Freesurfer

freesurfer@nmr.mgh.harvard.edu

16 participants
30084 discussions

longitudinal processing stream
by Dana W. Moore 22 May '09

22 May '09

Hi freesurfer team, I noticed in the new version release notes that the longitudinal stream is still a work in progress. Any idea of what the time-frame is for this fix? Also, I was wondering if there is a way after longitudinal processing to look at change maps in tkmedit or tksurfer (e.g. a color-coded segmentation that shows atrophy)? Thanks, Dana Dana W. Moore, Ph.D. Neuropsychology Fellow Cornell Neuropsychology Service Weill Medical College of Cornell University New York Presbyterian Hospital Department of Neurology & Neuroscience 428 East 72nd Street, Suite 500 New York, NY 10021 Phone: 212-746-2441 Fax: 212-746-5584 Email: dwm2003(a)med.cornell.edu

2 1

what's the parc_dir flag in mri_ca_train
by xforever＠ucla.edu 22 May '09

22 May '09

Dear Freesurfer Experts I'm trying to train the program to recognize subcorticle structures of Vervet monkeys using command mri_ca_train. I've manually made a bunch of labels, and as I use the mri_ca_train, it stopped for no reason. On the wiki page : http://surfer.nmr.mgh.harvard.edu/fswiki/mri_ca_train it says a parc_dir flag is required. what is this parc_dir, and what should I put in it? thanks in advance for the help sincerely, Andy S

