Freesurfer

freesurfer@nmr.mgh.harvard.edu

19 participants
30132 discussions

Using Freesurfer's label files to create one ROI
by Christophe Destrieux 04 Jun '10

04 Jun '10

Hi Stephan You could use mris_translate_annotation <subject> <hemi> <in annot> <translation file> <out annot> with : *<subject>* : the subject you want to work on *<hemi> *: the hemi you want to work on *<in annot> *: your initial annotation file (ie the one containing Medial OFC, Lateral OFC, anterior part of the Cingulate) *<translation file>* : a text file you have to create, that will list the labels( one per line) you want to group, and the new label you want to create. In fact you can't use the labels names but you have to use their RGB codes; each line will provide the input and output RGB values for instance the following file 221 220 60 223 220 60 221 220 160 223 220 60 221 220 100 223 220 60 will group 3 labels (with RGB codes 221 220 60, 221 220 160, and 221 220 100) in a single label (223 220 60) you can get the RGB value by clicking view->information->annotation on tksurfer interface after loading the surface and the annotation file. Be carefull not to use a RGB code previously used in your input annotation. You can get the RGB value of any label by clicking view->information->annotation on tksurfer interface after loading the surface and the annotation file. A field named annotation will be created on the interface with the RGV under brackets *<out annot>* : the output annotation (the one you want to create, with labels grouped together) cheers -- Christophe Destrieux, Directeur du Département Communication et Multimedia http://med.univ-tours.fr/M0S01/0/fiche___defaultstructureksup/&RH=120065115… Laboratoire d'Anatomie - Faculté de Médecine - 10 Bd Tonnellé 37032 Tours - France tel (33) 2 47 36 61 36 - fax (33) 2 47 36 62 07

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recon-all -all -long error
by Gregory Dierksen 04 Jun '10

04 Jun '10

While running the following command: recon-all -all -long 2615_12202006 2615_12202006 -i .../dicom_raw/000001.dcm I'm getting this error durring the Cortical Ribbon mask: mris_volmask --label_left_white 2 --label_left_ribbon 3 --label_right_white 41 --label_right_ribbon 42 --save_ribbon --save_distance 2615_12202006.long.2615_12202006 SUBJECTS_DIR is /autofs/space/eesmith_001/users/dierksen/Petichial WARNING: the source volume info is not consistent between WARNING: the info contained in the surface data and that of the transform. WARNING: the source volume info is not consistent between WARNING: the info contained in the surface data and that of the transform. WARNING: the source volume info is not consistent between WARNING: the info contained in the surface data and that of the transform. WARNING: the source volume info is not consistent between WARNING: the info contained in the surface data and that of the transform. Segmentation fault This happened for three subjects. And I should mention that these subjects have significant hemorrhages that caused failed surface recons in the cross sectional processing stream. This was fixed by "patching" in the hemorrhage in the wm.mgz, effectively forcing the wm surface to wrap around the hemorrhage area. So, what's going on? What can I do to fix this? Thanks, Greg --

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Using Freesurfer's label files to create one ROI
by Stefan Du Plessis 04 Jun '10

04 Jun '10

Hello everyone I looked through the Wiki and mailing list archives and could not find a page that directly addresses this issue. I want to create a ROI that consists of the Medial OFC, Lateral OFC, anterior part of the Cingulate etc. using freesurfer's labels. I dont want to hand draw my own ROI just yet. Then I want to run a regression analysis across this with mri_glmfit. What is the simplest way of doing this on the command-line? It seems simple on QDEC, but I could not find it in the mri_glmfit command line documentation. (It just says --label **** add your label here...) PS When I upload a file for you to look at, would a READM.txt suffice to explain what I want you to look at? PPS I am having trouble finding the "Create your own ROI" tutorial page on the wiki. I know it exists, and that this is not described in it, though... thanks Stefan

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shared library error
by houman.ebrahimi 04 Jun '10

