Freesurfer February 2006

freesurfer@nmr.mgh.harvard.edu

40 participants
52 discussions

Viewing GCS / Atlas files
by Timothy R Jarvis 21 Feb '06

21 Feb '06

I've searched the WIKI and didn't see any instructions on how to view the following files: average/lh.atlas2002_simple.gcs - lh atlas average/rh.atlas2002_simple.gcs - rh atlas Is there a utility provided to do this, or can someone tell me what the file format / contents of these files is? Thanks --------------------------------------- Timothy R. Jarvis --------------------------------------- Graduate Research Assistant International Neuroimaging Consortium VA Medical Center 612-467-2619 http://www.neurovia.umn.edu ---------------------------------------

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mris_preproc file missing in my freesurfer package.
by Goradia, Dhruman D 20 Feb '06

20 Feb '06

Hi all, I have the following freesurfer version: OS: Mac OS X Platform: Tiger Release type: dev The mris_preproc file is missing. I would appreciate if some one can email me this file. Thank you. Dhruman.

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Output of mris_anatomical_stats
by Goradia, Dhruman D 17 Feb '06

17 Feb '06

Hi, The output of function "mris_anatomical_stats" contains the following measurements: integrated rectified mean curvature, integrated rectified Gaussian curvature, folding index and intrinsic curvature index. Can someone please give me a brief explanation of what these measurements are or suggest some reading material. -Dhruman Dhruman D. Goradia (M.S.) Research Specialist. Western Psychiatric Institute and Clinic. 3811 O'Hara St. Suite 431 Pittsburgh, PA 15213 Phone: 412-586-9017

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-legacy flag
by Vasanth Pappu 13 Feb '06

13 Feb '06

Hi, I started to run an old subject through autorecon1 and 2. I used the -legacy flag. However, I still got the error below, saying that I need some *mgz files in the orig/ directory. I thought -legacy would do this conversion. The orig/ had a COR volume, but the error said to have a 001.mgz and a 002.mgz. I tried to convert the dicoms with -i, but it would not write to the existing directory: recon-all -i /autofs/space/solo_004/users/dcm/CARG29/cdrom/03051411/21527384 -i /autofs/space/solo_004/users/dcm/CARG29/cdrom/03051411/21526253 -subjid CARG29_recon INFO: SUBJECTS_DIR is /autofs/space/biggs_008/users/vasanthp/NHS ERROR: /autofs/space/biggs_008/users/vasanthp/NHS/CARG29_recon exists So, I ended up converting the dicoms in another directory, copied the 001.mgz and 002.mgz to the CARG29_recon/, and then started to run recon-all -autorecon1 and 2. Is there a simpler way to do this? Thanks, Vasanth [biggs:mri] (nmr-dev-env) recon-all -subjid CARG29_recon -autorecon1 -autorecon2 INFO: SUBJECTS_DIR is /autofs/space/biggs_008/users/vasanthp/NHS Actual FREESURFER_HOME /autofs/space/freesurfer/centos4.0_x86_64/dev -rwxrwx--- 1 vasanthp cagn 76436 Feb 13 16:22 /autofs/space/biggs_008/users/vasanthp/NHS/CARG29_recon/scripts/recon-all.log Linux biggs 2.6.9-22.0.1.ELsmp #1 SMP Thu Oct 27 14:49:37 CDT 2005 x86_64 x86_64 x86_64 GNU/Linux INFO: current FREESURFER_HOME does not match that of previous processing. Current: /usr/local/freesurfer/dev Previous: /space/windu/6/users/freesurfer_cenagn/freesurfer_dev #-------------------------------------------- #@# MotionCor Mon Feb 13 16:23:34 EST 2006 ERROR: no run data found in /autofs/space/biggs_008/users/vasanthp/NHS/CARG29_recon/mri. Make sure to have a volume called 001.mgz in /autofs/space/biggs_008/users/vasanthp/NHS/CARG29_recon/mri/orig. If you have a second run of data call it 002.mgz, etc. See also: https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Conversion Linux biggs 2.6.9-22.0.1.ELsmp #1 SMP Thu Oct 27 14:49:37 CDT 2005 x86_64 x86_64 x86_64 GNU/Linux recon-all exited with ERRORS at Mon Feb 13 16:23:34 EST 2006 --

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Determining r and p values from GLM
by rhaynes＠neuro.gatech.edu 10 Feb '06

10 Feb '06

In Figure 4 of your recent paper "Thickness of ventromedial prefrontal cortex in humans...", the graphs display r and p values which are defined at a "peak vertex" in the paper. In tksurfer, if you compute statistics over a defined ROI you get similar graphs, but how do you find the peak vertex in this set of vertices and how do you obtain r and p? And is there a way to get statistics (r and p) for all the vertices in the region (summary statistics, upper/lower bounds, etc)? Thanks. Ryan Haynes Research Assistant Children's Healthcare of Atlanta

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DICOM file conversion problem
by Kerr, Catherine E. 10 Feb '06

10 Feb '06

I have what appear to be dicom files. The root directory of the CD ROM contains a file called dicomdir. The files are in a directory and named with non-consecutive 8-digit numbers. The directory is named with an 8 digit number as well. After converting the files to mgz format, running recon-all, and viewing the image, I see that the slices are not oriented correctly. In the coronal view, the image looks like a thin, incoherent stripe. In the sagital view there are several sagital slices and several coronal slices and most of the slices have no image on them. What is going on here?