3 2

problems with getting started with freesurfer
by Mayuresh Korgaonkar 21 May '09

21 May '09

Dear Freesurfer authors and users, I recently installed the CentOS 4*86_64 Freesurfer v4.3.0 on a RedHat machine. After following each installation step, I have reached the testingFreesurfer module. However I seem to be having problems in running the first few steps. On running the "tkmedit bert orig.mgz" & "tkmedit bert norm.mgz -segmentation aseg.mgz $FREESURFER_HOME/FreeSurferColorLUT.txt" commands, all I get is "Setting subject to bert" and nothing happens following that. Now, when I run the "tksurfer bert rh pial" I get errors (see at end of email). Any ideas whats going on and how I could fix this? Thanks, Mayuresh *********** error **************** [root@localhost ~]# tksurfer bert rh pial surfer: current subjects dir: /usr/local/freesurfer/subjects surfer: not in "scripts" dir ==> using cwd for session root surfer: session root data dir ($session) set to: surfer: /root surfer: all rgb files written to /root surfer: Reading header info from /usr/local/freesurfer/subjects/bert/mri/T1..mgz surfer: vertices=131860, faces=263716 Loading /usr/local/freesurfer/surface_labels.txt surfer: ### redraw failed: no gl window open surfer: single buffered window surfer: tkoInitWindow(bert) Tk_Init failed: this isn't a Tk applicationunknown color name "Black" Tix_Init failed: this isn't a Tk applicationunknown color name "Black" surfer: using interface /usr/local/freesurfer/lib/tcl/tksurfer.tcl Reading /usr/local/freesurfer/lib/tcl/tkm_common.tcl Reading /usr/local/freesurfer/lib/tcl/tkm_wrappers.tcl Reading /usr/local/freesurfer/lib/tcl/fsgdfPlot.tcl Error sourcing /usr/local/freesurfer/lib/tcl/tksurfer.tcl: this isn't a Tk applicationunknown color name "Black" surfer: Error sending tcl command tkm_SetEnableGroupStatus mg_InflatedVSetLoaded 0: can't read "glEnableGroups(mg_InflatedVSetLoaded)": no such variable surfer: Error sending tcl command tkm_SetEnableGroupStatus mg_PialVSetLoaded 0: can't read "glEnableGroups(mg_PialVSetLoaded)": no such variable surfer: Error sending tcl command tkm_SetEnableGroupStatus mg_TimeCourseLoaded 0: can't read "glEnableGroups(mg_TimeCourseLoaded)": no such variable surfer: Error sending tcl command tkm_SetEnableGroupStatus mg_OverlayLoaded 0: can't read "glEnableGroups(mg_OverlayLoaded)": no such variable surfer: Error sending tcl command tkm_SetEnableGroupStatus mg_CurvatureLoaded 0: can't read "glEnableGroups(mg_CurvatureLoaded)": no such variable surfer: Error sending tcl command tkm_SetEnableGroupStatus mg_LabelLoaded 0: can't read "glEnableGroups(mg_LabelLoaded)": no such variable surfer: Error sending tcl command tkm_SetEnableGroupStatus mg_FieldSignLoaded 0: can't read "glEnableGroups(mg_FieldSignLoaded)": no such variable surfer: Error sending tcl command tkm_SetEnableGroupStatus mg_FieldMaskLoaded 0: can't read "glEnableGroups(mg_FieldMaskLoaded)": no such variable surfer: Error sending tcl command UpdateUndoItemLabel "Nothing to Undo": invalid command name "UpdateUndoItemLabel" surfer: Error sending tcl command tkm_SetEnableGroupStatus mg_OriginalVSetLoaded 1: can't read "glEnableGroups(mg_OriginalVSetLoaded)": no such variable surfer: Error sending tcl command LblLst_SetStructures { 0 Unknown 1 G_cingularis 2 G_cuneus 3 G_frontalis_inf-pars_opercularis 4 G_frontalis_inf-pars_orbitalis 5 G_frontalis_inf-pars_triangularis 6 G_frontalis_medius 7 G_frontalis_sup-pars_lateralis 8 G_frontalis_sup-pars_medialis 9 G_frontomarginalis 10 G_hippocampi 11 G_insularis_breves 12 G_occipitalis_inf 13 G_occipitalis_medius-pars_inf 14 G_occipitalis_medius-pars_sup 15 G_occipitalis_sup 16 G_lateralis 17 G_lingualis 18 G_parahippocampi 19 G_orbitalis 20 G_paracentralis 21 G_parietalis_inf-pars_angularis 22 G_parietalis_inf-pars_supramarginalis 23 G_parietalis_sup 24 G_postcentralis 25 G_precentralis 26 G_precuneus 27 G_rectus_and_S_orbitalis_medialis 28 G_rectus_and_S_orbitalis_medialis2 29 G_subcentralis 30 G_supracingularis 31 G_temporalis_transversalis 32 G_temporalis_inf 33 G_temporalis_medius 34 G_temporalis_sup-pars_lateralis 35 G_temporalis_sup-planum_polare 36 G_temporalis_sup-planum_temporale 37 Plica_falciformis 38 Polus_occipitalis 39 Polus_temporalis 40 S_temporalis_transversalis 42 S_angularis 43 S_calcarinus 44 S_centralis_insulae_&_G_insularis_longus 46 S_centralis 47 S_cingularis 48 S_cingularis-pars_marginalis 49 S_circularis_insulae_ant 50 S_circularis_insulae_inf 51 S_circularis_insulae_sup 52 S_corpori_callosi 53 S_diagonalis 54 S_frontalis_inf 55 S_frontalis_medialis 56 S_frontalis_medius 57 S_frontalis_sup 58 S_frontomarginalis 59 S_intermedius_primus 60 S_intermedius_secundus 61 S_intracingularis 62 S_intraoccipitalis_medius 63 S_intraoccipitotemporalis_lateralis 64 S_intraparietalis 65 S_lateralis-pars_ant-ramus_horizontalis 66 S_lateralis-pars_ant-ramus_verticalis 67 S_lateralis-pars_horizontalis 68 S_lateralis-pars_post 69 S_lunatus 70 S_occipitalis_ant 71 S_occipitalis_inf 72 S_occipitalis_medius 73 S_occipitalis_sup 74 S_occipitalis_transversalis 75 S_occipitopolaris 76 S_occipitotemporalis_lateralis 77 S_occipitotemporalis_medialis 78 S_orbitales 79 S_orbitalis_lateralis 80 S_paracalcarinus 81 S_paracentralis 82 S_parietalis_transversalis 83 S_parieto_occipitalis 84 S_postcentralis 85 S_precentralis 86 S_retrocalcarinus 87 S_rhinalis 88 S_subcentralis_ant_&_post_ 89 S_suborbitalis 90 S_subparietalis 91 S_supracingularis 92 S_temporalis_inf 93 S_temporalis_sup 94 S_triangularis }: invalid command name "LblLst_SetStructures" reading white matter vertex locations... surfer: Error sending tcl command tkm_SetEnableGroupStatus mg_WhiteVSetLoaded 1: can't read "glEnableGroups(mg_WhiteVSetLoaded)": no such variable surfer: Error sending tcl command UpdateLinkedVarGroup all: invalid command name "UpdateLinkedVarGroup" % surfer: Error sending tcl command MoveToolWindow 663 681: invalid command name "MoveToolWindow" ************************************************************ Explore and discover exciting holidays and getaways with Yahoo! India Travel http://in.travel.yahoo.com/

