Freesurfer

freesurfer@nmr.mgh.harvard.edu

16 participants
30084 discussions

Trackvis/ Diffusion Toolkit
by Alan Francis 13 Nov '15

13 Nov '15

Hi Anastasia: It was great to meet you at the connectivity course at Martinos. I have been using Trackvis to examine the white matter tracks between the anterior insula and the Dorsal ACC. In line with your instruction, I created ROIS at each of these regions. However, the WM tracks generated do not appear to connect. I have attached a screenshot. What is the command that one would use to connect the ROIs? thanks so much, best regards, Alan -- |~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~| *Alan N. Francis PhD* NIDA T32 Fellow in Computational Neuroscience Brain Imaging Center McLean Hospital Harvard Medical School 115 Mill Street, Belmont, MA 02478 alanf(a)bwh.harvard.edu <ezra_wegbreit(a)brown.edu> afrancis(a)mclean.harvard.edu |~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|

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counting voxels in seeds
by André Schmidt 13 Nov '15

13 Nov '15

Dear FS experts, Using recon-all I defined 82 regions for a probabilistic tractography analysis. To address volume differences across regions, I like to normalize the obtained streamlines by the number of voxels in each regions. Is there an easy way to count voxels within each of my 82 regions? Thanks for your help André

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qdec analysis with ICV
by Hirsch, Gabriella 13 Nov '15

13 Nov '15

Hi Freesurfer Experts, I am hoping someone can help me solve this error I'm experiencing while conducting a simple qdec analysis. I have 4 subjects (3 vs 1) that I am trying to analyze for volume differences using a demeaned ICV as a nuisance factor (see attached fsgd file - note I changed the .dat extension as my email server didn't like the dat format). However, I am getting this error: Normalized matrix condition is 1e+08 Design matrix ------------------ 0.000 1.000 0.000 -28915.199; 0.000 1.000 0.000 194736.703; 0.000 1.000 0.000 -184311.000; 1.000 0.000 18489.000 0.000; -------------------------------- ERROR: matrix is ill-conditioned or badly scaled, condno = 1e+08 -------------------------------- Possible problem with experimental design: Check for duplicate entries and/or lack of range of continuous variables within a class. If you seek help with this problem, make sure to send: 1. Your command line: mri_glmfit --y /media/seagate_external_/freesurfer_subjects/qdec/Untitled/y.mgh --fsgd /media/seagate_external_/freesurfer_subjects/qdec/Untitled/qdec.fsgd dods --glmdir /media/seagate_external_/freesurfer_subjects/qdec/Untitled --surf fsaverage rh --label /media/seagate_external_/freesurfer_subjects/fsaverage/label/rh.aparc.label --C /media/seagate_external_/freesurfer_subjects/qdec/Untitled/contrasts/rh-Avg-Intercept-volume.mat --C /media/seagate_external_/freesurfer_subjects/qdec/Untitled/contrasts/rh-Avg-volume-ICV-Cor.mat --C /media/seagate_external_/freesurfer_subjects/qdec/Untitled/contrasts/rh-Diff-CVI-PVL-Intercept-volume.mat --C /media/seagate_external_/freesurfer_subjects/qdec/Untitled/contrasts/rh-Diff-CVI-PVL-Cor-volume-ICV.mat 2. The FSGD file (if using one) 3. And the design matrix above Error in Analyze: command failed: mri_glmfit --y /media/seagate_external_/freesurfer_subjects/qdec/Untitled/y.mgh --fsgd /media/seagate_external_/freesurfer_subjects/qdec/Untitled/qdec.fsgd dods --glmdir /media/seagate_external_/freesurfer_subjects/qdec/Untitled --surf fsaverage rh --label /media/seagate_external_/freesurfer_subjects/fsaverage/label/rh.aparc.label --C /media/seagate_external_/freesurfer_subjects/qdec/Untitled/contrasts/rh-Avg-Intercept-volume.mat --C /media/seagate_external_/freesurfer_subjects/qdec/Untitled/contrasts/rh-Avg-volume-ICV-Cor.mat --C /media/seagate_external_/freesurfer_subjects/qdec/Untitled/contrasts/rh-Diff-CVI-PVL-Intercept-volume.mat --C /media/seagate_external_/freesurfer_subjects/qdec/Untitled/contrasts/rh-Diff-CVI-PVL-Cor-volume-ICV.mat There are no duplicate entries. I have done this same analysis with a higher number of subjects without problems. I have also tried using the inbuilt qdec ICV (which is not demeaned) and got the same error. Could this be a problem with the small subject count? If so, is there any way to remedy it? Thank you! Gabriella * Confidentiality Notice: If you have received this e-mail in error, please immediately notify the sender by replying to this e-mail, keeping the original message intact. Please do not "Reply All." After replying to the sender, please delete this e-mail from your files. Information contained in this e-mail is only for the use of the individual(s) or entity for whom it is intended, even if addressed incorrectly.

