Freesurfer

freesurfer@nmr.mgh.harvard.edu

3 participants
30135 discussions

OS version on Edits/Analysis
by Andrew Schoen 11 Nov '15

11 Nov '15

Hi all, I know there is good evidence to support analyzing and performing edits on the same version of freesurfer, and the same operating system. However, our systems are going to be updating to Scientific Linux 7, from Scientific Linux 6 in the coming weeks. We are planning to keep a legacy box (Linux 6) box for about a year to finish our current processing/edits. However, since many of our studies can take a while from processing to final analysis, and we may revisit datasets after a year or two, I was wondering if it is okay to finish all edits on a given version of Linux (6), and later run all analyses on a different version of Linux (7). Namely, we are interested to know how long we would need to keep the legacy box around, in case we want to revisit data for additional analyses (e.g. all edits/reprocessing would be done on one version, analyses on another). Thanks! Andrew Schoen Center for Investigating Healthy Minds Waisman Center University of Wisconsin - Madison

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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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