2 1

Regarding turning of labelling of hypointensities and choroid plexus
by Kathrine Skak Madsen 21 May '09

21 May '09

Hi FreeSurfer Experts Is there a way to turn of the labelling of hypointensities and choroid plexus? Thank you in advance. Best wishes Kathrine

2 2

flipping freesurfer format brain (mirror image)
by xforever＠ucla.edu 21 May '09

21 May '09

Hi everyone, my name's Andy, I am a researcher in UCLA brain mapping group using Freesurfer we successfully generated the Surface or the vervet monkey brain, and our next step is to perform a surface segmentation using an .gcs file we created by hand. If there's anyway to flip the freesurfer format surface like .pial, .white, we'd only need one .gcs file for both hemisphere and that'd save us a lot of time. I tried using mris_transform with a xfm file, but the results turned out very weird. thanks in advance for the help Andy

3 2

how to get fsaverage after recon-all
by karlkarl 21 May '09

21 May '09

Hello, I have finished the recon-all on all the participants and ready for the group analysis. But I didn't find the fsaverage. Did I miss someting in the recon-all? How can I get the fsaverage (If I have two groups, do I need fsaverage for each group)? thanks a lot! Karl _________________________________________________________________ Messenger安全保护中心，免费修复系统漏洞，保护Messenger安全！ http://im.live.cn/safe/

