321_xu_Object4catmulti_01 flirt.fsl -ref bold/018/tmp.bbregister.1228/fslregister/refvol.fslregister.nii -in bold/018/tmp.bbregister.1228/fslregister/movvol.fslregister.nii -bins 256 -cost corratio -dof 6 -searchrx -90 90 -searchry -90 90 -searchrz -90 90 -verbose 0 -omat bold/018/tmp.bbregister.1228/reg.init.dat.fsl.mat -init bold/018/tmp.bbregister.1228/fslregister/fslmat0.trans.mat -schedule /ncf/apps/freesurfer-5.1.0//bin/flirt.newdefault.20080811.sch terminate called after throwing an instance of 'NEWMAT::SingularException' Abort ERROR: flirt bellow is the register-sess log file. I have only included the section for the registration of the last run. I have looked at the raw data of this run and it does not look different from the other runs (all other runs are successfully registered). I am running freesurfer 5.1. Any idea how I can fix the error? Thanks, Maryam $Id: bbregister,v 1.49 2011/03/06 23:38:41 greve Exp $ Linux ncfws08.rc.fas.harvard.edu http://ncfws08.rc.fas.harvard.edu 2.6.18-274.17.1.el5 #1 SMP Tue Jan 10 17:25:58 EST 2012 x86_64 x86_64 x86_64 GNU/Linux FREESURFER_HOME /ncf/apps/freesurfer-5.1.0/ mri_convert bold/018/template.nii.gz bold/018/tmp.bbregister.1228/template.nii mri_convert bold/018/template.nii.gz bold/018/tmp.bbregister.1228/template.nii $Id: mri_convert.c,v 1.179.2.2 2011/05/16 20:53:47 greve Exp $ reading from bold/018/template.nii.gz... TR=2000.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-0.998239, -0.0522464, 0.0280991) j_ras = (0.0500393, -0.995986, -0.0742193) k_ras = (0.031864, -0.0726825, 0.996846) writing to bold/018/tmp.bbregister.1228/template.nii... fslregister --s blue_street_kcb --mov bold/018/tmp.bbregister.1228/template.nii --reg bold/018/tmp.bbregister.1228/reg.init.dat --niters 1 --maxangle 90 --nobetmov --tmp bold/018/tmp.bbregister.1228/fslregister --dof 6 Log file is bold/018/tmp.bbregister.1228/reg.init.dat.fslregister.log Fri Mar 22 14:42:18 EDT 2013 --s blue_street_kcb --mov bold/018/tmp.bbregister.1228/template.nii --reg bold/018/tmp.bbregister.1228/reg.init.dat --niters 1 --maxangle 90 --nobetmov --tmp bold/018/tmp.bbregister.1228/fslregister --dof 6 $Id: fslregister,v 1.34.2.1 2011/03/28 20:35:36 greve Exp $ ncfws08.rc.fas.harvard.edu http://ncfws08.rc.fas.harvard.edu Linux ncfws08.rc.fas.harvard.edu http://ncfws08.rc.fas.harvard.edu 2.6.18-274.17.1.el5 #1 SMP Tue Jan 10 17:25:58 EST 2012 x86_64 x86_64 x86_64 GNU/Linux nIters 1 -- /ncf/vcn/Maryam/mri-space/studies/Obj4catmulti/unpackdata/130321_xu_Object4catmulti_01 mri_convert /ncf/vcn/Maryam/mri-space/subjects/blue_street_kcb/mri/brainmask.mgz bold/018/tmp.bbregister.1228/fslregister/refvol.fslregister.nii mri_convert /ncf/vcn/Maryam/mri-space/subjects/blue_street_kcb/mri/brainmask.mgz bold/018/tmp.bbregister.1228/fslregister/refvol.fslregister.nii $Id: mri_convert.c,v 1.179.2.2 2011/05/16 20:53:47 greve Exp $ reading from /ncf/vcn/Maryam/mri-space/subjects/blue_street_kcb/mri/brainmask.mgz... TR=2530.00, TE=3.45, TI=1100.00, flip angle=7.00 i_ras = (-1, 4.47035e-08, -4.65661e-08) j_ras = (-5.58793e-08, -4.05125e-08, -1) k_ras = (-5.96046e-08, 1, 1.11759e-08) writing to bold/018/tmp.bbregister.1228/fslregister/refvol.fslregister.nii... -- /ncf/vcn/Maryam/mri-space/studies/Obj4catmulti/unpackdata/130321_xu_Object4catmulti_01 mri_convert bold/018/tmp.bbregister.1228/template.nii bold/018/tmp.bbregister.1228/fslregister/movvol.fslregister.nii --frame 0 mri_convert bold/018/tmp.bbregister.1228/template.nii bold/018/tmp.bbregister.1228/fslregister/movvol.fslregister.nii --frame 0 $Id: mri_convert.c,v 1.179.2.2 2011/05/16 20:53:47 greve Exp $ reading from bold/018/tmp.bbregister.1228/template.nii... TR=2000.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-0.998239, -0.0522464, 0.0280991) j_ras =
Re: [Freesurfer] Problem with tracula: incomplete or lacking tracts
Hi Stefano - As I recall, we established that your bvecs were wrong. Did you fix them? a.y On Mon, 25 Mar 2013, std...@virgilio.it wrote: Hi Anastasia, I ran again trac-all, after checking all bvecs. Some tract are incomplete. Is possible that it depends from an error in my configuration file? I'm using to create bvecs file DTI TABLE CREATOR. Do you advice mi another one? Thanks, Stefano On Fri, 22 Mar 2013, std...@virgilio.it wrote: Thank you Anastasia. I'm checking bvecs/bvals. I obtain it by DTI table creator (http://godzilla.kennedykrieger.org/~jfarrell/OTHERphilips/GUI.html) bvecs/bvals should be done. Gradients can be the unique responsable? Stefano Messaggio originale Da: ayend...@nmr.mgh.harvard.edu Data: 22-mar-2013 17.07 A: std...@virgilio.it Cc: freesurfer@nmr.mgh.harvard.edu Ogg: Re: [Freesurfer] R: Re: R: Re: R: Re: R: R: Re: Problem with tracula: incomplete or lacking tracts Your gradient table is wrong. See where I've marked the corpus callosum in your screenshot. The eigenvectors are not pointing along the corpus callosum, but perpendicular to it. So they're off by 90 degrees, which means the same is true about the vectors in your gradient table. On Fri, 22 Mar 2013, std...@virgilio.it wrote: Hi Anastasia - I attacked the screenshots. Thanks, Stefano Messaggio originale Da: ayend...@nmr.mgh.harvard.edu Data: 22-mar-2013 1.39 A: std...@virgilio.it Cc: freesurfer@nmr.mgh.harvard.edu Ogg: Re: [Freesurfer] R: Re: R: Re: R: R: Re: Problem with tracula: incomplete or lacking tracts Hi Stefano - There's nothing in these screenshots that tells you that the eigenvectors are correct. These are vectors, so the way to check them is to display them as lines. You display dtifit_V1 as lines, overlaid on dtifit_FA. Then you see if the lines point in the right direction. a.y On Fri, 22 Mar 2013, std...@virgilio.it wrote: Here they are attacked. Thanks, Stefano Messaggio originale Da: ayend...@nmr.mgh.harvard.edu Data: 21-mar-2013 21.50 A: std...@virgilio.it Cc: freesurfer@nmr.mgh.harvard.edu Ogg: Re: R: Re: [Freesurfer] R: R: Re: Problem with tracula: incomplete or lacking tracts Can you send a screenshot that shows dtifit_V1 and dtifit_FA? On Thu, 21 Mar 2013, std...@virgilio.it wrote: I have checked the gradient directions. How can I resolve the brain mask problem. Can I send you my files of this subject? Stefano Messaggio originale Da: ayend...@nmr.mgh.harvard.edu Data: 20-mar-2013 22.46 A: std...@virgilio.it Cc: freesurfer@nmr.mgh.harvard.edu Ogg: Re: [Freesurfer] R: R: Re: Problem with tracula: incomplete or lacking tracts There are chunks of the brain missing from the brain mask. This may cause some tracts to be incomplete or missing. But you should still check that the gradient directions are correct, so you know if you have multiple problems or just one. The FA map can't tell you if the gradient table was correct, you have to check the eigenvectors in dtifit_V1 for that. On Wed, 20 Mar 2013, std...@virgilio.it wrote: File attacked Messaggio originale Da: std...@virgilio.it Data: 20-mar-2013 22.34 A: ayend...@nmr.mgh.harvard.edu Cc: freesurfer@nmr.mgh.harvard.edu Ogg: [Freesurfer] R: Re: Problem with tracula: incomplete or lacking tracts Thank you Anastasia. I'm checking gradient table but I would like underline that I'm noting some holes in dti_FA.nii.gz and not in dwi.nii.gz (I have attacked the relative images). Stefano Messaggio originale Da: ayend...@nmr.mgh.harvard.edu Data: 20-mar-2013 16.40 A: std...@virgilio.it Cc: freesurfer@nmr.mgh.harvard.edu Ogg: Re: [Freesurfer] Problem with tracula: incomplete or lacking tracts Hi Stefano - Have you checked that your gradient table is correct by looking at the output of the tensor fit? a.y On Wed, 20 Mar 2013, std...@virgilio.it wrote: Hi list and Anastasia, if you remember the last week I had same problems with tracula output: the final tract are lacking or incomplete for same subjects. Some of these are less wrong (only forceps major), other have more evident error (you can see this in picture that I have attacked). To resolve this issue I have: 1-checked the correct overlap of dwi and dwi_mask 2-rerun data with new version 5.2 3-rerun new registration using bbregister (fsl/spm option): for example, in the subject of the picture attacked, the .mincost file now contains as first value 0.87 (previous it was 1.1) Please, give me an advise Thanks
Re: [Freesurfer] Xhemi stat questions
I mean of a given subject, I suppose that on the fsaverage_sym, I would read the lh.lh-rh.thickness.mgh. But, As I'm thinking about this, I'm wondering if it has sense, or if I should obtain the lh-rh thickness differences? Nevertheless, I have no idea how to get any of those measurements.Regards,GabrielEl 25/03/13, Douglas N Greve gr...@nmr.mgh.harvard.edu escribió:Do you mean you want the right hemi thicknesses on the left hemisphere of a given subject or on the fsaverage_sym?dougOn 03/25/2013 11:25 AM, Gabriel Gonzalez Escamilla wrote: Thank you, so I'm keeping the one I had. Sorry for my bad explanation. When I do a normal cortical thickness study, I know the average thickness for a label, e.g. cortex, and the values at each vertex of each hemisphere are stored in $subject/surf/?l.thickness. I would like to know if it is possible to obtain the same cortical thickness measure from the lh-rh registered hemispheres of each subject. Regards, Gabriel El 25/03/13, *Douglas N Greve * gr...@nmr.mgh.harvard.edu escribió: On 03/25/2013 10:52 AM, Gabriel Gonzalez Escamilla wrote: Thanks a lot for your answer, I'm sending you attached the diff of the two mris_preproc. Those differences are just added features and won't change your results. When I wrote CT, I was meaning cortical thickness, as normally this values are in surf/?h.thickness, But how do I know the Xhemi-registered thickness values of each subject for lh-rh, or area or any of those indices? I'm not sure what you mean. When you run mris_preproc, you specify whether you want thickness, etc. doug Regards, Gabriel El 25/03/13, *Douglas N Greve * gr...@nmr.mgh.harvard.edu escribió: On 03/22/2013 06:45 AM, Gabriel Gonzalez Escamilla wrote: Dear Doug, I've seen that you restore the files to download, for the Xhemi registration. While I'm checking for the statistical process, I've seen that the one I have is: Date: 2012/12/06 16:06:52, Revision: 1.59.2.4, and the one that is on your ftp server is Date: 2012/12/06 16:06:17, Revision: 1.66, So mine is a lower version but recent hour, and the actual is newer version but seems that was created before the one I have. My question is, Which one should I keep? Can you send me a diff of the two files? If I change the mris_precproc version. Shall I re-run this step before statistical analyses, to create a new lh.lh-rh.thickness.sm00.mgh? On the other hand I have some doubts about the statistical procedure. It's supposed that if I apply the Xhemi registration, as result the left and right hemispheres are equals to each other on every subject, so: A) Where can I get the CT values after the Xhemi registration to FSaverage_sym for the left and right hemispheres? what are CT values?B) Given that I have two groups, Patients and Control, with two levels each, i.e male-female (Gp1male Gp1female Gp2male Gp2female Gp1maleVar1 Gp1femaleVar1 Grp2maleVar1 Grp2femaleVar1), and that I can set the contrasts and fsgd files as with a normal CT analisis, but only on my lh.lh-rh.thickness.smXX.mgh, wich is suppose to contain the left-right differences across subjects, right? Wich would be the right interpretation? of: The interpretation does not really change because it is a xhemi analysis 1) 5 .5 -.5 -.5 0 0 0 0 Is the L-R difference between Grp1 and Grp2 different than 0 (regressing out Var1 and gender) 2) 5 -.5 .5 -.5 0 0 0 0 Is the L-R difference between Males and Females different than 0 (regressing out Var1 and Group) 3) 0 0 0 0 .5 .5 -.5 -.5 Does the slope of the L-R difference with Var1 differ between Grp1 and Grp2(regressing out gender) 4) 0 0 0 0 5 -.5 .5 -.5 Does the slope of the L-R difference with Var1 differ between Male and Female(regressing out group) Many thanks in advanced. Gabriel. -- 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 Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ___ 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. -- -- PhD. student Gabriel González-Escamilla Laboratory of Functional Neuroscience Department of Physiology, Anatomy, and Cell Biology University Pablo de Olavide Ctra. de Utrera, Km.1 41013 - Seville - Spain - Email: ggon...@upo.es http://www.upo.es/neuroaging/es/
[Freesurfer] ERROR: Help with asegstats2table segmentation error
Could anybody help me with the --segno option during a asegstats2table process. I've run my subjects under recon-all and I am pretty sure the data exists under the stats folder but when I ran: asegstats2table --subjects MysubjectFolderName --tablefile aseg.txt --skip --segno 41 (I've tried it with different segnos a s wellŠ) I got the following error: SUBJECTS_DIR : THE_CORRECT_FOLDER_LOCATION Parsing the .stats files Building the table.. ERROR: cannot find the corresponding segmentation for the id:41 you provided in any of the .stats files parsed Rodrigo Dennis Perea Graduate Research Assistant rpe...@kumc.edu Bioengineering Program Alzheimer's Research Center The University of Kansas On 3/25/13 11:34 AM, freesurfer-requ...@nmr.mgh.harvard.edu freesurfer-requ...@nmr.mgh.harvard.edu wrote: freesurfer@nmr.mgh.harvard.edu ___ 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] bbregister error with hardi data
Hello all, I am attempting to run bbregister on 4D HARDI data that has already been motion, eddy, and epi-distortion corrected in fsl. I run the command: bbregister --s lindsay --mov hardi/ffiltered_func_data_01.nii.gz --dti --init-fsl --reg register.dat and get a number of errors that seem to begin in the mri_convert section as seen below. Any insight? Cheers, Corinna FREESURFER_HOME /usr/local/freesurfer mri_convert hardi/ffiltered_func_data_01.nii.gz ./tmp.bbregister.15356/template.nii mri_convert hardi/ffiltered_func_data_01.nii.gz ./tmp.bbregister.15356/template.nii $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from hardi/ffiltered_func_data_01.nii.gz... TR=17843.91, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-0.991204, -0.025762, 0.129811) j_ras = (-0.0259819, 0.999662, 0) k_ras = (0.129768, 0.00337275, 0.991539) writing to ./tmp.bbregister.15356/template.nii... fslregister --s lindsay --mov ./tmp.bbregister.15356/template.nii --reg ./tmp.bbregister.15356/reg.init.dat --niters 1 --maxangle 90 --nobetmov --tmp ./tmp.bbregister.15356/fslregister --dof 6 --fsvol brainmask Log file is ./tmp.bbregister.15356/reg.init.dat.fslregister.log Mon Mar 25 12:22:23 EDT 2013 --s lindsay --mov ./tmp.bbregister.15356/template.nii --reg ./tmp.bbregister.15356/reg.init.dat --niters 1 --maxangle 90 --nobetmov --tmp ./tmp.bbregister.15356/fslregister --dof 6 --fsvol brainmask $Id: fslregister,v 1.34.2.2 2012/11/08 16:18:56 greve Exp $ lotfi Linux lotfi 3.2.0-38-generic #61-Ubuntu SMP Tue Feb 19 12:18:21 UTC 2013 x86_64 x86_64 x86_64 GNU/Linux nIters 1 -- /usr/local/freesurfer/subjects/symmetry/lindsay mri_convert ERROR: could not determine file for /usr/local/freesurfer/subjects/symmetry/lindsay/mri/ERROR: ./tmp.bbregister.15356/fslregister/refvol.fslregister.nii mri_convert ERROR: could not determine file for /usr/local/freesurfer/subjects/symmetry/lindsay/mri/ERROR: ./tmp.bbregister.15356/fslregister/refvol.fslregister.nii mri_convert: extra arguments (not and following) type mri_convert -u for usage -- /usr/local/freesurfer/subjects/symmetry/lindsay mri_convert ./tmp.bbregister.15356/template.nii ./tmp.bbregister.15356/fslregister/movvol.fslregister.nii --frame 0 mri_convert ./tmp.bbregister.15356/template.nii ./tmp.bbregister.15356/fslregister/movvol.fslregister.nii --frame 0 $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from ./tmp.bbregister.15356/template.nii... TR=17843.91, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-0.991204, -0.025762, 0.129811) j_ras = (-0.0259819, 0.999662, 0) k_ras = (0.129768, 0.00337275, 0.991539) keeping frame 0 writing to ./tmp.bbregister.15356/fslregister/movvol.fslregister.nii... Mov determinant is -6.125 /usr/local/freesurfer/subjects/symmetry/lindsay tkregister2_cmdl --mov ./tmp.bbregister.15356/fslregister/movvol.fslregister.nii --reg ./tmp.bbregister.15356/fslregister/reg0.15393.dat --regheader --fslregout ./tmp.bbregister.15356/reg.init.dat.fsl.mat0 --s lindsay --noedit tkregister_tcl /usr/local/freesurfer/tktools/tkregister2.tcl INFO: no target volume specified, assuming FreeSurfer orig volume. target volume orig movable volume ./tmp.bbregister.15356/fslregister/movvol.fslregister.nii reg file ./tmp.bbregister.15356/fslregister/reg0.15393.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 /usr/local/freesurfer/subjects/symmetry/lindsay/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 ./tmp.bbregister.15356/fslregister/movvol.fslregister.nii Tmov: -1.750 0.000 0.000 112.000; 0.000 0.000 2.000 -60.000; 0.000 -1.750 0.000 112.000; 0.000 0.000 0.000 1.000; mkheaderreg = 1, float2int = 0 Computing reg from header (and possibly input matrix) Input registration matrix (computed) 0.991 0.026 -0.130 2.508; 0.130 0.003 0.992 -30.941; 0.026 -1.000 -0.000 1.279; 0.000 0.000 0.000 1.000; --- Input registration matrix 0.991 0.026 -0.130 2.508; 0.130 0.003 0.992 -30.941; 0.026 -1.000 -0.000 1.279; 0.000 0.000 0.000 1.000; Determinant 1 subject = lindsay RegMat --- 0.991 0.026 -0.130 2.508; 0.130 0.003 0.992 -30.941; 0.026 -1.000 -0.000 1.279; 0.000 0.000 0.000 1.000; FSLOUTPUTTYPE NIFTI tkreg2FSL: mov det = -6.125, ref det = -1 Mon Mar 25 12:22:34 EDT 2013 /usr/local/freesurfer/subjects/symmetry/lindsay flirt.fsl -ref ./tmp.bbregister.15356/fslregister/refvol.fslregister.nii -in ./tmp.bbregister.15356/fslregister/movvol.fslregister.nii -bins 256 -cost corratio -dof 6 -searchrx -90 90 -searchry -90 90 -searchrz -90 90
