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30065 discussions

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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Cannot view average curvature after make_average_subject
by Johannes Klein 11 Sep '06

11 Sep '06

Hi all, I'm setting up a small study where I want to compare a subject to some matched controls. I've been following the Group analysis tutorial and I've run make_average_subject on my controls. Now, I'd like to check my data and view averaged curvature and thickness measurements. When I try to load the lh.avg_curv onto lh white in tksurfer, I get the following error: ERROR: number of vertices in XX/lh.avg_curv does not match surface (173612,163842)surfer: error reading curvature file The same applies to lh.avg_thickness However, there is a file called lh.curv that I can load. What am I doing wrong here? How can I view the average curvature and thickness measurements? Thanks a lot everyone, Johannes

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Re: [Freesurfer] aseg total volumes
by Graham Wideman 09 Sep '06

09 Sep '06

Bruce: That's pretty interesting... >this is probably due to the partial volume correction we do when >computing the volumes. Is this algorithm described somewhere? I can see the intent, but your description doesn't completely illuminate how you decide which input voxels contribute to which output voxels, and how much. Graham >Basically we assume that each voxel is a linear >combination of the tissue at that voxel and the next most likely label that >neighbors that voxel. The weighting is computed as mixture weight for the >local class mean for each class that explains the voxel intensity. Our >internal studies show that this improves test-retest reliability and >presumably also accuracy. > >cheers, >Bruce

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FS using uncompressed (not mgz) MRI files?
by Graham Wideman 06 Sep '06

06 Sep '06

Folks -- probably Nick? I'd like to be able to work with some FS sessions using uncompressed data, ie: not using mgz files. (Why? So that I can conveniently use some other tools for troubleshooting and inspection, tools that don't know how to uncompress mgz files). Questions: 1. If I just try to gunzip mgz files, some of their names collide with the directories that mksubjdirs has set up. Historically, most of these dirs used to act as containers for per-slice COR files, so they don't seem useful anymore. Can they just be deleted without consequence? 2. I'm assuming that the uncompressed files should be given the extension ".mgh". Do the FS pipeline scripts and programs automatically adapt to uncompressed files? Thanks, Graham

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nan issue
by Derin Cobia 06 Sep '06

06 Sep '06

Bruce, I worked my way backwards through the stream on each .mgz file. The aseg.mgz (and aseg.auto.mgz) file came up in pieces, some parts were there, others weren't; brain.mgz was blank, there was nothing there, as well as the values being 0; the same for norm.mgz. However, both brainmask & nu.mgz appeared normal, which makes me suspect the talairach.lta file. Is this bad output because of the talairach registration? -Derin

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tkmedit problem, crash on loading aseg
by Johannes Klein 05 Sep '06

05 Sep '06

Hi everyone, I have a rather obscure problem. There are some subjects whose aseg subcortical parcellations will not load up in tkmedit, causing it to crash. This happens when using a Mac with X11 to view them, not on my Linux machine. Interestingly though, this does not happen for all subjects, some do get displayed correctly on the Mac, too. Here's what I do: tkmedit mysubj T1.mgz Then, use tkmedit's File-Load Segmentation There, select aseg.mgz and tkmeditColorsCMA tkmedit then crashes, producing the following log: tkmedit started: Tue Sep 5 17:26:20 2006 tkmedit PAT_XXXX T1.mgz lh.white -aux-surface rh.white $Id: tkmedit.c,v 1.274.2.1 2006/03/06 19:52:48 kteich Exp $ $Name: stable3 $ Set user home dir to /Volumes/JalapenoSAN/Scratch/XXXXXX/fs Set subject home dir to /Scratch/XXXXXX/fs/PAT_XXXX Using interface file /usr/local/freesurfer/lib/tcl/tkmedit.tcl Tcl: Successfully parsed tkmedit.tcl Tcl: Successfully parsed tkm_functional.tcl Error 1 in CLUT_GetLabel: Invalid pointer to object. I wonder if this is a known problem for Macs? Thanks, Johannes

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