[Freesurfer] Convert label file to STL file
Dear Freesurfer Experts, I'm trying to convert .label file to .stl file. In more detail of my purpose, I want to get separate stl files of whole brain. Now, I want to make stl files of label files which made from ?h.aparc.a2009s.annot. First, I tried to convert lh.pial to lh.pial.stl, I've got it (this was just check how mris_convert works). Second, I copied lh. white file from surf dir into label dir. Then, I runed next command: cd subjid/label mris_convert --label lh.bankssts.label bankssts lh.white lh.bankssts.label.stl And got the error message: ERROR: unknown file annot file type specified for output: lh.bankssts.label.stl Do you know what could have gone wrong? Thank you, Yuki. ___ 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] Research position at Columbia University Medical Center {Disarmed}
The Molecular Imaging and Neuropathology Division at Columbia University Medical Center is seeking a full-time image analyst to begin working immediately. The position involves assisting in the processing of brain imaging data, including positron emission tomography (PET) and structural and functional magnetic resonance imaging (MRI). Some background in brain imaging data processing is highly desired, as well as exceptional programming and other computer skills. Applicants should have experience coding in relevant languages, including Matlab, Python, unix command line scripting, HTML and PHP. A bachelor's degree in a scientific subject and and a strong academic record are required. Candidates invited to an interview will be asked to provide references, which will be contacted. Please fill out the official application at this link (https://jobs.columbia.edu/applicants/Central?quickFind=142939) as soon as possible. We are currently interviewing candidates and seek to fill the position within the next week. ___ 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] Group analysis tutorial
Hi Qijing, Under the 'Freeview dev build' section on this wiki page you can download an updated version of freeview. http://freesurfer.net/fswiki/Download -Louis On Mon, 7 Jul 2014, Qijing Yu wrote: Hi Doug, By new version, do you mean v5.3.0? Qijing On Mon, Jul 7, 2014 at 11:31 AM, Douglas N Greve gr...@nmr.mgh.harvard.edu wrote: Yea, that is actually a feature in the new version On 07/02/2014 02:17 PM, Joshua S wrote: Hi all, I was following the group analysis tutorial when I got an error when trying to view the uncorrected significance map with freeview. I used the command freeview -f $SUBJECTS_DIR/fsaverage/surf/lh.inflated:annot=aparc.annot:overlay=lh.gende r_age.glmdir/lh-Avg-thickness-age-Cor/sig.mgh:overlay_threshold=4,5 -viewport 3d. I removed the annot_outline=1, because it gave an error. Sig.mgh would not load, and I would get the attached image. I tried to manually add sig.mgh through add surface, but the program immediatley closed, and I got the message in the attached error.log. Text below. Thank you for any help, Josh Did not find any volume geometry information in the surface ???Tgreading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan _killiany.txt) colortable with 36 entries read (originally /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan _killiany.txt) Did not find color table in track volume. [0]PETSC ERROR: [0]PETSC ERROR: Caught signal number 11 SEGV: Segmentation Violation, probably memory access out of range [0]PETSC ERROR: Try option -start_in_debugger or -on_error_attach_debugger [0]PETSC ERROR: or see http://www.mcs.anl.gov/petsc/petsc-as/documentation/troubleshooting.html#Si gnal[0]PETSC ERROR: or try http://valgrind.org on linux or man libgmalloc on Apple to find memory corruption errors [0]PETSC ERROR: configure using --with-debugging=yes, recompile, link, and run [0]PETSC ERROR: to get more information on the crash. [0]PETSC ERROR: - Error Message [0]PETSC ERROR: Signal received! [0]PETSC ERROR: [0]PETSC ERROR: Petsc Release Version 2.3.3, Patch 13, Thu May 15 17:29:26 CDT 2008 HG revision: 4466c6289a0922df26e20626fd4a0b4dd03c8124 [0]PETSC ERROR: See docs/changes/index.html for recent updates. [0]PETSC ERROR: See docs/faq.html for hints about trouble shooting. [0]PETSC ERROR: See docs/index.html for manual pages. [0]PETSC ERROR: [0]PETSC ERROR: Unknown Name on a linux-gnu named farklemt.nmr.mgh.harvard.edu http://farklemt.nmr.mgh.harvard.edu by dc325 Wed Jul 