Freesurfer November 2015

freesurfer@nmr.mgh.harvard.edu

138 participants
239 discussions

Re: [Freesurfer] Freesurfer Digest, Vol 141, Issue 22
by Gonzalo Rojas Costa 11 Nov '15

11 Nov '15

Hi Martin: But, between version 5.3 and 6.0 there are any differences in the algorithms for subcortical volume, cortical thickness, etc., or only additions to that, such as the hippocampus or brainstem subfields ?... and in general, if I segment for example the same healthy control in freesurfer 5.3 and 6.0 in the same operating system, there will be any difference in subcortical volumes and/or cortical thickness ?... Sincerely, 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 On Wed, Nov 11, 2015 at 7:57 AM, <freesurfer-request(a)nmr.mgh.harvard.edu> wrote: > ------------------------------ > > Message: 24 > Date: Tue, 10 Nov 2015 16:57:43 -0500 > From: Martin Reuter <mreuter(a)nmr.mgh.harvard.edu> > Subject: Re: [Freesurfer] 5.3 vs 6.0 volumetric differences... > To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> > Message-ID: <56426857.3030804(a)nmr.mgh.harvard.edu> > Content-Type: text/plain; charset=utf-8; format=flowed > > Hi Gonzalo, > > of course. > > There is even a difference when running the same FS version with a > different operating system (due to differences in the numerical > libraries, optimizations etc). > > Are changes big or small? > In a single case they can be very big (it could be a case that failed in > 5.3 and works with 6.0 - or the other way) > > Are changes directional (significantly larger or smaller volumes/thickness)? > Hard to say and hard to detect if small, but it can happen due to a new > algorithm that measurements are consistently larger (/smaller) than in > another version. We try to avoid this, but it can theoretically happen. > > That is why it is so important to stick with the same version and > operating system when processing data. > > Best, Martin > > On 11/10/2015 04:48 PM, Gonzalo Rojas Costa wrote: >> 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 >> > > -- > Martin Reuter, PhD > Assistant Professor of Radiology, Harvard Medical School > Assistant Professor of Neurology, Harvard Medical School > A.A.Martinos Center for Biomedical Imaging > Massachusetts General Hospital > Research Affiliate, CSAIL, MIT > Phone: +1-617-724-5652 > Web : http://reuter.mit.edu

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Re: [Freesurfer] group mean greater than X
by Dace Apshvalka 11 Nov '15

11 Nov '15

That's what I will do. Just wanted to enquire whether there is an option to specify the value directly for the one-sample ttest. Thank you! Dace > Could you also just subtract 5 from all your input data? Then when you test > against zero (and only look at positive p values) you'll really be testing > whether the values are greater than 5? > > Kx > > On 11 November 2015 at 21:35, Douglas Greve <greve at nmr.mgh.harvard.edu> > wrote: > >> I guess you could subtract 5 from the gamma.mgh, then recompute the t = >> gamma-5.mgh/sqrt(gammavar.mgh). You'd then need to convert the t to a p >> or sig given the dof. >> doug >> >> ps. Please remember to include previous correspondences so we know the >> context of the question >> >> On 11/11/15 4:10 PM, Dace Apshvalka wrote: >> > Sorry, I was not very clear. >> > >> > I meant, how do I test whether the group mean is greater than 5, for >> > example. >> > >> > The default is 0, but can I change it somehow? >> > >> > >> > Dace >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer at 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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group mean greater than X
by Dace Apshvalka 11 Nov '15

11 Nov '15

Hi, How would I make a one sided t-test to see whether group mean is greater than X (any other number than 0)? Thanks, Dace

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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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Freesurfer November 2015