Freesurfer

freesurfer@nmr.mgh.harvard.edu

16 participants
30084 discussions

TalX TalY TalZ
by Yang, Daniel 11 Nov '15

11 Nov '15

Dear FreeSurfer Experts, Are these coordinates reported in mri_surfcluster in MNI305 space? (with —fixmni) Thanks, Daniel -- Daniel Yang, Ph.D. Yale Child Study Center E-mail: daniel.yj.yang(a)yale.edu

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mri_vol2surf Matlab Function
by Fatemeh.Molaei-Vaneghi 11 Nov '15

11 Nov '15

Dear FreeSurfers, I am using "mri_vol2surf" to map my SPM processed t images onto 9 intermediate surfaces created by "mris_expand". When every step is done manually it works perfectly. However, for very large datasets I would need to run mri_vol2surf for multiple subjects, multiple conditions, multiple ROIs, and etc. Therefore, automising the command to be executed on multiple datasets at once is a requirement. Unfortunately there is no Matlab function for mri_vol2surf, this brings me to my question: how can I use mri_vol2surf in Matlab for multiple datasets, how the command must be written, how the variables and directories must be redefined so Matlab and FreeSurfer both have access to what they need. In other words, how mri_vol2surf should be used, either in Matlab or in shell, in order to be executed on multiple datasets at once? As a side note I am using Mac OS 10.9.5 with FreeSurfer v5.3.0. Thank you in advance for your guidance. Kind Regards, Fatemeh Molaei-Vaneghi Max Planck Institute for Biological Cybernetics Tübingen Germany

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Advice for FreeSurfer developers
by Gronenschild Ed (NP) 11 Nov '15

11 Nov '15

Dear developers, Is it possible to check the presence of Matlab runtime right at the start of recon-all in FreeSurfer v6 instead of a long way down in the pipeline. After 36 hours for a high-res data processing I got this unexpected error message. Thanks in advance. Cheers Ed

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Re: [Freesurfer] Freesurfer@nmr.mgh.harvard.edu
by Douglas Greve 11 Nov '15

11 Nov '15

does that file exist? Did you run recon-all -qcache ? On 11/11/15 7:54 AM, Heidi Foo wrote: > Apologies, the error message should be /Error in analyze: couldn't > open > /Users/nnidementia/Documents/PDFS/FSVASE_002/surf/lh.thickness.fwhm10.fsaverage.mgz > or .mgh file./ > > On Wed, Nov 11, 2015 at 8:48 PM, Heidi Foo <heidifoo92(a)gmail.com > <mailto:heidifoo92@gmail.com>> wrote: > > Hi Dr Greve, > > Thank you for your advice, it is deeply appreciated. I removed the > blank lines of wmh.levels and included a carriage return at the > end of the long.qdec.table.txt. > > However, there is still /error in analyze: Couldn't open > /Users/nnidementia/Documents/PDFS/FS_PD002_1.nii/surf/lh.thickness.fwhm10.fsaverage.mgz > or .mgh file./ > / > / > I checked my qdec.table.txt (both cross and long) but I did not > see any fsaverage included in the list of subjects. Am I missing > something? > > Thank you. > > Regards, > Heidi Foo > / > / > > On Wed, Nov 11, 2015 at 12:28 AM, Douglas N Greve > <greve(a)nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> wrote: > > Also, try removing the blank line at the end of wmh.levels, > and make sure you have a carriage return at the end of > long.qdec.table.txt. This may fix the 2nd error > > On 11/09/2015 10:38 PM, Heidi Foo wrote: > > Dear Dr Greve, > > Thanks for your reply. I have already linked fsaverage to > my SUBJECTS_DIR but the error still persists. > > Attached is my qdec (long and cross) files. > > Thanks. > > Regards, > Heidi Foo > > > > On Tue, Nov 10, 2015 at 6:36 AM, Douglas N Greve > <greve(a)nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu> > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu>>> wrote: > > > > On 11/06/2015 09:35 PM, Heidi Foo wrote: > > Dear FreeSurfer experts, > > I am trying to compare between stable WMH group > and rapid > progressed WMH group in regards to the cortical > thickness as > well as volume changes in the gray matter. The > nuisance > variable in my case is age. I ran my analysis > using QDEC but > encountered a few problems: > > 1. There is error in analyze: couldn't open file > > It looks like it cannot find fsaverage. Link it to your > SUBJECTS_DIR if you have not already. > > 2. If this error doesn't appear, another one does. > QdecGlmDesign::Create: zero factors! > (Attached the screenshot of the errors for your > perusal) > > please send the qdec file > > > I am hoping that you could give me a solution to > my problems. > > Thank you so much. > > Regards, > Heidi > > > -- Douglas N. Greve, Ph.D. > MGH-NMR Center > greve(a)nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu> > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu>> > Phone Number: 617-724-2358 <tel:617-724-2358> > <tel:617-724-2358 <tel:617-724-2358>> > Fax: 617-726-7422 <tel:617-726-7422> <tel:617-726-7422 > <tel:617-726-7422>> > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 > www.nmr.mgh.harvard.edu/facility/filedrop/index.html > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > Outgoing: > ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > > > > The information in this e-mail is intended only for > the person to > whom it is > addressed. If you believe this e-mail was sent to you > in error and > the e-mail > contains patient information, please contact the Partners > Compliance HelpLine at > http://www.partners.org/complianceline . If the e-mail was > sent to > you in error > but does not contain patient information, please > contact the > sender and properly > dispose of the e-mail. > > > > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > greve(a)nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> > Phone Number: 617-724-2358 <tel:617-724-2358> > Fax: 617-726-7422 <tel:617-726-7422> > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 > www.nmr.mgh.harvard.edu/facility/filedrop/index.html > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > Outgoing: > ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > > >

