Freesurfer July 2013

freesurfer@nmr.mgh.harvard.edu

165 participants
332 discussions

MRI_Convert error
by Pom Sailasuta 25 Jul '13

25 Jul '13

Hello, I am resending this post since there is no reply for 2 days, I really appreciate your help. thanks so much. I have several errors using mri_convert to convert 3T Philips T1-wt, DTI and fMRI images. The last one on T1-wt images tells me to send email to freesurfer, so here is the error messages: [pom@PomLinux /home/pom]% !mri mri_convert -it dicom -i IM_0001 -ot mgz -o 001.mgz mri_convert -it dicom -i IM_0001 -ot mgz -o 001.mgz $Id: mri_convert.c,v 1.179.2.2 2011/05/16 20:53:47 greve Exp $ reading from IM_0001... Starting DICOMRead2() dcmfile = /home/pom/Software/freesurfer/ subjects/S009002A/mri/orig/orig2/IM_0001 dcmdir = /home/pom/Software/freesurfer/subjects/S009002A/mri/orig/orig2 WARNING: tag image orientation not found Ref Series No = 2 ERROR: bits = 8 not supported. Send email to freesurfer(a)nmr.mgh.harvard.edu for DTI images, here is the errors: MRIalloc(0, 0, 1855): bad parm [pom@PomLinux /home/pom]% mri_convert -it dicom -i IM_0001 -ot mgz -o 001.mgz mri_convert -it dicom -i IM_0001 -ot mgz -o 001.mgz $Id: mri_convert.c,v 1.179.2.2 2011/05/16 20:53:47 greve Exp $ reading from IM_0001... Starting DICOMRead2() dcmfile = /home/pom/Software/freesurfer/subjects/S009002A/mri/orig/IM_0001 dcmdir = /home/pom/Software/freesurfer/subjects/S009002A/mri/orig Ref Series No = 501 Found 1874 files, checking for dicoms WARNING: tag image orientation not found WARNING: tag image orientation not found WARNING: tag image orientation not found WARNING: tag image orientation not found WARNING: tag image orientation not found WARNING: tag image orientation not found WARNING: tag image orientation not found WARNING: tag image orientation not found WARNING: tag image orientation not found WARNING: tag SeriesNumber not found WARNING: tag image orientation not found Found 1855 dicom files in series. WARNING: tag image orientation not found WARNING: tag image orientation not found WARNING: tag image orientation not found WARNING: tag image orientation not found WARNING: tag image orientation not found WARNING: tag image orientation not found WARNING: tag image orientation not found WARNING: tag image orientation not found WARNING: tag image orientation not found WARNING: tag SeriesNumber not found WARNING: tag image orientation not found First Sorting Computing Slice Direction Vs: -117.09 -112.869 17.456 Vs: -0.715854 -0.690047 0.106721 Second Sorting Counting frames nframes = 1 nslices = 1855 ndcmfiles = 1855 MRIalloc(0, 0, 1855): bad parm ERROR: mri alloc failed I would greatly appreciate any help. -- Pom

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need help
by Haielom Embaie 25 Jul '13

25 Jul '13

Hi there, I was trying to learn the freesurfer, I have hard time to download at the beginning, later after that, I also have no knowledge of how to import images and analyse them. I really need your help tremendously. Thanks, Haielom

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bug reporting
by Kyllo, Hannah M 25 Jul '13

25 Jul '13

Hello, I've received the following error using Ubuntu 13.04: "WARNING: tcsh v6.17.06 has an exit code bug! Please update tcsh! ERROR: cannot find subj001.nii.gz Linux neuron 3.2.0-49-generic #75-Ubuntu SMP Tue Jun 18 17:39:32 UTC 2013 x86_64 x86_64 x86_64 GNU/Linux recon-all -s exited with ERRORS at Thu Jul 25 11:15:50 CDT 2013" thanks in advance for your input, - Hannah Kyllo The information in this e-mail may be privileged and confidential, intended only for the use of the addressee(s) above. Any unauthorized use or disclosure of this information is prohibited. If you have received this e-mail by mistake, please delete it and immediately contact the sender.

