Freesurfer

freesurfer@nmr.mgh.harvard.edu

17 participants
30099 discussions

Fwd: mpr2mni305 failed error
by Francesco Deleo 21 Aug '14

21 Aug '14

---------- Forwarded message ---------- From: Francesco Deleo <franc.deleo(a)gmail.com> Date: 2014-08-08 18:06 GMT+02:00 Subject: Re: [Freesurfer] mpr2mni305 failed error To: freesurfer <freesurfer(a)nmr.mgh.harvard.edu> It is not ok... It seems to have a contrast problem... I can send a snapshot, or if you want I can send the rawavg.mgz Francesco 2014-08-08 17:53 GMT+02:00 Bruce Fischl <fischl(a)nmr.mgh.harvard.edu>: what does the rawavg.mgz look like? If it is ok, can you email it to us? > > On Fri, 8 Aug 2014, Francesco Deleo wrote: > > Thank you all for attention and help! >> Maybe we're finding the problem: in cases I received the mpr2mni305 error >> the orig.mgz is unintelligible (it is white with some black point). But my >> dicoms are ok (I've checked!). I've already tried converting dicom to tiff >> but I got the same error message and the same unintelligible orig.mgz (and >> the tiff are ok too!). >> So I think the likely problem is in the recon-all -i command! >> Any idea? >> >> It remains a mistery for me why I have this problem only in some (and not >> in >> every one) MRI scans even if all the parameters are the same. >> >> thanks again >> >> Francesco >> >> >> 2014-08-07 17:16 GMT+02:00 Douglas N Greve <greve(a)nmr.mgh.harvard.edu>: >> Have you looked in transforms/talairach_avi.log? >> >> On 08/07/2014 07:57 AM, Francesco Deleo wrote: >> > Thank you Doug! >> > but i tried it in many cases but I've always received the same >> error >> > message... >> > Is there something else I can try? >> > >> > Francesco >> > >> > >> > 2014-08-07 0:46 GMT+02:00 Douglas N Greve >> <greve(a)nmr.mgh.harvard.edu >> > <mailto:greve@nmr.mgh.harvard.edu>>: >> > >> > Try it with -notal-check >> > doug >> > >> > On 08/06/2014 04:39 PM, Francesco Deleo wrote: >> > > I all! >> > > >> > > I am a new freesurfer user. >> > > I have a problem when I perform the recon-all -all, in about >> 15% of >> > > MRI scans, all made with the same scanning protocol (T1 MPRAGE >> in a >> > > SIEMENS Avanto 1,5 T). >> > > >> > > I can't recognize any difference between those scans which >> work >> > > correctly and those not. >> > > I have never found the same error on 3T MRI scans. >> > > >> > > I've already tried to add these flags to the recon-all -all >> command: >> > > -use-mritotal >> > > -talairach -use-mritotal >> > > -notalairach >> > > but I've always received an error message >> > > >> > > Thank you very much >> > > >> > > ERROR: mpr2mni305 failed, see transforms/talairach_avi.log >> > > Darwin pro-di-villani.besta.local 13.3.0 Darwin Kernel Version >> > 13.3.0: >> > > Tue Jun 3 21:27:35 PDT 2014; >> > root:xnu-2422.110.17~1/RELEASE_X86_64 x86_64 >> > > >> > > Thanks very much for your attention >> > > >> > > Francesco >> > > Milan, Italy >> > > >> > > >> > >> --------------------------------------------------------------------- >> > > >> > > FREESURFER_HOME: /Applications/freesurfer >> > > >> > > Build stamp: freesurfer-Darwin-lion-stable-pub-v5.3.0 >> > > >> > > Kernel info: Darwin 13.3.0 x86_64 >> > > >> > > >> > >> --------------------------------------------------------------------- >> > > >> > > >> > > LAST LINES IN TALAIRACH_AVI.LOG >> > > >> > > parameters >> > > 9.0270 134.9373 110.8627 -84.3566 -7.5458 -11.3475 >> > > eta,q 0.95791 3.72402 >> > > 0.0485 0.0470 0.0477 0.0513 0.0470 0.0452 >> > > 0.0475 0.0471 0.0478 0.0513 0.0457 0.0435 >> > > 0.0472 0.0472 0.0476 0.0428 0.0434 0.0415 >> > > 0.0471 0.0471 0.0476 0.0435 0.0430 0.0415 >> > > 0.0470 0.0478 0.0457 0.0525 0.0415 0.0430 >> > > 0.0473 0.0511 0.0430 0.0548 0.0442 0.0453 >> > > 0.0486 0.0426 0.0406 0.0672 0.0431 0.0503 >> > > niter,ni,del,rscale 7 3 12.0000 1.2000 >> > > imgrege: no voxels in register >> > > ERROR: 'imgreg_4dfp >> > > /Applications/freesurfer/average/711-2C_as_mni_average_305 >> > > >> /Applications/freesurfer/average/711-2B_as_mni_average_305_mask >> > > talsrcimg_g11 none talsrcimg_to_711-2C_as_mni_average_305_t4 >> 1283' >> > > failed! status=254 >> > > ERROR: mpr2mni305 execution aborted >> > > >> > > >> > > _______________________________________________ >> > > Freesurfer mailing list >> > > Freesurfer(a)nmr.mgh.harvard.edu >> > <mailto:Freesurfer@nmr.mgh.harvard.edu> >> > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> > >> > -- >> > 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/ >> > >> > _______________________________________________ >> > Freesurfer mailing list >> > Freesurfer(a)nmr.mgh.harvard.edu >> <mailto:Freesurfer@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. >> > >> > >> > >> > >> > _______________________________________________ >> > Freesurfer mailing list >> > Freesurfer(a)nmr.mgh.harvard.edu >> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> -- >> 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/ >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer(a)nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> >> >> > _______________________________________________ > 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. > >