Re: [Freesurfer] bbregister error with hardi data
Hi Corinna, can you run fslregister --debug --s lindsay --mov hardi/ffiltered_func_data_01.nii.gz --reg fsl.reg.dat --niters 1 --maxangle 90 --nobetmov --tmp ./tmp.fslregister --dof 6 --fsvol brainmask | tee dng.log and send me the dng.log? doug On 03/25/2013 12:39 PM, Corinna Bauer wrote: Hello all, I am attempting to run bbregister on 4D HARDI data that has already been motion, eddy, and epi-distortion corrected in fsl. I run the command: bbregister --s lindsay --mov hardi/ffiltered_func_data_01.nii.gz --dti --init-fsl --reg register.dat and get a number of errors that seem to begin in the mri_convert section as seen below. Any insight? Cheers, Corinna FREESURFER_HOME /usr/local/freesurfer mri_convert hardi/ffiltered_func_data_01.nii.gz ./tmp.bbregister.15356/template.nii mri_convert hardi/ffiltered_func_data_01.nii.gz ./tmp.bbregister.15356/template.nii $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from hardi/ffiltered_func_data_01.nii.gz... TR=17843.91, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-0.991204, -0.025762, 0.129811) j_ras = (-0.0259819, 0.999662, 0) k_ras = (0.129768, 0.00337275, 0.991539) writing to ./tmp.bbregister.15356/template.nii... fslregister --s lindsay --mov ./tmp.bbregister.15356/template.nii --reg ./tmp.bbregister.15356/reg.init.dat --niters 1 --maxangle 90 --nobetmov --tmp ./tmp.bbregister.15356/fslregister --dof 6 --fsvol brainmask Log file is ./tmp.bbregister.15356/reg.init.dat.fslregister.log Mon Mar 25 12:22:23 EDT 2013 --s lindsay --mov ./tmp.bbregister.15356/template.nii --reg ./tmp.bbregister.15356/reg.init.dat --niters 1 --maxangle 90 --nobetmov --tmp ./tmp.bbregister.15356/fslregister --dof 6 --fsvol brainmask $Id: fslregister,v 1.34.2.2 2012/11/08 16:18:56 greve Exp $ lotfi Linux lotfi 3.2.0-38-generic #61-Ubuntu SMP Tue Feb 19 12:18:21 UTC 2013 x86_64 x86_64 x86_64 GNU/Linux nIters 1 -- /usr/local/freesurfer/subjects/symmetry/lindsay mri_convert ERROR: could not determine file for /usr/local/freesurfer/subjects/symmetry/lindsay/mri/ERROR: ./tmp.bbregister.15356/fslregister/refvol.fslregister.nii mri_convert ERROR: could not determine file for /usr/local/freesurfer/subjects/symmetry/lindsay/mri/ERROR: ./tmp.bbregister.15356/fslregister/refvol.fslregister.nii mri_convert: extra arguments (not and following) type mri_convert -u for usage -- /usr/local/freesurfer/subjects/symmetry/lindsay mri_convert ./tmp.bbregister.15356/template.nii ./tmp.bbregister.15356/fslregister/movvol.fslregister.nii --frame 0 mri_convert ./tmp.bbregister.15356/template.nii ./tmp.bbregister.15356/fslregister/movvol.fslregister.nii --frame 0 $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from ./tmp.bbregister.15356/template.nii... TR=17843.91, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-0.991204, -0.025762, 0.129811) j_ras = (-0.0259819, 0.999662, 0) k_ras = (0.129768, 0.00337275, 0.991539) keeping frame 0 writing to ./tmp.bbregister.15356/fslregister/movvol.fslregister.nii... Mov determinant is -6.125 /usr/local/freesurfer/subjects/symmetry/lindsay tkregister2_cmdl --mov ./tmp.bbregister.15356/fslregister/movvol.fslregister.nii --reg ./tmp.bbregister.15356/fslregister/reg0.15393.dat --regheader --fslregout ./tmp.bbregister.15356/reg.init.dat.fsl.mat0 --s lindsay --noedit tkregister_tcl /usr/local/freesurfer/tktools/tkregister2.tcl INFO: no target volume specified, assuming FreeSurfer orig volume. target volume orig movable volume ./tmp.bbregister.15356/fslregister/movvol.fslregister.nii reg file ./tmp.bbregister.15356/fslregister/reg0.15393.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 /usr/local/freesurfer/subjects/symmetry/lindsay/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 ./tmp.bbregister.15356/fslregister/movvol.fslregister.nii Tmov: -1.750 0.000 0.000 112.000; 0.000 0.000 2.000 -60.000; 0.000 -1.750 0.000 112.000; 0.000 0.000 0.000 1.000; mkheaderreg = 1, float2int = 0 Computing reg from header (and possibly input matrix) Input registration matrix (computed) 0.991 0.026 -0.130 2.508; 0.130 0.003 0.992 -30.941; 0.026 -1.000 -0.000 1.279; 0.000 0.000 0.000 1.000; --- Input registration matrix 0.991 0.026 -0.130 2.508; 0.130 0.003 0.992 -30.941; 0.026 -1.000 -0.000 1.279; 0.000 0.000 0.000 1.000; Determinant 1 subject = lindsay RegMat --- 0.991 0.026 -0.130 2.508; 0.130 0.003 0.992
Re: [Freesurfer] ERROR: Help with asegstats2table segmentation error
41 is the code for Right-Cerebral-White-Matter. We do not explicitly represent that in the aseg.stats. Rather, it is rhCorticalWhiteMatter that is stored in the header portion. If you run asegstats2table with any other segno (eg, 17), it will give you 17 plus a lot of global measures. One of those global measures will be rhCorticalWhiteMatter. doug On 03/25/2013 12:38 PM, Rodrigo Perea wrote: Could anybody help me with the --segno option during a asegstats2table process. I've run my subjects under recon-all and I am pretty sure the data exists under the stats folder but when I ran: asegstats2table --subjects MysubjectFolderName --tablefile aseg.txt --skip --segno 41 (I've tried it with different segnos a s wellŠ) I got the following error: SUBJECTS_DIR : THE_CORRECT_FOLDER_LOCATION Parsing the .stats files Building the table.. ERROR: cannot find the corresponding segmentation for the id:41 you provided in any of the .stats files parsed Rodrigo Dennis Perea Graduate Research Assistant rpe...@kumc.edu Bioengineering Program Alzheimer's Research Center The University of Kansas On 3/25/13 11:34 AM, freesurfer-requ...@nmr.mgh.harvard.edu freesurfer-requ...@nmr.mgh.harvard.edu wrote: freesurfer@nmr.mgh.harvard.edu ___ 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 Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ___ 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] Freesurfer Digest, Vol 109, Issue 21
Yes, .4 is probably too high. What is fa_FOLDER-NAME.mask.nii? In your code below, there is no indication of how it was generated. There could be several things going on. One is that the registration is off. Have you check the reg? What is the first value of register.dat.mincost? The second thing is that it could be that the bvects/bvals. Finally, it could be your data that is off. doug On 03/24/2013 07:43 AM, Rotem Saar wrote: Hi Doug, Thanks for your answer. I changed the last step as u suggested, but I think I need to clarify my question: Indeed values of the CC looks OK, but don't u think other values, like the ventricles are too high ? When I first run the script, I got all values and looked the the CC - it looked fine. Then, I wanted to validate with some other regions, just to show that I got the appropriate (low) FA values for regions I don't expect to see high values in - and things looked odd (too high). I remember Bruce also writing me that the values seems a little high, but we didn't further discuss. I read the following this link: http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/MultiModalDtiIndividual The CC has an average FA of about 0.75, gyral parcellations are about 0.4, the left putamen is 0.27, and the ventricle is 0.2. This is as expected because the CC is highly directional with no crossing fibers so we would expect the CC to have the highest FA. The gyral white matter is also directional but has fibers crossing in them, so one expects the FA to be lower than CC. The gray matter (putamen) is still lower. The ventricle has no fibers, so we expect it to have the lowest FA. All my values are above 0.4 Additionally, if in the last step I'm writing --seg /usr/local/freesurfer/subjects/Rotem_try/mri/wmparc.mgz why do I get 182 regions ? in my wmparc.stats I have only 70... I'm probably doing something wrong, but I can't really point to the problem, thus asking for your help. Attached is the table again, Thanks Rotem The values look about right in the table. Your pipeline looks ok, thought the last step uses fa_FOLDER-NAME.mask.nii instead of the output of mri_vol2vol (fa_FOLDER-NAME.nii). doug On 03/17/2013 02:16 AM, Rotem Saar wrote: Hi all, I run into somthing that seems odd to me and wanted to consult - I run the following script for getting the FA values from my DTI scans: 1) dt_recon --i /usr/local/freesurfer/subjects/FOLDER-NAME/DTI/I1.dcm --s FOLDER-NAME --o /usr/local/freesurfer/subjects/FOLDER-NAME/DTI --b /usr/local/freesurfer/subjects/FOLDER-NAME/DTI/bvals.bval /usr/local/freesurfer/subjects/FOLDER-NAME/DTI/bvecs.bvec 2) tkregister2 --s fsaverage --surf white --reg /usr/local/freesurfer/subjects/FOLDER-NAME/DTI/fa-tal.nii.reg --mov /usr/local/freesurfer/subjects/FOLDER-NAME/DTI/fa-tal.nii 3) tkmedit FOLDER-NAME orig.mgz -aux brain.mgz -seg wmparc.mgz -reg /usr/local/freesurfer/subjects/FOLDER-NAME/DTI/register.dat -overlay /usr/local/freesurfer/subjects/FOLDER-NAME/DTI/fa.nii -fthresh 0.2 -fmax 1 4) mri_vol2vol --mov /usr/local/freesurfer/subjects/FOLDER-NAME/DTI/fa.nii --targ /usr/local/freesurfer/subjects/FOLDER-NAME/mri/orig.mgz --s FOLDER-NAME --interp nearest --o /usr/local/freesurfer/subjects/FOLDER-NAME/DTI/fa_FOLDER-NAME.nii --reg /usr/local/freesurfer/subjects/FOLDER-NAME/DTI/register.dat 5) tkregister2 --mov /usr/local/freesurfer/subjects/FOLDER-NAME/DTI/fa_FOLDER-NAME.nii --targ /usr/local/freesurfer/subjects/FOLDER-NAME/mri/orig.mgz --reg /usr/local/freesurfer/subjects/FOLDER-NAME/DTI/fa_FOLDER-NAME.nii.reg 6) mri_segstats --seg /usr/local/freesurfer/subjects/FOLDER-NAME/mri/wmparc.mgz --ctab $FREESURFER_HOME/FreeSurferColorLUT.txt --i /usr/local/freesurfer/subjects/FOLDER-NAME/DTI/fa_FOLDER-NAME.mask.nii --sum /usr/local/freesurfer/subjects/FOLDER-NAME/stats/all_stats_fa_FOLDER-NAME I got a table with all the FA values (see attached), for each segment, but I suspect a problem: I think that the values are too high (I set the threshold to 0.2-1), am I right ? Can u guide me regarding what I can do to solve the problem ? in addition I attached a figure of the corpus-callosum, in which I'm interested - i't seems that the green area in not big enough, is this fixable ? Thanks ! Rotem ___ 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
Re: [Freesurfer] How to get transform matrix from Vertex Index to Vertex RAS
The index is just a number that is an index into a type of lookup table. The lookup table is just the surface, eg, lh.white, which stores the RAS. doug On 03/24/2013 10:01 AM, ZhiLiangLong wrote: Hi all: I am studying the coordinate system transforms within subject across imaging modalities on web page: http://surfer.nmr.mgh.harvard.edu/fswiki/CoordinateSystems. I met a problem. First, i run tksurfer : tksurfer subjectname lh inflated -reg register.dat -ov mov.nii , then i chose a point on the surface and save it. There would be Vertex Index value and Vertex RAS value on the panel of TKSurfer Tool. For example: Vertex Index 96063 Vertex RAS (-56.05 0.42 62.6) Now, i want to know how the values between Vertex Index and Vertex RAS transformed each other. I need help. Best wishes! ___ 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 Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ___ 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] R: Re: Problem with tracula: incomplete or lacking tracts
I also remember that your brain masks had some big chunks of brain missing. Was whatever caused that fixed as well? On Mon, 25 Mar 2013, std...@virgilio.it wrote: Yes, I fix them. I'm attacking the maps after the last trac-all. Stefano Messaggio originale Da: ayend...@nmr.mgh.harvard.edu Data: 25-mar-2013 17.26 A: std...@virgilio.it Cc: freesurfer@nmr.mgh.harvard.edu Ogg: Re: Problem with tracula: incomplete or lacking tracts Hi Stefano - As I recall, we established that your bvecs were wrong. Did you fix them? a.y On Mon, 25 Mar 2013, std...@virgilio.it wrote: Hi Anastasia, I ran again trac-all, after checking all bvecs. Some tract are incomplete. Is possible that it depends from an error in my configuration file? I'm using to create bvecs file DTI TABLE CREATOR. Do you advice mi another one? Thanks, Stefano On Fri, 22 Mar 2013, std...@virgilio.it wrote: Thank you Anastasia. I'm checking bvecs/bvals. I obtain it by DTI table creator (http://godzilla.kennedykrieger.org/~jfarrell/OTHERphilips/GUI.html) bvecs/bvals should be done. Gradients can be the unique responsable? Stefano Messaggio originale Da: ayend...@nmr.mgh.harvard.edu Data: 22-mar-2013 17.07 A: std...@virgilio.it Cc: freesurfer@nmr.mgh.harvard.edu Ogg: Re: [Freesurfer] R: Re: R: Re: R: Re: R: R: Re: Problem with tracula: incomplete or lacking tracts Your gradient table is wrong. See where I've marked the corpus callosum in your screenshot. The eigenvectors are not pointing along the corpus callosum, but perpendicular to it. So they're off by 90 degrees, which means the same is true about the vectors in your gradient table. On Fri, 22 Mar 2013, std...@virgilio.it wrote: Hi Anastasia - I attacked the screenshots. Thanks, Stefano Messaggio originale Da: ayend...@nmr.mgh.harvard.edu Data: 22-mar-2013 1.39 A: std...@virgilio.it Cc: freesurfer@nmr.mgh.harvard.edu Ogg: Re: [Freesurfer] R: Re: R: Re: R: R: Re: Problem with tracula: incomplete or lacking tracts Hi Stefano - There's nothing in these screenshots that tells you that the eigenvectors are correct. These are vectors, so the way to check them is to display them as lines. You display dtifit_V1 as lines, overlaid on dtifit_FA. Then you see if the lines point in the right direction. a.y On Fri, 22 Mar 2013, std...@virgilio.it wrote: Here they are attacked. Thanks, Stefano Messaggio originale Da: ayend...@nmr.mgh.harvard.edu Data: 21-mar-2013 21.50 A: std...@virgilio.it Cc: freesurfer@nmr.mgh.harvard.edu Ogg: Re: R: Re: [Freesurfer] R: R: Re: Problem with tracula: incomplete or lacking tracts Can you send a screenshot that shows dtifit_V1 and dtifit_FA? On Thu, 21 Mar 2013, std...@virgilio.it wrote: I have checked the gradient directions. How can I resolve the brain mask problem. Can I send you my files of this subject? Stefano Messaggio originale Da: ayend...@nmr.mgh.harvard.edu Data: 20-mar-2013 22.46 A: std...@virgilio.it Cc: freesurfer@nmr.mgh.harvard.edu Ogg: Re: [Freesurfer] R: R: Re: Problem with tracula: incomplete or lacking tracts There are chunks of the brain missing from the brain mask. This may cause some tracts to be incomplete or missing. But you should still check that the gradient directions are correct, so you know if you have multiple problems or just one. The FA map can't tell you if the gradient table was correct, you have to check the eigenvectors in dtifit_V1 for that. On Wed, 20 Mar 2013, std...@virgilio.it wrote: File attacked Messaggio originale Da: std...@virgilio.it Data: 20-mar-2013 22.34 A: ayend...@nmr.mgh.harvard.edu Cc: freesurfer@nmr.mgh.harvard.edu Ogg: [Freesurfer] R: Re: Problem with tracula: incomplete or lacking tracts Thank you Anastasia. I'm checking gradient table but I would like underline that I'm noting some holes in dti_FA.nii.gz and not in dwi.nii.gz (I have attacked the relative images). Stefano Messaggio originale Da: ayend...@nmr.mgh.harvard.edu Data: 20-mar-2013 16.40 A: std...@virgilio.it Cc: freesurfer@nmr.mgh.harvard.edu Ogg: Re: [Freesurfer] Problem with tracula: incomplete or lacking tracts Hi Stefano - Have you checked that your gradient table is correct by looking at the output of the tensor fit? a.y On Wed, 20 Mar 2013, std...@virgilio.it wrote: Hi list and Anastasia, if you remember the last week I had same problems with tracula output: the final tract are lacking or
Re: [Freesurfer] Freesurfer Digest, Vol 109, Issue 21
