Freesurfer

freesurfer@nmr.mgh.harvard.edu

19 participants
30088 discussions

Combining 'accelerated' vs 'non-accelerated' data in ongitudinal analyses
by Irwin, William 23 Jul '11

23 Jul '11

Hello- Our group occasionally encounters patients with various syndromes such that 'excessive' head movement is an issue. One solution on which we rely is acquiring an "accelerated" MPRAGE sequences (Siemens GRAPPA) which takes about ½ the time. For those not familiar with this method, the resulting image is noisier and the contrast-to-noise is reduced. Quantitatively, because of the increased noise in the accelerated acquisition, comparisons of the correlation between regional cortical thickness reveals that the covariance is different between data acquired with the accelerated vs. non-accelerated sequences. If the longitudinal processing stream is used, is the issue of differing covariance between the 2 acquisitions method an issue? If so, does anyone have a suggestion about to deal with this issue? I should add, there is no systematic issue such as one patient group always requires using the accelerated sequence. Regards, Wil

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Aseg and Cerebellum
by Murray, Michael 22 Jul '11

22 Jul '11

Hi all, We've using version 5.1 to conduct a longitudinal study involving over 150 subjects with up to three time points apiece, and we're having some issues with regards to aseg in the areas around the cerebellum. Attached is an image of the problem - some dura or something else is being classified as cerebellum. It's particularly troubling because this issue is present in most of our images, but to varying degrees. We've tried adjusting the watershed parameters (using multistrip) as well as using gcut, but neither method was effective in removing the offending voxels. It seems like our only other option is to manually edit the brainmask.mgz, but with so many subjects and time points, we're wondering if there is another automated fix that we haven't tried. Otherwise, is this something that we'll have to manually fix, or can it be left alone? Thank you, Michael Murray

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PySurfer - A package for visualizing surfaces
by Michael Waskom 22 Jul '11

22 Jul '11

Dear Freesurfers, We are pleased to announce the 0.1 release of PySurfer, a Python-based package for the visualization of surface data from Freesurfer. Please see our website at http://pysurfer.github.com/ for information on how to install the package and a gallery of examples. We hope you'll find it useful in your research! Best, Michael Waskom Alexandre Gramfort Scott Burns

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Re: [Freesurfer] dcm conversion to nii
by Bruce Fischl 22 Jul '11

22 Jul '11

Hi Antonella, for each acquisition you give mri_convert *one* dicom file in that series and it will figure out the rest. You will then have one volume file per series. Something like: mri_convert <one .dcm file in the Ax_PD series) Ax_PD.nii.gz cheers Bruce On Thu, 21 Jul 2011, Antonella Kis wrote: > Good morning Bruce, > > Thank you for your answer and yes, I am posting my question to the list. > > For all my other subjects I had the MRI data converted by somebody else into one file .nii.gz for each subject. My question is how I can > convert the MRI data (.dcm) for a new subject in a .nii.gz file? I have multiple file from MRI: 3DAx_T1, 3DSag_T1, Ax_Flair, Ax_PD, Ax_T2, > BOLD, DTI_15, DTI_32 each of them containing lots of .dcm files. Do I need to convert all of them? If I give mri_convert one slice in each > dicom series and convert each one to it's own volume how I can further use this data? Do I get an .nii.gz for each dicom file? > > I attached a type of file .nii.gz from another subject so you can see what type of files I need to get by conversion. > > Thank you very much. > Antonella > > > From: Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> > To: Antonella Kis <atorok9(a)yahoo.com> > Sent: Wednesday, July 20, 2011 4:12 PM > Subject: Re: dcm conversion to nii > > Hi Antonella > > can you post this type of question to the list so others can answer? I don't think you want them in one file as they probably have > different resolution etc... Give mri_convert one slice in each dicom series and convert each one to it's own volume. > > cheers > Bruce > On Wed, 20 Jul 2011, Antonella Kis wrote: > > > Dear Bruce, > > > > I have the MRI data (.dcm) for my subject p27 within the following files: > > > > 3DAx_T1, 3DSag_T1, Ax_Flair, Ax_PD, Ax_T2, BOLD, DTI_15, DTI_32. > > > > I would like to convert this data into one file.nii.gz. It will be correct if I will run: > > > > mri_convert p27 NPI027.nii.gz? > > > > Will FS know to convert based on this statement all my dcm files into one nii.gz file? If not how should I do it? > > > > > > Many thanks. > > Antonella > > > > > > > > > > > > > > > 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. > > > >