1 0

Orientation of neural dipoles from Freesurfer
by Daniel Lindh 13 Nov '15

13 Nov '15

Hi, I am looking for a way of figuring out the orientation vector of the neurons within a voxel. That is, in which direction is the dipole of the neurons pointing at. This could be possible to calculate if there is a way of determining the position of the inner and outer layer for each voxel, which I am assuming is something Freesurfer does when it calculates gray matter thickness. If you could direct me to some relevant literature or an online tutorial I would be extremely grateful. best regards Daniel

2 2

Longitudinally processed thickness measures
by Worker, Amanda 13 Nov '15

13 Nov '15

Hi All, I have processed some longitudinal data (0, 1 week, 4 weeks) using the advised longitudinal stream. This is a healthy control sample and I wasn't expecting to see any differences in cortical thickness over the time points. Looking at some of the measures I have noticed that something doesn't seem quite right e.g. for one subject the insula measures: Cross-sectional Longitudinal Base A 2.835 3.016 B 2.721 1.864 C 3.050 3.107 3.098 The majority the longitudinally processed data looks reasonable, but there are a few instances where one timepoint looks completely different. Do you have any ideas if something may have gone wrong? I have attached the recon-all.log files for the template and the 3 longitudinally processed timepoints. Thanks in advance for your help, Amanda

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Re: [Freesurfer] Talairach_afd error (Bruce Fischl)
by Anna I. Garcia Diaz 13 Nov '15

