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question about surface based segmentation...
by Shahabuddin Ansari 13 Sep '06

13 Sep '06

Hi, I have done volume-based segmentation using freesurfer and now am interested in surface-based segmentation. I have used the following set of commands in volume-based segmentation: #!/bin/csh # Shahab Ansari, August 22, 2006 #The following command creates a directory structure for the subject, and strip skull, normalize intesity and normalize coordinates recon-all -i /ensc/IMAGE/2998977_02/2998977_02.img -s 2998977_02 > 2998977_02.log recon-all -subjid 2998977_02 -autorecon1 >> 2998977_02.log #this command segments the subcortical brain and takes about 10 hrs recon-all -subcortseg -s 2998977_02 >> 2998977_02.log #this will translate the segmentation back to the original MRI space mri_convert -rl /ensc/IMAGE/opt/FREESURFER/subjects/2998977_02/mri/rawavg.mgz -rt nearest /ensc/IMAGE/opt/FREESURFER/subjects/2998977_02/mri/aseg.mgz /ensc/IMAGE/opt/FREESURFER/subjects/2998977_02/mri/aseg_raw.mgz >> 2998977_02.log I need some know what else I need to do to segment the cortical surface. I appreciate any help pointer. Thanks Shahab __________________________________________________ Do You Yahoo!? Tired of spam? Yahoo! Mail has the best spam protection around http://mail.yahoo.com

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Re: [Freesurfer] Odd brainmask.auto and brainmask data and behavior
by Graham Wideman 13 Sep '06

13 Sep '06

Jenni: Thanks for your reply and explanation of the brainmask logic and rationale. As for this: >> Question 1: Is there a rationale for 255 values? (in the brainmask volume) > >I'm not sure where these are coming from in your volume - I assume you >havent done any editting on this one. These subjects' data may well have been edited (not by me, hence my not knowing exactly what's what here). And I suppose it's the brainmask.mgz volume that would have been edited, and the act of editing it sets voxels to 255 perhaps? (The 255's are in the appropriate locations to add additional grey matter to the edges.) That leads me to believe that the answer to this: > Question 0: Is the detailed image data in brainmask.mgz ever used, or is > it simply a zero/not-zero mask? Ie: is the meaning "masked brain", or > "mask using non-zero values to show where brain is". ... is that brainmask.mgz is used by subsequent steps as a mask in combination with some other image volume providing the actual image. In that case the actual intensities of brainmask.mgz are ignored. And I now see in the script that mri_ca_normalize does indeed use brainmask.mgz with the mask flag, so I guess I'm probably right that the actual intensities are unimportant. (And nu.mgz provides the actual image). Phew, I think I now have that straight... for this week :-) Graham

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coordinates
by Frederick Klauschen 13 Sep '06

13 Sep '06

Hi, I have to bring up an issue again which we had some discussion about before, but which we haven't yet found a satisfying solution. I would like pose my question a little more precisely again: 1) I have a dataset that is in 181x217x181 coordinates. 2) I am processing it as follows: > mri_convert name.img name/mri/orig/001.mgz > recon-all -motioncor -subjid name 3) after step 2, the resulting dataset is somehow transformed to a 256x256x256 dataset, i. e. the 181x217x181 is embedded into the 256^3 array: it is rotated and the origin in 181x217x181 is not the origin in the 256x256x256 array. 4) Since I would like to do a voxelwise comparison between the recon-all result and my initial dataset 1), I need to backtransform the result into the 181x217x181 coordinates (and of course, the backtransformation should be the exact inverse of the transformation in 2). I haven't found any info about how this transformation is done by FS, mri_info does not provide it. Thanks, Frederick __________________________________________________ Do You Yahoo!? Tired of spam? Yahoo! Mail has the best spam protection around http://mail.yahoo.com

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Looking for older versions of mri_normalize
by Andrew H Bell 13 Sep '06

