[Freesurfer] mris_volmask error

Hi, I ran recon-all, and it exited with an error at this command: mris_volmask --label_left_white 2 --label_left_ribbon 3 --label_right_white 41 --label_right_ribbon 42 --save_ribbon --save_distance subj10 The error message reads: mris_volmask.bin: error while loading shared librar

RE: [Freesurfer] w file to label

Hi Doug, I'm starting analysis of a new study after a long FSFAST hiatus, and am noting your remark about moving away from using w files. In the FSwiki page for paint-sess, it seems like its output is still w files. Does the current way to present functional data include a command instead of pa

RE: [Freesurfer] mri_annotation2label

, 2006 3:24 PM To: Dahlia Sharon Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] mri_annotation2label   Which version are you using? The dev version should not require a --table option doug Dahlia Sharon wrote: Hi,   I have two annotations, ?h.aparc.annot and

[Freesurfer] mri_annotation2label

Hi,   I have two annotations, ?h.aparc.annot and ?h.aparc.a2005s.annot, created by recon-all with the –cortparc and –cortparc2 command options. I would like to convert each of these to a set of labels.   For aparc.a2005s.annot I run (hopefully this is correct): mri_annotation2label --s

[Freesurfer] tables for mri_annotation2label (fwd)

l/aparc-rh-008.label LabelWrite: saving to /homes/6/dahlia/structurals//subj25_bay2/label/aparc-rh-008.label 9 0 --- skipping 10 0 --- skipping -- Forwarded message -- Date: Thu, 26 Oct 2006 16:13:05 -0400 (EDT) From: Dahlia Sharon <[EMAIL PROTECTED]>

[Freesurfer] tables for mri_annotation2label

Hi, When running mri_annotation2label, what is the correct table to give the --table option for ?h.aparc.annot ? $FREESURFER_HOME/Simple_surface_labels2005.txt is the table for ?h.aparc.a2005s.annot, right? Thanks! Dahlia. ___ Freesurfer mailing l

Re: [Freesurfer] visualizing surfaces

for BEMs it'll work... On Fri, 25 Aug 2006, Bruce Fischl wrote: only if they have the same # of faces/vertices though. Scuba is much more general. On Fri, 25 Aug 2006, Dahlia Sharon wrote: Hi Camilo, You can load a 3rd surface by going to: File > Aux Surface > Load

Re: [Freesurfer] visualizing surfaces

Hi Camilo, You can load a 3rd surface by going to: File > Aux Surface > Load Aux Surface Configuration > Pial Vertices and then choosing whatever surface you want (doesn't have to be pial, can be a BEM). Dahlia. On Fri, 25 Aug 2006 [EMAIL PROTECTED] wrote: Hi Freesurfer, Is there a way to

RE: [Freesurfer] BEMs

Hi Camilo, In my experience the mri_make_bem_surfaces command results in much more accurate surfaces than mri_watershed. I.e. by eye they seem to conform much better to the inner and outer skull. Like you said, you'll need the flash 5 sequence for mri_make_bem_surface; as far as I remember you use

[Freesurfer] retinotopy starting with blanks

Hi, I'm analyzing a retinotopy data-set in which each scan started with 2 TRs of a blank screen, and then proceeded to 8 cycles as usual. Is there any possibility to tell a retinotopy analysis to ignore these 2 TRs? Thanks! Dahlia. PS - I can't answer as to why these 2 blank TRs were put the

[Freesurfer] segmentation fault for: mris_convert

Hi, I'm trying to use mris_convert and am getting a segmentation fault error. The precise steps are pasted below. Can anyone figure out why this is happening now? Thanks! Dahlia. mirabai:dahlia[81] setenv SUBJECTS_DIR ~/structurals/ mirabai:dahlia[82] nmrenv freesurfer-Linux-centos4

[Freesurfer] tksurfer: left arrow in dev version

Hi, When working under nmr-dev-env, tksurfer gives me the following error message when I press the left arrow button (and doesn't move the surface): "Error: can't read 'extTransform(translate,dist)': no such variable". Am I doing something wrong? Thanks! Dahlia. _

[Freesurfer] saving open lines

Hi, Is there a way to save an open line drawn on a subject's surface to load on the surface in a future tksurfer use? Thanks, Dahlia. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesur

Re: [Freesurfer] recalculating surfaces

similar to the September ones. okay! On Thu, 27 Oct 2005, Dahlia Sharon wrote: Hi Ev, recon-all.log says I ran recon-all stage 2 on Saturday, overwriting the good files from September. The subject I had really WANTED to edit at the time is already edited and fixed etc. My problem is with

Re: [Freesurfer] recalculating surfaces

con all these subjects. okay! On Thu, 27 Oct 2005, Dahlia Sharon wrote: Hi, I overwrote several surface files (.inflated, .sulc, .curv, .smoothwm, .orig) by mistake while editing another subject. The volume in mri/wm/ is still the correct one. I should be able to run some of the recon

[Freesurfer] recalculating surfaces

Hi, I overwrote several surface files (.inflated, .sulc, .curv, .smoothwm, .orig) by mistake while editing another subject. The volume in mri/wm/ is still the correct one. I should be able to run some of the recon steps again to get the correct surfaces back, but I don't want to do this withou