13 Nov '15

Hi Bruce, The recon-all.log file from the tailaraich processes on reads as follows: #@# Talairach Tue Sep 22 13:07:35 CEST 2015 /psiquiatria/home/anna/subjects/prova/mri talairach --i orig.mgz --xfm transforms/talairach.auto.xfm /psiquiatria/home/anna/subjects/prova/mri /psiquiatria/software/freesurfer/bin/talairach --i orig.mgz --xfm transforms/talairach.auto.xfm $Id: talairach,v 1.7 2011/03/02 20:16:40 nicks Exp $ Linux blade01 2.6.32.12-0.7-default #1 SMP 2010-05-20 11:14:20 +0200 x86_64 x86_64 x86_64 GNU/Linux Tue Sep 22 13:07:36 CEST 2015 tmpdir is transforms/tmp.talairach.22322 /psiquiatria/home/anna/subjects/prova/mri mri_convert orig.mgz transforms/tmp.talairach.22322/src.mnc mri_convert orig.mgz transforms/tmp.talairach.22322/src.mnc input_transform(): error reading transform elem [1,1] input_transform: error reading transform. error loading transform from /psiquiatria/home/anna/subjects/prova/mri/transforms/talairach.xfm $Id: mri_convert.c,v 1.179.2.2 2011/05/16 20:53:47 greve Exp $ reading from orig.mgz... TR=2300.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 5.40604e-09, 3.72529e-09) j_ras = (0, 0, -1) k_ras = (-6.90488e-09, 1, 4.65661e-10) writing to transforms/tmp.talairach.22322/src.mnc... -------------------------------------------- mritotal -verbose -debug -clobber -modeldir /psiquiatria/software/freesurfer/mni/bin/../share/mni_autoreg -protocol icbm transforms/tmp.talairach.22322/src.mnc transforms/talairach.auto.xfm Tue Sep 22 13:08:01 CEST 2015 talairach done INFO: transforms/talairach.xfm already exists! The new transforms/talairach.auto.xfm will not be copied to transforms/talairach.xfm This is done to retain any edits made to transforms/talairach.xfm Add the -clean-tal flag to recon-all to overwrite transforms/talairach.xfm #-------------------------------------------- #@# Talairach Failure Detection Tue Sep 22 13:08:02 CEST 2015 /psiquiatria/home/anna/subjects/prova/mri talairach_afd -T 0.005 -xfm transforms/talairach.xfm ltMNIreadEx: could not read row 1 from transforms/talairach.xfm (Linear_Transform = ) ERROR: talairach_afd::Load_xfm(): could not parse transforms/talairach.xfm Manual Talairach alignment may be necessary, or include the -notal-check flag to skip this test, making sure the -notal-check flag follows -all or -autorecon1 in the command string. See http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Talairach Linux blade01 2.6.32.12-0.7-default #1 SMP 2010-05-20 11:14:20 +0200 x86_64 x86_64 x86_64 GNU/Linux recon-all -s prova exited with ERRORS at Tue Sep 22 13:08:04 CEST 2015 For more details, see the log file /psiquiatria/home/anna/subjects/prova/scripts/recon-all.log To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting Also, a recon-all.error file was created, and says the following: SUBJECT prova DATE Mon Sep 28 18:56:32 CEST 2015 USER anna HOST blade07 PROCESSOR x86_64 OS Linux Linux blade07 2.6.32.12-0.7-default #1 SMP 2010-05-20 11:14:20 +0200 x86_64 x86_64 x86_64 GNU/Linux $Id: recon-all,v 1.379.2.17 2011/05/20 22:48:18 nicks Exp $ /psiquiatria/software/freesurfer/bin/recon-all PWD /psiquiatria/home/anna/subjects/prova/mri CMD mri_nu_correct.mni --i orig.mgz --o nu.mgz --uchar transforms/talairach.xfm --n 2 (The same exact recon-all.error file appears when using the -notal-check flag) Kind regards, Anna Garcia On Wed, Oct 28, 2015 at 2:36 PM, <freesurfer-request(a)nmr.mgh.harvard.edu> wrote: > Send Freesurfer mailing list submissions to > freesurfer(a)nmr.mgh.harvard.edu > > To subscribe or unsubscribe via the World Wide Web, visit > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > or, via email, send a message with subject or body 'help' to > freesurfer-request(a)nmr.mgh.harvard.edu > > You can reach the person managing the list at > freesurfer-owner(a)nmr.mgh.harvard.edu > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of Freesurfer digest..." > > > Today's Topics: > > 1. mri_parse_sdcmdir splitting a single series into two? > (Oliver Hinds) > 2. Postdoc Positions for the Adolescent Brain Cognitive > Development (ABCD) study (Don Hagler) > 3. Re: FreeSurfer pve correction tool (Mohamed Ali Bahri) > 4. Re: A mixed effect model