Freesurfer April 2017

freesurfer@nmr.mgh.harvard.edu

123 participants
217 discussions

Can anyone help with this error - trying to compare 2 scans in same person
by Brad Matushewski 04 Apr '17

04 Apr '17

From: freesurfer-bounces(a)nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] On Behalf Of Brad Matushewski Sent: March 30, 2017 2:38 PM To: freesurfer(a)nmr.mgh.harvard.edu Subject: [Freesurfer] Trying to compare 2 scans from same person, 6 months apart. First scan is 005_IHD_1 Second scan is 005_IHD_1_post These were in $SUBJECTS / ihd I moved them into $SUBJECTS (i.e. no subfolder within $SUBJECTS folder). I am following this; https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/LongProcessing FsTutorial/LongProcessing - Free Surfer Wiki<https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/LongProcessing> surfer.nmr.mgh.harvard.edu Processing your data consists of three steps: First, run all your data independently (we also say cross sectionally) using "recon-all -all" (i.e. all time points for ... I ran a normal recon all on both scans first. I then ran this command: recon-all -base 005_IHD_1_base-tp 005_IHD_1 -tp 005_IHD_1_post -all and all seemed well. I then tried to run this command. recon-all -long <tpNid> <templateID> -all This is how I entered the command: recon-all -long 005_IHD_1 005_IHD_1_base -all It resulted in errors...here is the last bit of the error log: Applying LTAtransformInterp (resample_type 5) MRItoBSpline degree 3 writing to /usr/local/freesurfer/subjects/005_IHD_1.long.005_IHD_1_base/mri/rawavg.mgz... mri_add_xform_to_header -c /usr/local/freesurfer/subjects/005_IHD_1.long.005_IHD_1_base/mri/transforms/talairach.xfm /usr/local/freesurfer/subjects/005_IHD_1.long.005_IHD_1_base/mri/orig.mgz /usr/local/freesurfer/subjects/005_IHD_1.long.005_IHD_1_base/mri/orig.mgz INFO: extension is mgz #-------------------------------------------- #@# Talairach Thu Mar 30 14:31:07 EDT 2017 /usr/local/freesurfer/subjects/005_IHD_1.long.005_IHD_1_base/mri cp /usr/local/freesurfer/subjects/005_IHD_1_base/mri/transforms/talairach.auto.xfm /usr/local/freesurfer/subjects/005_IHD_1.long.005_IHD_1_base/mri/transforms/talairach.auto.xfm cp: cannot stat '/usr/local/freesurfer/subjects/005_IHD_1_base/mri/transforms/talairach.auto.xfm': No such file or directory Linux bjmatush-System-Product-Name 4.4.0-51-generic #72~14.04.1-Ubuntu SMP Thu Nov 24 19:22:30 UTC 2016 x86_64 x86_64 x86_64 GNU/Linux recon-all -s 005_IHD_1.long.005_IHD_1_base exited with ERRORS at Thu Mar 30 14:31:07 EDT 2017 What went wrong?

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Re: [Freesurfer] wm edits not incorporated
by Octavian Lie 04 Apr '17

04 Apr '17

Dear Bruce, > > I just transferred subject r02.tar.gz. > > Again, wm.mgz edits (all deleted voxels, no additions) are not > incorporated on reruns using any of the > recon-all -autorecon-wm -aitorecon3 > recon-all -autorecon2 -autorecon3 > recon-all -make all > > For example, the complete command line for a rerun on this particular > subject is > > recon-all -autorecon2-wm -autorecon3 -3T -bigventricles -cw256 -subjid r02 > -parallel > output.txt & > > > Here are some of the edited voxels which are not excluded from the wm on > rerun: > > > -40.14, -2.67, 116.29 coronal slice 132 > 12.73, -23.67, 126.16 coronal slice 171 > 14.05, 12.33, 11.61 coronal slice 147 > > > I mention this is not the only subject where I have this problem. > Thank you for your help. > Octavian > > >

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Creating an illustration on what Freesurfer has considered to be intracranial volume
by Erik Lindberg 04 Apr '17

04 Apr '17

Dear Freesurfer experts, I would like to create an image on tissue that Freesurfer has been included into the intracranial volume calculation. Is there anyway to summarize segmentations masks so I get one mask containing all tissue that has been included into the intracranial volume? best Erik

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A question regarding LUT/Freeview
by amir hosein 04 Apr '17