ps. you are getting 182 segs because that's how many there are in wmparc; it includes cortical and subortical gray. You don't get that many in wmparc.stats because we only report WM structures. doug On 03/25/2013 12:59 PM, Douglas N Greve wrote: Yes, .4 is probably too high. What is fa_FOLDER-NAME.mask.nii? In your code below, there is no indication of how it was generated. There could be several things going on. One is that the registration is off. Have you check the reg? What is the first value of register.dat.mincost? The second thing is that it could be that the bvects/bvals. Finally, it could be your data that is off. doug On 03/24/2013 07:43 AM, Rotem Saar wrote: Hi Doug, Thanks for your answer. I changed the last step as u suggested, but I think I need to clarify my question: Indeed values of the CC looks OK, but don't u think other values, like the ventricles are too high ? When I first run the script, I got all values and looked the the CC - it looked fine. Then, I wanted to validate with some other regions, just to show that I got the appropriate (low) FA values for regions I don't expect to see high values in - and things looked odd (too high). I remember Bruce also writing me that the values seems a little high, but we didn't further discuss. I read the following this link: http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/MultiModalDtiIndividual The CC has an average FA of about 0.75, gyral parcellations are about 0.4, the left putamen is 0.27, and the ventricle is 0.2. This is as expected because the CC is highly directional with no crossing fibers so we would expect the CC to have the highest FA. The gyral white matter is also directional but has fibers crossing in them, so one expects the FA to be lower than CC. The gray matter (putamen) is still lower. The ventricle has no fibers, so we expect it to have the lowest FA. All my values are above 0.4 Additionally, if in the last step I'm writing --seg /usr/local/freesurfer/subjects/Rotem_try/mri/wmparc.mgz why do I get 182 regions ? in my wmparc.stats I have only 70... I'm probably doing something wrong, but I can't really point to the problem, thus asking for your help. Attached is the table again, Thanks Rotem The values look about right in the table. Your pipeline looks ok, thought the last step uses fa_FOLDER-NAME.mask.nii instead of the output of mri_vol2vol (fa_FOLDER-NAME.nii). doug On 03/17/2013 02:16 AM, Rotem Saar wrote: Hi all, I run into somthing that seems odd to me and wanted to consult - I run the following script for getting the FA values from my DTI scans: 1) dt_recon --i /usr/local/freesurfer/subjects/FOLDER-NAME/DTI/I1.dcm --s FOLDER-NAME --o /usr/local/freesurfer/subjects/FOLDER-NAME/DTI --b /usr/local/freesurfer/subjects/FOLDER-NAME/DTI/bvals.bval /usr/local/freesurfer/subjects/FOLDER-NAME/DTI/bvecs.bvec 2) tkregister2 --s fsaverage --surf white --reg /usr/local/freesurfer/subjects/FOLDER-NAME/DTI/fa-tal.nii.reg --mov /usr/local/freesurfer/subjects/FOLDER-NAME/DTI/fa-tal.nii 3) tkmedit FOLDER-NAME orig.mgz -aux brain.mgz -seg wmparc.mgz -reg /usr/local/freesurfer/subjects/FOLDER-NAME/DTI/register.dat -overlay /usr/local/freesurfer/subjects/FOLDER-NAME/DTI/fa.nii -fthresh 0.2 -fmax 1 4) mri_vol2vol --mov /usr/local/freesurfer/subjects/FOLDER-NAME/DTI/fa.nii --targ /usr/local/freesurfer/subjects/FOLDER-NAME/mri/orig.mgz --s FOLDER-NAME --interp nearest --o /usr/local/freesurfer/subjects/FOLDER-NAME/DTI/fa_FOLDER-NAME.nii --reg /usr/local/freesurfer/subjects/FOLDER-NAME/DTI/register.dat 5) tkregister2 --mov /usr/local/freesurfer/subjects/FOLDER-NAME/DTI/fa_FOLDER-NAME.nii --targ /usr/local/freesurfer/subjects/FOLDER-NAME/mri/orig.mgz --reg /usr/local/freesurfer/subjects/FOLDER-NAME/DTI/fa_FOLDER-NAME.nii.reg 6) mri_segstats --seg /usr/local/freesurfer/subjects/FOLDER-NAME/mri/wmparc.mgz --ctab $FREESURFER_HOME/FreeSurferColorLUT.txt --i /usr/local/freesurfer/subjects/FOLDER-NAME/DTI/fa_FOLDER-NAME.mask.nii --sum /usr/local/freesurfer/subjects/FOLDER-NAME/stats/all_stats_fa_FOLDER-NAME I got a table with all the FA values (see attached), for each segment, but I suspect a problem: I think that the values are too high (I set the threshold to 0.2-1), am I right ? Can u guide me regarding what I can do to solve the problem ? in addition I attached a figure of the corpus-callosum, in which I'm interested - i't seems that the green area in not big enough, is this
Re: [Freesurfer] bbregister error with hardi data
Can you verify that /usr/local/freesurfer/subjects/symmetry/lindsay/mri/brainmask.mgz exists? doug On 03/25/2013 12:55 PM, Corinna Bauer wrote: sure. Here is the dng.log. Corinna On Mon, Mar 25, 2013 at 12:45 PM, Douglas N Greve gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu wrote: Hi Corinna, can you run fslregister --debug --s lindsay --mov hardi/ffiltered_func_data_01.nii.gz --reg fsl.reg.dat --niters 1 --maxangle 90 --nobetmov --tmp ./tmp.fslregister --dof 6 --fsvol brainmask | tee dng.log and send me the dng.log? doug On 03/25/2013 12:39 PM, Corinna Bauer wrote: Hello all, I am attempting to run bbregister on 4D HARDI data that has already been motion, eddy, and epi-distortion corrected in fsl. I run the command: bbregister --s lindsay --mov hardi/ffiltered_func_data_01.nii.gz --dti --init-fsl --reg register.dat and get a number of errors that seem to begin in the mri_convert section as seen below. Any insight? Cheers, Corinna FREESURFER_HOME /usr/local/freesurfer mri_convert hardi/ffiltered_func_data_01.nii.gz ./tmp.bbregister.15356/template.nii mri_convert hardi/ffiltered_func_data_01.nii.gz ./tmp.bbregister.15356/template.nii $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from hardi/ffiltered_func_data_01.nii.gz... TR=17843.91, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-0.991204, -0.025762, 0.129811) j_ras = (-0.0259819, 0.999662, 0) k_ras = (0.129768, 0.00337275, 0.991539) writing to ./tmp.bbregister.15356/template.nii... fslregister --s lindsay --mov ./tmp.bbregister.15356/template.nii --reg ./tmp.bbregister.15356/reg.init.dat --niters 1 --maxangle 90 --nobetmov --tmp ./tmp.bbregister.15356/fslregister --dof 6 --fsvol brainmask Log file is ./tmp.bbregister.15356/reg.init.dat.fslregister.log Mon Mar 25 12:22:23 EDT 2013 --s lindsay --mov ./tmp.bbregister.15356/template.nii --reg ./tmp.bbregister.15356/reg.init.dat --niters 1 --maxangle 90 --nobetmov --tmp ./tmp.bbregister.15356/fslregister --dof 6 --fsvol brainmask $Id: fslregister,v 1.34.2.2 2012/11/08 16:18:56 greve Exp $ lotfi Linux lotfi 3.2.0-38-generic #61-Ubuntu SMP Tue Feb 19 12:18:21 UTC 2013 x86_64 x86_64 x86_64 GNU/Linux nIters 1 -- /usr/local/freesurfer/subjects/symmetry/lindsay mri_convert ERROR: could not determine file for /usr/local/freesurfer/subjects/symmetry/lindsay/mri/ERROR: ./tmp.bbregister.15356/fslregister/refvol.fslregister.nii mri_convert ERROR: could not determine file for /usr/local/freesurfer/subjects/symmetry/lindsay/mri/ERROR: ./tmp.bbregister.15356/fslregister/refvol.fslregister.nii mri_convert: extra arguments (not and following) type mri_convert -u for usage -- /usr/local/freesurfer/subjects/symmetry/lindsay mri_convert ./tmp.bbregister.15356/template.nii ./tmp.bbregister.15356/fslregister/movvol.fslregister.nii --frame 0 mri_convert ./tmp.bbregister.15356/template.nii ./tmp.bbregister.15356/fslregister/movvol.fslregister.nii --frame 0 $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from ./tmp.bbregister.15356/template.nii... TR=17843.91, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-0.991204, -0.025762, 0.129811) j_ras = (-0.0259819, 0.999662, 0) k_ras = (0.129768, 0.00337275, 0.991539) keeping frame 0 writing to ./tmp.bbregister.15356/fslregister/movvol.fslregister.nii... Mov determinant is -6.125 /usr/local/freesurfer/subjects/symmetry/lindsay tkregister2_cmdl --mov ./tmp.bbregister.15356/fslregister/movvol.fslregister.nii --reg ./tmp.bbregister.15356/fslregister/reg0.15393.dat --regheader --fslregout ./tmp.bbregister.15356/reg.init.dat.fsl.mat0 --s lindsay --noedit tkregister_tcl /usr/local/freesurfer/tktools/tkregister2.tcl INFO: no target volume specified, assuming FreeSurfer orig volume. target volume orig movable volume ./tmp.bbregister.15356/fslregister/movvol.fslregister.nii reg file ./tmp.bbregister.15356/fslregister/reg0.15393.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 /usr/local/freesurfer/subjects/symmetry/lindsay/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
Re: [Freesurfer] bbregister error with hardi data
yes, this file exists. On Mon, Mar 25, 2013 at 1:10 PM, Douglas N Greve gr...@nmr.mgh.harvard.eduwrote: Can you verify that /usr/local/freesurfer/**subjects/symmetry/lindsay/mri/**brainmask.mgz exists? doug On 03/25/2013 12:55 PM, Corinna Bauer wrote: sure. Here is the dng.log. Corinna On Mon, Mar 25, 2013 at 12:45 PM, Douglas N Greve gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.**edugr...@nmr.mgh.harvard.edu wrote: Hi Corinna, can you run fslregister --debug --s lindsay --mov hardi/ffiltered_func_data_01.**nii.gz --reg fsl.reg.dat --niters 1 --maxangle 90 --nobetmov --tmp ./tmp.fslregister --dof 6 --fsvol brainmask | tee dng.log and send me the dng.log? doug On 03/25/2013 12:39 PM, Corinna Bauer wrote: Hello all, I am attempting to run bbregister on 4D HARDI data that has already been motion, eddy, and epi-distortion corrected in fsl. I run the command: bbregister --s lindsay --mov hardi/ffiltered_func_data_01.**nii.gz --dti --init-fsl --reg register.dat and get a number of errors that seem to begin in the mri_convert section as seen below. Any insight? Cheers, Corinna FREESURFER_HOME /usr/local/freesurfer mri_convert hardi/ffiltered_func_data_01.**nii.gz ./tmp.bbregister.15356/**template.nii mri_convert hardi/ffiltered_func_data_01.**nii.gz ./tmp.bbregister.15356/**template.nii $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from hardi/ffiltered_func_data_01.**nii.gz... TR=17843.91, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-0.991204, -0.025762, 0.129811) j_ras = (-0.0259819, 0.999662, 0) k_ras = (0.129768, 0.00337275, 0.991539) writing to ./tmp.bbregister.15356/**template.nii... fslregister --s lindsay --mov ./tmp.bbregister.15356/**template.nii --reg ./tmp.bbregister.15356/reg.**init.dat --niters 1 --maxangle 90 --nobetmov --tmp ./tmp.bbregister.15356/**fslregister --dof 6 --fsvol brainmask Log file is ./tmp.bbregister.15356/reg.**init.dat.fslregister.log Mon Mar 25 12:22:23 EDT 2013 --s lindsay --mov ./tmp.bbregister.15356/**template.nii --reg ./tmp.bbregister.15356/reg.**init.dat --niters 1 --maxangle 90 --nobetmov --tmp ./tmp.bbregister.15356/**fslregister --dof 6 --fsvol brainmask $Id: fslregister,v 1.34.2.2 2012/11/08 16:18:56 greve Exp $ lotfi Linux lotfi 3.2.0-38-generic #61-Ubuntu SMP Tue Feb 19 12:18:21 UTC 2013 x86_64 x86_64 x86_64 GNU/Linux nIters 1 --** /usr/local/freesurfer/**subjects/symmetry/lindsay mri_convert ERROR: could not determine file for /usr/local/freesurfer/**subjects/symmetry/lindsay/mri/**ERROR: ./tmp.bbregister.15356/**fslregister/refvol.**fslregister.nii mri_convert ERROR: could not determine file for /usr/local/freesurfer/**subjects/symmetry/lindsay/mri/**ERROR: ./tmp.bbregister.15356/**fslregister/refvol.**fslregister.nii mri_convert: extra arguments (not and following) type mri_convert -u for usage --** /usr/local/freesurfer/**subjects/symmetry/lindsay mri_convert ./tmp.bbregister.15356/**template.nii ./tmp.bbregister.15356/**fslregister/movvol.**fslregister.nii --frame 0 mri_convert ./tmp.bbregister.15356/**template.nii ./tmp.bbregister.15356/**fslregister/movvol.**fslregister.nii --frame 0 $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from ./tmp.bbregister.15356/**template.nii... TR=17843.91, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-0.991204, -0.025762, 0.129811) j_ras = (-0.0259819, 0.999662, 0) k_ras = (0.129768, 0.00337275, 0.991539) keeping frame 0 writing to ./tmp.bbregister.15356/**fslregister/movvol.**fslregister.nii... Mov determinant is -6.125 /usr/local/freesurfer/**subjects/symmetry/lindsay tkregister2_cmdl --mov ./tmp.bbregister.15356/**fslregister/movvol.**fslregister.nii --reg ./tmp.bbregister.15356/**fslregister/reg0.15393.dat --regheader --fslregout ./tmp.bbregister.15356/reg.**init.dat.fsl.mat0 --s lindsay --noedit tkregister_tcl /usr/local/freesurfer/tktools/**tkregister2.tcl INFO: no target volume specified, assuming FreeSurfer orig volume. target volume orig movable volume ./tmp.bbregister.15356/**fslregister/movvol.**fslregister.nii reg file ./tmp.bbregister.15356/**fslregister/reg0.15393.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 /usr/local/freesurfer/**subjects/symmetry/lindsay/mri/**orig.mgz Ttarg:
[Freesurfer] Fwd: Brodmann area thickness, surface area and volume
Hello list! Any suggestions on what I may be doing wrong? Thanks! Andreia - Mensagem encaminhada de _andre...@sapo.pt - Data: Sun, 24 Mar 2013 19:11:13 + De: _andre...@sapo.pt Assunto: Re: [Freesurfer] Brodmann area thickness, surface area and volume Para: Anastasia Yendiki ayend...@nmr.mgh.harvard.edu, freesurfer freesurfer@nmr.mgh.harvard.edu Cc: Bruce Fischl fis...@nmr.mgh.harvard.edu Hi all, I want to study Brodmann Areas cortical thickness, surface area and volume. I've added the 5.2 BAxxx.threshold.label to my 5.0 fsaverage and run the recon-all BA labels command. Now I run aparcstats2table and get a table with the values but they are the same as before running the BAxxx.threshold.label. So, everything is working but the values haven't changed. Am I missing something? Do I need to run any other command so to the threshold have effect? Andreia Quoting Anastasia Yendiki ayend...@nmr.mgh.harvard.edu: Sounds like centos4 is probably the safest bet for you, although you should ask the list this question. Sorry, I don't know what values you want to get in a table. On Sat, 23 Mar 2013, _andre...@sapo.pt wrote: Ah ok! Anyway, I'm thinking of working with 5.2, should I download the version for centOS 4 then? After running the new BAxxx.thresh.label files how can I get the values in a table? Quoting Anastasia Yendiki ayend...@nmr.mgh.harvard.edu: It doesn't matter. You just need to use those .label files from the fsaverage directory in the 5.2 distritbution. You don't need to run any of the executables from the 5.2 distribution. On Sat, 23 Mar 2013, _andre...@sapo.pt wrote: I'm using Centos5, which file should I download? The one for CentOS 6 or 4? Quoting Anastasia Yendiki ayend...@nmr.mgh.harvard.edu: You'll need to go to the section of recon-all.log under the heading BA labels. You'll need to rerun the commands in that section, but instead of using the BAxxx.label files, us the BAxxx.thresh.label files, which you'll find in the fsaverage subject dir in the 5.2 distribution. On Sat, 23 Mar 2013, _andre...@sapo.pt wrote: Hello Anastasia, How should I proceed to get the different BAs measures output with FS 5.0? Thank you very much! Andreia Quoting Anastasia Yendiki ayend...@nmr.mgh.harvard.edu: The thresholded labels are in the 5.2 version of fsaverage under: $FREESURFER_HOME/subjects/fsaverage/label/*.thresh.label On Sat, 23 Mar 2013, Bruce Fischl wrote: Anastasia? On Sat, 23 Mar 2013, _andre...@sapo.pt wrote: Ok, that was my guess... I am running against a deadline, any news on automatically computing the correct threshold script? Will I be able to use it in 5.0? Thanks you! Andreia Quoting Bruce Fischl fis...@nmr.mgh.harvard.edu: yes. Surface area will be the affected much more than thickness (and volume of course scales with area) On Fri, 22 Mar 2013, _andre...@sapo.pt wrote: Hi Bruce, Thank you for the quick response! In the meanwhile, does that also apply to cortical thickness and volume? Thank you! Andreia Quoting Bruce Fischl fis...@nmr.mgh.harvard.edu: Hi Andreia the issue is that the BA labels contain every point that has any non-zero probability (no matter how small!) of being in that label. So the total label area is almost certainly always bigger than theactual BA. Anastasia has some scripts for automatically computing the correct threshold, and I believe she and Nick integrated them into 5.2 so that the stats are computed both thresholded and unthresholded, hopefully they can comment. Bruce On Fri, 22 Mar 2013, _andre...@sapo.pt wrote: Hi all, I'm using FS 5.0 and some time ago I was told by Bruce that I had to threshold the BA in order to have an approximate areawhen overlaying in the inflated surface. To get surface area values Ialso need touse the label_area and put a
Re: [Freesurfer] Fwd: Brodmann area thickness, surface area and volume