approach in within subject dataset > {Disarmed} (Martin Reuter) > 5. Re: FreeSurfer pve correction tool (Douglas N Greve) > 6. Understanding the brainstem AtlasMesh file structure format > (Jonathan Plasencia) > 7. Re: comparison of 4 groups: mri_glmfit or Qdec? (Sandy Schramm) > 8. Re: Talairach_afd error (Bruce Fischl) (Bruce Fischl) > 9. error finding Matlab (Jason Haberman) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Tue, 27 Oct 2015 15:14:25 -0400 (EDT) > From: Oliver Hinds <ohinds(a)nmr.mgh.harvard.edu> > Subject: [Freesurfer] mri_parse_sdcmdir splitting a single series into > two? > To: freesurfer(a)nmr.mgh.harvard.edu > Message-ID: > <alpine.LRH.2.20.1510271455210.6558(a)gate.nmr.mgh.harvard.edu> > Content-Type: text/plain; charset=US-ASCII > > Hi, > > I'm running into an issue where the slices from one DICOM series are being > parsed by mri_parse_sdcmdir (and mri_info and mri_convert) as two separate > series. > > A few example lines from a scan.out: > > 6 AR_t.s40.c0 ok 64 64 41 1 <long file name> > 7 AR_t.s40.c0 ok 64 64 23 1 <different long file name> > > The scan AR_t.s40.c0 was run as a single series on the scanner, with 64 > slices. Inspection of the dicom header shows that the series UID is the > same for the DICOM files in each, except there is an extra string '.0.0.0' > at the end of series UID in the DICOMS that are parsed into the second > series. > > Has anyone else experienced this behavior? If so, is there a workaround? > > Thanks, > Oliver > > > > > ------------------------------ > > Message: 2 > Date: Tue, 27 Oct 2015 13:41:36 -0700 > From: Don Hagler <dhaglerjr(a)hotmail.com> > Subject: [Freesurfer] Postdoc Positions for the Adolescent Brain > Cognitive Development (ABCD) study > To: freesurfer(a)nmr.mgh.harvard.edu > Message-ID: <BLU436-SMTP65024FB31221FBD3A8E848A6220(a)phx.gbl> > Content-Type: text/plain; charset="us-ascii" > > Postdoc Positions for the Adolescent Brain Cognitive Development (ABCD) > study > > > > University of California, San Diego > > > > Several funded postdoctoral positions are available in image analysis > method development, including automated cortical- and subcortical > segmentation, advanced diffusion tractography, and fMRI mapping and time > series analysis. We are looking to build a team to help build the next > generation of analysis pipelines and visualization tools for a newly funded > study to follow 10,000 children with longitudinal structural and functional > imaging across 19 sites across the US. The study will use a cross-platform > Harmonized Human Connectome Protocol, optimized for quantitative accuracy > and consistency of imaging biomarkers across scanners and time. To learn > more about the ABCD study, please see > http://www.drugabuse.gov/news-events/news-releases/2015/09/nih-launches-lan… > < > http://www.drugabuse.gov/news-events/news-releases/2015/09/nih-launches-lan… > >. > > > > Requirements: Applicants should have research experience in any of the > above fields, with a Ph.D. or equivalent degree. They should be comfortable > working in a distributed team environment, and should have a track record > of quality scientific publications. Candidates are expected to be > experienced in programming with Matlab, Python, and/or <> C/C++. Experience > with FreeSurfer, FSL, and the Human Connectome analysis pipelines is > strongly preferred. > > > > To formally apply, submit a current CV, a personal statement describing > your research experience and interests, and contact information for 2-3 > references to abcd(a)ucsd.edu <mailto:abcd@ucsd.edu>. Or feel free to email > Dr. Donald Hagler (dhagler(a)ucsd.edu <mailto:dhagler@ucsd.edu>) or Anders > M. Dale (amdale(a)ucsd.edu <mailto:amdale@ucsd.edu>) for more information. > > > > The University of California, San Diego is an Equal > Opportunity/Affirmative Action Employer advancing inclusive excellence. All > qualified applicants will receive consideration for employment without > regard to race, color, religion, sex, sexual orientation, gender identity, > national origin, disability, age, protected veteran status, or other > protected categories covered by the UC nondiscrimination policy. >

