Freesurfer May 2007

freesurfer@nmr.mgh.harvard.edu

53 participants
97 discussions

Matlab and Freesurfer
by Robert Baldwin 09 Mar '08

09 Mar '08

Hello- I am new to Freesurfer and Matlab. I have Matlab 7.4.0 installed on an Intel Mac. I just installed Freesurfer. Now when I start Matlab I get the following warnings: Warning: Name is nonexistent or not a directory: /matlab. In path at 110 In startup at 4 In matlabrc at 255 Warning: Name is non existent or not a directory: /toolbox. In path at 110 In startup at 11 In Matlabrc at 255 I have tried adding the freesurfer folder to these files to the path for matlab, but the error still occurs. Any suggestions on how to get this error to quit? Thanks! -Robert

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calculation of total cortical gray matter volume
by Michael Harms 24 Jul '07

24 Jul '07

Hello FS-list, Could you please confirm the recommended current approach for calculating the total cortical gray matter volume. Based on the following Wiki page http://surfer.nmr.mgh.harvard.edu/fswiki/MorphometryStats? action=highlight&value=mris_volume I presume that the recommended calculation (illustrated using tcsh syntax) is: @ total_cort_gm_vol = `mris_volume ?h.pial` - `mris_volume ?h.white` My only hesitation is that I noticed the resulting value doesn't quite match the value of "total gray matter volume" that is output by mris_anatomical_stats. Is this because mris_anatomical_stats uses a older approach that is no longer considered quite as accurate? thanks, Mike Harms

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Making labels from the commandline
by Morgan Hough 27 Jun '07

27 Jun '07

I was wondering if I can make a cortical label from a volume ROI from the commandline. I would like to extract thickness values from a region defined in each subject's volume space. Thanks in advance. Cheers, -Morgan

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RE: [Freesurfer] ROI of SI cortex
by Rahul Desikan 27 Jun '07

27 Jun '07

Hi Xin, I will Doug handle this one. And please email the list in your replies. Best, rahul On Mon, 30 Apr 2007, Wang, Xin wrote: > Many thanks, Rahul. I found readings in /stats/*h.aparc.stats. I am a freesurfer beginner. I have another question. I want to compare the cortical thickness between two small groups (2X2). I can not work through the steps in the tutorial on my data. The mri_glmfit commend always returns with "bad design, ill-constructed," and stops. Do you have any detail instructions of two group comparison? > Thank you again, > > Xin > > ________________________________ > > From: Rahul Desikan [mailto:rahul@nmr.mgh.harvard.edu] > Sent: Mon 4/30/2007 4:06 PM > To: Wang, Xin > Cc: freesurfer(a)nmr.mgh.harvard.edu > Subject: RE: [Freesurfer] ROI of SI cortex > > > > Hi Xin, > > Within the *h.aparc.annot files for each subject, there should be > individual label files for *h.precentral.label and *h.postcentral.label. > If you take a look at your *h.aparc.stats, there should be a value for the > thickness and volume. You can, of course, take this *h.aparc.stats file > and upload it into matlab, spss or any other stats package and do > statistics on these values. > > Best, > > rahul > > On Mon, 30 Apr 2007, Wang, Xin wrote: > >> Dear Rahul >> The SI is primary somatosensory cortex (or postcentral gyrus) and MI is primary motor cortex (or precentral gyrus). I want to compare the thickness and volume of these two areas from left side to right side. >> Thank you, >> >> Xin >> >> ________________________________ >> >> From: Rahul Desikan [mailto:rahul@nmr.mgh.harvard.edu] >> Sent: Mon 4/30/2007 3:52 PM >> To: Wang, Xin >> Cc: freesurfer(a)nmr.mgh.harvard.edu >> Subject: Re: [Freesurfer] ROI of SI cortex >> >> >> >> Hi Xin, >> >> What exactly do SI and MI cortices refer to? >> >> rahul >> >> On Mon, 30 Apr 2007, Wang, Xin wrote: >> >>> Hello, group >>> I need to compare thickness of left v.s. the right SI and MI cortices. I saw some matlab tools for comparsion of left and right hippocampus in Lundervold.pdf. I could not find similar tools in the matlab folder of Freesurfer stable release 3.0.5 that I just installed. Could anybody kindly tell me the tools I could use for my study? >>> Thank you in advance. >>> Xin Wang >>> >> >> -- >> >> >> >> >> >> >> >> >> >> > > -- > > > > > > > > > > --

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slice thickness
by T. Song 21 Jun '07

21 Jun '07

Hi All: I have a question about the slice thickness. To get a "good" freesurfer reconstruction, especially the "accurate" statistic analysis, what it the maximum slice thickness can I use when acquire the DICOM image? Thanks! Tao

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Turn Off Verbose Output
by James Porter 07 Jun '07

07 Jun '07

Howdy- I didn't see any flags in the help files, but are there some 'hidden' commands I could use to attenuate the verbosity of reg-feat2anat and aseg2feat? Thanks, Jim Porter TRiCAM Lab Coordinator Elliott Hall N437 612.624.3892 www.psych.umn.edu/research/tricam <http://www.psych.umn.edu/research/tricam>