Hi Andreia - What you're rerunning is using BAxxx.label instead of BAxxx.thresh.label. So of course the results will be the same as before you copied over the BAxxx.thresh.label files, b/c these new files aren't being used in 5.0. You'll need to find the BA labels section in recon-all.log and rerun those commands yourself, changing every BAxxx.label to BAxxx.thresh.label. Hope this helps, a.y On Mon, 25 Mar 2013, _andre...@sapo.pt wrote: Hello list! Any suggestions on what I may be doing wrong? Thanks! Andreia - Mensagem encaminhada de _andre...@sapo.pt - Data: Sun, 24 Mar 2013 19:11:13 + De: _andre...@sapo.pt Assunto: Re: [Freesurfer] Brodmann area thickness, surface area and volume Para: Anastasia Yendiki ayend...@nmr.mgh.harvard.edu, freesurfer freesurfer@nmr.mgh.harvard.edu Cc: Bruce Fischl fis...@nmr.mgh.harvard.edu Hi all, I want to study Brodmann Areas cortical thickness, surface area and volume. I've added the 5.2 BAxxx.threshold.label to my 5.0 fsaverage and run the recon-all BA labels command. Now I run aparcstats2table and get a table with the values but they are the same as before running the BAxxx.threshold.label. So, everything is working but the values haven't changed. Am I missing something? Do I need to run any other command so to the threshold have effect? Andreia Quoting Anastasia Yendiki ayend...@nmr.mgh.harvard.edu: Sounds like centos4 is probably the safest bet for you, although you should ask the list this question. Sorry, I don't know what values you want to get in a table. On Sat, 23 Mar 2013, _andre...@sapo.pt wrote: Ah ok! Anyway, I'm thinking of working with 5.2, should I download the version for centOS 4 then? After running the new BAxxx.thresh.label files how can I get the values in a table? Quoting Anastasia Yendiki ayend...@nmr.mgh.harvard.edu: It doesn't matter. You just need to use those .label files from the fsaverage directory in the 5.2 distritbution. You don't need to run any of the executables from the 5.2 distribution. On Sat, 23 Mar 2013, _andre...@sapo.pt wrote: I'm using Centos5, which file should I download? The one for CentOS 6 or 4? Quoting Anastasia Yendiki ayend...@nmr.mgh.harvard.edu: You'll need to go to the section of recon-all.log under the heading BA labels. You'll need to rerun the commands in that section, but instead of using the BAxxx.label files, us the BAxxx.thresh.label files, which you'll find in the fsaverage subject dir in the 5.2 distribution. On Sat, 23 Mar 2013, _andre...@sapo.pt wrote: Hello Anastasia, How should I proceed to get the different BAs measures output with FS 5.0? Thank you very much! Andreia Quoting Anastasia Yendiki ayend...@nmr.mgh.harvard.edu: The thresholded labels are in the 5.2 version of fsaverage under: $FREESURFER_HOME/subjects/fsaverage/label/*.thresh.label On Sat, 23 Mar 2013, Bruce Fischl wrote: Anastasia? On Sat, 23 Mar 2013, _andre...@sapo.pt wrote: Ok, that was my guess... I am running against a deadline, any news on automatically computing the correct threshold script? Will I be able to use it in 5.0? Thanks you! Andreia Quoting Bruce Fischl fis...@nmr.mgh.harvard.edu: yes. Surface area will be the affected much more than thickness (and volume of course scales with area) On Fri, 22 Mar 2013, _andre...@sapo.pt wrote: Hi Bruce, Thank you for the quick response! In the meanwhile, does that also apply to cortical thickness and volume? Thank you! Andreia Quoting Bruce Fischl fis...@nmr.mgh.harvard.edu: Hi Andreia the issue is that the BA labels contain every point that has any non-zero probability (no matter how small!) of being in that label. So the total label area is almost certainly always bigger than theactual BA. Anastasia has some scripts for automatically computing the correct threshold, and I believe she and Nick integrated them into 5.2 so that the stats are computed both thresholded and unthresholded, hopefully they can comment. Bruce On Fri, 22 Mar 2013, _andre...@sapo.pt wrote: Hi all, I'm using FS 5.0 and some time ago I was told by Bruce that I had to threshold the BA in order to have an approximate areawhen overlaying in the inflated surface. To get surface area values Ialso need touse the label_area
Re: [Freesurfer] bbregister error with hardi data
Corinna, can you edit $FREESURFER_HOME/bin/bbregister? If so, change the following line From set cmd = (fslregister --s $subject --mov $regvol --reg $InitReg \ --niters 1 --maxangle 90 --tmp $tmpdir/fslregister \ --dof $FSLDOF --fsvol $fsvol) To set cmd = (fslregister --s $subject --mov $regvol --reg $InitReg \ --niters 1 --maxangle 90 --tmp $tmpdir/fslregister \ --dof $FSLDOF --fsvol $fsvol.mgz) It is just the very last part that is changed where I added .mgz to $fsvol Re-run bbregister and let me know if this works. doug On 03/25/2013 01:11 PM, Corinna Bauer wrote: yes, this file exists. On Mon, Mar 25, 2013 at 1:10 PM, Douglas N Greve gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu wrote: Can you verify that /usr/local/freesurfer/subjects/symmetry/lindsay/mri/brainmask.mgz exists? doug On 03/25/2013 12:55 PM, Corinna Bauer wrote: sure. Here is the dng.log. Corinna On Mon, Mar 25, 2013 at 12:45 PM, Douglas N Greve gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu wrote: Hi Corinna, can you run fslregister --debug --s lindsay --mov hardi/ffiltered_func_data_01.nii.gz --reg fsl.reg.dat --niters 1 --maxangle 90 --nobetmov --tmp ./tmp.fslregister --dof 6 --fsvol brainmask | tee dng.log and send me the dng.log? doug On 03/25/2013 12:39 PM, Corinna Bauer wrote: Hello all, I am attempting to run bbregister on 4D HARDI data that has already been motion, eddy, and epi-distortion corrected in fsl. I run the command: bbregister --s lindsay --mov hardi/ffiltered_func_data_01.nii.gz --dti --init-fsl --reg register.dat and get a number of errors that seem to begin in the mri_convert section as seen below. Any insight? Cheers, Corinna FREESURFER_HOME /usr/local/freesurfer mri_convert hardi/ffiltered_func_data_01.nii.gz ./tmp.bbregister.15356/template.nii mri_convert hardi/ffiltered_func_data_01.nii.gz ./tmp.bbregister.15356/template.nii $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from hardi/ffiltered_func_data_01.nii.gz... TR=17843.91, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-0.991204, -0.025762, 0.129811) j_ras = (-0.0259819, 0.999662, 0) k_ras = (0.129768, 0.00337275, 0.991539) writing to ./tmp.bbregister.15356/template.nii... fslregister --s lindsay --mov ./tmp.bbregister.15356/template.nii --reg ./tmp.bbregister.15356/reg.init.dat --niters 1 --maxangle 90 --nobetmov --tmp ./tmp.bbregister.15356/fslregister --dof 6 --fsvol brainmask Log file is ./tmp.bbregister.15356/reg.init.dat.fslregister.log Mon Mar 25 12:22:23 EDT 2013 --s lindsay --mov ./tmp.bbregister.15356/template.nii --reg ./tmp.bbregister.15356/reg.init.dat --niters 1 --maxangle 90 --nobetmov --tmp ./tmp.bbregister.15356/fslregister --dof 6 --fsvol brainmask $Id: fslregister,v 1.34.2.2 2012/11/08 16:18:56 greve Exp $ lotfi Linux lotfi 3.2.0-38-generic #61-Ubuntu SMP Tue Feb 19 12:18:21 UTC 2013 x86_64 x86_64 x86_64 GNU/Linux nIters 1 -- /usr/local/freesurfer/subjects/symmetry/lindsay mri_convert ERROR: could not determine file for /usr/local/freesurfer/subjects/symmetry/lindsay/mri/ERROR: ./tmp.bbregister.15356/fslregister/refvol.fslregister.nii mri_convert ERROR: could not determine file for /usr/local/freesurfer/subjects/symmetry/lindsay/mri/ERROR: ./tmp.bbregister.15356/fslregister/refvol.fslregister.nii mri_convert: extra arguments (not and following) type mri_convert -u for usage -- /usr/local/freesurfer/subjects/symmetry/lindsay mri_convert ./tmp.bbregister.15356/template.nii ./tmp.bbregister.15356/fslregister/movvol.fslregister.nii --frame 0 mri_convert ./tmp.bbregister.15356/template.nii
Re: [Freesurfer] Fwd: Brodmann area thickness, surface area and volume
Hi Anastasia! The command in the recon-all.log is this one: mri_label2label --srcsubject fsaverage --srclabel /home/user/visao/Freesurfer/fsaverage/label/rh.BA1.label --trgsubject SUSANAFERREIRA --trglabel ./rh.BA1.label --hemi rh --regmethod surface And I tried substituing BAxxx.label by BAxxx.thresh.label like this: mri_label2label --srcsubject fsaverage --srclabel /home/user/visao/Freesurfer/fsaverage/label/_lh.BA1.threshold.label_--trgsubject SUSANAFERREIRA --trglabel ._/lh.BA1.thresolh.label_ --hemi lh --regmethod surface gave an error : SUBJECTS_DIR /home/user/visao/Freesurfer/ FREESURFER_HOME /usr/local/freesurfer Loading source label. No such file or directory mri_label2label: could not open label file /home/user/visao/Freesurfer/fsaverage/label/lh.BA1.threshold.label Illegal seek ERROR reading /home/user/visao/Freesurfer/fsaverage/label/lh.BA1.threshold.label Thus, I substitued only in the second BAxxx.label and it worked. I thought that was it, but then the values were the same. I'm sorry, I'm not sure what is missing. Thank you! Andreia Quoting Anastasia Yendiki ayend...@nmr.mgh.harvard.edu: Hi Andreia - What you're rerunning is using BAxxx.label instead of BAxxx.thresh.label. So of course the results will be the same as before you copied over the BAxxx.thresh.label files, b/c these new files aren't being used in 5.0. You'll need to find the BA labels section in recon-all.log and rerun those commands yourself, changing every BAxxx.label to BAxxx.thresh.label. Hope this helps, a.y On Mon, 25 Mar 2013, _andre...@sapo.pt wrote: Hello list! Any suggestions on what I may be doing wrong? Thanks! Andreia - Mensagem encaminhada de _andre...@sapo.pt - Data: Sun, 24 Mar 2013 19:11:13 + De: _andre...@sapo.pt Assunto: Re: [Freesurfer] Brodmann area thickness, surface area and volume Para: Anastasia Yendiki ayend...@nmr.mgh.harvard.edu, freesurfer freesurfer@nmr.mgh.harvard.edu Cc: Bruce Fischl fis...@nmr.mgh.harvard.edu Hi all, I want to study Brodmann Areas cortical thickness, surface area and volume. I've added the 5.2 BAxxx.threshold.label to my 5.0 fsaverage and run the recon-all BA labels command. Now I run aparcstats2table and get a table with the values but they are the same as before running the BAxxx.threshold.label. So, everything is working but the values haven't changed. Am I missing something? Do I need to run any other command so to the threshold have effect? Andreia Quoting Anastasia Yendiki ayend...@nmr.mgh.harvard.edu: Sounds like centos4 is probably the safest bet for you, although you should ask the list this question. Sorry, I don't know what values you want to get in a table. On Sat, 23 Mar 2013, _andre...@sapo.pt wrote: Ah ok! Anyway, I'm thinking of working with 5.2, should I download the version for centOS 4 then? After running the new BAxxx.thresh.label files how can I get the values in a table? Quoting Anastasia Yendiki ayend...@nmr.mgh.harvard.edu: It doesn't matter. You just need to use those .label files from the fsaverage directory in the 5.2 distritbution. You don't need to run any of the executables from the 5.2 distribution. On Sat, 23 Mar 2013, _andre...@sapo.pt wrote: I'm using Centos5, which file should I download? The one for CentOS 6 or 4? Quoting Anastasia Yendiki ayend...@nmr.mgh.harvard.edu: You'll need to go to the section of recon-all.log under the heading BA labels. You'll need to rerun the commands in that section, but instead of using the BAxxx.label files, us the BAxxx.thresh.label files, which you'll find in the fsaverage subject dir in the 5.2 distribution. On Sat, 23 Mar 2013, _andre...@sapo.pt wrote: Hello Anastasia, How should I proceed to get the different BAs measures output with FS 5.0? Thank you very much! Andreia Quoting Anastasia Yendiki ayend...@nmr.mgh.harvard.edu: The thresholded labels are in the 5.2 version of fsaverage under: $FREESURFER_HOME/subjects/fsaverage/label/*.thresh.label On Sat, 23 Mar 2013, Bruce Fischl wrote: Anastasia? On Sat, 23 Mar 2013, _andre...@sapo.pt wrote: Ok, that was my guess... I am running against a deadline, any news on automatically computing the correct threshold script? Will I be able to use it in 5.0? Thanks you! Andreia Quoting Bruce Fischl fis...@nmr.mgh.harvard.edu: yes. Surface area will be the affected much more than thickness (and volume of course scales with area) On Fri, 22 Mar 2013, _andre...@sapo.pt wrote: Hi Bruce, Thank you for the quick response! In the meanwhile, does that also apply to cortical thickness and volume? Thank you! Andreia Quoting
Re: [Freesurfer] Fwd: Brodmann area thickness, surface area and volume
It's .thresh.label, not .threshold.label. On Mon, 25 Mar 2013, _andre...@sapo.pt wrote: Hi Anastasia! The command in the recon-all.log is this one: mri_label2label --srcsubject fsaverage --srclabel /home/user/visao/Freesurfer/fsaverage/label/rh.BA1.label --trgsubject SUSANAFERREIRA --trglabel ./rh.BA1.label --hemi rh --regmethod surface And I tried substituing BAxxx.label by BAxxx.thresh.label like this: mri_label2label --srcsubject fsaverage --srclabel /home/user/visao/Freesurfer/fsaverage/label/lh.BA1.threshold.label --trgsubject SUSANAFERREIRA --trglabel ./lh.BA1.thresolh.label --hemi lh --regmethod surface gave an error : SUBJECTS_DIR /home/user/visao/Freesurfer/ FREESURFER_HOME /usr/local/freesurfer Loading source label. No such file or directory mri_label2label: could not open label file /home/user/visao/Freesurfer/fsaverage/label/lh.BA1.threshold.label Illegal seek ERROR reading /home/user/visao/Freesurfer/fsaverage/label/lh.BA1.threshold.label Thus, I substitued only in the second BAxxx.label and it worked. I thought that was it, but then the values were the same. I'm sorry, I'm not sure what is missing. Thank you! Andreia Quoting Anastasia Yendiki ayend...@nmr.mgh.harvard.edu: Hi Andreia - What you're rerunning is using BAxxx.label instead of BAxxx.thresh.label. So of course the results will be the same as before you copied over the BAxxx.thresh.label files, b/c these new files aren't being used in 5.0. You'll need to find the BA labels section in recon-all.log and rerun those commands yourself, changing every BAxxx.label to BAxxx.thresh.label. Hope this helps, a.y On Mon, 25 Mar 2013, _andre...@sapo.pt wrote: Hello list! Any suggestions on what I may be doing wrong? Thanks! Andreia - Mensagem encaminhada de _andre...@sapo.pt - Data: Sun, 24 Mar 2013 19:11:13 + De: _andre...@sapo.pt Assunto: Re: [Freesurfer] Brodmann area thickness, surface area and volume Para: Anastasia Yendiki ayend...@nmr.mgh.harvard.edu, freesurfer freesurfer@nmr.mgh.harvard.edu Cc: Bruce Fischl fis...@nmr.mgh.harvard.edu Hi all, I want to study Brodmann Areas cortical thickness, surface area and volume. I've added the 5.2 BAxxx.threshold.label to my 5.0 fsaverage and run the recon-all BA labels command. Now I run aparcstats2table and get a table with the values but they are the same as before running the BAxxx.threshold.label. So, everything is working but the values haven't changed. Am I missing something? Do I need to run any other command so to the threshold have effect? Andreia Quoting Anastasia Yendiki ayend...@nmr.mgh.harvard.edu: Sounds like centos4 is probably the safest bet for you, although you should ask the list this question. Sorry, I don't know what values you want to get in a table. On Sat, 23 Mar 2013, _andre...@sapo.pt wrote: Ah ok! Anyway, I'm thinking of working with 5.2, should I download the version for centOS 4 then? After running the new BAxxx.thresh.label files how can I get the values in a table? Quoting Anastasia Yendiki ayend...@nmr.mgh.harvard.edu: It doesn't matter. You just need to use those .label files from the fsaverage directory in the 5.2 distritbution. You don't need to run any of the executables from the 5.2 distribution. On Sat, 23 Mar 2013, _andre...@sapo.pt wrote: I'm using Centos5, which file should I download? The one for CentOS 6 or 4? Quoting Anastasia Yendiki ayend...@nmr.mgh.harvard.edu: You'll need to go to the section of recon-all.log under the heading BA labels. You'll need to rerun the commands in that section, but instead of using the BAxxx.label files, us the BAxxx.thresh.label files, which you'll find in the fsaverage subject dir in the 5.2 distribution. On Sat, 23 Mar 2013, _andre...@sapo.pt wrote: Hello Anastasia, How should I proceed to get the different BAs measures output with FS 5.0? Thank you very much! Andreia Quoting Anastasia Yendiki ayend...@nmr.mgh.harvard.edu: The thresholded labels are in the 5.2 version of fsaverage under: $FREESURFER_HOME/subjects/fsaverage/label/*.thresh.label On Sat, 23 Mar 2013, Bruce Fischl wrote: Anastasia? On Sat, 23 Mar 2013, _andre...@sapo.pt wrote: Ok, that was my guess... I am running against a deadline, any news on automatically computing the correct threshold script? Will I be able to use it in 5.0? Thanks you! Andreia Quoting Bruce Fischl fis...@nmr.mgh.harvard.edu: yes. Surface area will be the affected much more than thickness (and volume of course scales with area) On Fri, 22 Mar 2013, _andre...@sapo.pt wrote: Hi Bruce, Thank you for the quick response! In the meanwhile, does that also apply to cortical thickness and volume? Thank you! Andreia Quoting Bruce Fischl
Re: [Freesurfer] bbregister error with hardi data
