Freesurfer November 2012

freesurfer@nmr.mgh.harvard.edu

105 participants
177 discussions

voxel number estimation kvlQuantifyPosteriorProbabilityImages
by lorenzo pasquini 29 Nov '12

29 Nov '12

Dear freesurfer users, I have a question regarding the kvlQuantifyPosteriorProbabilityImages command to quantify hippocampal subfield volumes. Are all voxels with a probability value bigger than 0 counted? Or is the command applying any threshold for the estimation? I have transformed the subfield .mgz images in .nii images. The number of voxels with a probability bigger than 0 in the nii images do not correspond to the estimations extracted with the kvlQuantifyPosteriorProbabilityImages command. Thank you! yours, Lorenzo Pasquini Can. Ph. D., Medical Life Science and Technology (Technische Universität Muenchen) Neuroimaging Lab, Neuroradiology Klinikum r. d. Isar (Technische Universität) 81675 München Tel.: 0049 (0) 89 4140-7666

1 0

What provides mri_annot2aparc?
by Chris McNorgan 28 Nov '12

28 Nov '12

Hello all, I've posted this question on the cmtk-users google group as well. In that forum there was an author who had been working on applying the Lausanne 2008 parcellation scheme to a functional data analysis. After running the connectomemapper toolkit to subdivide the Freesurfer parcellation into smaller ROIs, nodes along the white-matter/pial boundary are assigned to one of ~1000 1.5cm^2 ROIs. The next step is to propagate these ROI assignments outwards to the gray matter surface, and the solution entails running mri_annot2aparc on the cmtk .annot files according to the thread posted at: https://groups.google.com/forum/#!topic/cmtk-users/rjaVwDdhQOo The problem I am having is that I have been unable to find any executable or script named mri_annot2aparc anywhere in my filesystem, nor have I been able to find any clues online as to what package provides this resource. Does anyone have any insight? Thanks, Chris

2 1

FW: TRACULA some fiber volumes being too small
by Fernando Ventrice 28 Nov '12

28 Nov '12

Dear Freesurfer/Tracula users, Finally I could successfully test Tracula and I think it is amazing what it can do automatically. These are the commands I used: export FREESURFER_HOME=${HOME}/Programs/freesurfer_510 && source $FREESURFER_HOME/SetUpFreeSurfer.sh source /etc/fsl/fsl.sh export FSLPARALLEL=condor trac-all -prep -c /home/labneuroimg/STATION_FLENI/Tensores/Fernando_Ventrice/dmrirc_Fernando_Ventrice trac-all -bedp -c /home/labneuroimg/STATION_FLENI/Tensores/Fernando_Ventrice/dmrirc_Fernando_Ventrice # "trac-all -bedp" gave some errors so I used bedpostx directly: bedpostx /home/labneuroimg/STATION_FLENI/Tensores/Fernando_Ventrice/20120112_VENTRICE_FERNANDO/dmri trac-all -path -c /home/labneuroimg/STATION_FLENI/Tensores/Fernando_Ventrice/dmrirc_Fernando_Ventrice freeview -tv /home/labneuroimg/STATION_FLENI/Tensores/Fernando_Ventrice/20120112_VENTRICE_FERNANDO/dpath/merged_avg33_mni_flt.mgz -v /home/labneuroimg/STATION_FLENI/Tensores/Fernando_Ventrice/20120112_VENTRICE_FERNANDO/dmri/dtifit_FA.nii.gz & All finished without errors, but there seems to be a problem with CC Forceps Mayor volume, which gave very small values. Is this OK or I made some mistake? First I tested with some patient and other fiber tracks also gave very small volumes. I attached some pictures and the dmrirc and trac-all log files. Best, Fernando Ventrice El contenido del presente mensaje y el de sus adjuntos, es confidencial, privado y de uso exclusivo de los destinatarios a los cuales está dirigido, pudiendo contener información legalmente protegida. Queda prohibida la revisión, divulgación, publicación, modificación, copia, distribución o acción en relación con esta información, por personas o entidades distintas al destinatario. Si usted, por alguna razón, lo ha recibido por error, por favor tenga la amabilidad de eliminarlo de su sistema. Las opiniones contenidas, son exclusivas de su autor, y no representa necesariamente, la opinión de FLENI. http://www.fleni.org.ar

3 6

preproc-sess and option -mni305-1mm results in an error
by Jörg Pfannmöller 28 Nov '12