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trac-all -bedp error
by phoebe＠nmr.mgh.harvard.edu 21 Jul '11

21 Jul '11

Hi, I run the trac-all bedp process and it comes up with the following errors: 56 slices processed 56 slices processed 57 slices processed Queuing post processing stage 58 slices processed For some reason the bedpostX process DOES NOT appear to have successfully completed. Please examine your results carefully. /usr/local/freesurfer/stable5_1_0/bin/bedpostx_seychelles: line 281: kill: (12876) - No such process When I look at the processed data in dmri.bedpostx, I couldn't identify the problem. Kindly help. Phoebe. -- ___________________________________ Phoebe Suk-tak Chan, Ph.D. Athinoula A. Martinos Center for Biomedical Imaging Massachusetts General Hospital Bldg. 149, 13th St., mailcode 149-2301 Charlestown, MA 02129 phoebe(a)nmr.mgh.harvard.edu

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Re: [Freesurfer] Problem registering labels to native space
by John Richey 21 Jul '11

21 Jul '11

Quick update: this fix worked brilliantly. Many thanks for the help, J Richey -----Original Message----- From: Douglas N Greve [mailto:greve@nmr.mgh.harvard.edu] Sent: Monday, July 18, 2011 5:20 PM To: John Richey Cc: 'Bruce Fischl'; 'freesurfer(a)nmr.mgh.harvard.edu' Subject: Re: [Freesurfer] Problem registering labels to native space In that case, try this instead doug # Create a register.dat to fsaverage/mni305 cd $SUBJECTS_DIR/subject/mri tkregister2 --s subject --targ orig.mgz \ --ixfm transforms/talairach.xfm --zero-cras \ --reg transforms/talairach.reg.dat \ --mov $FREESURFER_HOME/subjects/fsaverage/mri/orig.mgz \ --noedit # Create a register.dat to the 2mm version of fsaverage/mni305 mri_matrix_multiply \ -im $FREESURFER_HOME/subjects/fsaverage/mri.2mm/reg.2mm.dat \ -im transforms/talairach.reg.dat \ -om transforms/mni305.2mm.reg.dat # Check tkregister2 --reg transforms/mni305.2mm.reg.dat \ --mov $FREESURFER_HOME/subjects/fsaverage/mri.2mm/orig.mgz \ --surfs # Run label2label mri_label2label --srclabel mni305.2mm.label \ --trglabel $SUBJECTS_DIR/subject/labels/mni305.2mm.label \ --regmethod volume \ --reg $SUBJECTS_DIR/subject/mri/transforms/mni305.2mm.reg.dat \ --xfm-invert John Richey wrote: > Hi Doug, this is indeed an fsfast analysis. I used the fsaverage > subject included with the 5.1 distribution. Here is the code that I > used to produce the registration matrix for one subject. Note that I > did use mri_convert to change the .mgz files into .nii.gz > > The use of flirt (below) is more of an ad-hoc solution to register > each subject's anatomical image to fsaverage. I'm not wedded to this > method if there's a better alternative. > > bet ${SUBJECTS_DIR}/${SUBJECT}/mri/nu.nii.gz \ > ${SUBJECTS_DIR}/${SUBJECT}/mri/nu_bet.nii.gz \ -f 0.3 -g 0 > > flirt -in ${SUBJECTS_DIR}/${SUBJECT}/mri/nu_bet.nii.gz \ -ref > ${SUBJECTS_DIR}/fsaverage/mri/brain.nii.gz \ -out > ${SUBJECTS_DIR}/${SUBJECT}/mri/nu_bet_reg.nii.gz \ -omat > ${SUBJECTS_DIR}/${SUBJECT}/mri/nu_bet_reg.mat \ -bins 256 -cost > corratio -searchrx -90 90 -searchry -90 90 \ -searchrz -90 90 -dof 12 > -interp trilinear > > cd $SUBJECTS_DIR > tkregister2 --targ $SUBJECTS_DIR/${SUBJECT}/mri/nu_bet_reg.nii.gz \ > --mov $SUBJECTS_DIR/fsaverage/mri/brain.nii.gz \ --fsl > $SUBJECTS_DIR/${SUBJECT}/mri/nu_bet_reg.mat \ --reg > $SUBJECTS_DIR/${SUBJECT}/mri/nu_bet_reg.dat \ --noedit > > > > -----Original Message----- > From: Douglas N Greve [mailto:greve@nmr.mgh.harvard.edu] > Sent: Monday, July 18, 2011 3:11 PM > To: John Richey > Cc: 'Bruce Fischl'; 'freesurfer(a)nmr.mgh.harvard.edu' > Subject: Re: [Freesurfer] Problem registering labels to native space > > How did you create it? What is the actual "fsaverage space"? Is this > an FSFAST analysis? > doug > > John Richey wrote: > >> Hi Doug, the .dat file that I mention below had already been >> converted >> > into > >> a fs matrix using tkregister2. >> >> -----Original Message----- >> From: Douglas N Greve [mailto:greve@nmr.mgh.harvard.edu] >> Sent: Monday, July 18, 2011 12:38 PM >> To: John Richey >> Cc: 'Bruce Fischl'; 'freesurfer(a)nmr.mgh.harvard.edu' >> Subject: Re: [Freesurfer] Problem registering labels to native space >> >> You can't use a flirt matrix with mri_label2label. You can convert a >> flirt matrix to the proper format with tkregister2 using the --fsl >> option (this will allow you to check the reg