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registration format conversion
by S.V.Shepherd [work] 10 Nov '15

10 Nov '15

Hi, I understand lta_convert can generalize between FSL (.mat), tkregister2 (.dat) and FreeSurfer 5 (.lta) format registration matrices. How can I get this file? The location archived in *Re: [Freesurfer] Lta_convert *is no longer available. stephen *stephen v. shepherd phd* The Rockefeller University / 1230 York Avenue / New York NY 10065-6307 USA // 212.327.7699

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Error viewing uncorrected sign map with freeview
by Gay,Charles Wysaw 10 Nov '15

10 Nov '15

Dear Freesurfer group - I am receiving the following error when I try view results of a mri_glmfit. Any assistance would be greatly appreciated. Thanks, Chaz freeview -f $SUBJECTS_DIR/fsaverage/surf/lh.inflated:annot=aparc.annot:annot_outline=1:overlay=lh.gender_worstpain_age.glmdir/worstpain/sig.mgh:overlay_threshold=4,5 -viewport 3d Unrecognized sub-option flag 'annot_outline'. FREESURFER_HOME: /Volumes/projects/painimaging/Bishop/FreeSurfer_R01/freesurfer Build stamp: freesurfer-Darwin-lion-stable-pub-v5.3.0 Kernel info: Darwin 14.5.0 x86_64 --------------------------------------------------------------------- Please include the following additional information in your report: 1) subject name 2) the entire command-line executed 3) the error message generated 4) optionally include the subject's /script/recon-all.log

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5.3 vs 6.0 volumetric differences...
by Gonzalo Rojas Costa 10 Nov '15

10 Nov '15

Hi: There are any difference between subcortical structures volume, cortical thickness, supratentorial volume, gray matter volume, etc. computed with freesurfer 5.3 and 6.0 ?... Sincerely, Gonzalo Rojas Costa -- Gonzalo Rojas Costa Laboratory for Advanced Medical Image Processing Department of Radiology Clínica las Condes Lo Fontecilla 441, Las Condes, Santiago, Chile. Tel: 56-2-2105170 Cel: 56-9-97771785 www.clc.cl

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unpacksdcmdir
by Li, Baojuan 10 Nov '15