13 Sep '06

To FreeSurfer Community, I've looking for older versions of mri_normalize - in particular mri_normalize.041022 I am working with monkey volumes and have found that this version gives me the best results. Thanks Andy Andrew H. Bell, PhD Visiting Post-Doctoral Fellow Laboratory of Brain and Cognition National Institute of Mental Health 49 Convent Drive Building 49, RM 1B80 Bethesda, MD 20892 office: (301) 496-5625 ext.260 fax: (301) 402-0046 mobile: (202) 679-1279 bellah(a)mail.nih.gov

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writing curvature format
by Marie Schaer 13 Sep '06

13 Sep '06

Hello everybody, I am using the "write_curv" matlab code posted by Doug Greve on 01/10/2003 to convert a curvature vector back into freesurfer .curv format, using the following syntax in matlab: write_curv('lh.curv',myvector,facenumber); and when I try to launch mris_glm --meas curv --hemi lh ..., I get the following reading curvature error: MRISreadNewCurvature: vals/vertex 3 unsupported (must be 1) ... However, I am sure that my vector has the size "verticesnumber x 1", and I also thought that the line 23 of write_curv "fwrite(fid, 1, 'int32');" will anyway assign only one value per vertex. Could anyone help me? Many thanks, Marie Schaer

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Odd brainmask.auto and brainmask data and behavior
by Graham Wideman 13 Sep '06

13 Sep '06

Folks: I'd appreciate if someone could explain the brainmask.auto.mgz, and brainmask.mgz logic? Somewhat alarming is that in a brainmask volume, I'm seeing some full-brightness (255) values on the edge of the mask (border of brain and nothing), which are certainly not in the input volume T1.mgz volume. Question 0: Is the detailed image data in brainmask.mgz ever used, or is it simply a zero/not-zero mask? Ie: is the meaning "masked brain", or "mask using non-zero values to show where brain is". Question 1: Is there a rationale for 255 values? That led me to look at the brainmask.auto volume, and the "bad" values are not there either. The recon-all script is a bit puzzling and convoluted in this area -- Question 2: It appears that the Skull Stripping section of the script uses a "-keep" flag on mri_watershed. This isn't explained on the wiki doc page -- what does it do? (And why does mri_watershed get BMA and two BM's?) Question 3: In the normal case, does brainmask.auto.mgz just get copied to brainmask.mgz? If so it's a puzzle to me how these wind up different (in the cases I looked at the mgz files are not the same size). <more scratching of head> Thanks, Graham

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Freesurfer and Red Hat Enterprise
by Juergen Haenggi 13 Sep '06

13 Sep '06

> Dear Freesurfer user > > I intend to use Freesurfer software. Does FreeSurfer also run > with RedHat Enterprise Academic Desktop ot Workstation? > If no, where we can RedHat Linux 9 any longer? > > Thanks in advance > Best regards > Juergen > > ---------------------------------------------- > Juergen Haenggi, Ph.D. student > Neuropsychology and Imaging > Division of Psychiatry Research > Psychiatric University Hospital > University of Zurich, Switzerland > P.O. Box 1931 > Lenggstrasse 31, 8032 Zurich > 0041 44 384 26 10 (office phone) > 0041 76 445 86 84 (mobile phone) > 0041 44 384 26 86 (fax) > H 115 (office room number) > juergen.haenggi(a)bli.unizh.ch (division email) > http://www.dpr.unizh.ch/ (division website) > http://www.juergenhaenggi.ch (private website) > ---------------------------------------------- > >

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Re: retinotopic questions in Freesurfer
by Jonathan Polimeni 13 Sep '06