Ok I adjusted the bbregister file to say fsvol.mgz in the location you specified and got this error a bit later on in the bbregister output: setenv SUBJECTS_DIR /usr/local/freesurfer/subjects/symmetry cd /usr/local/freesurfer/subjects/symmetry/lindsay /usr/local/freesurfer/bin/bbregister --s lindsay --mov hardi/ffiltered_func_data_01.nii.gz --dti --init-fsl --reg register.dat $Id: bbregister,v 1.49.2.2 2013/02/23 01:32:22 mreuter Exp $ Linux lotfi 3.2.0-38-generic #61-Ubuntu SMP Tue Feb 19 12:18:21 UTC 2013 x86_64 x86_64 x86_64 GNU/Linux FREESURFER_HOME /usr/local/freesurfer mri_convert hardi/ffiltered_func_data_01.nii.gz ./tmp.bbregister.15807/template.nii mri_convert hardi/ffiltered_func_data_01.nii.gz ./tmp.bbregister.15807/template.nii $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from hardi/ffiltered_func_data_01.nii.gz... TR=17843.91, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-0.991204, -0.025762, 0.129811) j_ras = (-0.0259819, 0.999662, 0) k_ras = (0.129768, 0.00337275, 0.991539) writing to ./tmp.bbregister.15807/template.nii... fslregister --s lindsay --mov ./tmp.bbregister.15807/template.nii --reg ./tmp.bbregister.15807/reg.init.dat --niters 1 --maxangle 90 --nobetmov --tmp ./tmp.bbregister.15807/fslregister --dof 6 --fsvol.mgz brainmask ERROR: Flag --fsvol.mgz unrecognized. --s lindsay --mov ./tmp.bbregister.15807/template.nii --reg ./tmp.bbregister.15807/reg.init.dat --niters 1 --maxangle 90 --nobetmov --tmp ./tmp.bbregister.15807/fslregister --dof 6 --fsvol.mgz brainmask mri_segreg --mov ./tmp.bbregister.15807/template.nii --init-reg ./tmp.bbregister.15807/reg.init.dat --out-reg ./tmp.bbregister.15807/bbr.pass1.dat --subsamp-brute 100 --subsamp 100 --tol 1e-4 --tol1d 1e-3 --brute -4 4 4 --surf white --gm-proj-frac 0.5 --gm-gt-wm 0.5 regio_read_register(): No such file or directory Could not open ./tmp.bbregister.15807/reg.init.dat mri_segreg --mov ./tmp.bbregister.15807/template.nii --init-reg ./tmp.bbregister.15807/bbr.pass1.dat --out-reg register.dat --brute -0.1 0.1 0.1 --interp trilinear --wm-proj-abs 2 --tol 1e-8 --tol1d 1e-3 --c0 0 --mincost register.dat.mincost --dof 6 --nmax 36 --param register.dat.param --surf white --cur-reg ./tmp.bbregister.15807/reg.curopt.dat --gm-proj-frac 0.5 --nsub 1 --gm-gt-wm 0.5 regio_read_register(): No such file or directory Could not open ./tmp.bbregister.15807/bbr.pass1.dat Cleaning up Started at Mon Mar 25 13:24:53 EDT 2013 Ended at Mon Mar 25 13:25:00 EDT 2013 BBR-Run-Time-Sec 7 bbregister Done To check results, run: tkregister2 --mov hardi/ffiltered_func_data_01.nii.gz --reg register.dat --surf On Mon, Mar 25, 2013 at 1:22 PM, Douglas N Greve gr...@nmr.mgh.harvard.eduwrote: Corinna, can you edit $FREESURFER_HOME/bin/**bbregister? If so, change the following line From set cmd = (fslregister --s $subject --mov $regvol --reg $InitReg \ --niters 1 --maxangle 90 --tmp $tmpdir/fslregister \ --dof $FSLDOF --fsvol $fsvol) To set cmd = (fslregister --s $subject --mov $regvol --reg $InitReg \ --niters 1 --maxangle 90 --tmp $tmpdir/fslregister \ --dof $FSLDOF --fsvol $fsvol.mgz) It is just the very last part that is changed where I added .mgz to $fsvol Re-run bbregister and let me know if this works. doug On 03/25/2013 01:11 PM, Corinna Bauer wrote: yes, this file exists. On Mon, Mar 25, 2013 at 1:10 PM, Douglas N Greve gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.**edugr...@nmr.mgh.harvard.edu wrote: Can you verify that /usr/local/freesurfer/**subjects/symmetry/lindsay/mri/**brainmask.mgz exists? doug On 03/25/2013 12:55 PM, Corinna Bauer wrote: sure. Here is the dng.log. Corinna On Mon, Mar 25, 2013 at 12:45 PM, Douglas N Greve gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.**edugr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.**edu gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.**edu gr...@nmr.mgh.harvard.edu wrote: Hi Corinna, can you run fslregister --debug --s lindsay --mov hardi/ffiltered_func_data_01.**nii.gz --reg fsl.reg.dat --niters 1 --maxangle 90 --nobetmov --tmp ./tmp.fslregister --dof 6 --fsvol brainmask | tee dng.log and send me the dng.log? doug On 03/25/2013 12:39 PM, Corinna Bauer wrote: Hello all, I am attempting to run bbregister on 4D HARDI data that has already been motion, eddy, and epi-distortion corrected in fsl. I run the command: bbregister --s lindsay --mov hardi/ffiltered_func_data_01.**nii.gz --dti --init-fsl --reg register.dat and get a number of errors that seem to begin in the mri_convert section as seen below.
Re: [Freesurfer] Fwd: Brodmann area thickness, surface area and volume
Ah ok! Sorry... In both places? Quoting Anastasia Yendiki ayend...@nmr.mgh.harvard.edu: It's .thresh.label, not .threshold.label. On Mon, 25 Mar 2013, _andre...@sapo.pt wrote: Hi Anastasia! The command in the recon-all.log is this one: mri_label2label --srcsubject fsaverage --srclabel /home/user/visao/Freesurfer/fsaverage/label/rh.BA1.label --trgsubject SUSANAFERREIRA --trglabel ./rh.BA1.label --hemi rh --regmethod surface And I tried substituing BAxxx.label by BAxxx.thresh.label like this: mri_label2label --srcsubject fsaverage --srclabel /home/user/visao/Freesurfer/fsaverage/label/lh.BA1.threshold.label --trgsubject SUSANAFERREIRA --trglabel ./lh.BA1.thresolh.label --hemi lh --regmethod surface gave an error : SUBJECTS_DIR /home/user/visao/Freesurfer/ FREESURFER_HOME /usr/local/freesurfer Loading source label. No such file or directory mri_label2label: could not open label file /home/user/visao/Freesurfer/fsaverage/label/lh.BA1.threshold.label Illegal seek ERROR reading /home/user/visao/Freesurfer/fsaverage/label/lh.BA1.threshold.label Thus, I substitued only in the second BAxxx.label and it worked. I thought that was it, but then the values were the same. I'm sorry, I'm not sure what is missing. Thank you! Andreia Quoting Anastasia Yendiki ayend...@nmr.mgh.harvard.edu: Hi Andreia - What you're rerunning is using BAxxx.label instead of BAxxx.thresh.label. So of course the results will be the same as before you copied over the BAxxx.thresh.label files, b/c these new files aren't being used in 5.0. You'll need to find the BA labels section in recon-all.log and rerun those commands yourself, changing every BAxxx.label to BAxxx.thresh.label. Hope this helps, a.y On Mon, 25 Mar 2013, _andre...@sapo.pt wrote: Hello list! Any suggestions on what I may be doing wrong? Thanks! Andreia - Mensagem encaminhada de _andre...@sapo.pt - Data: Sun, 24 Mar 2013 19:11:13 + De: _andre...@sapo.pt Assunto: Re: [Freesurfer] Brodmann area thickness, surface area and volume Para: Anastasia Yendiki ayend...@nmr.mgh.harvard.edu, freesurfer freesurfer@nmr.mgh.harvard.edu Cc: Bruce Fischl fis...@nmr.mgh.harvard.edu Hi all, I want to study Brodmann Areas cortical thickness, surface area and volume. I've added the 5.2 BAxxx.threshold.label to my 5.0 fsaverage and run the recon-all BA labels command. Now I run aparcstats2table and get a table with the values but they are the same as before running the BAxxx.threshold.label. So, everything is working but the values haven't changed. Am I missing something? Do I need to run any other command so to the threshold have effect? Andreia Quoting Anastasia Yendiki ayend...@nmr.mgh.harvard.edu: Sounds like centos4 is probably the safest bet for you, although you should ask the list this question. Sorry, I don't know what values you want to get in a table. On Sat, 23 Mar 2013, _andre...@sapo.pt wrote: Ah ok! Anyway, I'm thinking of working with 5.2, should I download the version for centOS 4 then? After running the new BAxxx.thresh.label files how can I get the values in a table? Quoting Anastasia Yendiki ayend...@nmr.mgh.harvard.edu: It doesn't matter. You just need to use those .label files from the fsaverage directory in the 5.2 distritbution. You don't need to run any of the executables from the 5.2 distribution. On Sat, 23 Mar 2013, _andre...@sapo.pt wrote: I'm using Centos5, which file should I download? The one for CentOS 6 or 4? Quoting Anastasia Yendiki ayend...@nmr.mgh.harvard.edu: You'll need to go to the section of recon-all.log under the heading BA labels. You'll need to rerun the commands in that section, but instead of using the BAxxx.label files, us the BAxxx.thresh.label files, which you'll find in the fsaverage subject dir in the 5.2 distribution. On Sat, 23 Mar 2013, _andre...@sapo.pt wrote: Hello Anastasia, How should I proceed to get the different BAs measures output with FS 5.0? Thank you very much! Andreia Quoting Anastasia Yendiki ayend...@nmr.mgh.harvard.edu: The thresholded labels are in the 5.2 version of fsaverage under: $FREESURFER_HOME/subjects/fsaverage/label/*.thresh.label On Sat, 23 Mar 2013, Bruce Fischl wrote: Anastasia? On Sat, 23 Mar 2013, _andre...@sapo.pt wrote: Ok, that was my guess... I am running against a deadline, any news on automatically computing the correct threshold script? Will I be able to use it in 5.0? Thanks you! Andreia Quoting Bruce Fischl fis...@nmr.mgh.harvard.edu: yes. Surface area will be the affected much more than thickness (and volume of course scales with area) On Fri, 22 Mar 2013, _andre...@sapo.pt wrote: Hi Bruce, Thank you for the quick response! In the meanwhile, does that also apply
Re: [Freesurfer] Fwd: Brodmann area thickness, surface area and volume
What you call the output label is up to you. What you call the input label is more important - it has to be a file that actually exists. On Mon, 25 Mar 2013, _andre...@sapo.pt wrote: Ah ok! Sorry... In both places? Quoting Anastasia Yendiki ayend...@nmr.mgh.harvard.edu: It's .thresh.label, not .threshold.label. On Mon, 25 Mar 2013, _andre...@sapo.pt wrote: Hi Anastasia! The command in the recon-all.log is this one: mri_label2label --srcsubject fsaverage --srclabel /home/user/visao/Freesurfer/fsaverage/label/rh.BA1.label --trgsubject SUSANAFERREIRA --trglabel ./rh.BA1.label --hemi rh --regmethod surface And I tried substituing BAxxx.label by BAxxx.thresh.label like this: mri_label2label --srcsubject fsaverage --srclabel /home/user/visao/Freesurfer/fsaverage/label/lh.BA1.threshold.label --trgsubject SUSANAFERREIRA --trglabel ./lh.BA1.thresolh.label --hemi lh --regmethod surface gave an error : SUBJECTS_DIR /home/user/visao/Freesurfer/ FREESURFER_HOME /usr/local/freesurfer Loading source label. No such file or directory mri_label2label: could not open label file /home/user/visao/Freesurfer/fsaverage/label/lh.BA1.threshold.label Illegal seek ERROR reading /home/user/visao/Freesurfer/fsaverage/label/lh.BA1.threshold.label Thus, I substitued only in the second BAxxx.label and it worked. I thought that was it, but then the values were the same. I'm sorry, I'm not sure what is missing. Thank you! Andreia Quoting Anastasia Yendiki ayend...@nmr.mgh.harvard.edu: Hi Andreia - What you're rerunning is using BAxxx.label instead of BAxxx.thresh.label. So of course the results will be the same as before you copied over the BAxxx.thresh.label files, b/c these new files aren't being used in 5.0. You'll need to find the BA labels section in recon-all.log and rerun those commands yourself, changing every BAxxx.label to BAxxx.thresh.label. Hope this helps, a.y On Mon, 25 Mar 2013, _andre...@sapo.pt wrote: Hello list! Any suggestions on what I may be doing wrong? Thanks! Andreia - Mensagem encaminhada de _andre...@sapo.pt - Data: Sun, 24 Mar 2013 19:11:13 + De: _andre...@sapo.pt Assunto: Re: [Freesurfer] Brodmann area thickness, surface area and volume Para: Anastasia Yendiki ayend...@nmr.mgh.harvard.edu, freesurfer freesurfer@nmr.mgh.harvard.edu Cc: Bruce Fischl fis...@nmr.mgh.harvard.edu Hi all, I want to study Brodmann Areas cortical thickness, surface area and volume. I've added the 5.2 BAxxx.threshold.label to my 5.0 fsaverage and run the recon-all BA labels command. Now I run aparcstats2table and get a table with the values but they are the same as before running the BAxxx.threshold.label. So, everything is working but the values haven't changed. Am I missing something? Do I need to run any other command so to the threshold have effect? Andreia Quoting Anastasia Yendiki ayend...@nmr.mgh.harvard.edu: Sounds like centos4 is probably the safest bet for you, although you should ask the list this question. Sorry, I don't know what values you want to get in a table. On Sat, 23 Mar 2013, _andre...@sapo.pt wrote: Ah ok! Anyway, I'm thinking of working with 5.2, should I download the version for centOS 4 then? After running the new BAxxx.thresh.label files how can I get the values in a table? Quoting Anastasia Yendiki ayend...@nmr.mgh.harvard.edu: It doesn't matter. You just need to use those .label files from the fsaverage directory in the 5.2 distritbution. You don't need to run any of the executables from the 5.2 distribution. On Sat, 23 Mar 2013, _andre...@sapo.pt wrote: I'm using Centos5, which file should I download? The one for CentOS 6 or 4? Quoting Anastasia Yendiki ayend...@nmr.mgh.harvard.edu: You'll need to go to the section of recon-all.log under the heading BA labels. You'll need to rerun the commands in that section, but instead of using the BAxxx.label files, us the BAxxx.thresh.label files, which you'll find in the fsaverage subject dir in the 5.2 distribution. On Sat, 23 Mar 2013, _andre...@sapo.pt wrote: Hello Anastasia, How should I proceed to get the different BAs measures output with FS 5.0? Thank you very much! Andreia Quoting Anastasia Yendiki ayend...@nmr.mgh.harvard.edu: The thresholded labels are in the 5.2 version of fsaverage under: $FREESURFER_HOME/subjects/fsaverage/label/*.thresh.label
Re: [Freesurfer] bbregister error with hardi data
Are you sure you made the right edit? It should be --fsvol $fsvol.mgz It looks like you might have changed it to --fsvol.mgz $fsvol On 03/25/2013 01:30 PM, Corinna Bauer wrote: Ok I adjusted the bbregister file to say fsvol.mgz in the location you specified and got this error a bit later on in the bbregister output: setenv SUBJECTS_DIR /usr/local/freesurfer/subjects/symmetry cd /usr/local/freesurfer/subjects/symmetry/lindsay /usr/local/freesurfer/bin/bbregister --s lindsay --mov hardi/ffiltered_func_data_01.nii.gz --dti --init-fsl --reg register.dat $Id: bbregister,v 1.49.2.2 2013/02/23 01:32:22 mreuter Exp $ Linux lotfi 3.2.0-38-generic #61-Ubuntu SMP Tue Feb 19 12:18:21 UTC 2013 x86_64 x86_64 x86_64 GNU/Linux FREESURFER_HOME /usr/local/freesurfer mri_convert hardi/ffiltered_func_data_01.nii.gz ./tmp.bbregister.15807/template.nii mri_convert hardi/ffiltered_func_data_01.nii.gz ./tmp.bbregister.15807/template.nii $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from hardi/ffiltered_func_data_01.nii.gz... TR=17843.91, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-0.991204, -0.025762, 0.129811) j_ras = (-0.0259819, 0.999662, 0) k_ras = (0.129768, 0.00337275, 0.991539) writing to ./tmp.bbregister.15807/template.nii... fslregister --s lindsay --mov ./tmp.bbregister.15807/template.nii --reg ./tmp.bbregister.15807/reg.init.dat --niters 1 --maxangle 90 --nobetmov --tmp ./tmp.bbregister.15807/fslregister --dof 6 --fsvol.mgz brainmask ERROR: Flag --fsvol.mgz unrecognized. --s lindsay --mov ./tmp.bbregister.15807/template.nii --reg ./tmp.bbregister.15807/reg.init.dat --niters 1 --maxangle 90 --nobetmov --tmp ./tmp.bbregister.15807/fslregister --dof 6 --fsvol.mgz brainmask mri_segreg --mov ./tmp.bbregister.15807/template.nii --init-reg ./tmp.bbregister.15807/reg.init.dat --out-reg ./tmp.bbregister.15807/bbr.pass1.dat --subsamp-brute 100 --subsamp 100 --tol 1e-4 --tol1d 1e-3 --brute -4 4 4 --surf white --gm-proj-frac 0.5 --gm-gt-wm 0.5 regio_read_register(): No such file or directory Could not open ./tmp.bbregister.15807/reg.init.dat mri_segreg --mov ./tmp.bbregister.15807/template.nii --init-reg ./tmp.bbregister.15807/bbr.pass1.dat --out-reg register.dat --brute -0.1 0.1 0.1 --interp trilinear --wm-proj-abs 2 --tol 1e-8 --tol1d 1e-3 --c0 0 --mincost register.dat.mincost --dof 6 --nmax 36 --param register.dat.param --surf white --cur-reg ./tmp.bbregister.15807/reg.curopt.dat --gm-proj-frac 0.5 --nsub 1 --gm-gt-wm 0.5 regio_read_register(): No such file or directory Could not open ./tmp.bbregister.15807/bbr.pass1.dat Cleaning up Started at Mon Mar 25 13:24:53 EDT 2013 Ended at Mon Mar 25 13:25:00 EDT 2013 BBR-Run-Time-Sec 7 bbregister Done To check results, run: tkregister2 --mov hardi/ffiltered_func_data_01.nii.gz --reg register.dat --surf On Mon, Mar 25, 2013 at 1:22 PM, Douglas N Greve gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu wrote: Corinna, can you edit $FREESURFER_HOME/bin/bbregister? If so, change the following line From set cmd = (fslregister --s $subject --mov $regvol --reg $InitReg \ --niters 1 --maxangle 90 --tmp $tmpdir/fslregister \ --dof $FSLDOF --fsvol $fsvol) To set cmd = (fslregister --s $subject --mov $regvol --reg $InitReg \ --niters 1 --maxangle 90 --tmp $tmpdir/fslregister \ --dof $FSLDOF --fsvol $fsvol.mgz) It is just the very last part that is changed where I added .mgz to $fsvol Re-run bbregister and let me know if this works. doug On 03/25/2013 01:11 PM, Corinna Bauer wrote: yes, this file exists. On Mon, Mar 25, 2013 at 1:10 PM, Douglas N Greve gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu wrote: Can you verify that /usr/local/freesurfer/subjects/symmetry/lindsay/mri/brainmask.mgz exists? doug On 03/25/2013 12:55 PM, Corinna Bauer wrote: sure. Here is the dng.log. Corinna On Mon, Mar 25, 2013 at 12:45 PM, Douglas N Greve gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu wrote: Hi Corinna, can you run fslregister --debug --s lindsay --mov hardi/ffiltered_func_data_01.nii.gz --reg fsl.reg.dat --niters 1 --maxangle 90 --nobetmov --tmp ./tmp.fslregister --dof 6 --fsvol