10 Nov '15

Hi all, I am using unpacksdcmdir to unpack our data (collected using a Siemens scanner) but running into an error. I have two questions and hope someone can kindly help me with them: 1. Why can not I successully unpack images for run10? 2. I got the DTI.nii image, the bvecs and bvals for run4 now. Can I use them for my analyses? Seems this run has an error. Does this error matter? Thank you so much for your help! Best wishes, Baojuan The logfile is as follows: Done scanning Mon Nov 9 19:10:43 EST 2015 ------------------------------------------ 1 localizer ok 512 512 3 1 MR.1.3.12.2.1107.5.2.32.35162.2012120515075082139361714 2 AAScout ok 128 128 128 2 MR.1.3.12.2.1107.5.2.32.35162.2012120515084521701761763 3 T1_MPRAGE_sag ok 256 256 128 1 MR.1.3.12.2.1107.5.2.32.35162.2012120515211411553363371 4 DIFFUSION_HighRes err 128 128 64 70 MR.1.3.12.2.1107.5.2.32.35162.2012120515244054044164212 5 DIFFUSION_HighRes ok 128 128 64 1 MR.1.3.12.2.1107.5.2.32.35162.2012120515335954318286428 6 DIFFUSION_HighRes ok 128 128 64 1 MR.1.3.12.2.1107.5.2.32.35162.2012120515335954396886429 7 DIFFUSION_HighRes ok 128 128 64 1 MR.1.3.12.2.1107.5.2.32.35162.2012120515335954482386430 8 DIFFUSION_HighRes ok 128 128 64 1 MR.1.3.12.2.1107.5.2.32.35162.2012120515335954528786431 9 DIFFUSION_HighRes ok 128 128 64 1 MR.1.3.12.2.1107.5.2.32.35162.2012120515335954607786432 10 DIFFUSION_HighRes ok 128 128 1 64 MR.1.3.12.2.1107.5.2.32.35162.2012120515335954660486433 11 ge_functionals ok 64 64 33 150 MR.1.3.12.2.1107.5.2.32.35162.2012120515373932869186918 unpacking config ------------------ {3 T1 mgz T1.mgz} {4 DTI nii DTI.nii} {10 DTI nii DTI.nii} ----------------------------------- --------------------------------------------------------- Run 3 ----------------------------------------- Mon Nov 9 19:10:43 EST 2015 3 T1 mgz T1.mgz mri_convert /cluster/archive/302/siemens/TrioTim-35162-20121205-150656-604000/MR.1.3.12.2.1107.5.2.32.35162.2012120515211411553363371 /autofs/space/quadra_001/users/baojuan/old_lab_datatset/T1/003/T1.mgz --sdcmlist /autofs/space/quadra_001/users/baojuan/old_lab_datatset/T1/003/flf -ot mgz --nspmzeropad 3 --in_type siemens_dicom --------------------------------------------------------- Run 4 ----------------------------------------- Mon Nov 9 19:10:56 EST 2015 4 DTI nii DTI.nii INFO: this run has an error, but trying anyway mri_convert /cluster/archive/302/siemens/TrioTim-35162-20121205-150656-604000/MR.1.3.12.2.1107.5.2.32.35162.2012120515244054044164212 /autofs/space/quadra_001/users/baojuan/old_lab_datatset/DTI/004/DTI.nii --sdcmlist /autofs/space/quadra_001/users/baojuan/old_lab_datatset/DTI/004/flf -ot nii --nspmzeropad 3 --in_type siemens_dicom --------------------------------------------------------- Run 10 ----------------------------------------- Mon Nov 9 19:11:19 EST 2015 10 DTI nii DTI.nii ERROR: reading /cluster/archive/302/siemens/TrioTim-35162-20121205-150656-604000/MR.1.3.12.2.1107.5.2.32.35162.2012120515335954660486433 tag 28 30

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applying longitudinal processing on twins
by Örjan de Manzano 10 Nov '15

10 Nov '15

Dear FreeSurfers, I'm about to analyze cortical thickness in monozygotic twins discordant for certain expertise. The within-pair similarities in brain morphology are striking (e.g. twin1 x twin2 intracranial volume correlation r=.99) and you could easily play a memory game with the images. Nonetheless, there are notable within-pair differences in gyrification etc. I'm trying to figure out if the longitudinal stream, or some version of it, might still be a viable option in this situation. The sample is fairly small and I want to do what I can to maximize sensitivity. Do any of you have experience with a similar data set or ideas/opinions/recommendations? Best regards, Örjan

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mri_label2label
by Ray Razlighi 10 Nov '15

