[Freesurfer] recon-all error

Hello! I just setup "freesurfer-Linux-centos4-stable-pub-v4.4.0" on linux 2.6.21-1.3194.fc7 . to test freesurfer, I successfully run "recon-all -s bert -autorecon1" and "recon-all -s bert -autorecon3", but "recon-all -s bert -autorecon2", exited with ERRORS,as follows: "writing output transfor

[Freesurfer] image matrix

Hi, I want to check the image matrix after doing autorecon-all. When I look at the text, I see that “Original Data has (1, 1, 1) mm size and (224, 256, 160) voxels. Data is conformed to 1 mm size and 256 voxels for all directions”. This is said that that image matrix is 256 x 256 x 256. Righ

[Freesurfer] autorecon1 error

Hi, I had problems running autorecon 1 with my own subject group, so I decided to see if I could run the tutorial with Bert. I ran the motion correction, and then tried autorecon 1 and got the following error (please see the attached word document to see my output). ERROR: converting nu to COR

Re: [Freesurfer] recon-all error

how much ram do you have on your machine? On Tue, 30 Jun 2009 whb...@mail.ustc.edu.cn wrote: Hello! I just setup "freesurfer-Linux-centos4-stable-pub-v4.4.0" on linux 2.6.21-1.3194.fc7 . to test freesurfer, I successfully run "recon-all -s bert -autorecon1" and "recon-all -s bert -autorecon3

Re: [Freesurfer] image matrix

Hi Feng-Xian, the surfaces all live in the surf subdirectory. To see how many vertices a surface contains you can run either mris_euler_numer of mris_info. The thickness is in the ?h.thickness ("curv" format file - one scalar per vertex) and the inflated is in ?h.inflated surface format. You c

Re: [Freesurfer] autorecon1 error

Hi Fatima, can you send us the recon-all.log? thanks Bruce On Tue, 30 Jun 2009, Ahmed, F, Me wrote: Hi, I had problems running autorecon 1 with my own subject group, so I decided to see if I could run the tutorial with Bert. I ran the motion correction, and then tried autorecon 1 and got

Re: [Freesurfer] mri_surf2surf

Hi Jidan, The surface in the native space is given by ?h.white. ?h.sphere and ?h.sphere.reg provide the "mapping" of those vertices of to a spherical representation, and registered spherical representation, respectively. There are ways to get at the Jacobian of these transformations if that is w

Re: [Freesurfer] talairach error during recon-all

Doug Yes, there is an error message in the talairach_avi.log--I am not sure what it means. The end of the log gives me this message: Dana imgrege: no voxels in register ERROR: 'imgreg_4dfp /usr/local/freesurfer/average/711-2C_as_mni_average_305 /usr/local/freesurfer/average/711-2B_as_mni_av

Re: [Freesurfer] talairach error during recon-all

Hi Avi, do you have any advise for Dana? thanks Bruce On Tue, 30 Jun 2009, Dana W. Moore wrote: Doug Yes, there is an error message in the talairach_avi.log--I am not sure what it means. The end of the log gives me this message: Dana imgrege: no voxels in register ERROR: 'imgreg_4dfp /u

[Freesurfer] freesurfer dice coefficient calculation

Hi freesurfer masters, Quick question on the way freesurfer calculates the dice coefficient. I am interested in getting an INTERsubject dice coefficient as a measure of similarity between 2 subjects. My question is, do I need to do an INTERsubject registration step before calculating the dice

[Freesurfer] mkbrainmask not finding fslmaths

Hi, I ran the following preproc-sess command and mkbrainmask-sess failed, with an error message of not finding fsmaths. I don't know where to be looking for this file and what previous command should have generated it. Can anyone help me out? Thanks! Dahlia. I ran: preproc-sess -sf sessid_subj31

Re: [Freesurfer] freesurfer dice coefficient calculation

Hi Jared, yes, the talairach.m3z is the intersubject registration we use for generating the aseg, and you could use it to compute a dice. cheers Bruce On Tue, 30 Jun 2009, Jared Price wrote: Hi freesurfer masters, Quick question on the way freesurfer calculates the dice coefficient. I am

[Freesurfer] MNI/Startup.PM error in FreeSurfer 4.4.0

Hello. I just installed FreeSurfer v4.4.0, following all the directions to the letter. When I run recon-all -i -s -autorecon1, I get the following error: Can't locate MNI/Startup.pm in @INC (@INC contains: /System/Library/Perl/5.8.6/darwin-thread-multi-2level /System/Library/Perl/5.8.6 /Librar

[Freesurfer] Re: mkbrainmask not finding fslmaths

Perhaps I should have asked: Do I need to separately install FSL? Thanks > Hi, > > I ran the following preproc-sess command and mkbrainmask-sess failed, with > an error message of not finding fsmaths. I don't know where to be looking > for this file and what previous command should have generated

[Freesurfer] Cannot allocate memory / can't allocate region

Dear FS experts I am using high resolution (0.75x0.75x0.75 mm) data within FS but the following error occurred: ... vertex spacing 0.69 +- 0.21 (0.00-->6.06) (max @ vno 265258 --> 114262) face area 0.19 +- 0.10 (0.00-->4.49) mris_make_surfaces(49536) malloc: *** mmap(size=1355776) failed (err