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FreeSurfer Version
by Rodrigo Perea 25 Jul '13

25 Jul '13

Is there any other way I can find the FreeSurfer version I am using? According to https://surfer.nmr.mgh.harvard.edu/fswiki/UserContributions/FAQ#Q.HowdoIkno… I have to run: recon-all -version, but I get the output below. Now the stable FreeSurfer Version is 5.3.0 so its not even close to the output. Any help? Rodrigo OUTPUT: recon-all -version $Id: recon-all,v 1.379.2.17 2011/05/20 22:48:18 nicks Exp $

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different results between 5.1.0 and 5.2.0
by clarissa yasuda 25 Jul '13

25 Jul '13

Dear FreeSurfer Experts As in some other posts, I have also observed some differences between the two releases. The values from cuneus (thickness) are similar to the post from Ritobrato Datta, Ph.D. on 18 march. But I also observed some differences in volume of right / left thalami. Did anybody observe such asymmetry?? I am now running analysis with patients and controls on data from 5.2.0 and got surprised with this asymmetry. Here I am showing the average I obtained: R PALLIDUM L PALLIDUM R THAL L THAL RH_CUNEUS LH_CUNEUS 5.1 (350 SUBJECTS) 1580 1688 6701 6970.31 1.845 1.857 5.2 (115 SUBJECTS, subgroup of 350) 1519 1367 6520 7401 2.42 2.40 Is there any approach to correct it on 5.2 ?? Thanks in advance clarissa

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R: Re: R: Re: problem with nu_correct
by Andrea Tateo 25 Jul '13

25 Jul '13

Normal 0 14 false false false IT X-NONE X-NONE MicrosoftInternetExplorer4 Hello Zeke, I must make a clarification: I use freesurfer on a PC cluster. I have submitted the same image several times and on different machines. Sometimes it was killed sometimes not. If I submit a second time the failed job it may happen that it is terminated with success. thank you very much /* Style Definitions */ table.MsoNormalTable {mso-style-name:"Tabella normale"; mso-tstyle-rowband-size:0; mso-tstyle-colband-size:0; mso-style-noshow:yes; mso-style-priority:99; mso-style-qformat:yes; mso-style-parent:""; mso-padding-alt:0cm 5.4pt 0cm 5.4pt; mso-para-margin-top:0cm; mso-para-margin-right:0cm; mso-para-margin-bottom:10.0pt; mso-para-margin-left:0cm; line-height:115%; mso-pagination:widow-orphan; font-size:11.0pt; font-family:"Calibri","sans-serif"; mso-ascii-font-family:Calibri; mso-ascii-theme-font:minor-latin; mso-fareast-font-family:"Times New Roman"; mso-fareast-theme-font:minor-fareast; mso-hansi-font-family:Calibri; mso-hansi-theme-font:minor-latin;} ----Messaggio originale---- Da: zkaufman(a)nmr.mgh.harvard.edu Data: 24-lug-2013 21.53 A: "Andrea Tateo"<andrea.tateo(a)virgilio.it> Cc: <freesurfer(a)nmr.mgh.harvard.edu> Ogg: Re: R: Re: [Freesurfer] problem with nu_correct Andrea, Hmmm. I am not able to duplicate this error on my end using local data. A few things: 1) What happens when you type "nu_evaluate -help"? Do you get help output or does it crash? 2) Does this error occur for all subjects or just this one used for this particular recon? 3) Does the brain image look "normal", meaning is there anything obviously wrong with the input data, which you can see by opening it with Freeview? -Zeke On 07/24/2013 11:22 AM, Andrea Tateo wrote: > Hello zkaufman, > > thanks for your involvement > > Andrea > > > > ----Messaggio originale---- > Da: zkaufman(a)nmr.mgh.harvard.edu > Data: 24-lug-2013 16.52 > A: "Andrea Tateo"<andrea.tateo(a)virgilio.it> > Cc: <freesurfer(a)nmr.mgh.harvard.edu> > Ogg: Re: [Freesurfer] problem with nu_correct > > Hello Andrea, > > Can you please attach the entire recon-all.log file? It will be located > in $SUBJECT_DIR/subject_name/scripts/recon-all.log > > -Zeke > > On 07/24/2013 09:35 AM, Andrea Tateo wrote: > > Hi FreeSurfer expert, > > > > I have a problem with command "recon-all". > > > > In recon-all.log I can to read > > > > nu_correct: crashed while running nu_evaluate (termination status=9) > > > > Thank for your help > > > > > > _______________________________________________ > > 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. > > >