2 3

CBF map computed on surface and projected on fsaverage
by Matthieu Vanhoutte 21 Aug '14

21 Aug '14

Dear experts, I try to project on fsaverage CBF maps computed on surface, but when trying to look at the mri_info of the output file "meanCBF_0_s1.5asl.rem.mc.s6.fsaverage.lh.nii" I got this error : *niiRead(): bad number of dimensions (13734) in /home/matthieu/NAS/pierre/Epilepsy/FreeSurfer5.0/Patients_fmri_dti//Delforterie_Julien/asl_COR_PVEnew/meanCBF_0_s1.5asl.rem.mc.s6.fsaverage.lh.nii* Here below the command lines used : *# CBF map * *computed on surface**# fsaverage & lh* *mri_surf2surf --srcsubject Delforterie_Julien --srchemi lh --srcsurfreg sphere.reg --trgsubject fsaverage --trghemi lh --trgsurfreg sphere.reg --sval meanCBF_0_s1.5asl.rem.mc.s6.lh.nii --sfmt curv --noreshape --no-cortex --tval meanCBF_0_s1.5asl.rem.mc.s6.fsaverage.lh.nii --tfmt curv* You can find data file joined to this mail. Thanks in advance for helping ! Best regards, ------------------------------------- Matthieu Vanhoutte, MSc Research Engineer - Department of Neuroradiology Regional University Hospital, Lille, France

2 2

mri_tessellate: max vertices 1000000 exceeded
by Michiel Kleinnijenhuis 20 Aug '14

20 Aug '14

Hi, While doing a high resolution ex vivo recon job, I came across the error mri_tessellate: max vertices 1000000 exceeded As mentioned in the threads http://www.mail-archive.com/freesurfer%40nmr.mgh.harvard.edu/msg35305.html<http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg35305.html> http://www.mail-archive.com/freesurfer%40nmr.mgh.harvard.edu/msg31331.html<http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg31331.html> there seems to be an easy fix. Does anyone have a compiled version of mri_tesselate with the vertex limit relaxed; for Mac (freesurfer-Darwin-lion-stable-pub-v5.3.0)? Thanks! Michiel Kleinnijenhuis == Michiel Kleinnijenhuis Postdoctoral researcher FMRIB Centre Nuffield Department of Clinical Neurosciences University of Oxford