13 Sep '06

hi lei, please see below. On Tue, 12 Sep 2006 Lei.Zhang(a)uniklinik-freiburg.de wrote: > Hi, Jonathan, > > I'm glad to know you via Nick's email and I want you could give me some > guidances with my retinotopic analysis. > I have scanned the retinotopic runs with eccen and polar, and the > parameters were as following. > Eccen run: TR 3, the first 8 TRs will discard, then follow Ncycles 7, 48 > sec per cycle, all scan 24+336 sec. > Polar run: TR 3, the first 8 TRs will discard, then follow Ncycles 6, 60 > sec per cycle, all scan 24+360 sec. one thing to note here: you mentioned that you have two rotating wedges presented simultaneously, and that the full stimulus rotates once per 60 seconds. each position in the visual field would then be stimulated *twice* per 60 seconds, so, if i am understanding correctly, it sounds like your 'ncycles' for the polar angle maps should therefore be 12. > Now I can view my final processed retinotopic results, but unfortunately > it looks not ideal. This is my first time to try Freesurfer, so I was > confused by some processing steps, and I want to get your kind help. > 1) in mkanalysis-sess.new command, -ncycles option, I don't know how to > fill it because my eccen run was 7 and polar run was 12 cycles (sorry, > here should be 6 cycles). doug attached to his previous email a new version of "mkanalysis-sess" in which he has added the ability to specify the 'ncycles' parameter value on a per-run basis. as he explained, the command no longer requires specification of 'ncycles' on the command line. this parameter value can now be specified within each paradigm file contained in the run directories. so you may produce, e.g., an 'rtopy_mixedncycles.par' file that, in the eccentricity map runs, looks like... stimtype eccen direction neg ncycles 7 ...and, in the polar angle map runs, looks like... stimtype polar direction neg ncycles 12 then just specify '-paradigm rtopy_mixedncycles.par' in your "mkanalysis-sess" command and leave out the '-ncycles' parameter. to take advantage of this new feature, you should use the updated version of "mkanalysis-sess" that doug provided in his email attachment. > 2) also in mkanalysis-sess.new, can I use -nskip? I want to discard the > first 8 time points (8 TRs) in eccen and polar runs. yup. just append '-nskip 8' to your "mkanalysis-sess" command on the command line. > 3) what can we find in sliceview-sess (intermediate results)? I mean > that the activations should be found in the occipital lobe if the > processing is OK? "sliceview-sess" is great for checking the significance maps calculated from the phase encoding analysis---which i believe are stored in those first 3 images of the analyzed phase encoding volume that is loaded---prior to computing the functional-structural registration. note that you can separately view the significance maps of the 'eccen' and 'polar' analyses within the functional volumes. however, to see that the phases are mapped out correctly you will probably need to view the 'eccen' and 'polar' phases along the cortical surface. these last two steps (involving "paint-sess" and "surf-sess") are described in the "FsFastIndividualRetinotopyAnalysis" workflow on the FreeSurfer wiki. > 4) can I process the eccen and polar runs separately? because I don't > know if ther will be interferences with different cycle time in the > analysis, my eccen run was 48 sec per cycles and polar was 60 sec per > cycle. sure. again, now that doug has extended "mkanalysis-sess" you can easily process both the eccentricity and polar angle maps at once even if they were acquired with different stimulus presentation frequencies. internally, the analysis processes each separately when it computes the corresponding phase maps, so there will be no interference. hope that helps. good luck! -jon

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tcl problems with surf-sess
by Lei.Zhang＠uniklinik-freiburg.de 11 Sep '06