2 11:35:56 2014 [0]PETSC ERROR: Libraries linked from /autofs/space/lyon_006/pubsw/Linux2-2.3-x86_64/packages/petsc/2.3.3-p13/src /petsc-2.3.3-p13/lib/linux-gnu-c-opt [0]PETSC ERROR: Configure run at Tue Aug 10 15:01:59 2010 [0]PETSC ERROR: Configure options --with-debugging=no --with-cc=gcc --with-fc=g77 --download-f-blas-lapack=0 --download-mpich=1 --with-mpi=1 --with-x=0 --with-gnu-copyright-code=0 --with-shared=0 COPTFLAGS=-O3 CXXOPTFLAGS=-O3 FOPTFLAGS=-O3 [0]PETSC ERROR: [0]PETSC ERROR: User provided function() line 0 in unknown directory unknown file [unset]: aborting job: application called MPI_Abort(MPI_COMM_WORLD, 59) - process 0 ___ 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: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/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
Re: [Freesurfer] bad freesurfer segmentation
Hi Bruce, Thanks for your reply. In my previous e-mail I already tried to attach one of my subjects, but got the response that the message was too big, and therefore it was rejected. So how should I upload the image? The images are T1-weighted, 3D, acquired with a 3T scanner, resolution 256 256. I discovered that FSL does a proper segmentation on this subjects, so I was looking for a way to import these segments from FSL into the Freesurfer pipeline, but I didn't succeed so far. I used the white matter segment from FSL as wm.mgz (in a subject in which I already ran recon-all), I used mri_vol2vol to get this segment in the right space, and normalized with mri_normalize. Then I rerun recon-all with -autorecon2-wm. But it gives me the error message: 'ERROR: mri_segment-MRIcheckVolDims: volume1 depth=160 != volume2 depth=256.' So apparently, the wm.mgz still doesn't have the right size. Do you have any experience with this? Or any ideas about this? Best regards, Doety On 9 jul. 2014, at 15:00, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: Hi Doety yes, that looks pretty bad. Can you tell us about the acquisition? What resolution/field strength/scan type was it? If you upload the subject we will take a look cheers Bruce On Wed, 9 Jul 2014, Doety Prins wrote: Dear freesurfer experts, I experienced some problems with the segmentation of my T1 scans, as both the white surface and the pial surface are placed incorrectly (see attached images). This seems to me to be a too big difference with what it should look like, that I think could not be fixed with the standard troubleshooting strategies. Do you have any solutions for this? Is it for instance possible to make changes to the recon-all script to shift the surfaces? Thanks in advance, Doety ___ 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] Convert label file to STL file
It probably thinks the STL file is just a mesh without coloring. Peace, Matt. From: Mat yuki matsuyuki2...@outlook.jp Reply-To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Date: Thursday, July 10, 2014 at 7:19 AM To: freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] Convert label file to STL file Dear Freesurfer Experts, I'm trying to convert .label file to .stl file. In more detail of my purpose, I want to get separate stl files of whole brain. Now, I want to make stl files of label files which made from ?h.aparc.a2009s.annot. First, I tried to convert lh.pial to lh.pial.stl, I've got it (this was just check how mris_convert works). Second, I copied lh. white file from surf dir into label dir. Then, I runed next command: cd subjid/label mris_convert --label lh.bankssts.label bankssts lh.white lh.bankssts.label.stl And got the error message: ERROR: unknown file annot file type specified for output: lh.bankssts.label.stl Do you know what could have gone wrong? Thank you, Yuki. ___ 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] bad freesurfer segmentation
