[Freesurfer] problems with getting started with freesurfer
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 $FREESURFER_HOME/FreeSurferColorLUT.txt" commands, all I get is
"Setting subject to bert" and nothing happens following that.
Now, when I run the "tksurfer bert rh pial" I get errors (see at end of email).
Any ideas whats going on and how I could fix this?
Thanks,
Mayuresh
*** error
[r...@localhost ~]# tksurfer bert rh pial
surfer: current subjects dir: /usr/local/freesurfer/subjects
surfer: not in "scripts" dir ==> using cwd for session root
surfer: session root data dir ($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_luna
[Freesurfer] exporting surface as an image volume
Dear Freesurfer users and authors, Is it possible to export a surface (eg. ?h.thickness) to an image volume - something which could be read into SPM? I came across mri_surf2vol function, however I am not to familiar with the usage. I understand that a volume registration file is required, what exactly is this file? If anyone can suggest an example usage of mri_surf2vol that will be very helpful. Thanks in advance, Mayuresh Explore and discover exciting holidays and getaways with Yahoo! India Travel http://in.travel.yahoo.com/ ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] exporting surface as an image volume
Hi Bruce, Thanks for your reply. I was planning on doing 1. voxel based statistics with our data in SPM, and 2. Overlaying the thickness data in original subject space. But I realised I could do the same statistics using Qdec. I had a few naive questions/clarifications about the ascii file generated for thickness, inflated and sphere surfaces. 1. The order of vertices in each of these files is the same? i.e. row 3 in thickness file should represent the same point on row 3 in the inflated and sphere files. 2. My understanding is that the coordinates are in the RAS space in each of the files? 3. The coordinates in "sphere.reg" file are in some average space? Is this MNI space? This would mean that the same coordinate in the sphere.reg files of different subjects represent the same anatomical area, right? Best regards, Mayuresh --- On Thu, 11/6/09, Bruce Fischl wrote: > From: Bruce Fischl > Subject: Re: [Freesurfer] exporting surface as an image volume > To: "Mayuresh Korgaonkar" > Cc: freesurfer@nmr.mgh.harvard.edu > Date: Thursday, 11 June, 2009, 8:45 PM > Hi Mayuresh, > > what do you want to do with it in SPM? The thickness > can be converted to > a volume format, but it will actually be a 1 x n vector, > where n is the # > of vertices in the surface. Not sure if that will be useful > or not. For > example from the surf dir you could do: > > mris_convert -c thickness lh.orig lh.thickness.mgz > mri_convert lh.thickness.mgz lh.thickness.nii > > to create a niftii file > > cheers > Bruce > > On Thu, 11 Jun 2009, Mayuresh Korgaonkar wrote: > > > > > > > Dear Freesurfer users and authors, > > > > Is it possible to export a surface (eg. ?h.thickness) > to an image volume - something which could be read into > SPM? > > I came across mri_surf2vol function, however I am not > to familiar with the usage. I understand that a volume > registration file is required, what exactly is this file? If > anyone can suggest an example usage of mri_surf2vol that > will be very helpful. > > > > Thanks in advance, > > Mayuresh > > > > > > Explore and discover exciting > holidays and getaways with Yahoo! India Travel http://in.travel.yahoo.com/ > > > > > > ___ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > > > Explore and discover exciting holidays and getaways with Yahoo! India Travel http://in.travel.yahoo.com/ ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] 4D to 3D
Dear Freesurfer authors, I have been working with the command line group analysis tutorial from the freesurfer wiki website. Unfortunately I did not "qcached" my data with recon-all. So I ran the "mris_preproc" and "mri_surf2surf" commands from the tutorial (see below) at the end of which I get a single 4D file "lh.gender_age.thickness.10B.mgh" concatenated over all subjects Is there a way to split this file into 3D files so that I have a thickness file for each individual subject? Thanks, Mayuresh mris_preproc --fsgd gender_age.fsgd \ --target fsaverage --hemi lh \ --meas thickness \ --out lh.gender_age.thickness.00.mgh mri_surf2surf --hemi lh \ --s fsaverage \ --sval lh.gender_age.thickness.00.mgh \ --fwhm 10 \ --cortex \ --tval lh.gender_age.thickness.10B.mgh Love Cricket? Check out live scores, photos, video highlights and more. Click here http://cricket.yahoo.com ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] Incorrect hemispheres
Hello Freesurfer authors, I have processed a few datasets without realising that the hemispheric orientation was provided incorrectly i.e the labelled left hemisphere is actually the right hemisphere. Does this mean all the analysis is incorrect and unusable? What should I do to correct for this hemispheric flip? Thanks in advance, Mayuresh The INTERNET now has a personality. YOURS! See your Yahoo! Homepage. http://in.yahoo.com/ ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