10 Nov '15

Hi Guys, I'm trying to map the vertices of temporal pole in one subject into the space of another subject using mri_label2label. When I do it, the output doesn't have the same number of vertices and the other of the vertex are completely messed up. See below as the first few lines in the source and transferred labels along with the command execution. What I need to know is that where for example vertex number 129756 mapped to in the target surface space. I can't extract those information from these two files. Thanks a lot -------------------------------------------------------------------------------------------------------------------------------- Source Label file: aparc-lh-032.label #!ascii label , from subject FreeSurferClean vox2ras=TkReg 217 129756 -13.048 63.016 -1.943 0.0000000000 129757 -13.268 63.132 -1.961 0.0000000000 129767 -13.120 63.091 -2.173 0.0000000000 129768 -13.470 63.274 -2.293 0.0000000000 129870 -7.339 63.337 5.869 0.0000000000 129879 -7.347 63.505 5.024 0.0000000000 129888 -7.731 63.526 4.092 0.0000000000 129889 -8.111 63.407 3.205 0.0000000000 129893 -8.317 63.382 2.401 0.0000000000 129896 -7.864 64.313 1.332 0.0000000000 129897 -8.180 63.672 1.427 0.0000000000 129898 -12.359 64.295 1.105 0.0000000000 129899 -12.777 64.061 1.152 0.0000000000 129902 -7.780 64.251 0.861 0.0000000000 129903 -7.979 63.500 0.404 0.0000000000 129904 -11.492 64.276 0.155 0.0000000000 129905 -12.091 63.982 0.540 0.0000000000 129906 -13.264 63.628 0.557 0.0000000000 -------------------------------------------------------------------------------------------------------------------------------- Transfered Label file: aparc-lh-032-reg3.label #!ascii label , from subject FreeSurferClean2 vox2ras=TkReg 333 132988 -7.268 83.361 -2.195 0.0000000000 132714 -7.766 83.079 -2.603 0.0000000000 132259 -4.885 81.451 7.416 0.0000000000 132260 -5.354 81.986 6.795 0.0000000000 132609 -5.461 82.480 5.323 0.0000000000 132904 -5.190 83.525 4.692 0.0000000000 132903 -4.503 83.934 4.047 0.0000000000 133205 -3.592 84.944 3.299 0.0000000000 132913 -3.623 84.596 3.095 0.0000000000 133222 -6.863 84.768 1.300 0.0000000000 133223 -7.284 84.611 1.941 0.0000000000 133204 -3.445 84.969 2.831 0.0000000000 133211 -3.895 84.688 2.151 0.0000000000 133250 -6.409 84.885 -0.260 0.0000000000 133236 -6.568 84.963 0.611 0.0000000000 132934 -7.418 83.679 1.113 0.0000000000 133456 -3.481 85.560 2.366 0.0000000000 133470 -3.739 85.730 0.320 0.0000000000 -------------------------------------------------------------------------------------------------------------------------------- ray@athens-b8-e8-56-47-e6-54:~/Data/P00001613\> mri_label2label --srclabel FreeSurferClean/label/aparc-lh-032.label --srcsubject FreeSurferClean --trglabel FreeSurferClean2/label/aparc-lh-032-reg3.label --trgsubject FreeSurferClean2 --regmethod surface --hemi lh srclabel = FreeSurferClean/label/aparc-lh-032.label srcsubject = FreeSurferClean trgsubject = FreeSurferClean2 trglabel = FreeSurferClean2/label/aparc-lh-032-reg3.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /Users/ray/Data/P00001613 FREESURFER_HOME /Applications/freesurfer Loading source label. Found 217 points in source label. Starting surface-based mapping Reading source registration /Users/ray/Data/P00001613/FreeSurferClean/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /Users/ray/Data/P00001613/FreeSurferClean2/surf/lh.white Reading target registration /Users/ray/Data/P00001613/FreeSurferClean2/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 217 nlabel points Performing mapping from target back to the source label 134519 Number of reverse mapping hits = 142 Checking for and removing duplicates Writing label file FreeSurferClean2/label/aparc-lh-032-reg3.label 359 mri_label2label: Done ---------------------------------------------------------------------------------------------------------------------- -- Sincerely, Ray

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