Hi Doety, Consider these options for uploading data: https://surfer.nmr.mgh.harvard.edu/fswiki/FtpFileExchange https://www.nmr.mgh.harvard.edu/facility/filedrop/index.html I think recon-all is expecting your wm.mgz to be conformed or 256^3. Something like: mri_convert wm.mgz wm.conform.mgz --conform You would need to rename wm.conform.mgz to wm.mgz, after renaming or saving a copy of the current non-conformed wm mask you got from FSL. -Louis On Thu, 10 Jul 2014, Doety Prins wrote: Hi Bruce, Thanks for your reply. In my previous e-mail I already tried to attach one of my subjects, but got the response that the message was too big, and therefore it was rejected. So how should I upload the image? The images are T1-weighted, 3D, acquired with a 3T scanner, resolution 256 256. I discovered that FSL does a proper segmentation on this subjects, so I was looking for a way to import these segments from FSL into the Freesurfer pipeline, but I didn't succeed so far. I used the white matter segment from FSL as wm.mgz (in a subject in which I already ran recon-all), I used mri_vol2vol to get this segment in the right space, and normalized with mri_normalize. Then I rerun recon-all with -autorecon2-wm. But it gives me the error message: 'ERROR: mri_segment-MRIcheckVolDims: volume1 depth=160 != volume2 depth=256.' So apparently, the wm.mgz still doesn't have the right size. Do you have any experience with this? Or any ideas about this? Best regards, Doety On 9 jul. 2014, at 15:00, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: Hi Doety yes, that looks pretty bad. Can you tell us about the acquisition? What resolution/field strength/scan type was it? If you upload the subject we will take a look cheers Bruce On Wed, 9 Jul 2014, Doety Prins wrote: Dear freesurfer experts, I experienced some problems with the segmentation of my T1 scans, as both the white surface and the pial surface are placed incorrectly (see attached images). This seems to me to be a too big difference with what it should look like, that I think could not be fixed with the standard troubleshooting strategies. Do you have any solutions for this? Is it for instance possible to make changes to the recon-all script to shift the surfaces? Thanks in advance, Doety ___ 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 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] combining aseg and seg_edited files for an atlas
If you have matlab, it would be pretty easy to do it there, something like
aseg = MRIread('aseg.mgz');
seg = MRIread('seg_edited.mgz');
% Your first seg inside cerebellum
indseg1 = find(seg.vol == 1 (aseg.vol == 8 | aseg.vol == 47));
% cerebellum cortex = 8 and 47, see $FREESURFER_HOME/FreeSurferColorLUT.txt
aseg.vol(indseg1) = X1; % X1 = whatever index you want for your first
segmentation, make it unique
MRIwrite(aseg,'newaseg.mgz')
On 07/09/2014 01:26 PM, N/A N/A wrote:
Hi Freesurfer forum,
I have never used the forum before but I am a long time user of
Freesurfer and I am currently working on making a new atlas for the
cerebellum. However I am having a problem loading my /seg_edited.mgz/
files into the /rebuild_gca_atlas.csh/ script. So I renamed my
/aseg.mgz/ file to /seg_edited/ and that worked but my resulting image
is not great.
I think it did not work with my original /seg_edited/ file because the
atlas needed cortex data to complete the process and my original
/seg_edited/ file did not have and my /aseg/ does.
I would like to try and combine my /aseg/ file and my original
/seg_edited/ files together but I realized that no one has apparently
asked about doing that before on your forums. Is there anyway to
combine those files?
I would appreciate any advise on the matter!
Thank you,
Alexarae Bryon
FIU student
___
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: https://gate.nmr.mgh.harvard.edu/filedrop2
www.nmr.mgh.harvard.edu/facility/filedrop/index.html
Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/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] Compiling data from lobesStrict
I don't think you need to do steps 2 and 3. Just run mri_annotomical_stats on the lobes annot just like it is done for aparc. Look in the recon-all.log file for the command line doug On 07/08/2014 02:42 PM, krista kelly wrote: Hi all, I'm trying to extract cortical thickness data from each lobe per participant. Here are the commands I used so far: 1) create annotation file for lobes: mri_annotation2label --subject $s --hemi lh --lobesStrict lh.lobesStrict.annot 2) extract lobe labels: mri_annotation2label --subject $s --hemi lh --annotation lobesStrict --outdir $s/label 3) create stats file for each lobe per participant: mris_anatomical_stats -a $s/label/lh.lobesStrict.annot -b -f $s/stats/lh.lobesStrict.stats PROBLEM: I'm stuck now on how to compile all of the data into one file. I've tried: aparcstats2table --subjects subjectlist --parc lobesStrict.annot --hemi lh –meas thickness --tablefile lh.lobesStrict.thickness.stats.txt I've also tried: asegstats2table --subjects subjectlist --subdir=stats --statsfile lh.lobesStrict --tablefile lh.lobesStrict.thickness.stats.txt None of these work. Can someone please tell me what I'm doing wrong? Thanks! Krista ___ 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: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/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] input anatomy orientation