3 2

Open MP parallel processing scaling factor?
by O'Shea,Andrew 20 Aug '14

20 Aug '14

Hello all, Traditionally I have only processed FS data using a single core per person, but processing many people at once. Now we have caught up with the backlog of scans, we have a continuos trickle of scans coming in 1 by 1. I was wondering if anyone has tested how the speed-up of open-mp varies with number of cores used simultaneously. For example how much faster is using 100 cores versus 10? I am trying to find a sweet spot of resource usage and speed. Thanks! -Andrew

3 3

tkmedit
by Ali Radaideh 20 Aug '14

20 Aug '14

Dear FreeSurfer experts, I have installed FreeSurfer on multiple machines in our image processing lab (15 PC, Linux Ubuntu) and made sure that the setting are fine. However, I have tried to test if freesurfer works or not by typing the following: tkmedit bert orig.mgz Unfortunately, I have got the following error message on all PCs A segfault has occurred. This is not your fault, : but is most likely an unrecoverable error and has : made the program unstable. So what would be the error? Many thanks in advance, Ali, -- *Ali M. Al-Radaideh. PhDAssistant ProfessorHead of Department of Medical ImagingVice Dean of the Faculty of Allied Health SciencesThe Hashemite University, Zarqa, JordanW.phone +962 5 3903333 ext.5422, 5355, 5364Email: ali.radaideh(a)hu.edu.jo <ali.radaideh(a)hu.edu.jo>* *webpage: http://staff.hu.edu.jo/Default.aspx?id=ABZUPDzYeqM= <http://staff.hu.edu.jo/Default.aspx?id=ABZUPDzYeqM=>*

4 10

problem downloading freesurfer
by gamaliel huerta urrea 20 Aug '14

20 Aug '14

Hi I tried for three days download freesurfer even today but pressing the download link in http://surfer.nmr.mgh.harvard.edu/fswiki/Download These are fallen and message "This web page is not available" I have understood that the site was in maintenance, however the links do not even respond. any help? I need to download for Mac OS XV FreeSurfer 10.9.4 64bit regards -- *Gamaliel Huerta* *Ingeniería Civil Biomédica* *Universidad de Valparaíso*

2 1

Custom aseg Color Lookup Table
by C.P. Frost 20 Aug '14

20 Aug '14

Hi all, I'm trying to use Freeview to display subcortical regions in aseg.mgz with a custom color lookup table. RGB colors will indicate on a jet scheme how well that region's volume correlates to performance on a behavioral measure. In other words, an R^2 coefficient of -1 is dark blue, 0 is green, and 1 is dark red. I adapted the approach for aseg structures from this method: http://brainder.org/2011/07/05/freesurfer-brains-in-arbitrary-colours/ When I try right now, by e.g. loading subjects_dir/average/mri/aseg.mgz, and choosing Color map > Lookup Table, Lookup Table > Load lookup table... and selecting my custom table file, it *almost* works. The file is copied below (it has no headers). 4 Left-Lateral-Ventricle 92 255 163 0 5 Left-Inf-Lat-Vent 224 255 31 0 7 Left-Cerebellum-White-Matter 112 255 143 0 8 Left-Cerebellum-Cortex 133 255 122 0 10 Left-Thalamus-Proper 153 255 102 0 11 Left-Caudate 102 255 153 0 12 Left-Putamen 61 255 194 0 13 Left-Pallidum 102 255 153 0 14 3rd-Ventricle 0 224 255 0 15 4th-Ventricle 61 255 194 0 16 Brain-Stem 71 255 184 0 17 Left-Hippocampus 102 255 153 0 18 Left-Amygdala 41 255 214 0 26 Left-Accumbens-area 92 255 163 0 28 Left-VentralDC 122 255 133 0 30 Left-vessel 102 255 153 0 31 Left-choroid-plexus 102 255 153 0 43 Right-Lateral-Ventricle 173 255 82 0 44 Right-Inf-Lat-Vent 122 255 133 0 41 Right-Cerebellum-White-Matter 82 255 173 0 42 Right-Cerebellum-Cortex 122 255 133 0 49 Right-Thalamus-Proper 173 255 82 0 50 Right-Caudate 143 255 112 0 51 Right-Putamen 92 255 163 0 52 Right-Pallidum 41 255 214 0 53 Right-Hippocampus 133 255 122 0 54 Right-Amygdala 20 255 235 0 58 Right-Accumbens-area 82 255 173 0 60 Right-VentralDC 122 255 133 0 62 Right-vessel 122 255 133 0 63 Right-choroid-plexus 143 255 112 0 72 5th-Ventricle 92 255 163 0 85 Optic-Chiasm 112 255 143 0 251 CC_Posterior 71 255 184 0 252 CC_Mid_Posterior 31 255 224 0 253 CC_Central 10 255 245 0 The index numbers were chosen to match those found in the default aseg LUT, as listed on the FS wiki: FSTutorial > AnatomicalROI > FreeSurferColorLUT. Some regions appear correctly, but others either a) display with incorrect labels, particularly Right-Cerebellum-White-Matter or Right-Cerebellum-Cortex on *cortical* white matter and ribbon, or b) display with no label in the info panel, which makes it unclear whether it's working. Notes: - Originally indices were simply 1 to n, but that caused a wider array of problems, and I inferred (perhaps incorrectly) freeview was matching regions with indices rather than label names. -This particular map is mostly green since most correlations are small, which is fine; others will have a broader range of values. -I'm not sure what the effect is of pressing the "Show existing labels only" toggle, which eliminates a couple areas from the label list, but it's unclear how it chooses them. Can anyone offer advice on how to ensure the correct colors are displayed in the correct regions? (Or an easier way to do this?) Cheers, C.P. Frost UW-Madison