04 Jun '10

Hi, I am constantly getting the same error when running recon-all on different subjects: #@# Cortical ribbon mask Sat May 29 15:08:06 EST 2010 /home/houman/Desktop/freesurfer/subjects/PS2038/mri mris_volmask --label_left_white 2 --label_left_ribbon 3 --label_right_white 41 --label_right_ribbon 42 --save_ribbon --save_distance PS2038 mris_volmaskbin: error while loading shared libraries: libtiff.so.3: cannot open shared object file: No such file or directory Linux ubuntu 2.6.32-22-generic #33-Ubuntu SMP Wed Apr 28 13:28:05 UTC 2010 x86_64 GNU/Linux recon-all exited with ERRORS at Sat May 29 15:08:07 EST 2010 I am running: freesurfer-Linux-centos4_x86_64-stable-pub-v.4.5.0-full.tar.gz i7 processor - Ubuntu 10.04 (Kernel Linux 2.6.32-22-generic, GNOME 2.30.0) I have referred to the suggested solutions at the following post: http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg07975.html but neither seem to correct the problem. I am interested mainly in the data in the stats/aseg.stats file (which is generate on the step before the error). Is this error likely to affect the data in that file? Thanks! Houman

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Change LUT
by Bauer, Andrew J 03 Jun '10

03 Jun '10

Hi, There are two parts to my question, and they have to do with cortical parcellation color labeling: I'd like to change the look-up table such that some regions (in my case, ALL white matter) that are originally labeled with unique color codes, are DE-labeled (as in, are given no color). I know how to manually change the color codes in a text editor. However, I don't know how to change the LUT so that there is NO color label is attached. Second, if I edit the LUT, will the region colors be automatically updated when I view the regions, either surface or volume? Regards, Andrew

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Re: [Freesurfer] Freesurfer Digest, Vol 76, Issue 4
by Marietta, Jacquie R 03 Jun '10

03 Jun '10

Thanks:) Jacquie Marietta Research Assistant University of Iowa Hospitals and Clinics Department of Psychiatry W 292 GH Iowa City, Iowa 52245 319 353 8513 jacquie-marietta(a)uiowa.edu -----Original Message----- From: freesurfer-bounces(a)nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] On Behalf Of freesurfer-request(a)nmr.mgh.harvard.edu Sent: Wednesday, June 02, 2010 4:02 PM To: freesurfer(a)nmr.mgh.harvard.edu Subject: Freesurfer Digest, Vol 76, Issue 4 Send Freesurfer mailing list submissions to freesurfer(a)nmr.mgh.harvard.edu To subscribe or unsubscribe via the World Wide Web, visit https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer or, via email, send a message with subject or body 'help' to freesurfer-request(a)nmr.mgh.harvard.edu You can reach the person managing the list at freesurfer-owner(a)nmr.mgh.harvard.edu When replying, please edit your Subject line so it is more specific than "Re: Contents of Freesurfer digest..." Today's Topics: 1. Re: autorecon2 error (Gabriel Go.Es.) 2. Re: autorecon2 error (Bruce Fischl) 3. Re: autorecon2 error (Gabriel Go.Es.) 4. Re: autorecon2 error (Bruce Fischl) 5. label2label with two subjects directories (Garth Coombs) ---------------------------------------------------------------------- Message: 1 Date: Wed, 2 Jun 2010 19:11:25 +0000 From: "Gabriel Go.Es." <gabriellbk(a)hotmail.com> Subject: Re: [Freesurfer] autorecon2 error To: <nicks(a)nmr.mgh.harvard.edu>, <reuter(a)mit.edu> Cc: free surfer <freesurfer(a)nmr.mgh.harvard.edu> Message-ID: <SNT124-W28C9EC56CF343A93A46AFADCD00(a)phx.gbl> Content-Type: text/plain; charset="iso-8859-1" Thank you I redownloaded the mri_ca_label file and worked, it seems that gets corrupted when donwloading, but now it appears a new error, from the autorecon2, any idea??? #@# Intensity Normalization2 Wed Jun 2 14:58:57 CEST 2010 /root/trabajo/freesurfer/subjects/T1_GE1/mri mri_normalize -aseg aseg.mgz -mask brainmask.mgz norm.mgz brain.mgz using segmentation for initial intensity normalization reading from norm.mgz... mri_normalize: aseg volume aseg.mgz must be conformed using MR volume brainmask.mgz to mask input volume... unconformed source detected - conforming... Linux localhost.localdomain 2.6.9-34.ELsmp #1 SMP Thu Mar 9 06:23:23 GMT 2006 x86_64 x86_64 x86_64 GNU/Linux recon-all exited with ERRORS at Wed Jun 2 14:59:06 CEST 2010 Best, Gabriel _________________________________________________________________ ?Quieres conocer trucos de Windows 7? ?Los que ya lo usan te los cuentan! http://www.sietesunpueblodeexpertos.com/index_windows7.html