This is expected, unfortunately. When you change the orientation, it changes the interpolation which changes things slightly. Those areas are all pretty small so the changes can appear to be large (though they are only a few percent). doug On 07/09/2014 01:42 PM, Kathy L. Pearson wrote: I have run FreeSurfer 5.3 recon-all, getting different stats output, for these cases of anatomy input: (1) mprage DICOM series converted with dcm2nii (2) fslreorient2std (RL PA IS) on the dcm2nii output (3) mprage DICOM series converted with mri_convert Differing example results include these from lh.BA.stats: case 1: BA1 1115583 2017 2.511 0.650 0.175 0.155 66 9.1 BA2 3686 2392 5986 2.342 0.615 0.123 0.047 44 7.2 case 2: BA1 1043585 2060 2.569 0.637 0.181 0.226 169 4.8 BA2 3569 2357 6064 2.397 0.612 0.123 0.050 38 5.9 case 3: BA1 1071558 1994 2.583 0.617 0.159 0.181 66 6.5 BA2 3654 2364 6191 2.461 0.631 0.121 0.058 42 6.9 Is this as expected? Are there any options that I should apply to indicate that the orientation is RL PA IS if I use the same anatomy.nii.gz file in case #2 as prepared for FSL? Or must I always either use mri_convert to generate the input for recon-all? Or is there a command I should be running first to reset my RL PA IS image to a particular orientation required by recon-all? Thanks, Kathy Pearson ___ 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: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/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] Categorical covariates with more than two levels on qdec
You cannot use qdec for this. You must use the command line stream. There is a tutorial for this as well as a presentation on our wiki. Basically, you will need to create your FSGD file, run mris_preproc, mri_surf2surf to smooth, mri_glmfit, and mri_glmfit-sim doug On 07/09/2014 03:43 AM, Isotalus, Hanna wrote: Subject: Categorical covariates with more than two levels on qdec Categorical covariates with more than two levels on qdec Dear Freesurfer experts, I am doing an analysis on a large data set gathered from eight different imaging centres. In my analysis I would like to covary for the imaging site but qdec only allows me to covary for categorical variables if they have two levels (and I have eight). I am also using age (continuous) and gender (categorical, two levels) as covariates. Is there a way of using the imaging site as a covariate using qdec? Do you have any suggestions on how I should proceed? Is treating imaging site as a continuous variable acceptable? Best wishes, Hanna ___ 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: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/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] Jacobian mri_cvs_register
Hi Andre You can run: mri_jacobian -tm3d 3d morph template volume output volume --Lilla On Thu, 10 Jul 2014, André Ribeiro wrote: Dear Freesurfer Community, How can I obtain the Jacobian of the deformation field estimated through mri_cvs_register for further use like VBM analysis? Regards, Andre Santos Ribeiro ___ 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] Jacobian mri_cvs_register
Dear Freesurfer Community, How can I obtain the Jacobian of the deformation field estimated through mri_cvs_register for further use like VBM analysis? Regards, Andre Santos Ribeiro ___ 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] Group analysis tutorial