Re: [Freesurfer] Fwd: Brodmann area thickness, surface area and volume
If you replace *every* occurence of BAxxx.label with BAxxx.thresh.label, this will keep things simple and you won't have to worry about which one is input and which one is output. Run *all* the commands from the BA labels section, all the way to the end of that section, this will get you to the stats. On Mon, 25 Mar 2013, _andre...@sapo.pt wrote: Ok. So the first is the input and the second is the output, correct? So I'll have a different file for each out put? Is it possible to have a table with the different measures after the threshold? Thank you very much and I apologize for the naive questions... Andreia Quoting Anastasia Yendiki ayend...@nmr.mgh.harvard.edu: What you call the output label is up to you. What you call the input label is more important - it has to be a file that actually exists. On Mon, 25 Mar 2013, _andre...@sapo.pt wrote: Ah ok! Sorry... In both places? Quoting Anastasia Yendiki ayend...@nmr.mgh.harvard.edu: It's .thresh.label, not .threshold.label. On Mon, 25 Mar 2013, _andre...@sapo.pt wrote: Hi Anastasia! The command in the recon-all.log is this one: mri_label2label --srcsubject fsaverage --srclabel /home/user/visao/Freesurfer/fsaverage/label/rh.BA1.label --trgsubject SUSANAFERREIRA --trglabel ./rh.BA1.label --hemi rh --regmethod surface And I tried substituing BAxxx.label by BAxxx.thresh.label like this: mri_label2label --srcsubject fsaverage --srclabel /home/user/visao/Freesurfer/fsaverage/label/lh.BA1.threshold.label --trgsubject SUSANAFERREIRA --trglabel ./lh.BA1.thresolh.label --hemi lh --regmethod surface gave an error : SUBJECTS_DIR /home/user/visao/Freesurfer/ FREESURFER_HOME /usr/local/freesurfer Loading source label. No such file or directory mri_label2label: could not open label file /home/user/visao/Freesurfer/fsaverage/label/lh.BA1.threshold.label Illegal seek ERROR reading /home/user/visao/Freesurfer/fsaverage/label/lh.BA1.threshold.label Thus, I substitued only in the second BAxxx.label and it worked. I thought that was it, but then the values were the same. I'm sorry, I'm not sure what is missing. Thank you! Andreia Quoting Anastasia Yendiki ayend...@nmr.mgh.harvard.edu: Hi Andreia - What you're rerunning is using BAxxx.label instead of BAxxx.thresh.label. So of course the results will be the same as before you copied over the BAxxx.thresh.label files, b/c these new files aren't being used in 5.0. You'll need to find the BA labels section in recon-all.log and rerun those commands yourself, changing every BAxxx.label to BAxxx.thresh.label. Hope this helps, a.y On Mon, 25 Mar 2013, _andre...@sapo.pt wrote: Hello list! Any suggestions on what I may be doing wrong? Thanks! Andreia - Mensagem encaminhada de _andre...@sapo.pt - Data: Sun, 24 Mar 2013 19:11:13 + De: _andre...@sapo.pt Assunto: Re: [Freesurfer] Brodmann area thickness, surface area andvolume Para: Anastasia Yendiki ayend...@nmr.mgh.harvard.edu, freesurfer freesurfer@nmr.mgh.harvard.edu Cc: Bruce Fischl fis...@nmr.mgh.harvard.edu Hi all, I want to study Brodmann Areas cortical thickness, surface area and volume. I've added the 5.2 BAxxx.threshold.label to my 5.0 fsaverage and run the recon-all BA labels command. Now I run aparcstats2table and get a table with the values but they are the same as before running the BAxxx.threshold.label. So, everything is working but the values haven't changed. Am Imissing something? Do I need to run any other command so to the thresholdhave effect? Andreia Quoting Anastasia Yendiki ayend...@nmr.mgh.harvard.edu: Sounds like centos4 is probably the safest bet for you, although you should ask the list this question. Sorry, I don't know what values you want to get in a table. On Sat, 23 Mar 2013, _andre...@sapo.pt wrote: Ah ok! Anyway, I'm thinking of working with 5.2, should I download the version for centOS 4 then? After running the new BAxxx.thresh.label files how can I get the values in a table? Quoting Anastasia Yendiki ayend...@nmr.mgh.harvard.edu: It doesn't matter. You just need to use those .label files from the fsaverage directory in the 5.2 distritbution. You don't need to run any of the executables
Re: [Freesurfer] advice in registering a binary mask to Freesurfer space.
Hi Doug. That was in fact what I decided to do. Thanks! Josh - J On Mon, Mar 25, 2013 at 7:38 AM, Douglas N Greve gr...@nmr.mgh.harvard.eduwrote: Can you compute the registration between the manually traced anat space and the FS conformed space? Eg, with BBR. If you can do that, then you can run mri_label2vol to convert the mask into FS conformed space (assuming that that is what you want to do). doug On 03/22/2013 04:43 PM, Joshua Lee wrote: Hi All, I wanted to get peoples advice on the best method of registration/interpolation to use on a manually traced segmentation (and its structural) that is not in the same space and orientation as the structurals I started Freesurfer with (although they both originally came from the same image. I want to maintain the integrity of the manual traced binary mask through this registration and reslice. For a number of reasons, I do not want to take Freesurfers output to the space of the manual segmentation. What do people think is a good technique? Flirt nearest neighbor interpolation? Something different from Freesurfer? ANTs? - Josh ___ 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 Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ___ 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 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] QDEC issues
Hi Tudor, On 03/22/2013 05:19 PM, Tudor Popescu wrote: Hello everyone, I created a qdec.table.dat for my design (a simple group analysis, with gender as categorical factor and age as continuous factor), and created a gender.levels file containing the values that are found in qdec.table.dat, spellt in exactly the same way (all files attached). However, when loading the file in QDEC, I get the error: /ERROR: Subject C01 has an invalid level 'controls' in the group column INFO: If 'group' is a discrete factor, then create a file named 'group.levels' containing the valid factor names one per line. Error loading the data table. / The strings under the fsid column (subject ID) correspond to those that I used after the –subjid xxx, in my previous call to recon-all (e.g. C01, C02, M01, M02..). The qdec.table.dat was created in Excel and saved as a tab-delimited txt file. Replacing the tabs with spaces/commas does not change the error message. What could be the problem? It looks like you made the group.levels file on a windows system. There are hidden characters that cause qdec to fail. Try creating it from scratch on a linux system or run dos2unix on the file. I also have a few more questions, if I may: - how much more accurate are the results of a QDEC analysis if an average subject is computed from the subjects of the sample, with make_average_subject, as opposed to using FS's default average subject, fsaverage? Accurate in what way? Changing the average subject in qdec just changes the gray scale curvature pattern. This will be a little more accurate if you use your subjects, but probably not much. It will change the stats a very small amount. Note that QDEC will not use a different registration even if you spec a new average subject. - the qdec.table.dat in the tutorial http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/QdecGroupAnalysiscontains more than just demographical information, for instance it contains the volumes of the left and right hippocampi; are these types of informations normally brought in from previous analyses (that may have been done in a package other than FS), or does one first have to obtain any such relevant predictors in FreeSurfer, before starting the QDEC analysis? They do not have to be. They are only there for convenience in case you have a hypothesis about them. - the QDEC tutorial seems to be for whole-brain analyses; the ROI analysis tutorial http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/AnatomicalROI mentions nothing of QDEC, however; can ROI analyses not also be done in QDEC? No, not yet. - in the Group Analysis (non-QDEC) tutorial http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis, the design matrix (Xg.dat) is in the form MembershipF| MembershipM|AgeF|AgeM, while the values in the contrast are said to correspond to the 4 parameters (intercept for F,M; slope for F,M). Either way, how can the contrast vector be interpreted to give the correlation between thickness and age? Each column in the Xg.dat is matched with a linear parameter (intercept or slope). If you have [0 0 1 0], it means to ignore the parameters matched with 0s and just test the parameter matched with 1, in this case, the AgeF (and so slope) parameter. - in the same tutorial, why is the value 0 being given to the first two elements in the matrix, when it should only be given to nuisance variables? Effectively yes. They might only be nuisance for that particular contrast. For other contrasts they might be variables of interest. doug Many thanks in advance for any help! Tudor ___ 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 Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ___ 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] Bug in DOSS implementation in QDEC
Dear FreeSurferers, it has just come to my attention that there may be a bug in the way that QDEC computes contrasts for DOSS. If you are using QDEC in this way, please hold off until I track down the problem. Also, please let me know if you are using it in this way. thanks and sorry for the inconvenience doug -- 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 Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ___ 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] -clean-* flags
Hi, I was wondering if the -clean-* flags should only be used when you've performed manual edits on your volumes, or if they are also necessary when you re-process your subjects? For instance, let's say I edit the Talairach transform and run the entire recon-all process (using the -all flag) on a subject I had previously processed using the previous release of Freesurfer. If I had done no other manual edits on volumes such as brainmask.mgz, wm.mgz, etc., will these volumes be automatically overwritten when I run the latest version of recon-all, or do I need to specify the corresponding -clean-* flags in order for this to take place? Thanks, Gabriel ___ 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] surf2vol
Dear All Apologies for what I'm sure is a very basic question. I'm new to using freesurfer, and would like to generate cortical parcellations for running in probtrakx. I have followed the instructions from various sources and have managed to generate the parcellations from recon-all, extract the label files from the parcellation, then use mri_mergelabels and label2surf to generate the the .gii files needed for probtrakx. I'd like to be able to display the surface files for illustrative purposes, but I'm struggling to apply the surf2vol command. From the terminal window I can see that the commands required are: surf2vol surf refvol outvol convention I presume that surf is the .gii file I'm trying to visualise, and outvol is to specify the name of the output volume the command will generate, but what should I be using as the refvol? I would be very grateful for any guidance. Please accept my apologies if I've missed a very obvious online explanation for this and thank you in advance. Dan Lumsden Clinical Research Fellow ___ 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] -clean-* flags
Hi Gabriel you should only need to specify -clean if you have done editing or manual intervention and you want to overwrite what you have done. Otherwise edits and such will be detected and preserved. cheers Bruce On Mon, 25 Mar 2013, obre...@nmr.mgh.harvard.edu wrote: Hi, I was wondering if the -clean-* flags should only be used when you've performed manual edits on your volumes, or if they are also necessary when you re-process your subjects? For instance, let's say I edit the Talairach transform and run the entire recon-all process (using the -all flag) on a subject I had previously processed using the previous release of Freesurfer. If I had done no other manual edits on volumes such as brainmask.mgz, wm.mgz, etc., will these volumes be automatically overwritten when I run the latest version of recon-all, or do I need to specify the corresponding -clean-* flags in order for this to take place? Thanks, Gabriel ___ 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] surf2vol
Hi Dan try using mri_surf2vol instead (it has a much bigger help, thanks to Doug0 Bruce On Mon, 25 Mar 2013, Daniel Lumsden wrote: Dear All Apologies for what I'm sure is a very basic question. I'm new to using freesurfer, and would like to generate cortical parcellations for running in probtrakx. I have followed the instructions from various sources and have managed to generate the parcellations from recon-all, extract the label files from the parcellation, then use mri_mergelabels and label2surf to generate the the .gii files needed for probtrakx. I'd like to be able to display the surface files for illustrative purposes, but I'm struggling to apply the surf2vol command. From the terminal window I can see that the commands required are: surf2vol surf refvol outvol convention I presume that surf is the .gii file I'm trying to visualise, and outvol is to specify the name of the output volume the command will generate, but what should I be using as the refvol? I would be very grateful for any guidance. Please accept my apologies if I've missed a very obvious online explanation for this and thank you in advance. Dan Lumsden Clinical Research Fellow ___ 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] problem with registration in preprocessing