as well). >> >> doug >> >> John Richey wrote: >> >> >>> Hi Bruce, >>> >>> The labels that I have fsaverage space are 3D/volume-based and not >>> surface-based labels. >>> >>> >>> -----Original Message----- >>> From: Bruce Fischl [mailto:fischl@nmr.mgh.harvard.edu] >>> Sent: Monday, July 18, 2011 12:00 PM >>> To: John Richey >>> Cc: 'freesurfer(a)nmr.mgh.harvard.edu' >>> Subject: RE: [Freesurfer] Problem registering labels to native space >>> >>> Hi John >>> >>> why are you using an affine volume registration for fsaverage? Why >>> not use surface registration? >>> >>> Bruce >>> >>> >>> On Mon, 18 Jul 2011, John Richey wrote: >>> >>> >>> >>> >>>> Hi Bruce - thanks for the reply. >>>> >>>> Here is my command line: >>>> >>>> mri_label2label --srcsubject fsaverage \ --trgsubject ${SUBJECT} >>>> --srclabel $SUBJECTS_DIR/group_analysis/${CONTRAST}/${LABEL} \ >>>> --trglabel $SUBJECTS_DIR/${SUBJECT}/label/${CONTRAST}_${LABEL} \ >>>> --regmethod volume \ --reg $SUBJECTS_DIR/$SUBJECT/mri/brain_reg.dat >>>> >>>> Where "brain_reg.dat" is the subject-specific matrix I created >>>> through FLIRT. However, as I mentioned, disincluding this matrix >>>> does not seem to change the result much. >>>> >>>> One other problem I encounter... Occasionally when I view the >>>> label in native space, the label itself seems to be eroded on a >>>> voxel-wise >>>> >>>> >>>> >>> basis. >>> >>> >>> >>>> That is, the label essentially appears as a series of >>>> non-contiguous dots (which if dialated would become contiguous). >>>> >>>> >>>> >>>> >>>> >>>> >>>> -----Original Message----- >>>> From: Bruce Fischl [mailto:fischl@nmr.mgh.harvard.edu] >>>> Sent: Monday, July 18, 2011 11:20 AM >>>> To: John Richey >>>> Cc: 'freesurfer(a)nmr.mgh.harvard.edu' >>>> Subject: Re: [Freesurfer] Problem registering labels to native >>>> space >>>> >>>> Hi John >>>> >>>> can you email us your label2label cmdline? >>>> >>>> cheers >>>> Bruce >>>> >>>> >>>> On Mon, 18 Jul 2011, John Richey >>>> wrote: >>>> >>>> >>>> >>>> >>>>> Dear freesurfer experts, >>>>> >>>>> I have a series of labels corresponding to clusters of significant >>>>> activation in fsaverage space. >>>>> >>>>> I want to map these back to native space using mri_label2label, >>>>> however when I view the individual (native) labels, the >>>>> registration is way off and the labels do not map into plausible space. >>>>> >>>>> I have tried using talairach space as an intemediary (by omitting >>>>> the --reg flag in mri_label2label), as well as using fsl tools >>>>> (FLIRT) to create a registration matrix but unfortunately I cannot >>>>> seem to get the label into the right space to query my ces maps in >>>>> >>>>> >> funcroi-sess. >> >> >>>>> Have others encountered this problem? And how might I create a >>>>> more robust registration between fsaverage and native space to >>>>> facilitate the spatial transformation of my labels? >>>>> >>>>> Thanks very much in advance, >>>>> John >>>>> _______________________________________________ >>>>> Freesurfer mailing list >>>>> Freesurfer(a)nmr.mgh.harvard.edu >>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>>>> >>>>> >>>>> >>>>> >>>>> >>>>> >>>> The information in this e-mail is intended only for the person to >>>> whom it is addressed. If you believe this e-mail was sent to you in >>>> error and the e-mail contains patient information, please contact >>>> the Partners Compliance HelpLine at >>>> http://www.partners.org/complianceline >>>> . If the e-mail was sent to you in error but does not contain >>>> patient information, please contact the sender and properly dispose >>>> of the >>>> >>>> >> e-mail. >> >> >>>> >>>> >>>> >>> _______________________________________________ >>> Freesurfer mailing list >>> Freesurfer(a)nmr.mgh.harvard.edu >>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>> >>> >>> >>> >>> >> -- >> Douglas N. Greve, Ph.D. >> MGH-NMR Center >> greve(a)nmr.mgh.harvard.edu >> Phone Number: 617-724-2358 >> Fax: 617-726-7422 >> >> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting >> FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html >> >> >> >> > > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > greve(a)nmr.mgh.harvard.edu > Phone Number: 617-724-2358 > Fax: 617-726-7422 > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html > > > -- Douglas N. Greve, Ph.D. MGH-NMR Center greve(a)nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html