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Group analysis---qdec questions
by liyari5018 03 Jun '10

03 Jun '10

Hi FS experts, when i use qdec to analysis my data: 45 norms and 45 patients, what does this means: Is there a diagnosis--gender interaction in the mean thickness? (PS: I got a corrected results in this item, but i don't know how to report it) Thanks for you reply! LJ

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Order of Image Processing in the Longitudinal Stream and Multi-site scanning
by Meg Dennison 03 Jun '10

03 Jun '10

Hi, My question relates to the order of processing images from different time points in the longitudinal stream. The base-line images I have were collected in 2006, but many of these images are of poorer quality than those collected in 2008 at follow up. Given this description from Han et al., 2006: "The longitudinal scheme differs from the original procedure in three major steps: preprocessing, intensity normalization and surface deformation. *Assuming that a series of scans of the same subject are obtained at different time points, the data from time point one is first processed using the original procedure. For the processing of later time points, the three major steps mentioned above are modified.* First, a linear registration is computed between the image volume of a later time point and that of the first time point. Note that the volume itself is not transformed, but only the registration matrix is stored and will be used in later steps. Second, at the intensity normalization step, instead of re-computing the WM control points, the control points (automatically computed) from time point one are mapped to the current volume using the previously computed linear registration, which are then used to estimate the bias field. Third, at the surface deformation step, instead of starting the deformation from the topology-corrected WM tessellation, the gray/white and pial surfaces reconstructed from time point one are first transformed using the linear registration and then used to initialize the deformation for the gray/white and pial surfaces respectively for the current time point. Such an initialization scheme reduces the problem of deformable model methods being sensitive to initialization and local optimality (Dale et al., 1999; Xu et al., 1999; Han et al., 2005a). It also eliminates variation in initial surface tessellation and topology correction since these two steps are no longer needed in the processing of later time points." Would it make sense to use the better quality images, which in this case are those collected at time point 2, as the "baseline" when processing in the longitudinal stream to get a more accurate result for time point 1? Additionally, is there any consensus about the degree to which the longitudinal processing stream assists in overcoming variance due to multi-site scanning? Thanks in advance for any help on these issues, Kind Regards, Meg Dennison ------------------------------- PhD Candidate / Masters Clinical Psychology Psychological Sciences Melbourne University -------------------------------

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label2label with two subjects directories
by Garth Coombs 02 Jun '10