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mri_label2vol
by marc ruiz 10 Feb '06

10 Feb '06

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RE: [Freesurfer] feat2surf
by Strien, N van 10 Feb '06

10 Feb '06

I sent this e-mail before, but it seems that it arrived nowhere. I hope you can have a look at it still - thanks. Niels Hi Doug, Thank you for your reply. Just to make sure, you linked a file called mri_surf2surf instead of mri_vol2surf. Is this what you intended? It seems as if the feat2surf script has some errors still - at least for me. The script as you made it searches for .img and .nii files. However when I run the script, the script stops when not finding any .img files. Or to be more precise: 1) it does not seem to look for any .nii files 2) it sets srcvol = mblok1+.feat/stats/*.img which will lead to errors later on in the script So the imglist variable is not filled with .nii images. When I run the script with set imglist = ($statsdir/*.nii), it finds my zstat*.nii images and properly sets e.g. srcvol = mblok1+.feat/stats/zsat1.nii etc Also, the script complains that the mkdir command receives too few arguments. This results in my case that the output of the mrui_vol2_surf command is stored in the $HOME dir. When using the mri_vol2surf manually I did manage to overlay the stats output. (only when using the mri_vol2surf of the previous (november) dev release). I would be grateful if you could send me the updated mri_vol2_surf. Thanks again for your help. The next step for me is a functional mri analysis in spherical space... so I might knock on your door again with that if I may. Niels

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mri_surf2surf
by Don Hagler 09 Feb '06

09 Feb '06

Hi guys, There seems to be a minor bug in mri_surf2surf when trg_type = w. If trgsurfval is given as a relative path name (e.g. no directory sepcified with intention to create in current working directory), the output file name can be prefixed by" lh." or "rh." and it can be put in the subjects surf directory. Being put in that directory only happens when trgsubject is not ico. Don

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rh.sphere.reg not running?
by Steve Smith 09 Feb '06

09 Feb '06

Hi - sorry if this is a stupid question, but when I use the latest recon-all I get the lh.sphere.reg fine but not the rh - the final listing is: ..... -rw-rw-r-- 1 steve analysis 563291 Feb 8 09:31 lh.thickness -rw-rw-r-- 1 steve analysis 5070714 Feb 8 09:31 lh.smoothwm -rw-rw-r-- 1 steve analysis 563291 Feb 8 09:34 lh.sulc -rw-rw-r-- 1 steve analysis 5071028 Feb 8 09:34 lh.inflated -rw-rw-r-- 1 steve analysis 5071339 Feb 8 11:42 lh.sphere -rw-rw-r-- 1 steve analysis 5071734 Feb 8 12:54 lh.sphere.reg -rw-rw-r-- 1 steve analysis 5071746 Feb 8 14:02 lh.rh.sphere.reg -rw-rw-r-- 1 steve analysis 563291 Feb 8 14:02 lh.avg_curv -rw-rw-r-- 1 steve analysis 3485297 Feb 8 14:09 rh.orig.nofix -rw-rw-r-- 1 steve analysis 2614948 Feb 8 14:10 rh.smoothwm.nofix -rw-rw-r-- 1 steve analysis 2615288 Feb 8 14:13 rh.inflated.nofix -rw-rw-r-- 1 steve analysis 2615615 Feb 8 14:37 rh.qsphere.nofix -rw-rw-r-- 1 steve analysis 580459 Feb 8 14:39 rh.defect_labels -rw-rw-r-- 1 steve analysis 580459 Feb 8 14:39 rh.defect_chull -rw-rw-r-- 1 steve analysis 580459 Feb 8 14:39 rh.defect_borders -rw-rw-r-- 1 steve analysis 5055170 Feb 8 20:54 rh.orig -rw-rw-r-- 1 steve analysis 121 Feb 8 20:54 mris_make_surfaces.rh.mrisurf.c.version -rw-rw-r-- 1 steve analysis 5055491 Feb 8 22:07 rh.white -rw-rw-r-- 1 steve analysis 561635 Feb 8 22:08 rh.curv -rw-rw-r-- 1 steve analysis 561635 Feb 8 22:08 rh.area -rw-rw-r-- 1 steve analysis 5055491 Feb 8 22:53 rh.pial -rw-rw-r-- 1 steve analysis 561635 Feb 8 22:53 rh.curv.pial -rw-rw-r-- 1 steve analysis 561635 Feb 8 22:53 rh.area.pial -rw-rw-r-- 1 steve analysis 561635 Feb 8 23:01 rh.thickness -rw-rw-r-- 1 steve analysis 5055810 Feb 8 23:01 rh.smoothwm -rw-rw-r-- 1 steve analysis 561635 Feb 8 23:04 rh.sulc -rw-rw-r-- 1 steve analysis 5056124 Feb 8 23:04 rh.inflated -rw-rw-r-- 1 steve analysis 5056435 Feb 9 00:53 rh.sphere looking at the supplied bert it does look like rh.sphere.reg should be there - am I being dumb? Cheers, Steve. ------------------------------------------------------------------------ ------------------ Stephen M. Smith, Professor of Biomedical Engineering Associate Director, Oxford University FMRIB Centre FMRIB, John Radcliffe Hospital, Headington, Oxford OX3 9DU, UK +44 (0) 1865 222726 (fax 222717) steve(a)fmrib.ox.ac.uk http://www.fmrib.ox.ac.uk/~steve ------------------------------------------------------------------------ ------------------

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Freesurfer February 2006