I have trouble uploading files on the freesurfer page. I have put the files here: http://www.wjh.harvard.edu/~mvaziri/preproctest.tar I was initially running the analysis on harvard ncf network on one of the workstations. The fsl version there is fsl-4.1.7 and the freesurfer version is freesurfer 5.1. I ran the preprocessing on this run separately and got the same error. However when I transferred the files to my macintosh computer (iMAC) and ran the analysis on my computer which has the same version of freesurfer I did not get any errors and the preprocessing completed successfully. This is very puzzling as it seems to be specific to the harvard network. Any idea where the problem might be? Maryam On Mon, Mar 25, 2013 at 12:23 PM, Douglas N Greve gr...@nmr.mgh.harvard.edu wrote: Can you tar up the subject and the last run and drop it to me on our file drop system? doug On 03/25/2013 12:07 PM, Maryam wrote: The raw images of the last run seems fine. And it is only the last run out of 12. M On Mar 25, 2013, at 10:36 AM, Douglas N Greve gr...@nmr.mgh.harvard.edu wrote: Hi Maryam, I'm not sure what is wrong. Can you check the image in bold/018 to make sure that there is not something horribly wrong? Eg, it is not a localizer or only has one slice. And it is only the last run? The others are ok? doug On 03/22/2013 03:05 PM, Maryam Vaziri Pashkam wrote: Hi Doug, I am running fsfast preprocessing on my data and I am getting an error on one of the runs. This is the preprocessing code that I run: preproc-sess -s 130321_xu_Object4catmulti_01 -per-run -sliceorder siemens -fsd bold -fwhm 0 -mni305-2mm -surface self lhrh The error seems to happen during the fsl registration on the last run (out of 12 runs): /ncf/vcn/Maryam/mri-space/**studies/Obj4catmulti/** unpackdata/130321_xu_**Object4catmulti_01 flirt.fsl -ref bold/018/tmp.bbregister.1228/**fslregister/refvol.**fslregister.nii -in bold/018/tmp.bbregister.1228/**fslregister/movvol.**fslregister.nii -bins 256 -cost corratio -dof 6 -searchrx -90 90 -searchry -90 90 -searchrz -90 90 -verbose 0 -omat bold/018/tmp.bbregister.1228/**reg.init.dat.fsl.mat -init bold/018/tmp.bbregister.1228/**fslregister/fslmat0.trans.mat -schedule /ncf/apps/freesurfer-5.1.0//**bin/flirt.newdefault.20080811.* *sch terminate called after throwing an instance of 'NEWMAT::SingularException' Abort ERROR: flirt bellow is the register-sess log file. I have only included the section for the registration of the last run. I have looked at the raw data of this run and it does not look different from the other runs (all other runs are successfully registered). I am running freesurfer 5.1. Any idea how I can fix the error? Thanks, Maryam $Id: bbregister,v 1.49 2011/03/06 23:38:41 greve Exp $ Linux ncfws08.rc.fas.harvard.edu http://ncfws08.rc.fas.**harvard.eduhttp://ncfws08.rc.fas.harvard.edu 2.6.18-274.17.1.el5 #1 SMP Tue Jan 10 17:25:58 EST 2012 x86_64 x86_64 x86_64 GNU/Linux FREESURFER_HOME /ncf/apps/freesurfer-5.1.0/ mri_convert bold/018/template.nii.gz bold/018/tmp.bbregister.1228/** template.nii mri_convert bold/018/template.nii.gz bold/018/tmp.bbregister.1228/** template.nii $Id: mri_convert.c,v 1.179.2.2 2011/05/16 20:53:47 greve Exp $ reading from bold/018/template.nii.gz... TR=2000.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-0.998239, -0.0522464, 0.0280991) j_ras = (0.0500393, -0.995986, -0.0742193) k_ras = (0.031864, -0.0726825, 0.996846) writing to bold/018/tmp.bbregister.1228/**template.nii... fslregister --s blue_street_kcb --mov bold/018/tmp.bbregister.1228/**template.nii --reg bold/018/tmp.bbregister.1228/**reg.init.dat --niters 1 --maxangle 90 --nobetmov --tmp bold/018/tmp.bbregister.1228/**fslregister --dof 6 Log file is bold/018/tmp.bbregister.1228/**reg.init.dat.fslregister.log Fri Mar 22 14:42:18 EDT 2013 --s blue_street_kcb --mov bold/018/tmp.bbregister.1228/**template.nii --reg bold/018/tmp.bbregister.1228/**reg.init.dat --niters 1 --maxangle 90 --nobetmov --tmp bold/018/tmp.bbregister.1228/**fslregister --dof 6 $Id: fslregister,v 1.34.2.1 2011/03/28 20:35:36 greve Exp $ ncfws08.rc.fas.harvard.edu http://ncfws08.rc.fas.**harvard.eduhttp://ncfws08.rc.fas.harvard.edu Linux ncfws08.rc.fas.harvard.edu http://ncfws08.rc.fas.**harvard.eduhttp://ncfws08.rc.fas.harvard.edu 2.6.18-274.17.1.el5 #1 SMP Tue Jan 10 17:25:58 EST 2012 x86_64 x86_64 x86_64 GNU/Linux nIters 1 --** /ncf/vcn/Maryam/mri-space/**studies/Obj4catmulti/** unpackdata/130321_xu_**Object4catmulti_01 mri_convert /ncf/vcn/Maryam/mri-space/**subjects/blue_street_kcb/mri/**brainmask.mgz bold/018/tmp.bbregister.1228/**fslregister/refvol.**fslregister.nii mri_convert /ncf/vcn/Maryam/mri-space/**subjects/blue_street_kcb/mri/**brainmask.mgz bold/018/tmp.bbregister.1228/**fslregister/refvol.**fslregister.nii $Id: mri_convert.c,v 1.179.2.2 2011/05/16 20:53:47 greve
[Freesurfer] R: Re: R: Re: Problem with tracula: incomplete or lacking tracts
Hi Anastasia,now I have correct the nodif mask and run again trac-all. Is normal WARN: Could not find satisfactory control point fit - try 83Finding center streamline during -prior? Stefano Messaggio originale Da: ayend...@nmr.mgh.harvard.edu Data: 25-mar-2013 18.02 A: std...@virgilio.it Cc: freesurfer@nmr.mgh.harvard.edu Ogg: Re: [Freesurfer] R: Re: Problem with tracula: incomplete or lacking tracts I also remember that your brain masks had some big chunks of brain missing. Was whatever caused that fixed as well? On Mon, 25 Mar 2013, std...@virgilio.it wrote: Yes, I fix them. I'm attacking the maps after the last trac-all. Stefano Messaggio originale Da: ayend...@nmr.mgh.harvard.edu Data: 25-mar-2013 17.26 A: std...@virgilio.it Cc: freesurfer@nmr.mgh.harvard.edu Ogg: Re: Problem with tracula: incomplete or lacking tracts Hi Stefano - As I recall, we established that your bvecs were wrong. Did you fix them? a.y On Mon, 25 Mar 2013, std...@virgilio.it wrote: Hi Anastasia, I ran again trac-all, after checking all bvecs. Some tract are incomplete. Is possible that it depends from an error in my configuration file? I'm using to create bvecs file DTI TABLE CREATOR. Do you advice mi another one? Thanks, Stefano On Fri, 22 Mar 2013, std...@virgilio.it wrote: Thank you Anastasia. I'm checking bvecs/bvals. I obtain it by DTI table creator (http://godzilla.kennedykrieger.org/~jfarrell/OTHERphilips/GUI.html) bvecs/bvals should be done. Gradients can be the unique responsable? Stefano Messaggio originale Da: ayend...@nmr.mgh.harvard.edu Data: 22-mar-2013 17.07 A: std...@virgilio.it Cc: freesurfer@nmr.mgh.harvard.edu Ogg: Re: [Freesurfer] R: Re: R: Re: R: Re: R: R: Re: Problem with tracula: incomplete or lacking tracts Your gradient table is wrong. See where I've marked the corpus callosum in your screenshot. The eigenvectors are not pointing along the corpus callosum, but perpendicular to it. So they're off by 90 degrees, which means the same is true about the vectors in your gradient table. On Fri, 22 Mar 2013, std...@virgilio.it wrote: Hi Anastasia - I attacked the screenshots. Thanks, Stefano Messaggio originale Da: ayend...@nmr.mgh.harvard.edu Data: 22-mar-2013 1.39 A: std...@virgilio.it Cc: freesurfer@nmr.mgh.harvard.edu Ogg: Re: [Freesurfer] R: Re: R: Re: R: R: Re: Problem with tracula: incomplete or lacking tracts Hi Stefano - There's nothing in these screenshots that tells you that the eigenvectors are correct. These are vectors, so the way to check them is to display them as lines. You display dtifit_V1 as lines, overlaid on dtifit_FA. Then you see if the lines point in the right direction. a.y On Fri, 22 Mar 2013, std...@virgilio.it wrote: Here they are attacked. Thanks, Stefano Messaggio originale Da: ayend...@nmr.mgh.harvard.edu Data: 21-mar-2013 21.50 A: std...@virgilio.it Cc: freesurfer@nmr.mgh.harvard.edu Ogg: Re: R: Re: [Freesurfer] R: R: Re: Problem with tracula: incomplete or lacking tracts Can you send a screenshot that shows dtifit_V1 and dtifit_FA? On Thu, 21 Mar 2013, std...@virgilio.it wrote: I have checked the gradient directions. How can I resolve the brain mask problem. Can I send you my files of this subject? Stefano Messaggio originale Da: ayend...@nmr.mgh.harvard.edu Data: 20-mar-2013 22.46 A: std...@virgilio.it Cc: freesurfer@nmr.mgh.harvard.edu Ogg: Re: [Freesurfer] R: R: Re: Problem with tracula: incomplete or lacking tracts There are chunks of the brain missing from the brain mask. This may cause some tracts to be incomplete or missing. But you should still check that the gradient directions are correct, so you know if you have multiple problems or just one. The FA map can't tell you if the gradient table was correct, you have to check the eigenvectors in dtifit_V1 for that. On Wed, 20 Mar 2013, std...@virgilio.it wrote: File attacked Messaggio originale Da: std...@virgilio.it Data: 20-mar-2013 22.34 A: ayend...@nmr.mgh.harvard.edu Cc: freesurfer@nmr.mgh.harvard.edu Ogg: [Freesurfer] R: Re: Problem with tracula: incomplete or lacking tracts Thank you Anastasia. I'm checking gradient table but I would like underline that I'm noting some holes in dti_FA.nii.gz and not in dwi.nii.gz (I have attacked the relative images).
Re: [Freesurfer] R: Re: R: Re: Problem with tracula: incomplete or lacking tracts
Yes, it's a warning, not an error. On Mon, 25 Mar 2013, std...@virgilio.it wrote: Hi Anastasia,now I have correct the nodif mask and run again trac-all. Is normal WARN: Could not find satisfactory control point fit - try 83Finding center streamline during -prior? Stefano Messaggio originale Da: ayend...@nmr.mgh.harvard.edu Data: 25-mar-2013 18.02 A: std...@virgilio.it Cc: freesurfer@nmr.mgh.harvard.edu Ogg: Re: [Freesurfer] R: Re: Problem with tracula: incomplete or lacking tracts I also remember that your brain masks had some big chunks of brain missing. Was whatever caused that fixed as well? On Mon, 25 Mar 2013, std...@virgilio.it wrote: Yes, I fix them. I'm attacking the maps after the last trac-all. Stefano Messaggio originale Da: ayend...@nmr.mgh.harvard.edu Data: 25-mar-2013 17.26 A: std...@virgilio.it Cc: freesurfer@nmr.mgh.harvard.edu Ogg: Re: Problem with tracula: incomplete or lacking tracts Hi Stefano - As I recall, we established that your bvecs were wrong. Did you fix them? a.y On Mon, 25 Mar 2013, std...@virgilio.it wrote: Hi Anastasia, I ran again trac-all, after checking all bvecs. Some tract are incomplete. Is possible that it depends from an error in my configuration file? I'm using to create bvecs file DTI TABLE CREATOR. Do you advice mi another one? Thanks, Stefano On Fri, 22 Mar 2013, std...@virgilio.it wrote: Thank you Anastasia. I'm checking bvecs/bvals. I obtain it by DTI table creator (http://godzilla.kennedykrieger.org/~jfarrell/OTHERphilips/GUI.html) bvecs/bvals should be done. Gradients can be the unique responsable? Stefano Messaggio originale Da: ayend...@nmr.mgh.harvard.edu Data: 22-mar-2013 17.07 A: std...@virgilio.it Cc: freesurfer@nmr.mgh.harvard.edu Ogg: Re: [Freesurfer] R: Re: R: Re: R: Re: R: R: Re: Problem with tracula: incomplete or lacking tracts Your gradient table is wrong. See where I've marked the corpus callosum in your screenshot. The eigenvectors are not pointing along the corpus callosum, but perpendicular to it. So they're off by 90 degrees, which means the same is true about the vectors in your gradient table. On Fri, 22 Mar 2013, std...@virgilio.it wrote: Hi Anastasia - I attacked the screenshots. Thanks, Stefano Messaggio originale Da: ayend...@nmr.mgh.harvard.edu Data: 22-mar-2013 1.39 A: std...@virgilio.it Cc: freesurfer@nmr.mgh.harvard.edu Ogg: Re: [Freesurfer] R: Re: R: Re: R: R: Re: Problem with tracula: incomplete or lacking tracts Hi Stefano - There's nothing in these screenshots that tells you that the eigenvectors are correct. These are vectors, so the way to check them is to display them as lines. You display dtifit_V1 as lines, overlaid on dtifit_FA. Then you see if the lines point in the right direction. a.y On Fri, 22 Mar 2013, std...@virgilio.it wrote: Here they are attacked. Thanks, Stefano Messaggio originale Da: ayend...@nmr.mgh.harvard.edu Data: 21-mar-2013 21.50 A: std...@virgilio.it Cc: freesurfer@nmr.mgh.harvard.edu Ogg: Re: R: Re: [Freesurfer] R: R: Re: Problem with tracula: incomplete or lacking tracts Can you send a screenshot that shows dtifit_V1 and dtifit_FA? On Thu, 21 Mar 2013, std...@virgilio.it wrote: I have checked the gradient directions. How can I resolve the brain mask problem. Can I send you my files of this subject? Stefano Messaggio originale Da: ayend...@nmr.mgh.harvard.edu Data: 20-mar-2013 22.46 A: std...@virgilio.it Cc: freesurfer@nmr.mgh.harvard.edu Ogg: Re: [Freesurfer] R: R: Re: Problem with tracula: incomplete or lacking tracts There are chunks of the brain missing from the brain mask. This may cause some tracts to be incomplete or missing. But you should still check that the gradient directions are correct, so you know if you have multiple problems or just one. The FA map can't tell you if the gradient table was correct, you have to check the eigenvectors in dtifit_V1 for that. On Wed, 20 Mar 2013, std...@virgilio.it wrote: File attacked Messaggio originale Da: std...@virgilio.it Data: 20-mar-2013 22.34 A: ayend...@nmr.mgh.harvard.edu Cc: freesurfer@nmr.mgh.harvard.edu Ogg: [Freesurfer] R: Re: Problem with tracula: incomplete or lacking tracts Thank you Anastasia. I'm checking gradient table but I would like underline that I'm noting some holes in dti_FA.nii.gz and not in dwi.nii.gz (I have attacked the relative images).
Re: [Freesurfer] advice in registering a binary mask to Freesurfer space.
Hi Doug, Is a standard 12 affine registration sufficient to get a subjects structural (in a different orientation) into the same space as norm.mgz, or will I need some non-linear registration? Basically, what kind of transforms are applied to go from orig to norm? - Joshua Lee Graduate Student Center for Mind and Brain Department of Psychology University of California, Davis 530.747.3805 On Mon, Mar 25, 2013 at 10:52 AM, Joshua Lee jki...@ucdavis.edu wrote: Hi Doug. That was in fact what I decided to do. Thanks! Josh - J On Mon, Mar 25, 2013 at 7:38 AM, Douglas N Greve gr...@nmr.mgh.harvard.edu wrote: Can you compute the registration between the manually traced anat space and the FS conformed space? Eg, with BBR. If you can do that, then you can run mri_label2vol to convert the mask into FS conformed space (assuming that that is what you want to do). doug On 03/22/2013 04:43 PM, Joshua Lee wrote: Hi All, I wanted to get peoples advice on the best method of registration/interpolation to use on a manually traced segmentation (and its structural) that is not in the same space and orientation as the structurals I started Freesurfer with (although they both originally came from the same image. I want to maintain the integrity of the manual traced binary mask through this registration and reslice. For a number of reasons, I do not want to take Freesurfers output to the space of the manual segmentation. What do people think is a good technique? Flirt nearest neighbor interpolation? Something different from Freesurfer? ANTs? - Josh ___ 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 Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ___ 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 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] bbregister error with hardi data
yep, looks right On 03/25/2013 03:12 PM, Corinna Bauer wrote: Also, I now want to apply the inverse transform to move the T1 into the HARDI space. Did I do this correctly? It looks good in tkregister. mri_vol2vol --mov hardi/ffiltered_func_data_01.nii.gz --targ mri/orig.mgz --reg register.dat --inv --o mri-in-hardi.nii On Mon, Mar 25, 2013 at 1:47 PM, Corinna Bauer corinna...@gmail.com mailto:corinna...@gmail.com wrote: ahhh, yes, that's it. sorry my oversight. On Mon, Mar 25, 2013 at 1:45 PM, Douglas N Greve gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu wrote: Are you sure you made the right edit? It should be --fsvol $fsvol.mgz It looks like you might have changed it to --fsvol.mgz $fsvol On 03/25/2013 01:30 PM, Corinna Bauer wrote: Ok I adjusted the bbregister file to say fsvol.mgz in the location you specified and got this error a bit later on in the bbregister output: setenv SUBJECTS_DIR /usr/local/freesurfer/subjects/symmetry cd /usr/local/freesurfer/subjects/symmetry/lindsay /usr/local/freesurfer/bin/bbregister --s lindsay --mov hardi/ffiltered_func_data_01.nii.gz --dti --init-fsl --reg register.dat $Id: bbregister,v 1.49.2.2 2013/02/23 01:32:22 mreuter Exp $ Linux lotfi 3.2.0-38-generic #61-Ubuntu SMP Tue Feb 19 12:18:21 UTC 2013 x86_64 x86_64 x86_64 GNU/Linux FREESURFER_HOME /usr/local/freesurfer mri_convert hardi/ffiltered_func_data_01.nii.gz ./tmp.bbregister.15807/template.nii mri_convert hardi/ffiltered_func_data_01.nii.gz ./tmp.bbregister.15807/template.nii $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from hardi/ffiltered_func_data_01.nii.gz... TR=17843.91, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-0.991204, -0.025762, 0.129811) j_ras = (-0.0259819, 0.999662, 0) k_ras = (0.129768, 0.00337275, 0.991539) writing to ./tmp.bbregister.15807/template.nii... fslregister --s lindsay --mov ./tmp.bbregister.15807/template.nii --reg ./tmp.bbregister.15807/reg.init.dat --niters 1 --maxangle 90 --nobetmov --tmp ./tmp.bbregister.15807/fslregister --dof 6 --fsvol.mgz brainmask ERROR: Flag --fsvol.mgz unrecognized. --s lindsay --mov ./tmp.bbregister.15807/template.nii --reg ./tmp.bbregister.15807/reg.init.dat --niters 1 --maxangle 90 --nobetmov --tmp ./tmp.bbregister.15807/fslregister --dof 6 --fsvol.mgz brainmask mri_segreg --mov ./tmp.bbregister.15807/template.nii --init-reg ./tmp.bbregister.15807/reg.init.dat --out-reg ./tmp.bbregister.15807/bbr.pass1.dat --subsamp-brute 100 --subsamp 100 --tol 1e-4 --tol1d 1e-3 --brute -4 4 4 --surf white --gm-proj-frac 0.5 --gm-gt-wm 0.5 regio_read_register(): No such file or directory Could not open ./tmp.bbregister.15807/reg.init.dat mri_segreg --mov ./tmp.bbregister.15807/template.nii --init-reg ./tmp.bbregister.15807/bbr.pass1.dat --out-reg register.dat --brute -0.1 0.1 0.1 --interp trilinear --wm-proj-abs 2 --tol 1e-8 --tol1d 1e-3 --c0 0 --mincost register.dat.mincost --dof 6 --nmax 36 --param register.dat.param --surf white --cur-reg ./tmp.bbregister.15807/reg.curopt.dat --gm-proj-frac 0.5 --nsub 1 --gm-gt-wm 0.5 regio_read_register(): No such file or directory Could not open ./tmp.bbregister.15807/bbr.pass1.dat Cleaning up Started at Mon Mar 25 13:24:53 EDT 2013 Ended at Mon Mar 25 13:25:00 EDT 2013 BBR-Run-Time-Sec 7 bbregister Done To check results, run: tkregister2 --mov hardi/ffiltered_func_data_01.nii.gz --reg register.dat --surf On Mon, Mar 25, 2013 at 1:22 PM, Douglas N Greve gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu wrote: Corinna, can you edit $FREESURFER_HOME/bin/bbregister? If so, change the following line From set cmd = (fslregister --s $subject --mov $regvol --reg $InitReg \ --niters 1 --maxangle 90 --tmp $tmpdir/fslregister \ --dof $FSLDOF --fsvol $fsvol) To set cmd = (fslregister --s $subject --mov $regvol --reg $InitReg \
Re: [Freesurfer] advice in registering a binary mask to Freesurfer space.