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MRI dimensions different from [256x256x256]
by François Tadel 24 Jul '13

24 Jul '13

Hello, Is it possible to run recon-all without modifying the size of the input MRI volume? I have in input a volume [181x217x181], and all the steps of recon-all save it in a [256x256x256] volume. I tried skipping all the first steps to avoid this behavior (recon-all -all -nomotioncor -nonuintensitycor -notalairach) but it still re-interpolates my volume... For what I have to do, it would really help me if I can avoid this re-interpolation + padding. If this can't be done, can the output volumes be cropped to the desired size, while keeping the correspondence MRI/surfaces? Thanks, Francois -- François Tadel, MSc MEG / McConnell Brain Imaging Center / MNI / McGill University 3801 rue University, Montreal, QC H3A2B4, Canada

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Binary mask of the skull
by Fotiadis, Panagiotis 24 Jul '13

24 Jul '13

Hi, I was wondering whether there was a command (or a flag in a command such as mri_binarize) that can give me the binary mask of my subject's skull. I was thinking of creating a binary ask of the subject's brain and then one of the brain and the skull and subtracting them, but I was wondering whether there is a faster way. Thanks, Panos

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R: Re: problem with nu_correct
by Andrea Tateo 24 Jul '13

24 Jul '13

Hello zkaufman, thanks for your involvement Andrea ----Messaggio originale---- Da: zkaufman(a)nmr.mgh.harvard.edu Data: 24-lug-2013 16.52 A: "Andrea Tateo"<andrea.tateo(a)virgilio.it> Cc: <freesurfer(a)nmr.mgh.harvard.edu> Ogg: Re: [Freesurfer] problem with nu_correct Hello Andrea, Can you please attach the entire recon-all.log file? It will be located in $SUBJECT_DIR/subject_name/scripts/recon-all.log -Zeke On 07/24/2013 09:35 AM, Andrea Tateo wrote: > Hi FreeSurfer expert, > > I have a problem with command "recon-all". > > In recon-all.log I can to read > > nu_correct: crashed while running nu_evaluate (termination status=9) > > Thank for your help > > > _______________________________________________ > 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.

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GCA atlas defined anatomical boundaries
by Zuzana Nedelska 24 Jul '13

24 Jul '13

Hello, I have attended short FSL/FreeSurfer course in New Zealand last year and have subscribed for mailing list, but in spite of all that I would I would appreciate very much to know. 1.) 1.)how GCA atlas that is used by FreeSurfer defines boundaries of subcortical volumes (especially amygdala and hippocampus). I work in Mayo Clinic Center for Advanced Imaging Research now and I need to know these details (if possible) this for publication methods. We use and cite FreeSurfer often, but never went into details like this. 2.) 2.)What is ment by region of ‘5th ventricle’ in FS aseg.stats outputs and LUTs color coding table? From anatomical point of view, I am not sure what 5th ventricle is 3.) 3.)Do I correctly understand that subcortical segmentation is based on manually labeled GCA atlas, and cortical parcellation is based either on Desikan-Killiany atlas with 33 ROIS/hemisphere, or Destrieux atlas with 73 ROIs/hemisphere? 4.) 4.)What is cortical region named ‘bankssts’ in Desikan-Killiany atlas? I would greatly appreciate your reply or suggestion where to find these information ASAP. Thank you, Zuzana Nedelska

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Freesurfer July 2013