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Segmentation Fault during mri_ca_normalize
by Tali Swisher 21 Jul '11

21 Jul '11

Hi all, I was having consistent errors with two cases during mri_ca_normalize, and after using an updated version (mri_ca_normalize_centos), one case went through smoothly. I'm having trouble with the second case, however; it now repeatedly reports a segmentation fault partway through mri_ca_normalize (error message below) - any ideas?? Thanks! Tali Swisher #@# CA Normalize Thu Jul 21 12:25:47 EDT 2011 /home/pnlstaff/freesurfer/subjects/umd_V2_20110711/mri mri_ca_normalize -mask brainmask.mgz nu.mgz /share/apps/freesurfer4.0.5/average/RB_all_2008-03-26.gca transforms/talairach.lta norm.mgz using MR volume brainmask.mgz to mask input volume... reading 1 input volumes reading atlas from '/share/apps/freesurfer4.0.5/average/RB_all_2008-03-26.gca'... reading transform from 'transforms/talairach.lta'... reading input volume from nu.mgz... resetting wm mean[0]: 102 --> 107 resetting gm mean[0]: 64 --> 64 input volume #1 is the most T1-like using real data threshold=19.0 using (122, 88, 141) as brain centroid... mean wm in atlas = 107, using box (106,72,120) --> (137, 104,162) to find MRI wm before smoothing, mri peak at 215 after smoothing, mri peak at 214, scaling input intensities by 0.500 scaling channel 0 by 0.5 using 244171 sample points... INFO: compute sample coordinates transform 1.134 0.005 0.006 -38.602; 0.006 1.132 0.138 -19.653; 0.004 -0.150 1.048 -20.038; 0.000 0.000 0.000 1.000; INFO: transform used finding control points in Left_Cerebral_White_Matter.... found 41584 control points for structure... bounding box (142, 46, 61) --> (202, 147, 218) Left_Cerebral_White_Matter: limiting intensities to 97.0 --> 111.0 19 of 76 (25.0%) samples deleted finding control points in Right_Cerebral_White_Matter.... found 40735 control points for structure... bounding box (87, 48, 60) --> (144, 148, 219) Right_Cerebral_White_Matter: limiting intensities to 95.0 --> 107.0 27 of 73 (37.0%) samples deleted finding control points in Left_Cerebellum_White_Matter.... found 3012 control points for structure... bounding box (146, 122, 85) --> (188, 161, 136) Left_Cerebellum_White_Matter: limiting intensities to 92.0 --> 105.0 5 of 18 (27.8%) samples deleted finding control points in Right_Cerebellum_White_Matter.... found 2764 control points for structure... bounding box (103, 122, 83) --> (144, 160, 137) Right_Cerebellum_White_Matter: limiting intensities to 95.0 --> 108.0 0 of 7 (0.0%) samples deleted finding control points in Brain_Stem.... found 3520 control points for structure... bounding box (130, 115, 118) --> (158, 176, 147) Segmentation fault Linux compute-2-1.local 2.6.9-34.ELsmp #1 SMP Fri Feb 24 16:56:28 EST 2006 x86_64 x86_64 x86_64 GNU/Linux recon-all exited with ERRORS at Thu Jul 21 12:28:18 EDT 2011 -- Talis M. Swisher, BA Research Assistant Psychiatry Neuroimaging Laboratory Harvard Medical School, Brigham and Women's Hospital 1249 Boylston St, 3rd Floor Boston, MA 02215 Office: (617) 525-6119 Cell: (336) 577-5071 Fax: (617) 525-6150