04 Apr '17

Dear All, A quick question. I Want to use Freeview to display a number of brain areas (that I have chosen for some purposes) on the brain. As I have studied in this forum, it is suggested that I should create a custom Look-Up-Table in which I only keep the labels that are my target and erase others, so that when I give the Freeview a range of lables, only my target labels are displayed. So far, so good. Now, this is how I have changed part of the LUT, as an example: … 2027 ctx-rh-rostralmiddlefrontal 75 50 125 0 2028 ctx-rh-superiorfrontal 20 220 160 0 2029 ctx-rh-superiorparietal 20 180 140 0 2032 ctx-rh-frontalpole 100 0 100 0 2033 ctx-rh-temporalpole 70 70 70 0 2034 ctx-rh-transversetemporal 150 150 200 0 2035 ctx-rh-insula 255 192 32 0 … As you can see, I have omitted the labels #2030 and 2031 from my LUT. Now, I load this LUT in Freeview, and on the box on the left side I do not see these two labels, as they are already omitted. However, when I give the freeview this range 2028:2035, still the two labels of 2031 and 2031 are displayed !! I have omitted them from the list, but they still want to come! Do you think I am doing something wrong? Many thanks, Amir

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eTIV estimation on same subject over time
by Melanie Ganz 04 Apr '17

04 Apr '17

Dear list, we are currently working with some longitudinal data where we would like to measure volume changes over time and compare the cross-sectional and longitudinal stream on. When we run the cross-sectional stream and just look at changes of eTIV within subjects over a period of 6 months to a year we get 3-4 subjects out of 110 that have eTIV changes of 20-30%. I've double checked the tailarach transforms using the talairach_afd tools and also manually checked the transforms with tkregister. Everything seems to be ok. I know when using the longitudinal stream we can use the single eTIV value for volume correction, but for comparison in case of the cross-sectional stream we want to use the single time point values of eTIV. Any ideas what else I can check or is this simply noise transferred from the linear estimation of eTIV? Cheers, Mel -- Melanie Ganz-Benjaminsen, MSc, Ph.D. Neurobiology Research Unit University of Copenhagen Rigshospitalet Rockefeller Center Juliane Maries Vej 28/30, 3. DK-2100 Copenhagen Denmark phone: +45 3545 6718 e-mail: Melanie.Ganz(a)nru.dk web: http://melanie.clausundmelanie.de/

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Fwd: recon-all error
by Patrícia Klobušiaková 04 Apr '17

04 Apr '17

Hello FreeSurfer Developers, I have installed Freesurfer on Windows using VMware - CentOS 64-bit (the one from FSLuser Linux installation). Everytime I run recon-all, there is an error. The same error occurs when I try to rum mri2mesh command in SIMNIBS toolbox which uses Fresurfer (recon-all), too. I'm sending screenshots and logfile attached. Version: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c uname -a: Linux fslvm6.localdomain 2.6.32-431.5.1.el6.x86_64 #1 SMP Wed Feb 12 00:41:43 UTC 2014 x86_64 x86_64 x86_64 GNU/Linux Thanks for your help. Best, Patricia

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Position in Genetics and Neuroimaging
by Juan Domingo Gispert López 04 Apr '17

04 Apr '17

The Barcelonaβeta Brain Research Centre (BBRC), research institution of the Pasqual Maragall Foundation (PMF) and the Centre for Genomic Regulation (CRG) invites applications for a full-time research position to study the genetic modulation of cerebral phenotypes based on genome-wide associations with neuroimaging data, as part of its clinical research program. The primary responsibility of this position includes the analysis and interpretation of genome-wide association studies (GWAS) data in association with quantitative phenotypes extracted from neuroimaging modalities. The candidate will be working under the guidance of the Principal Investigators Roderic Guigó of the CRG and the Neuroimaging Group Principal Investigator of the BBRC, Juan-Domingo Gispert. The aim of this project is to improve our understanding of genetic modulation of cerebral phenotypes in healthy subjects and to identify spatially varying patterns of genetic control that may not be evident from summary variables. For additional details please visit: https://recruitment.crg.eu/content/jobs/position/research-position-genetics… -- *Juan D Gispert* Head Neuroimaging Research *Barcelona**β**eta **Brain Research Center - Fundació Pasqual Maragall* T. (+34) 93 326 31 90 C/ Wellington, 30 08005 Barcelona *www.fpmaragall.org <http://www.fpmaragall.org/>*

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Re: [Freesurfer] FW: MPRAGE images dimension different {Disarmed}
by John Anderson 03 Apr '17