Thank you Doug and Louis!! was stuck in something else in the past few days. I will try the new version and let you know if I still have problems viewing the results. Thanks again! Really appreciate your help! On Thu, Jul 10, 2014 at 10:57 AM, Louis Nicholas Vinke vi...@nmr.mgh.harvard.edu wrote: Hi Qijing, Under the 'Freeview dev build' section on this wiki page you can download an updated version of freeview. http://freesurfer.net/fswiki/Download -Louis On Mon, 7 Jul 2014, Qijing Yu wrote: Hi Doug, By new version, do you mean v5.3.0? Qijing On Mon, Jul 7, 2014 at 11:31 AM, Douglas N Greve gr...@nmr.mgh.harvard.edu wrote: Yea, that is actually a feature in the new version On 07/02/2014 02:17 PM, Joshua S wrote: Hi all, I was following the group analysis tutorial when I got an error when trying to view the uncorrected significance map with freeview. I used the command freeview -f $SUBJECTS_DIR/fsaverage/surf/lh.inflated:annot=aparc.annot:overlay=lh.gende r_age.glmdir/lh-Avg-thickness-age-Cor/sig.mgh:overlay_threshold=4,5 -viewport 3d. I removed the annot_outline=1, because it gave an error. Sig.mgh would not load, and I would get the attached image. I tried to manually add sig.mgh through add surface, but the program immediatley closed, and I got the message in the attached error.log. Text below. Thank you for any help, Josh Did not find any volume geometry information in the surface ???Tgreading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan _killiany.txt) colortable with 36 entries read (originally /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan _killiany.txt) Did not find color table in track volume. [0]PETSC ERROR: [0]PETSC ERROR: Caught signal number 11 SEGV: Segmentation Violation, probably memory access out of range [0]PETSC ERROR: Try option -start_in_debugger or -on_error_attach_debugger [0]PETSC ERROR: or see http://www.mcs.anl.gov/petsc/petsc-as/documentation/troubleshooting.html#Si gnal[0]PETSC ERROR: or try http://valgrind.org on linux or man libgmalloc on Apple to find memory corruption errors [0]PETSC ERROR: configure using --with-debugging=yes, recompile, link, and run [0]PETSC ERROR: to get more information on the crash. [0]PETSC ERROR: - Error Message [0]PETSC ERROR: Signal received! [0]PETSC ERROR: [0]PETSC ERROR: Petsc Release Version 2.3.3, Patch 13, Thu May 15 17:29:26 CDT 2008 HG revision: 4466c6289a0922df26e20626fd4a0b4dd03c8124 [0]PETSC ERROR: See docs/changes/index.html for recent updates. [0]PETSC ERROR: See docs/faq.html for hints about trouble shooting. [0]PETSC ERROR: See docs/index.html for manual pages. [0]PETSC ERROR: [0]PETSC ERROR: Unknown Name on a linux-gnu named farklemt.nmr.mgh.harvard.edu http://farklemt.nmr.mgh.harvard.edu by dc325 Wed Jul 2 11:35:56 2014 [0]PETSC ERROR: Libraries linked from /autofs/space/lyon_006/pubsw/Linux2-2.3-x86_64/packages/petsc/2.3.3-p13/src /petsc-2.3.3-p13/lib/linux-gnu-c-opt [0]PETSC ERROR: Configure run at Tue Aug 10 15:01:59 2010 [0]PETSC ERROR: Configure options --with-debugging=no --with-cc=gcc --with-fc=g77 --download-f-blas-lapack=0 --download-mpich=1 --with-mpi=1 --with-x=0 --with-gnu-copyright-code=0 --with-shared=0 COPTFLAGS=-O3 CXXOPTFLAGS=-O3 FOPTFLAGS=-O3 [0]PETSC ERROR: [0]PETSC ERROR: User provided function() line 0 in unknown directory unknown file [unset]: aborting job: application called MPI_Abort(MPI_COMM_WORLD, 59) - process 0 ___ 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: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html
Re: [Freesurfer] combining aseg and seg_edited files for an atlas
Thank you Douglas for the suggestion, I will try this method!
Alexarae
On Thu, Jul 10, 2014 at 11:43 AM, Douglas N Greve gr...@nmr.mgh.harvard.edu
wrote:
If you have matlab, it would be pretty easy to do it there, something like
aseg = MRIread('aseg.mgz');
seg = MRIread('seg_edited.mgz');
% Your first seg inside cerebellum
indseg1 = find(seg.vol == 1 (aseg.vol == 8 | aseg.vol == 47));
% cerebellum cortex = 8 and 47, see $FREESURFER_HOME/FreeSurferColorLUT.txt
aseg.vol(indseg1) = X1; % X1 = whatever index you want for your first
segmentation, make it unique
MRIwrite(aseg,'newaseg.mgz')
On 07/09/2014 01:26 PM, N/A N/A wrote:
Hi Freesurfer forum,
I have never used the forum before but I am a long time user of
Freesurfer and I am currently working on making a new atlas for the
cerebellum. However I am having a problem loading my /seg_edited.mgz/
files into the /rebuild_gca_atlas.csh/ script. So I renamed my
/aseg.mgz/ file to /seg_edited/ and that worked but my resulting image
is not great.
I think it did not work with my original /seg_edited/ file because the
atlas needed cortex data to complete the process and my original
/seg_edited/ file did not have and my /aseg/ does.
I would like to try and combine my /aseg/ file and my original
/seg_edited/ files together but I realized that no one has apparently
asked about doing that before on your forums. Is there anyway to
combine those files?
I would appreciate any advise on the matter!
