Freesurfer

freesurfer@nmr.mgh.harvard.edu

19 participants
30088 discussions

mris_pmake error
by Steph Bickel 31 Oct '11

31 Oct '11

Hi, when trying to use mris_pmake I get error messages: when I run:mris_pmake I get: sh: cannot create lock: Permission denied mris_pmake I'm sorry, but an error condition has occurred. While I was checking on the options file, I couldn't access the options file. Does it exist? Exiting to system with code 40 When I run: sudo ./bin/mris_pmake I get: mris_pmake I'm sorry, but an error condition has occurred. While I was processing environment, it seems that the SUBJECTS_DIR env variable is not set. Exiting to system with code 10 I did specify SUBJECTS_DIR in SetUpFreesurfer.sh that I source in the bashrc file and the variable is set for the other freesurfer functions. I am using freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0 on ubuntu 11.04. Any help is much appreciated. thanks, Stephan

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FW: Question on mris_pmake
by Jungwon Ryu 31 Oct '11

31 Oct '11

Regarding my first question in my previous post below, the same error occurs even when I run my script (containing many repetition of mris_pmake command) on only one terminal window. From: Jungwon Ryu [mailto:rjungwon@snu.ac.kr] Sent: Tuesday, October 25, 2011 8:11 PM To: 'freesurfer(a)nmr.mgh.harvard.edu' Subject: Question on mris_pmake Hi, I'm trying to get distances on a cortical surface between sets of voxels in visual areas and I have two questions; 1) I have the following error message so often; === System error: Address already in use Fatal error encountered. SSocket `Unnamed SSocket_UDP_receive' (id: 0) Current function: c_SSocket_UDP_receive::c_SSocket_UDP_receive Problem binding to socket 1701 Error returned from system: Address already in use Throwing exception to (this) with code 1 terminate called after throwing an instance of 'c_SSocket*' runSh_Ori_1_02_01.sh: line 5789: 93334 Abort trap mris_pmake --subject JR20110819 --hemi rh --surface0 white --curv0 sulc --curv1 sulc --mpmOverlay euclidean --mpmProg pathFind --mpmArgs startVertex:907,endVertex:731 >> result_Ori_1_02_01.txt === I have around 10,000 voxel pairs to run mris_pmake( ) command. Since I have to call mris_pmake( ) so many times (one pair by one pair), I splitted the whole list of voxel pairs into four script files, containing many mris_pmake commands with 2,500 voxel pairs as arguments, then I ran scripts with four terminal windows saparately to parallelize the processing. All script files are located in the same diretory. Then I had the message as above. What might be the problem? (It seems as if multiple terminal instances share the socket port number) 2) How can I get interhemispheric distances between visual areas across hemispheres? Ryu PhD student Department of Brain and Cognitive Sciences, Seoul National University, Korea

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Sag3D_T1 or Axial_T1
by Antonella Kis 31 Oct '11

31 Oct '11

Dear Freesurfers, I have a set of MRI data collected in an Axial_T1 and some in Sag3D_T1. I wonder if after dcm to nii conversion when I get a 3D or 4D volume (if further use for FSL) it really matter how my data was acquired (Axial or Sag) since the NIFTI file is in fact a volume. Should I do a conversion for all the files in Axial or Sag? I am planning to use this data in Qdec and also in FSL to do some DTI studies, so I will need to register this data into MNI space. Also, how I can cut from the nii file's slices in order to bring two files to the same dimensions (x, Y, Z)? Many thanks, Antonella

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Cluster-wise simulation in small samples
by Alexander Lebedev 31 Oct '11

31 Oct '11

Dear Freesurfers, Could you please tell me about your experience with cluster-wise correction for multiple comparisons in relatively small samples. For instance, is it wise to use CWS for regression with one continuos variable in n=30 sample? --- Regards, Alex

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Re: [Freesurfer] white matter volume in a ROI
by Douglas N Greve 31 Oct '11