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TRACULA bedpostx error
by denizzgursel 13 Nov '15

13 Nov '15

Hello, I am running TRACULA on one subject, I ran trac-all -prep without problem. However, when I run trac-all -bedp, it is not successfully completed. Although it says, all slices processed, it gives the error: bedpostx_mgh: line 345: kill: (18735) - No such process I am missing many outputs such as mean_s0samples, mean_dsamples, dyads_dispersion that are necessary for reconstruction of the pathways. Does anybody have an idea how to solve this? Thanks. Best, -- Deniz

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R: Re: R: Re: R: Re: R: Re: error MRS voxel as seed in FS-FAST
by stdp82＠virgilio.it 13 Nov '15

13 Nov '15

Thanks. But the MRS_mask should be in Tal, MNI or native? Now I'm using a masks that overlaps orig.nii.gz. Second, if I would like to create a sphere and use it as seed, there is a specific command line? Stefano >----Messaggio originale---- >Da: greve(a)nmr.mgh.harvard.edu >Data: 9-nov-2015 23.24 >A: <freesurfer(a)nmr.mgh.harvard.edu> >Ogg: Re: [Freesurfer] R: Re: R: Re: R: Re: error MRS voxel as seed in FS-FAST > >So that mask has 22926 non-zero voxels? The only other thing I can think >of is that the registration is off. Have you checked that? > >On 11/06/2015 07:16 AM, stdp82(a)virgilio.it wrote: >> I hope that this information are fine >> >> fslinfo $SUBJECTS_DIR/Control22/MRS_MASK.nii.gz >> data_type FLOAT32 >> dim1 256 >> dim2 256 >> dim3 256 >> dim4 1 >> datatype 16 >> pixdim1 1.000000 >> pixdim2 1.000000 >> pixdim3 1.000000 >> pixdim4 0.000000 >> cal_max 0.0000 >> cal_min 0.0000 >> file_type NIFTI-1+ >> >> >> fslstats $SUBJECTS_DIR/Control22/MRS_MASK.nii.gz -V >> 22926 22926.000000 >> >> Thanks, >> >> >> Stefano >> >> >>> ----Messaggio originale---- >>> Da: greve(a)nmr.mgh.harvard.edu >>> Data: 5-nov-2015 23.43 >>> A: <freesurfer(a)nmr.mgh.harvard.edu> >>> Ogg: Re: [Freesurfer] R: Re: R: Re: error MRS voxel as seed in FS- >> FAST >>> How many non-zero voxels are in MRS_MASK.mgz? Is MRS_MASK.mgz 256^3, >> 1mm3 ? >>> On 11/05/2015 04:47 PM, stdp82(a)virgilio.it wrote: >>>> Please see the file attached. >>>> Thanks >>>> >>>> Stefanofile >>>> >>>> ----Messaggio originale---- >>>> Da: greve(a)nmr.mgh.harvard.edu >>>> Data: 5-nov-2015 15.43 >>>> A: <freesurfer(a)nmr.mgh.harvard.edu> >>>> Ogg: Re: [Freesurfer] R: Re: error MRS voxel as seed in FS- FAST >>>> >>>> sorry, should have been >>>> >>>> fcseed-sess -debug -s Control22_FS -cfg MRS_MASK.config |& tee >> doug.log >>>> >>>> >>>> On 11/4/15 6:05 PM, stdp82(a)virgilio.it wrote: >>>>> Hi Dough, >>>>> in summary: >>>>> I have the MRS_MASK.mgz within $SUBJECTS_DIR/Control22/mri >>>>> thus, I have copy this file in fMRI directory >> (fMRI/Control22_FS) the >>>>> MRS_MASK.mgz >>>>> and run: >>>>> fcseed-config -segid 1 -seg Control22_FS/MRS_MASK.mgz -fsd >> rest -mean - >>>>> cfg MRS_MASK.config >>>>> fcseed-sess -s Control22_FS -cfg MRS_MASK.config >>>>> >>>>> ...Writing to >>>>> >> /Applications/freesurfer/subjects/fMRI/Control22_FS/rest/001/tmp. >> fcseed- >>>>> sess.12305/avgwf.mgh >>>>> Segmentation fault >>>>> >>>>> Therefore, according with your suggestion, I have now run: >>>>> fcseed-sess -debug -s -cfg MRS_MASK.config | & tee doug.log >>>>> ERROR: cound not find session -cfg >>>>> >>>>> The doug.log is attached. >>>>> >>>>> Thanks, >>>>> >>>>> >>>>> Stefano >>>>> >>>>> >>>>> >>>>> >>>>>> ----Messaggio originale---- >>>>>> Da:greve@nmr.mgh.harvard.edu >>>>>> Data: 4-nov-2015 16.58 >>>>>> A:<freesurfer(a)nmr.mgh.harvard.edu> >>>>>> Ogg: Re: [Freesurfer] error MRS voxel as seed in FS-FAST >>>>>> >>>>>> First, when running fcseed-config, don't give it the full >> path, just >>>>> the >>>>>> path relative to subject/mri (in this case only MRS_MASK. mgz) >>>>>> >>>>>> However, I don't think that is the problem. Please run >>>>>> >>>>>> fcseed-sess -debug -s -cfg MRS_MASK.config |& tee doug.log >>>>>> >>>>>> and send me doug.log >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> On 11/04/2015 04:14 AM,stdp82(a)virgilio.it wrote: >>>>>>> Hi list, this error is still occurring: >>>>>>> >>>>>>> mri_convert $SUBJECTS_DIR/subj/mri/MRS_MASK.nii.gz >>>>>>> $SUBJECTS_DIR//subj/mri/MRS_MASK.mgz >>>>>>> fcseed-config -segid 1 -seg $SUBJECTS_DIR//subj/mri/MRS_MASK. >> mgz - >>>>> fsd >>>>>>> rest -mean -cfg MRS_MASK.config >>>>>>> fcseed-sess -s -cfg MRS_MASK.config >>>>>>> >>>>>>> During >>>>>>> >>>>>>> fcseed-sess -s subj -cfg MRS_MASK.config >>>>>>> >>>>>>> Voxel