02 Jun '10

Hi Doug & Freesurfer experts, Is there a way to run mri_label2label to copy a label from one subject to another in a different SUBJECTS_DIR, or do the subjects have to be in the same directory for label2label to work (e.g. vs_subject1 in SUBJECTS_DIR_A to subject1_anat in SUBJECTS_DIR_B)? I am having trouble with specifying the source and target registration/white matter files. The subjects in both directories are the same, the only difference being which version of freesurfer the recons were run with and a slight difference in the naming convention. I tried just copying the file, but when I tried to visualize the label, it looked incorrect. Below are the outputs I got when running mri_label2label. When I do not use the --srcsurfreg & --trgsurfreg flags, I get very similar errors, but with shorter path names that it cannot find. Thanks for your help! -Garth When I try: setenv SUBJECTS_DIR /space/dinah/1/users/balaji/SUBJECTS_DIR/subjects/ cd /autofs/space/brownie_003/users/gcoombs/SUBJECTS_DIR/ mri_label2label --srclabel /space/dinah/1/users/balaji/SUBJECTS_DIR/subjects/vs_aric/label/ffa_lh_indiv.label --srcsubject vs_aric --trglabel /space/brownie/3/users/gcoombs/SUBJECTS_DIR/aric_anat/label/ffa_lh_indiv.label --trgsubject aric_anat --regmethod surface --hemi lh --srcsurfreg /space/dinah/1/users/balaji/SUBJECTS_DIR/subjects/vs_aric/surf/lh.sphere.reg --trgsurfreg space/brownie/3/users/gcoombs/SUBJECTS_DIR/aric_anat/surf/lh.sphere.reg I get this error: srclabel = /space/dinah/1/users/balaji/SUBJECTS_DIR/subjects/vs_aric/label/ffa_lh_indiv.label srcsubject = vs_aric trgsubject = aric_anat trglabel = /space/brownie/3/users/gcoombs/SUBJECTS_DIR/aric_anat/label/ffa_lh_indiv.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = /space/dinah/1/users/balaji/SUBJECTS_DIR/subjects/vs_aric/surf/lh.sphere.reg trgsurfreg = /space/brownie/3/users/gcoombs/SUBJECTS_DIR/aric_anat/surf/lh.sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 SUBJECTS_DIR is /autofs/space/dinah_001/users/balaji/SUBJECTS_DIR/subjects FREESURFER_HOME is /usr/local/freesurfer/stable4 Loading source label. /space/dinah/1/users/balaji/SUBJECTS_DIR/subjects/vs_aric/label/ffa_lh_indiv.label /space/dinah/1/users/balaji/SUBJECTS_DIR/subjects/vs_aric/label/ffa_lh_indiv.label Found 158 points in source label. Starting surface-based mapping Reading source registration /autofs/space/dinah_001/users/balaji/SUBJECTS_DIR/subjects/vs_aric/surf/lh./space/dinah/1/users/balaji/SUBJECTS_DIR/subjects/vs_aric/surf/lh.sphere.reg MRISread(/autofs/space/dinah_001/users/balaji/SUBJECTS_DIR/subjects/vs_aric/surf/lh./space/dinah/1/users/balaji/SUBJECTS_DIR/subjects/vs_aric/surf/lh.sphere.reg): could not open file No such file or directory ERROR: could not read /autofs/space/dinah_001/users/balaji/SUBJECTS_DIR/subjects/vs_aric/surf/lh./space/dinah/1/users/balaji/SUBJECTS_DIR/subjects/vs_aric/surf/lh.sphere.reg When I try changing the subjects directory: setenv SUBJECTS_DIR /space/brownie/3/users/gcoombs/SUBJECTS_DIR/ cd $SUBJECTS_DIR mri_label2label --srclabel /space/dinah/1/users/balaji/SUBJECTS_DIR/subjects/vs_aric/label/ffa_lh_indiv.label --srcsubject vs_aric --trglabel /space/brownie/3/users/gcoombs/SUBJECTS_DIR/aric_anat/label/ffa_lh_indiv.label --trgsubject aric_anat --regmethod surface --hemi lh --srcsurfreg /space/dinah/1/users/balaji/SUBJECTS_DIR/subjects/vs_aric/surf/lh.sphere.reg --trgsurfreg space/brownie/3/users/gcoombs/SUBJECTS_DIR/aric_anat/surf/lh.sphere.reg I get this error: srclabel = /space/dinah/1/users/balaji/SUBJECTS_DIR/subjects/vs_aric/label/ffa_lh_indiv.label srcsubject = vs_aric trgsubject = aric_anat trglabel = /space/brownie/3/users/gcoombs/SUBJECTS_DIR/aric_anat/label/ffa_lh_indiv.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = /space/dinah/1/users/balaji/SUBJECTS_DIR/subjects/vs_aric/surf/lh.sphere.reg trgsurfreg = /space/brownie/3/users/gcoombs/SUBJECTS_DIR/aric_anat/surf/lh.sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 SUBJECTS_DIR is /autofs/space/brownie_003/users/gcoombs/SUBJECTS_DIR FREESURFER_HOME is /usr/local/freesurfer/stable4 Loading source label. /space/dinah/1/users/balaji/SUBJECTS_DIR/subjects/vs_aric/label/ffa_lh_indiv.label /space/dinah/1/users/balaji/SUBJECTS_DIR/subjects/vs_aric/label/ffa_lh_indiv.label Found 158 points in source label. Starting surface-based mapping Reading source registration /autofs/space/brownie_003/users/gcoombs/SUBJECTS_DIR/vs_aric/surf/lh./space/dinah/1/users/balaji/SUBJECTS_DIR/subjects/vs_aric/surf/lh.sphere.reg MRISread(/autofs/space/brownie_003/users/gcoombs/SUBJECTS_DIR/vs_aric/surf/lh./space/dinah/1/users/balaji/SUBJECTS_DIR/subjects/vs_aric/surf/lh.sphere.reg): could not open file No such file or directory ERROR: could not read /autofs/space/brownie_003/users/gcoombs/SUBJECTS_DIR/vs_aric/surf/lh./space/dinah/1/users/balaji/SUBJECTS_DIR/subjects/vs_aric/surf/lh.sphere.reg