2 1

Error unpacking dti scans
by Jesse Friedman 21 May '09

21 May '09

I've noticed that an error is consistently reported in the unpack log file when I unpack dti scans for any subject: INFO: this run has an error, but trying anyway For example, if I try to unpack the dti scan for subject RMCON032, whose data is in /space/archive/216/siemens/TrioTim-35006-20090508-140454-440000, the dcmdir-info output is: PatientName RMCON032 StudyDate 20090508 StudyTime 140454.440000 <snip> 000024 ep_b0#1 DIFFUSION_HighRes 440000-000024-000001.dcm 000025 ep_b0_700 DIFFUSION_HighRes 440000-000025-000001.dcm 000026 ep_b700t DIFFUSION_HighRes 440000-000026-000001.dcm 000027 ep_b0_700 DIFFUSION_HighRes 440000-000027-000001.dcm 000028 ep_b700 DIFFUSION_HighRes 440000-000028-000001.dcm 000029 ep_b0_700 DIFFUSION_HighRes 440000-000029-000001.dcm 000030 DIFFUSION_HighRes 440000-000030-000001.dcm <snip> And I enter the command: unpacksdcmdir -src . -targ $SUBJECTS_DIR/RMCON032 -run 24 dti_test nii f.nii -fsfast -log dti_test.log The unpack.log file contained the warnings and errors below (Also: I expected the log filed to be named dti_test.log so it wouldn't overwrite the unpack.log file I already had for the subject, but instead it was saved as unpack.log, overwriting the preexisting unpack.log) WARNING: Run 24 appears to be truncated Files Found: 70, Files Expected (lRep+1): 120 FileName ./440000-000024-000001.dcm Run 24 ----------------------------------------- Thu May 21 10:37:42 EDT 2009 24 dti_test nii f.nii INFO: this run has an error, but trying anyway RunNo = 23 WARNING: Run 1 appears to be truncated Files Found: 70, Files Expected (lRep+1): 120 FileName ./440000-000024-000001.dcm Are the dti scans I unpacked usable, or do I need to change my unpack command? Thanks, Jesse FREESURFER_HOME: /usr/local/freesurfer/stable4 Build stamp: freesurfer-Linux-centos4_x86_64-stable-v4.3.1-20090521 RedHat release: CentOS release 5.3 (Final) Kernel info: Linux 2.6.18-128.1.6.el5 x86_64 NMR Center info (/space/freesurfer exists): machine: vantz SUBJECTS_DIR: /space/ventzl/36/users/RespMon12C/subjects PWD: /space/archive/216/siemens/TrioTim-35006-20090508-140454-440000 ssh vantz setenv SUBJECTS_DIR /space/ventzl/36/users/RespMon12C/subjects cd /space/archive/216/siemens/TrioTim-35006-20090508-140454-440000

2 1

con and sig
by adrzezga＠nmr.mgh.harvard.edu 20 May '09

20 May '09

Dear All I have 2 specific question regarding transfer of SPM-results to Freesurfer and vice versa: 1.) I transfer SPM result images (con_00x images) to freeSurfer for illustration purposes. Conversion of the images using mri_vol2surf works nicely. Now I am just not sure on how to interpret the overlay in tksurfer regarding significance thresholds. Can someone advice me on how to "translate" the Min and Max-values in the "configure overlay display" tool into actual p-values, when using SPM-generated con-images ? 2.) The second question is probably related to 1.) Can I perform a direct correlation analysis between FreeSurfer-derived results (sig.mgh) and SPM-generated results (con_00x.img), i.e. are the values in the two image types comparable or do they have to be normalized to some common ground before actual correlation analysis can be carried out ? Thanks for any advice ! Alex Alexander Drzezga, MD Visiting Assistant Professor Harvard Medical School Massachusetts General Hospital/ Athinoula A. Martinos Center for Biomedical Imaging Building 149 13th Street, Room 2301 Charlestown, Massachusetts 02129 Tel: 617 378-1071 Fax: 617 726-7422 email:adrzezga@nmr.mgh.harvard.edu

1 0

question abt inflated brain registration
by Ritobrato Datta 20 May '09

20 May '09

Hello All, I am new to freesurfer. Is there a method to create a "registered inflated brain" from the lh.sphere.reg (which if I understood correctly, is the ?h.sphere data for a subject registered to the spherical atlas). If yes, is it also possible to display the corresponding functional data on this "registered inflated brain" ? Please let me know. Thanks Ri Ritobrato Datta, Ph.D. Post Doctoral Fellow Department of Neurology University of Pennsylvania School of Medicine 3rd Floor Gates Building 3400 Spruce St. Philadelphia Pa 19104

2 1

new release?
by Sebastian Moeller 20 May '09

20 May '09

Dear FeeSurfer team, I just realised that a new version appeared on the Download site. Does this include the fix for the fix for the MACOSX mri_normalize? Does freeview now work on the mac? One more thing, it would be marvellous if new releases could be announced on the freesurfer list to alert the users. Thanks for developing & supplying these great tools -- Sebastian Moeller telephone: 626-395-6713 German GSM: 0 15 77 - 1 90 31 41 moeller(a)caltech.edu Division of Biology MC 114-96 California Institute of Technology 1200 East California Boulevard CA 91125, Pasadena USA

2 1

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