Volume is 64.5752 mm^3 >>>>>>> Generating list of segmentation ids >>>>>>> Found 1 segmentations >>>>>>> Computing statistics for each segmentation >>>>>>> 0 1 0 >> 0.000 >>>>>>> MRIalloc(0, 1, 1): bad parm >>>>>>> Reporting on 0 segmentations >>>>>>> Computing spatial average of each frame >>>>>>> >>>>>>> Writing to >> /Applications/freesurfer/subjects/fMRI/sub/rest/001/tmp. >>>>>>> fcseed-sess.97908/avgwf.mgh >>>>>>> Segmentation fault >>>>>>> >>>>>>> I have read your previous message and you can check the MRS >> voxel >>>>>>> features. >>>>>>> MRS voxel mask is in subj directory where I have run recon >> all - >>>>> all. >>>>>>> data_type FLOAT32 >>>>>>> dim1 256 >>>>>>> dim2 256 >>>>>>> dim3 256 >>>>>>> dim4 1 >>>>>>> datatype 16 >>>>>>> pixdim1 1.000000 >>>>>>> pixdim2 1.000000 >>>>>>> pixdim3 1.000000 >>>>>>> pixdim4 0.010747 >>>>>>> cal_max 0.0000 >>>>>>> cal_min 0.0000 >>>>>>> file_type NIFTI-1+ >>>>>>> >>>>>>> >>>>>>> The features are same of other subject that runs fine. >>>>>>> data_type FLOAT32 >>>>>>> dim1 256 >>>>>>> dim2 256 >>>>>>> dim3 256 >>>>>>> dim4 1 >>>>>>> datatype 16 >>>>>>> pixdim1 1.000000 >>>>>>> pixdim2 1.000000 >>>>>>> pixdim3 1.000000 >>>>>>> pixdim4 0.010747 >>>>>>> cal_max 0.0000 >>>>>>> cal_min 0.0000 >>>>>>> file_type NIFTI-1+ >>>>>>> >>>>>>> Thank you very much. >>>>>>> >>>>>>> >>>>>>> Stefano >>>>>>> >>>>>>> >>>>>>>> ----Messaggio originale---- >>>>>>>> Da:stdp82@virgilio.it >>>>>>>> Data: 16-ott-2015 23.15 >>>>>>>> A:<freesurfer(a)nmr.mgh.harvard.edu> >>>>>>>> Ogg: [Freesurfer] R: Re: R: import FS-FAST results in FSL >>>>>>>> >>>>>>>> I'd like to open with FSLview the sig.nii.gz which is >> produced by >>>>>>>> selxavg3-sess. >>>>>>>> If I use mri_surf2vol, which is the template to added in -- >>>>> template? >>>>>>>> It should be in Tailairach space? Where can I find the >> template >>>>> that >>>>>>> I >>>>>>>> should added? >>>>>>>> Thanks, >>>>>>>> >>>>>>>> Stefano >>>>>>>> >>>>>>>> subj/rest/fc.seed.surf.lh/L_seed/sig.nii.gz >>>>>>>> data_type FLOAT32 >>>>>>>> dim1 27307 >>>>>>>> dim2 1 >>>>>>>> dim3 6 >>>>>>>> dim4 1 >>>>>>>> datatype 16 >>>>>>>> pixdim1 1.000000 >>>>>>>> pixdim2 1.000000 >>>>>>>> pixdim3 1.000000 >>>>>>>> pixdim4 1100.000000 >>>>>>>> cal_max 49.1815 >>>>>>>> cal_min -12.3855 >>>>>>>> file_type NIFTI-1+ >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> Thanks, >>>>>>>> >>>>>>>> Stefano >>>>>>>> >>>>>>>> >>>>>>>>> ----Messaggio originale---- >>>>>>>>> Da:greve@nmr.mgh.harvard.edu >>>>>>>>> Data: 29-set-2015 22.09 >>>>>>>>> A:<freesurfer(a)nmr.mgh.harvard.edu> >>>>>>>>> Ogg: Re: [Freesurfer] R: import FS-FAST results in FSL >>>>>>>>> >>>>>>>>> Do you mean surface-based analysis? You'd have to put them >> back >>>>>>> into >>>>>>>> the >>>>>>>>> volume using mri_surf2vol, write them out as nifti and >> then run >>>>>>>> fslview >>>>>>>>> on them >>>>>>>>> >>>>>>>>> On 09/29/2015 11:17 AM,stdp82(a)virgilio.it wrote: >>>>>>>>>> Hi list, >>>>>>>>>> >>>>>>>>>> I would like to import FS-FAST results (conjunction >> maps) >>>>> in >>>>>>>> FSL, >>>>>>>>>> opening them by fslview. >>>>>>>>>> Could you provide me any suggestion? >>>>>>>>>> >>>>>>>>>> Thank you very much >>>>>>>>>> Best regards, >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> Stefano >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> _______________________________________________ >>>>>>>>>> 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: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(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 >>>>>>> _______________________________________________ >>>>>>> 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: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(a)nmr.mgh.harvard.edu >>>>>> https://mail.nmr.mgh.harvard. edu/mailman/listinfo/freesurfer >>>>>> >>>>>> >>>>>> >>>>>> _______________________________________________ >>>>>> Freesurfer mailing list >>>>>> Freesurfer(a)nmr.mgh.harvard.edu >>>>>> https://mail.nmr.mgh.harvard. edu/mailman/listinfo/freesurfer >>>> >>>> >>>> >>>> >>>> _______________________________________________ >>>> 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: 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(a)nmr.mgh.harvard.edu >>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>> >> _______________________________________________ >> 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: 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(a)nmr.mgh.harvard.edu >https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >

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recon_checker missing output files
by Lauren Bystrom 12 Nov '15

12 Nov '15

Dear Experts, I am trying to run recon_checker on a set of subjects with brain tumors. Since FreeSurfer cannot deal with this, I am using recon_checker -s SUBJID -ignore lh. to try and ignore the processes on the hemisphere with the tumor, but it keeps checking for those files anyway. Also, it gives me an html file that is supposed to display my snapshot but the images aren't appearing where the code says they should be. Could this be caused by the absence of specific files that were missing in the recon_all, on both hemispheres, and if so is there a way to get my snapshot images without these files? Lauren Bystrom

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'mri_normalize' & 'mri_nu_correct', how do they work?
by Guido Orlando Pascariello 12 Nov '15

12 Nov '15

Hi FS Experts I'm bioengineering student and I'm working on my final project to get my degree. it's about process neuroimaging (IRM) in order to cuantific some parameter which could be helpful for medicine (clinical neurology). I'm using FreeSurfer to process my data. It works realy good. But it will be so much helpful to me if you can answer me a few question about it! *FIRST ONE*: I've been using 'mri_normalize' and I read the paper which describe it. But: 1. In step 4: Discard outliers from the array: You suppose variation in intensity due to magnetic field inhomogeneities is smooth across space. But, field inhomogeneities are corrected in 'NuCorrect' module using N3. 2. I understood the 1D normalization process. However the 3D normalization process works estimating a bias field like that which is corrected by 'NuCorrect' module. Could you tell me why did you that? and what are diferences with 'NuCorrect' module? *SECOND ONE*: It's abuou 'mri_nu_correct': I've read the description but I'm not sure about it. Does it use the N3 algorithm to work? In the description is written that "changing the number of iterations should be done carefully, because this can exacerbate artifacts". Could you tell me what are these artifact? and why is the default number of iteration four? I'll be grateful if you can help Being all for now, I await a reply Guido PASCARIELLO Facultad de Ingeniería - Universidad Nacional de Entre Ríos Argentina

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