Thank you,
Alexarae Bryon
FIU student
___
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: https://gate.nmr.mgh.harvard.edu/filedrop2
www.nmr.mgh.harvard.edu/facility/filedrop/index.html
Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/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.
[Freesurfer] Question about LGI
Hi FS Community, I was wondering whether LGI and Surface Area need to be corrected for total Intracranial Volume. Thanks in advance, Panos ___ 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] Question about LGI
Hi Panos, It all depends on what your question is: whether the between-group difference in LGI and surface area is an absolute difference (then don't correct), or whether you want to see if it holds after correction. In any case, by geometric definition, the relationship between surface area, and thus LGI, and volume is governed by a power law, which means that if you linearly correct for intracranial volume, some of its effect will remain. Hope it helps, Marie On Jul 10, 2014, at 10:57 AM, pfot...@nmr.mgh.harvard.edu wrote: Hi FS Community, I was wondering whether LGI and Surface Area need to be corrected for total Intracranial Volume. Thanks in advance, Panos ___ 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] Question about LGI
Hi Marie, Thank you for your reply. I wanted to compare the LGI and Surface Area between two cohorts, from which one has a significantly higher intracranial volume than the other. I was wondering about the correction because the results, especially in the case of SA, are the opposite before and after correcting for total intraranial volume, and for LGI, it just removed the significance of the association. Thanks again, Panos Hi Panos, It all depends on what your question is: whether the between-group difference in LGI and surface area is an absolute difference (then don't correct), or whether you want to see if it holds after correction. In any case, by geometric definition, the relationship between surface area, and thus LGI, and volume is governed by a power law, which means that if you linearly correct for intracranial volume, some of its effect will remain. Hope it helps, Marie On Jul 10, 2014, at 10:57 AM, pfot...@nmr.mgh.harvard.edu wrote: Hi FS Community, I was wondering whether LGI and Surface Area need to be corrected for total Intracranial Volume. Thanks in advance, Panos ___ 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 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] Understanding Hippocampal volume stats
Hi, Freesurfer reported the following hippocampal volumes for a subject volumeInVoxels: right_CA1: 2652.3 right_CA2_3: 7245.11 right_CA4_DG: 3967.28 right_fimbria: 423.555 right_hippocampal_fissure: 191.897 right_presubiculum: 3598.99 right_subiculum: 4868.1 Right-Hippocampus: 3258.77 I have two questions about it 1. I don’t understand why the right_subiculum volume is more than the Right-Hippocampus volume. 2. Since the voxel size for the volumes is 0.5^mm, do we have to divide these volumes by 8 to convert them to voxel size 1^mm so that we can do direct comparison with other freesurfer stats volume (for example the volumes in rh.aparc.stats)? Thanks --Mohammad Zia This e-mail message, including any attachments, is for the sole use of the intended recipient(s) and may contain confidential and privileged information. Any unauthorized review, use, disclosure or distribution is prohibited. If you are not the intended recipient, please contact the sender by e-mail and destroy all copies of the original. ___ 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] Tracula
Hello, I have a few questions about Tracula. I am very new to DTI, so I hope you can bare with me. 1.) I have been checking my registration at the prep stage. I am very new to this so it may be that I am not looking at the right files. I looked at my eddy current corrected diffusion data (which I believe is in data.nii.gz in the dmri folder) with the no_dif_brain_mask.nii, and noticed that the no_dif_brain_mask does not cover very well for some of my subjects. Should I individually tailor the Fractional Intensity Threshold for BET mask extraction from low-b images at the prep stage? 2.) In general what files should I be checking at each phase (prep, bedpost, path)? 3.)How do you generate the whole-brain ROIS to guide the tractography (is the white matter mask that is generated at the prep phase involved)? Thanks, Emily ___ 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] Question about LGI
