Freesurfer October 2011

freesurfer@nmr.mgh.harvard.edu

95 participants
160 discussions

internal capsule
by Vaidya, Jatin G 31 Oct '11

31 Oct '11

Hi, We recently processed some T1 data through Freesurfer but I did not see any labels for the internal capsule. Does Freesurfer still create a label for this region? Thanks, Jatin ________________________________ 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. ________________________________

3 3

Re: [Freesurfer] CUDA Error in file '/space/freesurfer/build/minerva/stable/dev/include/ctfactory.hpp' on line 92 : invalid texture reference
by Nick Schmansky 31 Oct '11

31 Oct '11

Hemant, We dont have any cards here that are compute capability 1.0. Our test cards are all 1.3 or higher. We do compile with -arch sm_11 (compute capability 1.1). I've recompiled mri_em_register_cuda and mri_ca_register_cuda with -arch sm_10 and put them here: https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/misc/linux-centos4_x… i dont know if they will work for you though. n. On Mon, 2011-10-31 at 12:29 -0400, R Edgar wrote: > On Mon, Oct 31, 2011 at 11:32 AM, Hemant Bokil <hemantbokil(a)gmail.com> wrote: > > > There was another thread a while back on the freesurfer website: A user > > reported a similar problem to mine and another user responded that the > > problem was with CUDA Compute Capability (See the link below- > > http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg14906.html) > > > > My card is a Quadro 4600 which has Compute Capability 1.0. Do I need a card > > with a higher Compute Capability ? > > I didn't catch that. You absolutely need a more capable card. You > should check with Nick as to the minimum supported, but you don't get > the full benefits until you get to Comp. Cap. 2.0. > > Richard > >

2 4

mri_surfcluster .w input from MEG/EEG data
by raij＠nmr.mgh.harvard.edu 31 Oct '11

31 Oct '11

Hi Doug and Matti, I am using mri_surfcluster to threshold and extract ROIs from MEG/EEG source analysis data. The same code used to work fine in Jan 2009, but now I am running into unexpected errors. I wonder if something happened along the way of FreeSurfer and/or MNE stream upgrades and now mne_analyze .w files and mri_surfcluster no longer talk to each other. I first run the usual MEG/EEG analysis using the MNE stream and then save the resulting dSPM map on the surface of the subject as a .w file (using the mne_analyze GUI). For sanity check, I download the overlay in tksurfer and observe that it looks fine (which makes me think that the problem originates at the mri_surfcluster side rather than at mne_analyze; however, see below for evidence suggesting the opposite). on machine adapt nmr-std-env (=FreeSurfer 5.1) mne_setup cd /cluster/scratch/monday/raij/MEEG setenv SUBJECTS_DIR /cluster/scratch/monday/raij/MRIs/ setenv SUBJECT Wyss_000 mri_surfcluster \ --subject Wyss_000 \ --hemi lh \ --in AVL_GA_List1-00150.0-lh.w \ --frame 0 \ --thmin 2 \ --thsign abs \ --minarea 100 \ --olab test01 \ thsign = abs, id = 0 version $Id: mri_surfcluster.c,v 1.51.2.1 2011/03/28 15:32:36 greve Exp $ hemi = lh srcid = AVL_GA_List1-00150.0-lh.w srcsubjid = Wyss_000 srcsurf = white srcframe = 0 thsign = abs thmin = 2 thmax = -1 fdr = -1 minarea = 100 xfmfile = talairach.xfm nth = -1 subjectsdir = /cluster/scratch/monday/raij/MRIs/ FixMNI = 1 ------------- XFM matrix (RAS2RAS) --------------- /cluster/scratch/monday/raij/MRIs//Wyss_000/mri/transforms/talairach.xfm 0.973 -0.031 -0.031 0.033; 0.001 0.989 0.327 -34.515; 0.008 -0.285 1.073 -30.192; 0.000 0.000 0.000 1.000; ---------------------------------------------------- Reading source surface /cluster/scratch/monday/raij/MRIs//Wyss_000/surf/lh.white Done reading source surface Computing metric properties Loading source values mri_read(): couldn't determine type of file /autofs/cluster/scratch/monday/raij/MEEG/AVL_GA_List1-00150.0-lh.w ERROR: could not read AVL_GA_List1-00150.0-lh.w as type If I try to convert .w to .mgz I get the error mri_convert AVL_GA_List1-00150.0-lh.w AVL_GA_List1-00150.0-lh.mgz file not found or unknown file type for file AVL_GA_List1-00150.0-lh.w (which makes me think that perhaps the .w file from mne_analyze is incompatible with much of FreeSurfer 5.1 code) Any suggestions? As always, thank you for the advice in advance! Best regards, Tommi --- Tommi Raij, MD, PhD MGH/MIT/HMS Athinoula A. Martinos Center for Biomedical Imaging Bldg 149, 13th St Charlestown, MA 02129 U.S.A.

2 4

Fornix in corpus callosum segmentation
by Miguel Burgaleta 31 Oct '11

31 Oct '11

Hi Freesurfers, I'm using FS 4.5.0 to calculate the volume of the corpus callosum, but in about 70% of my subjects (n = 100) I get mild to severe inclusions of the fornix in the central and/or mid-posterior sections of the CC. Is there any workaround for this particular issue, before start considering manual editing? Thanks, Miguel

2 1

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

31 Oct '11

Your ROI must be listed in the color table, so you'll need to create a custom color table. For this you will need the ID eventually assigned to your ROI. To find this out, load the wmparc your created in tkmedit as both a segmentation and as the aux volume. When you click on your ROI, the tkmedit control window should show the name of your ROI. The "aux" field will show a value. This is the value you need. doug dolphinede(a)aol.com wrote: > Hi Doug, > > thanks a lot for your reply. > > I have run the following command to get wm volume stats of my ROI: > > > mri_segstats --seg > /Users/dolphinede/Desktop/Probanden/ARS23/mri/wmparc.mgz --sum > /Users/dolphinede/Desktop/Probanden/ARS23/stats/wmparc.stats --pv > /Users/dolphinede/Desktop/Probanden/ARS23/mri/norm.mgz --excludeid 0 > --brain-vol-from-seg --brainmask > /Users/dolphinede/Desktop/Probanden/ARS23/mri/brainmask.mgz --in > /Users/dolphinede/Desktop/Probanden/ARS23/mri/norm.mgz > --in-intensity-name norm --in-intensity-units MR --etiv --subject > ARS23 --surf-wm-vol --ctab > /Applications/freesurfer//FreeSurferColorLUT.txt > > But I think it is not right cause my ROI, my annotation is not listed > there in the wmparc.stats. I thought that with my annotation i did > modify my wmparc.mgz and this yields to a new wmparc.stats. > > > 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: Mo, 31 Okt 2011 3:20 pm > Betreff: Re: [Freesurfer] white matter volume in a ROI > > 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 <mailto:dolphinede@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 <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: 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> <mailto:dolphinede@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> <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?>>>; 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 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?>> <mailto:dolphinede@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?>> > <mailto:greve@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?>> > <mailto:dolphinede@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?>> > <mailto:freesurfer@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?>> <mailto:dolphinede@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?>> > <mailto:Freesurfer@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?>> > <mailto:greve@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> > > <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?>> > <mailto:greve@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> > > <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> <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

1 0

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

3 7

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

2 1

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

2 2

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

2 1

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

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 October 2011