2 1

Creating the FSDG file for more than one discrete variable
by Isotalus, Hanna 20 Aug '14

20 Aug '14

Dear Freesurfer gurus, I am trying to create an FSDG file for my data set and I have a question regarding discrete variables. So say this is my data: Two discrete variables (two with two levels, one with eight), one continuous variable. I'm interested in one discrete variable (Patient/Control) with two levels and want to account for the effect of the others in the analysis. How should I construct my FSDG file? Can I have three columns for discrete variables (1) or should I have one column (2)? Or is there another way? (1) So should I do: GroupDescriptorFile 1 Title GroupAnalysis Class Male Class Female Class Patient Class Control Class ImagingsiteOne Class ImagingsiteTwo [and so on...] Class OccupationEight Variables Age Subject1 Male Patient ImagingsiteThree 16 Subject2 Male Control ImagingsiteSeven 18 Subject3 Female Patient ImagingsiteThree 23 And so on OR (2) Should I do GroupDescriptorFile 1 Title GroupAnalysis Class MalePatientImagingsiteOne Class MalePatient?ImagingsiteTwo [and so on..] Class MalePatient?ImagingsiteEight Class MaleControlImagingsiteOne [and so on...] Class FemalePatient?ImagingsiteOne [and so on until...] Class FemaleControl?ImagingsiteEight Variables Age Subject1 MalePatientImagingsiteThree 16 Subject2 MaleControlImagingsiteSeven 18 Subject3 FemalePatientImagingsiteThree ?23 And so on Thank you! Best wishes, Hanna

2 1

tracula update link not working
by Kirstie Whitaker 20 Aug '14

20 Aug '14

Hi, I apologise if this is only on my end but I can't seem to download any of the updates from http://surfer.nmr.mgh.harvard.edu/fswiki/Tracula. I was successful last week so I wonder if something's changed? Thanks Kx -- Kirstie Whitaker, PhD Research Associate Department of Psychiatry University of Cambridge Mailing Address Brain Mapping Unit Department of Psychiatry Sir William Hardy Building Downing Street Cambridge CB2 3EB Phone: +44 7583 535 307 Website: www.kirstiewhitaker.com

2 2

Error with the brainmask
by Mads Jensen 20 Aug '14

20 Aug '14

Dear list, I have problem with the brainmask from a subject where there is removed to much of the gray matter. So, I would like to hear if someone has a good idea where I should start to fix this issue? I have attached a jpgs of the brainmask and orig, and a link to the recon-all.log best regards, mads https://dl.dropboxusercontent.com/u/915037/recon-all.log

1 0

Jump to page:

2026

2025

2024

2023

2022

2021

2020

2019

2018

2017

2016

2015

2014

2013

2012

2011

2010

2009

2008

2007

2006

2005

2004

Freesurfer