03 Apr '17

Dear Dhaval, when your recon-all finishs the process you will get images 256^3 and 1mm isootropic. The you can simply follow the instructions mentioned here https://surfer.nmr.mgh.harvard.edu/fswiki/FsAnat-to-NativeAnat to send your images back to native space. All the best, John > > On Mon, Apr 3, 2017 at 4:35 PM, Dhaval Shah <dshah(a)bnac.net> wrote: > Hi All, > > I am new and a very basic question about freesurfer processing. > > I ran recon-all on a high res-T1 image(128x128x80 matrix size), but > after recon-all the folder mri contains resulted (brain.mgz and > orig.mgz) T1 images has (127x128x128 matrix size). > > 1) how come the dimensions are changed? Is it normal? > 2) how can i keep the dimensions same as the original? > 3) is it possible that i will always get the higher matrix size image > data? > > for simplicity, i converted resulted orig.mgz to nii format and loaded > it in to fslview. Please find the first image (Original) and the > second image (after recon-all but orig.mgz). > > Your help is greatly appreciated. > > -- > Kind regards, > Dhaval Shah > > MRI Research fellow,MRI Physicist,Clinical Trial Research Staff > Buffalo Neuroimaging Analysis Center > State University of New York at Buffalo > Department of Neurology > 100 High St., D-2, Buffalo, NY 14203 > [MailScanner has detected a possible fraud attempt from "dshah(a)bnac.net" claiming to be MailScanner has detected a possible fraud attempt from "dshah(a)bnac.net" claiming to be dshah@bnac.net//http://mbl.bnac.net](http://dshah@bnac.net/http:/mbl.bnac.net) > > > > > -- > Kind regards, > Dhaval Shah > > MRI Research fellow,MRI Physicist,Clinical Trial Research Staff > Buffalo Neuroimaging Analysis Center > State University of New York at Buffalo > Department of Neurology > 100 High St., D-2, Buffalo, NY 14203 > [MailScanner has detected a possible fraud attempt from "dshah(a)bnac.net" claiming to be MailScanner has detected a possible fraud attempt from "dshah(a)bnac.net" claiming to be dshah@bnac.net//http://mbl.bnac.net](http://dshah@bnac.net/http:/mbl.bnac.net) > > _______________________________________________ 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. -- Kind regards, Dhaval Shah MRI Research fellow,MRI Physicist,Clinical Trial Research Staff Buffalo Neuroimaging Analysis Center State University of New York at Buffalo Department of Neurology 100 High St., D-2, Buffalo, NY 14203 dshah(a)bnac.net // http://mbl.bnac.net

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MPRAGE images dimension different
by Dhaval Shah 03 Apr '17

03 Apr '17

Hi All, I am new and a very basic question about freesurfer processing. I ran recon-all on a high res-T1 image(128x128x80 matrix size), but after recon-all the folder mri contains resulted (brain.mgz and orig.mgz) T1 images has (127x128x128 matrix size). 1) how come the dimensions are changed? Is it normal? 2) how can i keep the dimensions same as the original? 3) is it possible that i will always get the higher matrix size image data? for simplicity, i converted resulted orig.mgz to nii format and loaded it in to fslview. Please find the first image (Original) and the second image (after recon-all but orig.mgz). Your help is greatly appreciated. -- Kind regards, Dhaval Shah MRI Research fellow,MRI Physicist,Clinical Trial Research Staff Buffalo Neuroimaging Analysis Center State University of New York at Buffalo Department of Neurology 100 High St., D-2, Buffalo, NY 14203dshah@bnac.net//http://mbl.bnac.net

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mri_vol2vol --mni152reg flips volume
by Melanie Ganz 03 Apr '17

03 Apr '17

Hi all, my colleague Vincent wanted to register a volume in MNI305 to MNI152, unfortunately the final image appears flipped up-down and anterior-posterior when using the --mni152reg flag with mri_vol2vol. For example, trying to resample fsaverage orig.mgz to MNI152 using mri_vol2vol --mov $SUBJECTS_DIR/fsaverage/mri/orig.mgz --mni152reg --o fsaverage.orig.MNI152.nii.gz ends up yielding the attached image (red is the output file and background is FSL MNI152 template). Anything obvious he's doing wrong? Cheers, Melanie -- Melanie Ganz-Benjaminsen, MSc, Ph.D. Neurobiology Research Unit University of Copenhagen Rigshospitalet Rockefeller Center Juliane Maries Vej 28/30, 3. DK-2100 Copenhagen Denmark phone: +45 3545 6718 e-mail: Melanie.Ganz(a)nru.dk web: http://melanie.clausundmelanie.de/

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Freesurfer April 2017