Re: problems with register.csh
Hi Nick, This might be occuring because you have a newer version of mri_convert that does not support the -raw flag. You could use an older version with register.csh or try using mri_motion_correct2 (i think that is the name). The latter works really well, but you will need to install all of the MNI tools. check the archive for hints on mni installation. good luck. brian - Original Message - From: Nicholas Knouf [EMAIL PROTECTED] [EMAIL PROTECTED] To: [EMAIL PROTECTED] Sent: Wednesday, October 16, 2002 1:00 PM Subject: problems with register.csh Hi, I am trying to run register.csh (as per the FreeSurfer manual) to motion correct my anatomical scans before averaging them together. However, I get an error saying 'mri_convert: unknown flag -raw' (actual output below). Unfortunately, I can't make out from the information what options to mri_convert should actually be used. Thanks, Nick Knouf Lab Manager, Kanwisher Lab --- uninteresting data snipped -- ++ CPU time for realignment=279 s ++ Min : roll=-0.285 pitch=-0.072 yaw=-0.997 dS=+6.359 dL=+2.301 dP=+9.563 ++ Mean: roll=-0.285 pitch=-0.072 yaw=-0.997 dS=+6.359 dL=+2.301 dP=+9.563 ++ Max : roll=-0.285 pitch=-0.072 yaw=-0.997 dS=+6.359 dL=+2.301 dP=+9.563 ++ Writing dataset to disk in ./dset+orig.HEAD. ** Warning: will overwrite file regist.afni done registering rotating -0.285 -0.072 -0.997 6.359 2.301 9.563 atr_int == NULL atr_flo == NULL /pasque/nfs_data2/data/subjects/021015nk/mri/orig mri_convert -raw 256 256 256 uchar /tmp/reg.res+orig.BRIK motion_corrected_cor mri_convert: unknown flag -raw type mri_convert -u for usage pasque%
Re: trouble converting to COR, can't stat ??
Hi Scott, What version of freesurfer are you using? brian - Original Message - From: Scott Laurence Fairhall [EMAIL PROTECTED] To: [EMAIL PROTECTED] Sent: Tuesday, October 01, 2002 11:20 PM Subject: trouble converting to COR, can't stat ?? Hello, I'm probably doing something very stupid but I can't figure out what. When I attempted to load in my anatomical files through the GUI I recieved an error saying: Convert (scott) failed - working on: orig/a/I.%03d So I tried the tutorial (bert) files through the command line and got: --- [all@ikirk 001]$ mri_convert -it cor cor-001 . mri_convert -it cor cor-001 . reading from cor-001... corRead(): can't stat cor-001 --- and I have no clue what's going wrong. Any advice would be very much appreciated. Scott Fairhall
Re: mri_surfglm!!!
Hi Arvid, I did not find a correction for that problem yet. mris_convert may not be causing the problem, because I obtained the same result with an older version of it. Maybe something went wrong in the make final surfaces step. I am still looking for the source of the mismatch between the white and thickness vertices. However, the mri_surfglm program ran without crashing, despite the above problem. It seems like the mismatched vertices could be relevant for the parametric analyses, but I am not sure how/if it uses the pial or white surfaces. This program may use the ?h.sphere.reg which, because it is registered may not have the incompatible vertex number in file issue. I have to go back and look at the output. Sorry I couldn't be more helpful yet. Brian - Original Message - From: Arvid Lundervold [EMAIL PROTECTED] To: Brian Schweinsburg [EMAIL PROTECTED] Cc: [EMAIL PROTECTED] Sent: Monday, September 30, 2002 9:15 AM Subject: Re: mri_surfglm!!! Dear Brian Please tell me (us) what was your solution to the mris_convert failure (-c thickness rh.white rh.thickness.asc ) Best regards Arvid Lundervold Arvid Lundervold, MD PhD Department of Physiology, University of Bergen AArstadveien 19, N-5009 Bergen, Norway Tel: +47 55 58 63 53 Fax: +47 55 58 64 10 Mob: +47 915 61 824 E-mail: [EMAIL PROTECTED] On 29 Sep 2002, Brian Schweinsburg wrote: I was able to answer my own question regarding thickness parameter maps from the other day by poking through the Linux/bin directory. Looking forward to using it. brian
cortical thickness and between groups analyses