11 Sep '06

Hi, dear Freesurfer, I'm tring to analyse my retinotopic data with the new freesurfer version (freesurfer-Linux-centos4-stable-pub-v3.0.3-full.tar.gz) under Suse Linux10.1. I follewed the processing step of FsFastIndividualRetinotopyAnalysis on your freesurferwiki, and now when I run the last step 'surf-sess -s sessid -a rtopy -c polar -flat', I got the errors, not only for polar, eccen, fieldsign and twocond-flat.tcl which I tried were the same result---'couldn't read file "***.tcl": no such file or directory'. I checked the folder and I can find these files. How can I do next? Thanks for your help! ***Error message*** Session: RM07_retino ---- ------ lh hemisphere ------ /home/zhang/MYSTUDY/RM07_retino/bold/RM07_anal ---------------------------------------------------------- /home/zhang/MYSTUDY/RM07_retino/bold/RM07_anal tksurfer -RM07 lh inflated -tcl fs-flat.tcl ---------------------------------------------------------- Reading /usr/local/freesurfer/lib/tcl/tkm_common.tcl Reading /usr/local/freesurfer/lib/tcl/tkm_wrappers.tcl Reading /usr/local/freesurfer/lib/tcl/fsgdfPlot.tcl Reading /usr/local/freesurfer/lib/tcl/tkUtils.tcl Successfully parsed tksurfer.tcl surfer: current subjects dir: /usr/local/freesurfer/subjects surfer: not in "scripts" dir ==> using cwd for session root surfer: session root data dir ($session) set to: surfer: /home/zhang/MYSTUDY/RM07_retino/bold/RM07_anal surfer: Reading header info from /usr/local/freesurfer/subjects/RM07/mri/T1.mgz surfer: vertices=165187, faces=330370 surfer: single buffered window surfer: using interface /usr/local/freesurfer/lib/tcl/tksurfer.tcl tksurfer: run tcl script: fs-flat.tcl couldn't read file "fs-flat.tcl": no such file or directory% Session: RM07_retino ---- ------ lh hemisphere ------ /home/zhang/MYSTUDY/RM07_retino/bold/RM07_anal ---------------------------------------------------------- /home/zhang/MYSTUDY/RM07_retino/bold/RM07_anal tksurfer -RM07 lh inflated -tcl eccen-flat.tcl ---------------------------------------------------------- Reading /usr/local/freesurfer/lib/tcl/tkm_common.tcl Reading /usr/local/freesurfer/lib/tcl/tkm_wrappers.tcl Reading /usr/local/freesurfer/lib/tcl/fsgdfPlot.tcl Reading /usr/local/freesurfer/lib/tcl/tkUtils.tcl Successfully parsed tksurfer.tcl surfer: current subjects dir: /usr/local/freesurfer/subjects surfer: not in "scripts" dir ==> using cwd for session root surfer: session root data dir ($session) set to: surfer: /home/zhang/MYSTUDY/RM07_retino/bold/RM07_anal surfer: Reading header info from /usr/local/freesurfer/subjects/RM07/mri/T1.mgz surfer: vertices=165187, faces=330370 surfer: single buffered window surfer: using interface /usr/local/freesurfer/lib/tcl/tksurfer.tcl tksurfer: run tcl script: eccen-flat.tcl couldn't read file "eccen-flat.tcl": no such file or directory% *********** Lei Zhang Universitätsklinikum Freiburg Dept. of Diagnostic Radiology Medical Physics Hugstetter Strasse 55 79106 Freiburg, Germany

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FS-FAST group analysis paint question
by raij＠nmr.mgh.harvard.edu 11 Sep '06

11 Sep '06

Hi, I would like to paint group analysis results to the surface of the fsaverage brain to produce .w files. With individual subject analyses (that were calculated in individual space, i.e. not morphed), I have been able to use mri_vol2surf in this manner: mri_vol2surf --src V-REST/sig --src_type bfloat -srcreg ../register.dat --hemi lh --o ./V-REST-lh.w --out_type paint In the group analysis, the individual subjects' volumes were morphed into sperical space where the spatial alignment across subjects was done. I used the average brain "fsaverage" as the target brain. Here the above mri_vol2surf will not work. I am unsure how to do the corresponding paint job for the morphed group analysis data. Would the following command do what needs to be done? mri_surf2surf --srcsubject fsaverage --trgsubject fsaverage --srcsurfval V-REST/sig-lh --src_type bfloat --hemi lh --trgsurfval ./V-REST-lh.w --trg_type paint Thanks, Tommi --- Tommi Raij, M.D., Ph.D. MGH/MIT/HMS Athinoula A. Martinos Center for Biomedical Imaging Bldg 149, 13th St Charlestown, MA 02129 U.S.A. raij(a)nmr.mgh.harvard.edu

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