28 Nov '12

Hi, if I apply the following command: preproc-sess -s sessID -fsd bold -nostc -surface fsaverage lhrh -mni305-1mm -fwhm 0 -per-run -nosmooth -force The preprocessing runs into trouble at the following point mri_vol2vol done mri_mask /...path.../bold/001/masks/brain.mni305.1mm.nii /usr/local/freesurfer/subjects/fsaverage/mri.2mm/subcort.mask.mgz /...path.../bold/001/masks/brain.mni305.1mm.nii freadFloat: fread failed ERROR: dimension mismatch between source and mask As far as I can see freesurfer uses a 2mm mask for a 1mm brain, which results in the dimension mismatch. How can I get rid of this problem? Cheers Joerg

2 4

optseq2 using dependent trials
by Danielle Miller 28 Nov '12

28 Nov '12

Hi Freesurfer, I have a paradigm in which the conditions are dependent on each other. That is, trials (e.g., congruent or incongruent) are linked to each other in that I want an equal number of trials to follow each other (e.g., congruent- congruent, congruent- incongruent, incongruent-congruent, incongruent-incongruent). When trying optseq2, it of courses randomizes the presentation, and I do not get equal presentations of the "pairs" of trials. Is there a way to jitter dependent trials using optseq? If not, do you have any suggestions on how to address this issue? Thanks, Danielle -- Ph.D. Program in Behavioral Neuroscience Boston University School of Medicine L-815 72 E. Concord St Boston, MA 02118 VA Boston Healthcare System Jamaica Plain Memory Disorders Research Center 150 South Huntington Ave D11-103 Boston, MA 02130 OFFICE:(857) 364-2130

2 1

Info extraction hippocampus
by Andrea Tateo 28 Nov '12

28 Nov '12

Hello FS experts, I would like to extract from head's MRI a bunary image showing only hippocampus. I used command: ############### mri_convert FILE_NAME.nii path/directory/NAME_OUTPUT.mgz recon-all -s SUBJECT_name -autorecon-all mri_extract_label aseg.mgz 17 53 hippocampi.mgz ############# This command spends more then 12 computing houres. I would like to spend less computing time. Is there any procedure? thanks All the best Andre Tateo

2 1

TRACULA tract path failure
by Arman Eshaghi 28 Nov '12

28 Nov '12

Dear all, I have difficulty sorting out the problem with some tracts in several subjects, tracts are incomplete or missing. As it has come up quite a few times on the list, for this sort of problem I have first set "reinit=1" and then increased control points to 7, and re-ran trac-all with "-prior" flag. This has worked for some tracts in several subjects, however there are a few subjects that still have this problem. It would be great if someone could let me know what else I might be able to do in order to correct missing/faulty tracts in my subjects. (The problem is not limited to a specific tract, it varies in different subjects) All the best, -Arman