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Re: [Freesurfer] reg- feat2anat error
by Furlong, Carolyn 06 Jun '07

06 Jun '07

Hi niiRead(): unsupported timing pattern in Pre_DB/DB_Prelip_BET.feat/example_func.nii.gz sorry for the delay, Best wishes Carolyn can you send the log file? Furlong, Carolyn wrote: Hi, When I try to register my functional data to anatomical data using reg-feat2anat --feat feat_directory --subject subject_name I get the following error message ERROR: could not read ///example_func.nii.gz as 24 What does this mean? And how can I fix this? Best wishes Carolyn ________________________________ _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://owa.liv.ac.uk/exchweb/bin/redir.asp?URL=https://mail.nmr.mgh.harvar…> -- Douglas N. Greve, Ph.D. MGH-NMR Center greve(a)nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 In order to help us help you, please follow the steps in: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting

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tkmedit-sess question
by Avram Holmes 05 Jun '07

05 Jun '07

FreeSurfer Folks, I am attempting to look at some data with tkmedit-sess tkmedit-sess -analysis LowTraumaSPMHRF -contrast all_v_fix -d . -s FPPREW09 -map sig -fsd bold but I am getting the following error. corRead(): can't open file /exp/REfMRI/fMRI_FPPREW/structural//FPPREW09/mri/orig/COR-.info Error: Loading volume orig Couldn't read the anatomical volume. Tkmedit couldn't read the volume you specified. This could be because the image format wasn't recognized, or it couldn't find the proper header, or the file(s) were unreadable, or it was the wrong size. I can look at the data with tkmedit (without the sess) loading all the files manually. I have tried the tkmedit-sess several different ways but I always get an error. Does anyone have an idea about how I get this to work? Thanks, Avram ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Avram Holmes Department of Psychology Harvard University 1210 William James Hall Phone:(617) 495-0790 33 Kirkland Street Fax:(617) 495-3728 Cambridge, MA 02138, USA Email: holmes(a)fas.harvard.edu ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

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problem with tksurfer (fwd)
by Claus Tempelmann 04 Jun '07

04 Jun '07

Hello everybody, Having worked with quite old versions of freesurfer for a long time we decided recently to install a newer version on two new computers. Both are running under the 64 bit version of SUSE Linux 10.2, both have a Dual Opteron processor, they have 6 GB (system 1) or 8 GB (system 2) and most hardware and software is quite comparable in my opinion. There is one major difference with the graphic cards, system 1 has an MSI GEForce 6600, whereas system 2 has an GEForce FX 7600GS. I'd expect that both cards are more than sufficient for freesurfer and I doubt that this difference can be the reason for the difference I have observed but may be some of you have experienced a similar problem and can help me out. What's the problem? All analysis steps of the standard procedure seem to work fine on both systems. However, I see a reproducible strange problem on system 2 when I try to use tksurfer on the standard data set (bert) coming with the package (freesurfer-Linux-rh9-stable- pub-v3.0.5.-full.tar). When I run the command tkregister bert lh inflated on system 1, everything looks like expected. But on system 2 something is wrong, the program tells the number of vertices and faces as usual and the numbers are the same as on system 2 (as they should, I'm using the same data set). Nevertheless, the output looks quite different, I'll try to attach a screenshot. The window shows up as usual and a small part of the inflated brain is shown at the right edge of the window but the rest of the brain is never shown. When I rotate this surface the visible part of the inflated brain is rotated correctly but the rest is always missing. Can anybody help? Thanks in advance Claus ----------------------------------------------------------------------- Claus Tempelmann email: Claus.Tempelmann(a)medizin.uni-magdeburg.de Clinic for Neurology II MR department Tel.: +49-(0)391-6117183 OvG University Magdeburg +49-(0)391-6117177 Leipziger Strasse 44 39120 Magdeburg Fax: +49-(0)391-6117178 Germany

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mri_vol2surf question
by Morgan Hough 01 Jun '07

01 Jun '07

Hi there, I am trying to interpolate a volume of tstats to the average surface with mri_vol2surf but I am getting the error below. Does mri_vol2surf take all the inputs that mri_convert takes? Is this a float2int problem mentioned in the bugs section of the --help? If the latter, what argument should I specify with --float2int? Thanks in advance for your time. Cheers, -Morgan mri_vol2surf --src vbm_results_mni305_tl.nii.gz --trgsubject average --hemi lh --surf inflated --surfreg lh.sphere.reg --out lh.vbm_surf_results.mgh --srcreg reg.dat srcvol = vbm_results_mni305_tl.nii.gz srcreg = reg.dat srcregold = 0 srcwarp unspecified surf = inflated hemi = lh trgsubject = average surfreg = lh.sphere.reg interp = nearest float2int = round INFO: float2int code = 2 niiRead(): error opening file /home/fs11/mhough/Research/SOS/vbm_interp_results/vbm_results_mni305_tl.nii.gz ERROR: could not read vbm_results_mni305_tl.nii.gz as type 24

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Freesurfer May 2007