31 Oct '11

Use mri_segstats. You can look in the recon-all.log file in subject/scripts. Find the call to mri_segstats used to generate the wmparc stats, copy it and make the customizations you need. doug dolphinede(a)aol.com wrote: > Hi Doug, > > to get the white matter volume of my ROI-label, i have done the > following steps: > > 1. mris_label2annot > (mris_label2annot --s ZPN20 --h lh --ctab > /Users/dolphinede/Desktop/Probanden/ZPN20/label/aparc.annot.ctab --a > myaparc --l lh.cluster1.labe/.label --nhits nhits.mgh) > > > 2. mri_aparc2aseg, with my real ROI label and a dumy label for the > other hemisphere. > > mri_aparc2aseg --s ZPN20 --labelwm --hypo-as-wm --rip-unknown > --volmask --o mri/wmparc.mgz --ctxseg aparc+aseg.mgz --annot myaparc/ > > How do i get from the wmparc.mgz the white matter volume for my ROI > label/myaparc ? > Should i use mris_wm_volume? > > Best regards > > Daniel... > > > > > > -----Ursprüngliche Mitteilung----- > Von: Douglas N Greve <greve(a)nmr.mgh.harvard.edu> > An: dolphinede <dolphinede(a)aol.com>; freesurfer > <freesurfer(a)nmr.mgh.harvard.edu> > Verschickt: Di, 25 Okt 2011 5:05 pm > Betreff: Re: [Freesurfer] white matter volume in a ROI > > > Yes, I see what you mean. mri_aparc2aseg is hard coded to accept both > hemis. The easiest way around it is just to create a dummy label for the > right hemisphere. > doug > > dolphinede(a)aol.com <mailto:dolphinede@aol.com> wrote: > > Hi Doug, > > > > thanks a lot your advice. > > > > I created an annnotation of my ROI-label as called > > lh.cluster1.labe.label with the command line: > > > > /mris_label2annot --s ZPN20 --h lh --ctab > > //Users/dolphinede/Desktop/Probanden/ZPN20/label/aparc.annot.ctab --a > > myaparc --l lh.cluster1.labe/.label --nhits nhits.mgh > > > > This works fine. After that i have used your commmand in this way: > > > > m/ri_aparc2aseg --s ZPN20 --labelwm --hypo-as-wm --rip-unknown > > --volmask --o mri/wmparc.mgz --ctxseg aparc+aseg.mgz --annot myaparc/ > > > > and i get the following error, which is cause that i have no > > lh.cluster1.labe.label in the right hemisphere: > > > > /Loading lh annotations from > > /Users/dolphinede/Desktop/Probanden/ZPN20/label/lh.myaparc.annot > > reading colortable from annotation file... > > colortable with 36 entries read (originally > > //Users/dolphinede/Desktop/Probanden/ZPN20/label/aparc.annot.ctab) > > > > Reading rh white surface > > /Users/dolphinede/Desktop/Probanden/ZPN20/surf/rh.white > > > > Reading rh pial surface > > /Users/dolphinede/Desktop/Probanden/ZPN20/surf/rh.pial > > > > Loading rh annotations from > > /Users/dolphinede/Desktop/Probanden/ZPN20/label/rh.myaparc.annot > > could not read annot file > > /Users/dolphinede/Desktop/Probanden/ZPN20/label/rh.myaparc.annot > > No such file or directory > > ERROR: MRISreadAnnotation() failed > > /Users/dolphinede/Desktop/Probanden/ZPN20/label/rh.myaparc.annot/ > > > > The question i have is if all these steps are right and/if i have to > > do some more steps to get white matter volume of my annotation and > > where i can find it? > > > > Excuse my numerous questions but I am just a freesurfer-beginner... > > > > Best regards > > > > Daniel > > > > > > > > > > > > > > > > > > > > -----Ursprüngliche Mitteilung----- > > Von: Douglas N Greve <greve(a)nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> > > An: dolphinede <dolphinede(a)aol.com <mailto:dolphinede@aol.com>>; freesurfer > > <freesurfer(a)nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu>> > > Verschickt: Mo, 24 Okt 2011 10:04 pm > > Betreff: Re: [Freesurfer] white matter volume in a ROI > > > > It will be more involved than that. You will need to create an > > annotation that contains your label (maybe in addition to other labels), > > then uses mri_aparc2aseg with the --labelwm option, something like > > > > mri_aparc2aseg --s subject-anat --labelwm --hypo-as-wm --rip-unknown > > --volmask --o mri/wmparc.mgz --ctxseg aparc+aseg.mgz --annot yourannot > > > > doug > > > > dolphinede(a)aol.com <mailto:dolphinede@aol.com> <mailto:dolphinede@aol.com <mailto:dolphinede@aol.com?>> wrote: > > > Hi Doug, > > > > > > thanks a lot for your answer. > > > > > > So i understand you right that i can get "exact" knowledge about the > > > thickness, grey matter volume and pial surface area in my ROI, but in > > > case of "the" ROI white matter volume, i have to look to which > > > cortical label my ROI counts and then I use the wmparc.files for this > > > label? > > > > > > Best regards > > > > > > Daniel Klein > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > -----Ursprüngliche Mitteilung----- > > > Von: 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?>>> > > > An: dolphinede <dolphinede(a)aol.com <mailto:dolphinede@aol.com> <mailto:dolphinede@aol.com <mailto:dolphinede@aol.com?>>> > > > Cc: freesurfer <freesurfer(a)nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu> <mailto:freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu?>>> > > > Verschickt: Mo, 24 Okt 2011 4:48 pm > > > Betreff: Re: [Freesurfer] white matter volume in a ROI > > > > > > For GM area and volume, you can use mris_anatomical_stats. See the > > > recent thread on how. For the WM volume, how would you define the WM > > > volume that corresponds to you label? We have a routine that parcellates > > > WM based on closest proximity to a cortical label. > > > doug > > > > > > dolphinede(a)aol.com <mailto:dolphinede@aol.com> <mailto:dolphinede@aol.com <mailto:dolphinede@aol.com?>> wrote: > > > > Dear FreeSurfer experts, > > > > > > > > i have created a ROI in qdec , where i have found a significant > > > > correlation between lgi and age. > > > > > > > > I mapped this ROI to all subjects. > > > > > > > > I am interested to compare in this ROI the pial-surface area, the grey > > > > matter volume and if possible the white matter volume for this > > > > specific region and i am not sure how to do this? > > > > > > > > Best regards > > > > > > > > Daniel Klein > > > > ------------------------------------------------------------------------ > > > > > > > > _______________________________________________ > > > > Freesurfer mailing list > > > > Freesurfer(a)nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> <mailto:Freesurfer@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> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu?>> > > > Phone Number: 617-724-2358 > > > Fax: 617-726-7422 > > > > > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > > > FileDrop: 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> > > > > > > > > > > > > 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> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu?>> > > Phone Number: 617-724-2358 > > Fax: 617-726-7422 > > > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > > FileDrop: 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> > > > > -- > 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 > Fax: 617-726-7422 > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > -- 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: www.nmr.mgh.harvard.edu/facility/filedrop/index.html