Hi All, I am interested in being able to do parametric analyses with the cortical thickness data (e.g., one patient group, one control group, and a t-test for each registered vertex similar to Rosas et al. 2002). I have completed the process of fixing topology, sphering, and registering. I can export the thickness data into ascii using mris_convert -c thickness surf/rh.white surf/rh.thickness.asc. However, I am interested in exporting the "registered" thickness values, so all participants vertices and thickness measures are aligned with the atlas. I tried to use: mris_convert -c thickness surf/rh.sphere.reg surf/rh.thickness.asc, and although it seemed like a good idea, it didn't work. It yielded the same values as the mris_convert command using rh.white or rh.pial. ***What is the command to get at the registered values. When registered, I am assuming that for example, vertex number 12 is at the same xyz for all the subjects-is that true? After obtaining the registered values, I assume the next step in the processing flow is to import the data into a program like SPM or AFNI or even SPSS or Excel for analysis. ***What program would you suggest using for this? I was able to import the ascii data for a participant into AFNIby using 3dUndump -prefix thickness_fim_data -master anat_geometry_forsubject+orig -xyz rh.thickness.asc. You have to delete the leading column identifying the number of the vertex, and when you "see function" in the AFNI controller, it overlays the thickness values onto the "master" anatomical. It is misaligned and 3dUndump does not like decimals and negatives so you end up with only one quadrant of data, but It still looks cool! Thanks for all of your help. brian ****Brian C. Schweinsburg University of California, San DiegoPhone: 858.642.3736Fax: 858.552.7432
contrast and brightness
Hi Folks, When I convert and load images (from gelx, analyze, or brik format), the contrast and brightness are way off. In some cases the entire brain looks bright white. This creates a problem for segmentation edits because when I adjust the contrast for the auxiliary image (mri/orig) the main volume (segmentation) is adjusted, and actually disappears. What could be causing my images to be loaded with poor contrast/brightness? Is it a scaling problem? Is there a way to automatically adjust for this, say, using an environment variable? thanks for any help. brian Brian C. Schweinsburg UCSDPhone: 858.642.3736Fax: 858.552.7432
Re: contrast and brightness
Thanks. I overlooked the aux adustment for some reason. The environment variable would be nice because my contrasts are off for every participant, to varying extents. I suspect that the display contrast and brightness do not impact the segmentation, etc. Although, I would like to confirm this. brian - Original Message - From: Evelina Busa [EMAIL PROTECTED] To: freesurfer [EMAIL PROTECTED] Sent: Tuesday, August 13, 2002 9:39 AM Subject: Re: contrast and brightness Hi Brian The tkmedit View-- Configure Brightness Contrast option allows you to configure the main and/or aux volume(s) to your liking. I suppose you could set an environment variable once you determine to which degree you want the aux volume brightness reduced -- assuming this would be the same for all the subjects in your study. Would this be the case, necessarily? On Tue, 13 Aug 2002, Brian C. Schweinsburg wrote: Hi Folks, When I convert and load images (from gelx, analyze, or brik format), the contrast and brightness are way off. In some cases the entire brain looks bright white. This creates a problem for segmentation edits because when I adjust the contrast for the auxiliary image (mri/orig) the main volume (segmentation) is adjusted, and actually disappears. What could be causing my images to be loaded with poor contrast/brightness? Is it a scaling problem? Is there a way to automatically adjust for this, say, using an environment variable? thanks for any help. brian Brian C. Schweinsburg UCSD Phone: 858.642.3736 Fax: 858.552.7432 -- Evelina
cortical thickness-ROI analysis
What is the best way to extract ROI information from cortical thickness data? For instance, I would be interested in obtaining thickness data for "prefrontal" cortex to compare patient group X to a group ofcontrols. My approach thus far has been to cut a prefrontal surface and flatten, overlay ?.thickness for the subject which shows the thickness for that ROI, and save the "curv" file to rh.prefrontal.thickness. My hope was that I would be able to run mris_convert -c thickness on this file, converting it to ASCII and be able to obtain the average thickness for this region. Unfortunately, the flattening didn't work (convergence errors and ill-conditioned points error messages), and when i ran mris_convert -c thickness on the prefrontal patch, I got a segmentation fault. Is there a better way to do this? With so many valuable data points in the thickness files, it seems like there would be other ways to extract more fine ROI (a particular gyrus) rather than the gross prefrontal one I cut. Thanks, Brian ___Brian C. SchweinsburgOffice: (858) 552-8585 x3736Fax: (858) 552-7432http://mednmr3.ucsd.edu/brian/home.htm___