Hi Panos, Then I would say that it's interesting to understand why the results change depending on the correction. Here is a list of papers that may be relevant, but you'll certainly find many others: http://www.ncbi.nlm.nih.gov/pubmed/8159014 http://pages.jh.edu/~kechen/pnas-brains.pdf http://www.touchophthalmology.com/sites/www.touchoncology.com/files/migrated/articles_pdfs/schear.pdf Best, Marie On Jul 10, 2014, at 11:50 AM, pfot...@nmr.mgh.harvard.edu wrote: Hi Marie, Thank you for your reply. I wanted to compare the LGI and Surface Area between two cohorts, from which one has a significantly higher intracranial volume than the other. I was wondering about the correction because the results, especially in the case of SA, are the opposite before and after correcting for total intraranial volume, and for LGI, it just removed the significance of the association. Thanks again, Panos Hi Panos, It all depends on what your question is: whether the between-group difference in LGI and surface area is an absolute difference (then don't correct), or whether you want to see if it holds after correction. In any case, by geometric definition, the relationship between surface area, and thus LGI, and volume is governed by a power law, which means that if you linearly correct for intracranial volume, some of its effect will remain. Hope it helps, Marie On Jul 10, 2014, at 10:57 AM, pfot...@nmr.mgh.harvard.edu wrote: Hi FS Community, I was wondering whether LGI and Surface Area need to be corrected for total Intracranial Volume. Thanks in advance, Panos ___ 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 ___ 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
Re: [Freesurfer] Question about LGI
For surface area, you should correct with the ICV (note you should use ICV and not something like ICV^(2/3)) doug On 07/10/2014 04:52 PM, Marie Schaer wrote: Hi Panos, Then I would say that it's interesting to understand why the results change depending on the correction. Here is a list of papers that may be relevant, but you'll certainly find many others: http://www.ncbi.nlm.nih.gov/pubmed/8159014 http://pages.jh.edu/~kechen/pnas-brains.pdf http://www.touchophthalmology.com/sites/www.touchoncology.com/files/migrated/articles_pdfs/schear.pdf Best, Marie On Jul 10, 2014, at 11:50 AM, pfot...@nmr.mgh.harvard.edu wrote: Hi Marie, Thank you for your reply. I wanted to compare the LGI and Surface Area between two cohorts, from which one has a significantly higher intracranial volume than the other. I was wondering about the correction because the results, especially in the case of SA, are the opposite before and after correcting for total intraranial volume, and for LGI, it just removed the significance of the association. Thanks again, Panos Hi Panos, It all depends on what your question is: whether the between-group difference in LGI and surface area is an absolute difference (then don't correct), or whether you want to see if it holds after correction. In any case, by geometric definition, the relationship between surface area, and thus LGI, and volume is governed by a power law, which means that if you linearly correct for intracranial volume, some of its effect will remain. Hope it helps, Marie On Jul 10, 2014, at 10:57 AM, pfot...@nmr.mgh.harvard.edu wrote: Hi FS Community, I was wondering whether LGI and Surface Area need to be corrected for total Intracranial Volume. Thanks in advance, Panos ___ 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 ___ 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 -- 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: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] ACPC alignment in freeview?
Hello Freesurfer experts: I am wondering if I can do ACPC alignment in freeview. Perhaps using Tools Transform volume and then rotating using landmarks. Is this indeed possible? If so, can anyone provide guidance on the 3 landmarks to select (would it be anterior commissure superior posterior edges posterior commissure) and how to map these landmarks to coordinate axis vectors? I would appreciate it. Thanks in advance, Tracy Riggins ___ 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] Convert label file to STL file
Hi Matt, Thank you for your reply. It is impossible to convert label file to stl file, is it wright? If it was so, do you know how to get it? I want to get stl files which divided into each percellation, if its possible. Thanks in advance, Yuki. Date: Thu, 10 Jul 2014 10:25:19 -0500 From: m...@ma-tea.com To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Convert label file to STL file It probably thinks the STL file is just a mesh without coloring. Peace, Matt. From: Mat yuki matsuyuki2...@outlook.jp Reply-To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Date: Thursday, July 10, 2014 at 7:19 AM To: freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] Convert label file to STL file Dear Freesurfer Experts, I'm trying to convert .label file to .stl file. In more detail of my purpose, I want to get separate stl files of whole brain. Now, I want to make stl files of label files which made from ?h.aparc.a2009s.annot. First, I tried to convert lh.pial to lh.pial.stl, I've got it (this was just check how mris_convert works). Second, I copied lh. white file from surf dir into label dir. Then, I runed next command: cd subjid/label mris_convert --label lh.bankssts.label bankssts lh.white lh.bankssts.label.stl And got the error message: ERROR: unknown file annot file type specified for output: lh.bankssts.label.stl Do you know what could have gone wrong? Thank you, Yuki. ___ 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.___ 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.