2 1

Re: [Freesurfer] fieldsign-sess problem in retinotopy
by Zhou, Wei 28 Nov '12

28 Nov '12

Hi Doug, Thank you for reply. yes all 4 are in bold separately. I tried -run-wise with selxavg3-sess, but it failed with the following msg: Saving X matrix to /media/local_home/zhouw4/EM0220/analysis/retinotopy/SUBJ01/bold/rtopy.self.lh/pr001/Xtmp.mat Error using svd Input to SVD must not contain NaN or Inf. Error in cond (line 39) s = svd(A); Error in fast_selxavg3 (line 254) XCond = cond(XtX); I attach the mat file in the email. I am thinking that the error is similar as that I only put polar or eccen session in bold folder. Thank you for looking into it. Best Wei ________________ But all four runs into a single bold folder, then try running selxavg3-sess with the -run-wise option. This will create separate run analysis in the output directory. I have not tried it with retinotopy before, so get back to me if it fails. doug On 11/26/2012 05:53 PM, Zhou, Wei wrote: > Hi Doug, > I think I didnt explain clearly last time. > Here's the thing: > I have four runs: 2 eccen and 2 polars. I followed the > processhttp://surfer.nmr.mgh.harvard.edu/fswiki/FsFastIndividualRetinotopyA… > and I hope to view the result of an individual session, e.g. one polar, > which could display the activations with different angles. What should I do > after all the analysis is done? Or I should run a retinotopy analysis > different from the link above. > Thank you in advance. > Best > Wei > ---- > Hi Wei, do you have both polar and eccentricity? It looks like you only > have polar. > doug > On 11/19/2012 01:39 PM, Zhou, Wei wrote: > > Please find the Xtmp.mat in the attachment.Thank you, Doug. > > Best > > Wei > > ---- > > Can you send me the Xtmp.mat file? > > dloug > > > > On 11/16/2012 01:01 PM, Zhou, Wei wrote: > > > Hi Doug, > > > > > > It seems the previous fieldsign-sess problem is due to that I stored > > > data on one server while freesurfer is on the other server. > > > But when I put the data and freesurfer on the same server and run the > > > retinotopy analysis again, it reported fail msg for "selxavg3-ses" : > > > -- > > > ntptot = 80, nX = 27, DOF = 53 > > > Saving X matrix to > > > > > > > > /media/local_home/zhouw4/testf/retinotopy/SUBJ01/bold/rtopy.self.lh/Xtmp.mat > > > Error using svd > > > Input to SVD must not contain NaN or Inf. > > > > > > Error in cond (line 39) > > > s = svd(A); > > > > > > Error in fast_selxavg3 (line 254) > > > XCond = cond(XtX); > > > --- > > > I checked Xtmp.mat. There is NaN in Xn and XtX. > > > My rtopy par is: eccen and pos. > > > > > > Would you please give me some idea about this error? > > > > > > Best > > > Wei > > > > > > >> > > > Try using this version > > > > > > > > > > > ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/fieldsign-sess > > > > > > doug > > > > > > On 11/01/2012 11:47 AM, Zhou, Wei wrote: > > > > Hi Doug, > > > > > > > > The subject name for structural is "SUBJ1" when I did recon-all, > > which > > > > is also the content of file "subjectname". My dir structures of > > > > "structural" and "retinotopy" are the same as > > > > http://www.alivelearn.net/?p=65 . "SUBJ1" is stored under > > > > "structural". if I set SUBJECTS_DIR as "....../structural", > > > > $SUBJECT_DIR/SUBJ1 does exist, then still I get the same error > > msg. > > > > > > > > The following is the log file: > > > > > > > > fieldsign-sess log file $Id: fieldsign-sess,v 1.2 2010/05/04 > > 22:00:18 > > > > greve Exp $ Thu Nov 1 10:36:52 CDT 2012 Linux rii-appserv-02 > > > > 2.6.32-279.11.1.el6.x86_64 #1 SMP Sat Sep 22 07:10:26 EDT 2012 > > x86_64 > > > > x86_64 x86_64 GNU/Linux /media/users/zhouw4/testf/retinotopy > > > > /usr/local/freesurfer/fsfast/bin/fieldsign-sess -a rtopy.self.lh > > > > -occip -s SUBJ1 uid=20120(zhouw4) gid=22000(rii_users) > > > > groups=22000(rii_users),21100(rii_appservers),23000(domain^users) > > > > context=unconfined_u:unconfined_r:unconfined_t:s0-s0:c0.c1023 > > > > > > > > Best > > > > Wei > > > > > > > > > > > > >What is the name of FreeSurfer subject? This is not necessarily > > the > > > > same>> > > > > >as SUBJ01 in your command line below. That is the session (which > > may > > > or > > > > >may not be the same as the "subject name"). What ever the > > subjectname > > > > is, does SUBJECT_DIR/subject exist? > > > > On 10/31/2012 03:07 PM, Zhou, Wei wrote: > > > > > > > > > > Hi, Doug > > > > > > > > > > Thank you for your reply. I have tried exporting > > SUBJECTS_DIR to > > > the > > > > > directory of upper fold, retinotopy or SUBJ01 But none of > > them > > > works. > > > > > Still the same error msg. > > > > > > > > > > So what should SUBJECTS_DIR be exported to for this > > analysis? > > > > > > > > > > Best > > > > > > > > > > Wei > > > > > > > > > > > > > > > > > > > > >Hi Wei, this is a bug in the error msg. It is trying to > > say that > > > your > > > > > >source subject is not in the $SUBJECTS_DIR. > > > > > >doug > > > > > > > > > > >On 10/27/2012 02:27 PM, Zhou, Wei wrote: > > > > > > Dear freesurfers, > > > > > > > > > > > > I am trying retinotopy analysis in freesurfer. For > > > > "fieldsign-sess", I > > > > > > encounter the following problem when I type > > "fieldsign-sess > > > -a > > > > > > rtopy.self.lh -occip -s SUBJ01" or "fieldsign-sess > > -a > > > > rtopy.self.lh > > > > > > -occip -sf sessid": > > > > > > > > > > > > > > > > > > */media/users/zhouw4/testf/retinotopy/SUBJ01/log/fieldsign-sess.log* > > > > > > *subject: Undefined variable.* > > > > > > > > > > > > my structure of retinotopy fold is : > > > > > > retinotopy > > > > > > | |--sessid > > > > > > |--SUBJ01 > > > > > > |--subjectname > > > > > > > > > > > > |--bold > > > > > > |--001 > > > > > > |--f.nii > > > > > > |--rtopy.par| > > > > > > > > > > > > I really appreciate it if you could give me some > > idea about > > > that > > > > > > problem. Thanks a lot in advance. > > > > > > > > > > > > Best > > > > > > Wei Zhou > > > > > > Medical Physics Ph.D. Student > > > > > > Diagnostic Imaging Track > > > > > > cgxz...(a)gmail.com<mailto:cgxz...@gmail.com> > > > > > > > > > zho...(a)livemail.uthscsa.edu<mailto:zho...@livemail.uthscsa.edu> > > > > > > > > > > > > > > > > > > _______________________________________________ > > > > > > 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 > > > > > gr...(a)nmr.mgh.harvard.edu > > > > > Phone Number: 617-724-2358 > > > > > Fax: 617-726-7422 > > > > > > > > > > > > > > > > > > > > _______________________________________________ > > > > > Freesurfer mailing list > > > > > Freesurfer(a)nmr.mgh.harvard.edu > > > > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > > > > Best > > > > Wei Zhou > > > > Medical Physics Ph.D. Student > > > > cgxz...(a)gmail.com<mailto:cgxz...@gmail.com> > > > > zho...(a)livemail.uthscsa.edu<mailto:zho...@livemail.uthscsa.edu> > > > > > > > > > > > > _______________________________________________ > > > > Freesurfer mailing list > > > > Freesurfer(a)nmr.mgh.harvard.edu > > > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > > Best > > > Wei Zhou > > > > > > > > > > > > _______________________________________________ > > > 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 > > gr...(a)nmr.mgh.harvard.edu > > Phone Number: 617-724-2358 > > Fax: 617-726-7422 > > > > Best > > Wei Zhou