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Join my network on LinkedIn
by Mohan Boddu via LinkedIn 30 Oct '11

30 Oct '11

LinkedIn ------------ Mohan Boddu souhaite se connecter à vous sur LinkedIn : ------------------------------------------ I'd like to add you to my professional network on LinkedIn. Accepter l'invitation de Mohan Boddu http://www.linkedin.com/e/-qq80um-guerwfnb-f/qaAr-Z_86TRZ5lXG-dA9kZQ49qSe59… Voir l'invitation de Mohan Boddu http://www.linkedin.com/e/-qq80um-guerwfnb-f/qaAr-Z_86TRZ5lXG-dA9kZQ49qSe59… ------------------------------------------ Quel est l'intérêt de faire partie du réseau de Mohan Boddu ? Les contacts de Mohan Boddu consulteront votre profil : Votre arrivée dans le réseau de Mohan Boddu attirera l'attention d'autres membres de LinkedIn. Voir qui a consulté votre profil. http://www.linkedin.com/e/-qq80um-guerwfnb-f/wvp/inv18_wvmp/?hs=false&tok=3… -- (c) 2011, LinkedIn Corporation

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Fwd: gray matter/csf surface reconstruction
by Shani Ben Amitay 30 Oct '11

30 Oct '11

Hi , I have a diffusion weighted dataset and I would like to perform an analysis along the cortical normals. Any advice will be appreciated Thanks, shani On Sun, Oct 23, 2011 at 5:04 PM, Bruce Fischl <fischl(a)nmr.mgh.harvard.edu>wrote: > Hi Shani > > we described in in the recon1 NeuroImage paper (1999) and the PNAS paper, I > think the next year. We don't impose any constrains on the pial surface as > it evolves from the white surface (e.g. "link" terms in the energy > functional), but let the vertices move whereever they want to in order to > find an image intensity that is what we estimate the gray/csf boundary to be > in that region. > > Can you tell us a bit about what you want to do with the normals? We > typically don't use them for sampling of hires data for example, but rather > use mris_expand to generate a series of intermediate surfaces. > > > cheers > Bruce > > > > On Sun, 23 Oct 2011, Shani Ben Amitay wrote: > > Dear freesurfers, >> In order to generate cortical vector normals connecting homologous >> vertices >> of the inner and outer surface, I would like to better understand how the >> gray matter/csf surface is reconstructed and how correspondence between >> inner and outer surfaces is achieved. >> >> Does anyone can explain or give a reference? >> >> Thanks , >> Shani >> >> >> >> >> >> > > 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<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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Re: [Freesurfer] Any Pre-exisiting Public Amazon EC2 AMI with Freesurfer out there?
by Joshua Lee 30 Oct '11

30 Oct '11

I think I may have found it as a public ami with freesurfer 5.1. Testing it out on Bert right now. Thanks!! - Joshua Lee Graduate Student Center for Mind and Brain & Department of Psychology University of California, Davis 530.747.3805 2011/10/30 Joshua Lee <jkilee(a)ucdavis.edu> > I think I may have found it as a public ami with freesurfer 5.1. Testing > it out on Bert right now. Thanks!! > - > Joshua Lee > > > > 2011/10/28 Joshua Lee <jkilee(a)ucdavis.edu> > >> Thanks Pedro, that's fantastic! I'm still getting used to the ec2 thing. >> Is there a password Ill need for root access? >> Thanks, >> >> Josh >> - >> Joshua Lee >> Graduate Student >> Center for Mind and Brain & >> Department of Psychology >> University of California, Davis >> 530.747.3805 >> >> >> >> 2011/10/28 Pedro Paulo de Magalhães Oliveira Junior <ppj(a)netfilter.com.br >> > >> >>> I have one. I'll give you the link >>> >>> -- iOS 5.0 >>> >>> Em 28/10/2011, às 20:52, Joshua Lee <jkilee(a)ucdavis.edu> escreveu: >>> >>> Are there any existing Amazon EC2 AMI registered publicly that can be >>> used? I want to analyze a lot of data fast. >>> >>> Thanks, >>> - >>> Joshua Lee >>> >>> _______________________________________________ >>> 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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sub-cortical group analysis
by xian zhang 29 Oct '11

29 Oct '11

https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis is very helpful. However, is there any equivalent page detail how to: do group analysis view significant map alpha sim export table ? Appreciate your help.

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Bad vertex in mris_flatten
by Oya, Hiroyuki (UI Health Care) 28 Oct '11

28 Oct '11

Dear sir, Mris_flatten could not be completed due to the fact that only one bad vertex was found in the patch. Is there any quick way to correct the vertex? Thank you. Hiroyuki ________________________________ Notice: This UI Health Care e-mail (including attachments) is covered by the Electronic Communications Privacy Act, 18 U.S.C. 2510-2521, is confidential and may be legally privileged. If you are not the intended recipient, you are hereby notified that any retention, dissemination, distribution, or copying of this communication is strictly prohibited. Please reply to the sender that you have received the message in error, then delete it. Thank you. ________________________________

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