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Re: [Freesurfer] autorecon2 error
by Nick Schmansky 02 Jun '10

02 Jun '10

mri_ca_label can be downloaded from here: ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/misc/linux-centos4_x86… copy it your $FREESURFER_HOME/bin n. On Mon, 2010-05-31 at 03:25 -0400, Martin Reuter wrote: > Yes, looks like the one I fixed. Nick can point you to a download for the > fixed files. > > Best, Martin > > > ----- Original Message ----- > From: "Bruce Fischl" <fischl(a)nmr.mgh.harvard.edu> > To: "Gabriel Go.Es." <gabriellbk(a)hotmail.com> > Cc: "free surfer" <freesurfer(a)nmr.mgh.harvard.edu>; "Reuter, Martin -- > Martin Reuter" <mreuter(a)nmr.mgh.harvard.edu>; "Martin Reuter" > <reuter(a)mit.edu> > Sent: Sunday, May 30, 2010 4:50 PM > Subject: Re: [Freesurfer] autorecon2 error > > > Hi Gabriel, > > I think Martin fixed this bug, didn't you Martin? > > Bruce > > On Sun, 30 May 2010, Gabriel Go.Es. wrote: > > > > > > > Dear FreeSurfers > > I run an autorecon1 using the flag -no-wsgcaatlas > > for skullstripping, I'm using > > freesurfer-Linux-centos4_x86_64-stable-pub-v4.5.0, you may find attached > > the recon-all_status log > > for any information you may need > > Then I was trying to run the autorecon2: recon-all -subjid -autorecon2 > > when it gives the following error message: > > > > > > ------------------------------------------------------ > > > > Linux localhost.localdomain 2.6.9-34.ELsmp #1 SMP Thu Mar 9 06:23:23 GMT > > 2006 x86_64 x86_64 x86_64 GNU/Linux > > > > $Id: recon-all,v 1.133.2.57 2009/08/06 18:27:48 nicks Exp $ > > > > /root/trabajo/freesurfer/bin/recon-all > > > > PWD /root/trabajo/freesurfer/subjects/MP2RAGE_2/mri > > > > CMD mri_ca_label -align -nobigventricles norm.mgz transforms/talairach.m3z > > /root/trabajo/freesurfer/average/RB_all_2008-03-26.gca > > aseg.auto_noCCseg.mgz > > > > > > mri_ca_label GCA sequential renormalization: label 28 not consistently > > computed. > > > > not using caudate to estimate GM means > > setting label Left_Cerebellum_Cortex based on Right_Cerebellum_Cortex = > > 1.05 x + 0 > > estimating mean gm scale to be 1.16 x + 0.0 > > estimating mean wm scale to be 1.00 x + 0.0 > > estimating mean csf scale to be 0.43 x + 0.0 > > > > saving intensity scales to aseg.auto_noCCseg.label_intensities.txt > > Linux localhost.localdomain 2.6.9-34.ELsmp #1 SMP Thu Mar 9 06:23:23 GMT > > 2006 x86_64 x86_64 x86_64 GNU/Linux > > > > recon-all exited with ERRORS at Fri May 28 14:57:45 CEST 2010 > > > > ------------------------------------------------------------------- > > > > > > > > any suggestions and help will be so appreciated > > > > Best > > > > Gabriel > > > > ¿Sabes que La Gente de Hoy tiene GUARDAESPALDAS contra el Spam? > > Con las alertas de Hotmail no perderás detalle de tu correo. ¡Contrátalo > > ya! > > _________________________________________________________________ > > ¿Quieres conocer trucos de Windows 7? ¡Los que ya lo usan te los cuentan! > > http://www.sietesunpueblodeexpertos.com/index_windows7.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. > >

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