1 0

bad reconstructions
by Catherine Bois 28 Nov '12

28 Nov '12

Hi, sorry I have an additional question; when reconstructed 9with edits), if the scan seemingly is worse off than before the edits were made; is there a "recon clean" command; that one can use that takes away all the edits and "starts from scratch? Thank you, Cathy

2 1

Problem Visualizing Hippocampal Subfield Segmentation in FreeView
by Juan Deliz 27 Nov '12

27 Nov '12

Hi FS community, I was trying to view the results of the hippocampal subfield segmentation but had trouble overlaying the subfields on the nu.mgz file. I tried letting it run for a while but it still does not work. Below I have included the commands I used in Terminal: [dyn-128-59-230-112:subjects/bert/mri] learninglab2% freeview nu.mgz -p-labels posterior_left_* posterior_Left-Hippocampus.mgz -p-labels posterior_right_* posterior_Right-Hippocampus.mgz -p-prefix posterior_ -p-lut $FREESURFER_HOME/FreeSurferColorLUT.txt 2012-11-27 19:18:38.964 freeview.bin[20154:607] invalid drawable 2012-11-27 19:18:38.969 freeview.bin[20154:607] invalid drawable 2012-11-27 19:18:38.987 freeview.bin[20154:607] invalid drawable 2012-11-27 19:18:38.989 freeview.bin[20154:607] invalid drawable 2012-11-27 19:18:39.006 freeview.bin[20154:607] invalid drawable 2012-11-27 19:18:39.008 freeview.bin[20154:607] invalid drawable 2012-11-27 19:18:39.025 freeview.bin[20154:607] invalid drawable 2012-11-27 19:18:39.027 freeview.bin[20154:607] invalid drawable QObject::connect: Connecting from QAbstractButton::toggled(bool) to COMPAT slot (QGroupBox::setShown(bool)) QObject::connect: Connecting from QAbstractButton::toggled(bool) to COMPAT slot (QGroupBox::setShown(bool)) CTABrgbAtIndexi: index -1 was OOB CTABrgbAtIndexi: index -1 was OOB Can not find index for color name left_CA2-3 CTABrgbAtIndexi: index -1 was OOB QThread: Destroyed while thread is still running I looked over the mailing list and saw that someone had a similar problem in the past and tried to follow that solution. It did not seem to work for me: [dyn-128-59-230-112:/Applications] learninglab2% cd $FREESURFER_HOME/ [dyn-128-59-230-112:/Applications/freesurfer] learninglab2% sed -i "s/CA2_3/CA2\/3/g" FreeSurferColorLUT.txt sed: 1: "FreeSurferColorLUT.txt": invalid command code F [dyn-128-59-230-112:/Applications/freesurfer] learninglab2% sed -i "s/CA4_DG/CA4\/DG/g" FreeSurferColorLUT.txt sed: 1: "FreeSurferColorLUT.txt": invalid command code F Does anybody know what's going on? Thanks for your help, Juan

1 0

← Newer
1
2
3
4
5
6
7
8
...
18
Older →

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 November 2012