Hi Josh, there are no spatial transforms to go from orig to norm. They are in the same space. cheers Bruce On Mon, 25 Mar 2013, Joshua Lee wrote: Hi Doug, Is a standard 12 affine registration sufficient to get a subjects structural (in a different orientation) into the same space as norm.mgz, or will I need some non-linear registration? Basically, what kind of transforms are applied to go from orig to norm? - Joshua Lee Graduate Student Center for Mind and Brain Department of Psychology University of California, Davis 530.747.3805 On Mon, Mar 25, 2013 at 10:52 AM, Joshua Lee jki...@ucdavis.edu wrote: Hi Doug. That was in fact what I decided to do. Thanks! Josh - J On Mon, Mar 25, 2013 at 7:38 AM, Douglas N Greve gr...@nmr.mgh.harvard.edu wrote: Can you compute the registration between the manually traced anat space and the FS conformed space? Eg, with BBR. If you can do that, then you can run mri_label2vol to convert the mask into FS conformed space (assuming that that is what you want to do). doug On 03/22/2013 04:43 PM, Joshua Lee wrote: Hi All, I wanted to get peoples advice on the best method of registration/interpolation to use on a manually traced segmentation (and its structural) that is not in the same space and orientation as the structurals I started Freesurfer with (although they both originally came from the same image. I want to maintain the integrity of the manual traced binary mask through this registration and reslice. For a number of reasons, I do not want to take Freesurfers output to the space of the manual segmentation. What do people think is a good technique? Flirt nearest neighbor interpolation? Something different from Freesurfer? ANTs? - Josh ___ 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 Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ___ 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] Incomplete and poorly formed tracts
Hi Susan - Good to hear that you get good results for most of your subjects. Have you checked the aparc+aseg and the diffusion-to-anatomical registration for the subjects that are failing? I'd check the aparc+aseg_mask (in the dlabel/diff directory) over the FA map to see if there are any holes or misregistration. a.y On Mon, 25 Mar 2013, Susan Kuo wrote: Hi FreeSurfers and Anastasia, TRACULA is working great for me, generating tracts for a sample of 20 subject brains I'm working with. However, for 3 of the brains, I'm receiving incomplete and poorly formed tracts. I've re-run trac-all at least 2x on each subject in case there was a mistake in my original configuration. However, I am reproducing the same results. Does anybody have an idea why I would see these spotty tracts? Thank you for all your help! -- Susie Kuo NIH ___ 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] problem with registration in preprocessing
I ran it in 5.2, and it works, but it does crash with the same error using 5.1. I have an explanation for what is happening, but it is not very satisfying:). There is a part of the FSL code that is inverting a matrix. If the matrix does not have certain properties, then it cannot be inverted. FreeSurfer creates the matrix that FSL is trying to invert. This matrix is very slightly different in 5.1 vs 5.2 (by slight, I mean one of the values is 239.199 instead of 239.198). This appears to be enough to push the matrix over the edge and make it non-invertible. I'm not sure what to tell you to do. For this subject, you can use -init-spm instead. doug On 03/25/2013 03:12 PM, Maryam Vaziri Pashkam wrote: I have trouble uploading files on the freesurfer page. I have put the files here: http://www.wjh.harvard.edu/~mvaziri/preproctest.tar http://www.wjh.harvard.edu/%7Emvaziri/preproctest.tar I was initially running the analysis on harvard ncf network on one of the workstations. The fsl version there is fsl-4.1.7 and the freesurfer version is freesurfer 5.1. I ran the preprocessing on this run separately and got the same error. However when I transferred the files to my macintosh computer (iMAC) and ran the analysis on my computer which has the same version of freesurfer I did not get any errors and the preprocessing completed successfully. This is very puzzling as it seems to be specific to the harvard network. Any idea where the problem might be? Maryam On Mon, Mar 25, 2013 at 12:23 PM, Douglas N Greve gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu wrote: Can you tar up the subject and the last run and drop it to me on our file drop system? doug On 03/25/2013 12:07 PM, Maryam wrote: The raw images of the last run seems fine. And it is only the last run out of 12. M On Mar 25, 2013, at 10:36 AM, Douglas N Greve gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu wrote: Hi Maryam, I'm not sure what is wrong. Can you check the image in bold/018 to make sure that there is not something horribly wrong? Eg, it is not a localizer or only has one slice. And it is only the last run? The others are ok? doug On 03/22/2013 03:05 PM, Maryam Vaziri Pashkam wrote: Hi Doug, I am running fsfast preprocessing on my data and I am getting an error on one of the runs. This is the preprocessing code that I run: preproc-sess -s 130321_xu_Object4catmulti_01 -per-run -sliceorder siemens -fsd bold -fwhm 0 -mni305-2mm -surface self lhrh The error seems to happen during the fsl registration on the last run (out of 12 runs): /ncf/vcn/Maryam/mri-space/studies/Obj4catmulti/unpackdata/130321_xu_Object4catmulti_01 flirt.fsl -ref bold/018/tmp.bbregister.1228/fslregister/refvol.fslregister.nii -in bold/018/tmp.bbregister.1228/fslregister/movvol.fslregister.nii -bins 256 -cost corratio -dof 6 -searchrx -90 90 -searchry -90 90 -searchrz -90 90 -verbose 0 -omat bold/018/tmp.bbregister.1228/reg.init.dat.fsl.mat -init bold/018/tmp.bbregister.1228/fslregister/fslmat0.trans.mat -schedule /ncf/apps/freesurfer-5.1.0//bin/flirt.newdefault.20080811.sch terminate called after throwing an instance of 'NEWMAT::SingularException' Abort ERROR: flirt bellow is the register-sess log file. I have only included the section for the registration of the last run. I have looked at the raw data of this run and it does not look different from the other runs (all other runs are successfully registered). I am running freesurfer 5.1. Any idea how I can fix the error? Thanks, Maryam $Id: bbregister,v 1.49 2011/03/06 23:38:41 greve Exp $ Linux ncfws08.rc.fas.harvard.edu http://ncfws08.rc.fas.harvard.edu http://ncfws08.rc.fas.harvard.edu 2.6.18-274.17.1.el5 #1 SMP Tue Jan 10 17:25:58 EST 2012 x86_64 x86_64 x86_64 GNU/Linux FREESURFER_HOME /ncf/apps/freesurfer-5.1.0/ mri_convert bold/018/template.nii.gz bold/018/tmp.bbregister.1228/template.nii mri_convert bold/018/template.nii.gz bold/018/tmp.bbregister.1228/template.nii $Id: mri_convert.c,v 1.179.2.2 2011/05/16 20:53:47 greve
Re: [Freesurfer] advice in registering a binary mask to Freesurfer space.
yes, the norm means intensity normalized, not spatially normalized:) doug On 03/25/2013 04:56 PM, Bruce Fischl wrote: Hi Josh, there are no spatial transforms to go from orig to norm. They are in the same space. cheers Bruce On Mon, 25 Mar 2013, Joshua Lee wrote: Hi Doug, Is a standard 12 affine registration sufficient to get a subjects structural (in a different orientation) into the same space as norm.mgz, or will I need some non-linear registration? Basically, what kind of transforms are applied to go from orig to norm? - Joshua Lee Graduate Student Center for Mind and Brain Department of Psychology University of California, Davis 530.747.3805 On Mon, Mar 25, 2013 at 10:52 AM, Joshua Lee jki...@ucdavis.edu wrote: Hi Doug. That was in fact what I decided to do. Thanks! Josh - J On Mon, Mar 25, 2013 at 7:38 AM, Douglas N Greve gr...@nmr.mgh.harvard.edu wrote: Can you compute the registration between the manually traced anat space and the FS conformed space? Eg, with BBR. If you can do that, then you can run mri_label2vol to convert the mask into FS conformed space (assuming that that is what you want to do). doug On 03/22/2013 04:43 PM, Joshua Lee wrote: Hi All, I wanted to get peoples advice on the best method of registration/interpolation to use on a manually traced segmentation (and its structural) that is not in the same space and orientation as the structurals I started Freesurfer with (although they both originally came from the same image. I want to maintain the integrity of the manual traced binary mask through this registration and reslice. For a number of reasons, I do not want to take Freesurfers output to the space of the manual segmentation. What do people think is a good technique? Flirt nearest neighbor interpolation? Something different from Freesurfer? ANTs? - Josh ___ 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 Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ___ 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. -- 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 Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] advice in registering a binary mask to Freesurfer space.
I see. To clarify. orig is the conformed version of the original input file, which means just sampling to 1 mm as needed, and cropping to 256 matrix. norm.mgz has some intensity corrections, but does not include spatial changes. I had read http://surfer.nmr.mgh.harvard.edu/fswiki/FsAnat-to-NativeAnat and I thought that maybe that spatial warping was involved beyond resampling to the original dimensions/resolution to get to native space. This simplifies things greatly. Thank you both. On Mon, Mar 25, 2013 at 1:56 PM, Bruce Fischl fis...@nmr.mgh.harvard.eduwrote: Hi Josh, there are no spatial transforms to go from orig to norm. They are in the same space. cheers Bruce On Mon, 25 Mar 2013, Joshua Lee wrote: Hi Doug, Is a standard 12 affine registration sufficient to get a subjects structural (in a different orientation) into the same space as norm.mgz, or will I need some non-linear registration? Basically, what kind of transforms are applied to go from orig to norm? - Joshua Lee Graduate Student Center for Mind and Brain Department of Psychology University of California, Davis 530.747.3805 On Mon, Mar 25, 2013 at 10:52 AM, Joshua Lee jki...@ucdavis.edu wrote: Hi Doug. That was in fact what I decided to do. Thanks! Josh - J On Mon, Mar 25, 2013 at 7:38 AM, Douglas N Greve gr...@nmr.mgh.harvard.edu wrote: Can you compute the registration between the manually traced anat space and the FS conformed space? Eg, with BBR. If you can do that, then you can run mri_label2vol to convert the mask into FS conformed space (assuming that that is what you want to do). doug On 03/22/2013 04:43 PM, Joshua Lee wrote: Hi All, I wanted to get peoples advice on the best method of registration/interpolation to use on a manually traced segmentation (and its structural) that is not in the same space and orientation as the structurals I started Freesurfer with (although they both originally came from the same image. I want to maintain the integrity of the manual traced binary mask through this registration and reslice. For a number of reasons, I do not want to take Freesurfers output to the space of the manual segmentation. What do people think is a good technique? Flirt nearest neighbor interpolation? Something different from Freesurfer? ANTs? - Josh __**_ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.**edu/mailman/listinfo/**freesurferhttps://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/BugReportinghttp://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/**facility/filedrop/index.htmlhttp://www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.**edu/transfer/outgoing/flat/**greve/ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ __**_ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.**edu/mailman/listinfo/**freesurferhttps://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/**compliancelinehttp://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] advice in registering a binary mask to Freesurfer space.
the orig.mgz is also changed to 1 byte/voxel. The norm.mgz is in the same space, but with the skull removed and the subcortical intensity normalization run on it. All the volumes in fact in the mri dir except rawavg.mgz are in the same coords cheers Bruce On Mon, 25 Mar 2013, Joshua Lee wrote: I see. To clarify. orig is the conformed version of the original input file, which means just sampling to 1 mm as needed, and cropping to 256 matrix. norm.mgz has some intensity corrections, but does not include spatial changes. I had read http://surfer.nmr.mgh.harvard.edu/fswiki/FsAnat-to-NativeAnat and I thought that maybe that spatial warping was involved beyond resampling to the original dimensions/resolution to get to native space. This simplifies things greatly. Thank you both. On Mon, Mar 25, 2013 at 1:56 PM, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: Hi Josh, there are no spatial transforms to go from orig to norm. They are in the same space. cheers Bruce On Mon, 25 Mar 2013, Joshua Lee wrote: Hi Doug, Is a standard 12 affine registration sufficient to get a subjects structural (in a different orientation) into the same space as norm.mgz, or will I need some non-linear registration? Basically, what kind of transforms are applied to go from orig to norm? - Joshua Lee Graduate Student Center for Mind and Brain Department of Psychology University of California, Davis 530.747.3805 On Mon, Mar 25, 2013 at 10:52 AM, Joshua Lee jki...@ucdavis.edu wrote: Hi Doug. That was in fact what I decided to do. Thanks! Josh - J On Mon, Mar 25, 2013 at 7:38 AM, Douglas N Greve gr...@nmr.mgh.harvard.edu wrote: Can you compute the registration between the manually traced anat space and the FS conformed space? Eg, with BBR. If you can do that, then you can run mri_label2vol to convert the mask into FS conformed space (assuming that that is what you want to do). doug On 03/22/2013 04:43 PM, Joshua Lee wrote: Hi All, I wanted to get peoples advice on the best method of registration/interpolation to use on a manually traced segmentation (and its structural) that is not in the same space and orientation as the structurals I started Freesurfer with (although they both originally came from the same image. I want to maintain the integrity of the manual traced binary mask through this registration and reslice. For a number of reasons, I do not want to take Freesurfers output to the space of the manual segmentation. What do people think is a good technique? Flirt nearest neighbor interpolation? Something different from Freesurfer? ANTs? - Josh ___ 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 Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ___ 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] algorithm mris_anatomical_stats
Hi, Is it possible to get the algorithm of mris_anatomicacl_Stats. Just ot know which files it uses to compute metrics ... Thanks. VP___ 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] Pial error (over estimation)
That is pretty bad. I'll try to investigate soon if you can upload the subject Bruce On Mar 25, 2013, at 9:44 PM, Charles Malpas c.mal...@student.unimelb.edu.au wrote: Dear Freesurfer experts, I am having a strange problem with a single brain. Freesurfer is over estimating the pial surface by a great deal. Two things are weird: (a) it occurs to the same brain scanned 6 months apart, and (b) it doesn't occur is 5.1 (I am using 5.2 now). I have attached some screen shots. Any help would be greatly appreciated! Kind regards, - Charles ***apologies if you receive this message twice, I seem to have problems posting to the list*** -- Charles Malpas Master of Psychology (Clinical Neuropsychology) / PhD Candidate Melbourne School of Psychological Sciences Department of Medicine (RMH) The University of Melbourne 3010 Melbourne Brain Centre @ RMH Neuropsychiatry Research Group Level 4, Main Building, Royal Melbourne Hospital Phone: 0451 116 434 Email: c.mal...@student.unimelb.edu.au Skype: charles.malpas 1.png 2.png ___ 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] Pial error (over estimation)
Thanks Bruce, I have uploaded the directory (I think) to the ftp site (/incoming/incoming/407-M087). Please let me know if it doesn't arrive and I will try again. Kind regards, - Charles On 26 March 2013 12:53, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: That is pretty bad. I'll try to investigate soon if you can upload the subject Bruce On Mar 25, 2013, at 9:44 PM, Charles Malpas c.mal...@student.unimelb.edu.au wrote: Dear Freesurfer experts, I am having a strange problem with a single brain. Freesurfer is over estimating the pial surface by a great deal. Two things are weird: (a) it occurs to the same brain scanned 6 months apart, and (b) it doesn't occur is 5.1 (I am using 5.2 now). I have attached some screen shots. Any help would be greatly appreciated! Kind regards, - Charles ***apologies if you receive this message twice, I seem to have problems posting to the list*** -- *Charles Malpas * Master of Psychology (Clinical Neuropsychology) / PhD Candidate Melbourne School of Psychological Sciences Department of Medicine (RMH) The University of Melbourne 3010 *Melbourne Brain Centre @ RMH* Neuropsychiatry Research Group* * Level 4, Main Building, Royal Melbourne Hospital Phone: 0451 116 434 Email: c.mal...@student.unimelb.edu.au Skype: charles.malpas 1.png 2.png ___ 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. -- *Charles Malpas * Master of Psychology (Clinical Neuropsychology) / PhD Candidate Melbourne School of Psychological Sciences Department of Medicine (RMH) The University of Melbourne 3010 *Melbourne Brain Centre @ RMH* Neuropsychiatry Research Group* * Level 4, Main Building, Royal Melbourne Hospital Phone: 0451 116 434 Email: c.mal...@student.unimelb.edu.au Skype: charles.malpas ___ 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] Linear Mixed modal
Dear experts Whether can the design of contrast in freesurfer 5.2 the same as SPM? it is difficult to make the contrast in freesurfer if the categorical variables were much more, specifically compute the interaction or F-test in study. Thanks！ Bo Xiang ___ 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.