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literature about multiple comparison correction
by Tetiana Dadakova 21 Jul '11

21 Jul '11

Dear list, Could you please recommend the literature about multiple comparisons correction, especially about Monte-Carlo simulation. Thank you, Tanja.

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Re: [Freesurfer] Calculate WM, GM and CSF volume
by Fellhauer, Iven 21 Jul '11

21 Jul '11

Hi Bruce, Yes, I would like to reduce the required calculation time, until desired results are available. Best regards, Iven -----Ursprüngliche Nachricht----- Von: Bruce Fischl [mailto:fischl@nmr.mgh.harvard.edu] Gesendet: Mittwoch, 20. Juli 2011 15:19 An: Fellhauer, Iven Cc: freesurfer(a)nmr.mgh.harvard.edu Betreff: Re: [Freesurfer] Calculate WM, GM and CSF volume Hi Iven, is there a reason you don't want to just run recon-all -all? It's more time for the computer, but no more for you and will give you a lot more measures cheers Bruce On Wed, 20 Jul 2011, Fellhauer, Iven wrote: > Dear All, > > I want to calculate the volume of WM, GM and CSF. First of all I have converted the .mri files to .mgz files. I have checked the ReconAllDevTable page to get the recon-all switches to calculate the volume of GM, WM and CFS. > > I want to use the following switches to calculate the volume, but I' m not sure if this works/is right: > recon-all -autorecon1 - gcareg -canorm -careg -rmneck -skull-lta > -calabel -segstatts -subject <subject> > > Did I miss something? Is there a better/faster way to get/calculate the volumes? The command returns the correct results? > > Best regards, > > Iven Fellhauer > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.

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Tracula with individual bvecs files
by Jürgen Hänggi 21 Jul '11

21 Jul '11

Dear FS and Tracula experts Because of correction for slice angulation during scanning, I have as many bvecs files as subjects. Therefore I created a list for the bvecs set bvecslist = (b101/bvecs b102/bvecs) but tracula reports the following error: mv: rename /Users/juergenhaenggi/Desktop/Tracula/Results/b101/dmri/dwi_orig_flip.mghdti .bvecs to /Users/juergenhaenggi/Desktop/Tracula/Results/b101/dmri/bvecs: No such file or directory However, when using set bvecsfile, everthing works fine. Any idea how to deal with more than one bvecs file? Thanks in advance Regards Jürgen ---------------------------------------------------------------------------- Jürgen Hänggi, Ph.D. Division Neuropsychology Institute of Psychology University of Zurich Binzmuehlestrasse 14, PO Box 25 8050 Zurich, Switzerland 0041 44 635 73 97 (phone office) 0041 76 445 86 84 (phone mobile) 0041 44 635 74 09 (fax office) BIN 4.D.04 (office room number) j.haenggi[at]psychologie.uzh.ch (email) http://www.psychologie.uzh.ch/neuropsy/ (website) http://www.juergenhaenggi.ch (private website) This e-mail (and any attachment/s) contains confidential and/or privileged information. If you are not the intended recipient (or have received this e-mail in error) please notify the sender immediately and destroy this e-mail. Any unauthorised copying, disclosure or distribution of the material in this e-mail is strictly forbidden. ----------------------------------------------------------------------------

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