Freesurfer November 2015

freesurfer@nmr.mgh.harvard.edu

138 participants
239 discussions

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

2 1

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

2 3

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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mri_surf2surf - Interpolation
by Gardus III, John D 10 Nov '15

10 Nov '15

Hello all, I'm in the process of mapping some non-FreeSurfer derived outcomes to a curv file containing the vertices of the pial surface mesh. I have values at roughly 100 vertices, leaving some 37000 with 'nan'. I then run an intra-subject surf2surf command in an attempt to interpolate between vertices for which I have values. The problem is that the NaNs pull the existing values down, resulting in a smearing/dilution of my outcomes. Is there any way to interpolate and make the intervening vertices purely a function of nearby vertices for which values exist? Thanks, John 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.

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Region specific stats
by Hassan bakhshi 10 Nov '15

10 Nov '15

Hi everyone, I could get all features from asegstats2table and aparcstats2table, Now I need stats by region, for example frontal lobe stats and etc. How can I get them??? Should I select by myself or there is an easy way?

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Re: [Freesurfer] Freesurfer@nmr.mgh.harvard.edu
by Douglas N Greve 10 Nov '15

10 Nov '15

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>> 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> > 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/ > > > > 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 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/

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Re: [Freesurfer] Freesurfer@nmr.mgh.harvard.edu
by Douglas N Greve 10 Nov '15

10 Nov '15

Are those the qdec files that generate the first error? That error implies that fsaverage is included as a subject in the qdec file. Is this possible? 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>> 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> > 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/ > > > > 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 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/

1 0

mri_surfcluster statistics and label question
by Yang, Daniel 10 Nov '15

10 Nov '15

Dear FreeSurfer experts, In the output mri_surfcluster (e.g., https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysisClusterSu…) what is the statistics behind the Max? Is it either t-statistic (if only 1 line of contrast) or F-statistic (if two lines of contrast), but not Z-statistics? Also, I notice that the annotation is picking only one of the anatomical regions in which the cluster is located. Is it possible to tell all the anatomical regions that a label has? Thanks, Daniel -- Daniel Yang, Ph.D. Yale Child Study Center E-mail: daniel.yj.yang(a)yale.edu

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Tracula bedpostx terminated
by denizzgursel 10 Nov '15

10 Nov '15

Dear Freesurfer experts, I am running tracula v5.3.0 on OpenSuse. I successfully ra n freesurfer reconstruction and trac-all-prep. However, when I try to run trac-all -bedp -c dmrirc_file, I get the following message: .... 47 s lices processed 48 s lices processed 50 s lices processed 53 slices processed Queuing post processing stage sw/freesurfer/5.3.0/bin/bedpostx_mgh: line440: 8026 Terminated ${subjdir}.bedpostX/monitor I am not running bedpostx on a cluster but locally. Any suggestions why it might be terminated? Thank you, -- D.

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Freesurfer November 2015