Freesurfer November 2004

freesurfer@nmr.mgh.harvard.edu

22 participants
53 discussions

Preprocessing steps of freesurfer on Macs
by Kushal Koolwal 10 Nov '04

10 Nov '04

Greetings, Let me apologize in advance for bothering you all agian with a technical question, but we seem to have reached an impasse and I am hopeful that you might be able to point us in the correct direction. We are struggling to get freesurfer up and running on Mac OS X, and have encountered difficulties with several of the preprocessing steps as mentioned in the Freesurfer tutorial(the steps for averaging and motion correcting Bert's data). I am wondering if you know anyone who has successfully ported the application to the Mac and that might be willing to suggest a fix or two? Also earlier someone had suggest using mri_motion_correct utility but to my surprise there was no such thing in the Mac installaion of freesurfer. All I could find was mri_motion_correct2 utility but even that didn't work. Can anyone please give proper pointers and directions in this matter. We are in a process of almost setting our lab with Mac so that we can start our work on freesurfer. Thanks Kushal __________________________________ Do you Yahoo!? Check out the new Yahoo! Front Page. www.yahoo.com

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Another question
by Calabrese Massimiliano 08 Nov '04

08 Nov '04

I'm sorry but I have another question for you. Sometimes the cutting planes are not correct and it doesn't delete the cerebellum. Whay can I do? Manual editing is my only chance? Thanks a lot Massimiliano Calabrese Neuroimaging Group Neuroimmunology Branch NINDS, NIH

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Re: [Freesurfer] FsFast file conversion/preprocessing
by Margaret Duff 08 Nov '04

08 Nov '04

Hi, so, instead of converting the files, i unpacked them into bshort and it gave me, i think, the right amount of files. then i used the command preproc-sess --sf sessid --df sesspar --fwhm 6. it ran for a while, gave me the sections converting input to afni, motion correcting, and matlab file. after it opens matlab it has the errors saying the mc-sess failed. i am running this from /space/troy. it does create the file fmc.mcdat and it looks like its complete. it just stops after that and doesn't make the actual motion corrected files. thanks for your help. margaret SPM stores each *frame* in a separate file, but all slices for a given frame in the same file. Thus, the number of files will equal the number of frames. bshort/bfloat stores each *slice* in a separate file, but all frames for a given slice in the same file. Thus the number of files will equal the number of slices. Does this resolve the difference? It sounds like your bshorts are not being converted to AFNI properly. Can you send me your preproc-sess command-line and the location you are running it from? doug Margaret Duff wrote: > > Hi, I have 12 runs of functional data I am trying to convert to FSFast > formats and then preprocess. I have been using mri_convert to make my > .img files into bshorts. However mri_convert makes only 30 files when my > folders originally contained 37 or 73 files. Is this what it is supposed > to do? I am also then trying to run preproc-sess on these files but i > keep getting an error during the motion correction of the first run. it > says can't register a 1 brick dataset to itself, and ERROR: 3dvolreg > existed with status 1. I am using the command "preproc-sess -sf sessid > -df sesspar -fwhm 6" for preprocessing and "mri_convert 028/f001.img > 028/f_001.bshort" for file conversion. Does anyone know why my steps > aren't working or knows of a better way to do these steps? Thank you so > much, Margaret Duff > > _______________________________________________ > Freesurfer mailing list > [EMAIL PROTECTED] > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center [EMAIL PROTECTED] Phone Number: 617-724-2358 Fax: 617-726-7422 _______________________________________________ Freesurfer mailing list [EMAIL PROTECTED] https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Multiple Sclerosis's lesion
by Calabrese Massimiliano 08 Nov '04

08 Nov '04

Goodmorning everybody. Do you think I have to fill ( during manual editing) the white matter lesion (black hole) which are outlined in green? Thanks a lot for your help. Massimiliano Calabrese Imaging group Neuroloimmunology Branch NINDS, NIH

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Re: mri_vol2surf warning
by Joongnam Yang 03 Nov '04

03 Nov '04

Hi Doub, When I ran recon-all -stage1 -subjid ID I got the following error. Would someone give me any suggestion? It complains about Stratup.pm at the beginning and later it complains it can't locate the file?????? Any comment would be appreciated ==================================================== ............................ perl: warning: Falling back to the standard locale ("C"). defined(@array) is deprecated at /usr/local/mni/lib/mni_autoreg/Startup.pm line 231. (Maybe you should just omit the defined()?) -------------------------------------------- mri_add_xform_to_header /home/nam/blobby/mri/transforms/talairach.xfm /home/nam/blobby/mri/orig /home/nam/blobby/mri/orig Tue Nov 2 14:57:47 EST 2004 --------------------------------------------- Nu Intensity Correction Tue Nov 2 14:57:48 EST 2004 mri_convert orig nu/nu0.mnc mri_convert orig nu/nu0.mnc reading from orig... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (0, 0, -1) k_ras = (0, 1, 0) writing to nu/nu0.mnc... nu_correct -clobber nu/nu0.mnc nu/nu1.mnc perl: warning: Setting locale failed. perl: warning: Please check that your locale settings: LANGUAGE = (unset), LC_ALL = (unset), LANG = "eng_US" are supported and installed on your system. perl: warning: Falling back to the standard locale ("C"). Can't locate MNI/Startup.pm in @INC (@INC contains: /usr/lib/perl5/5.8.0/i386-linux-thread-multi /usr/lib/perl5/5.8.0 /usr/lib/perl5/site_perl/5.8.0/i386-linux-thread-multi /usr/lib/perl5/site_perl/5.8.0 /usr/lib/perl5/site_perl /usr/lib/perl5/vendor_perl/5.8.0/i386-linux-thread-multi /usr/lib/perl5/vendor_perl/5.8.0 /usr/lib/perl5/vendor_perl /usr/lib/perl5/5.8.0/i386-linux-thread-multi /usr/lib/perl5/5.8.0 .) at /usr/local/mni/bin/nu_correct line 37. BEGIN failed--compilation aborted at /usr/local/mni/bin/nu_correct line 37.ERROR: nu_correct ------------------------------------------ Filesystem 1K-blocks Used Available Use% Mounted on /dev/hda6 10080488 7703596 1864824 81% / ------------------------------------------ recon-all exited with errors at Tue Nov 2 14:57:57 EST 2004 ===================================================

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tksurf doesn't recognise mouse position
by Glenn Lawyer 03 Nov '04

03 Nov '04

Hi, I'm having a problem choosing points with tksurfer. Essentially, it does not register the mouse position. More specifically, when I start the program [badger@dhcp-1017-4 ~/freesurfer]$ tksurfer HU0018 lh inflated The tool/command window shows the cursor vertex index as none and the mouse vertex index as none. When I move the mouse over the display window (no clicking yet!), the mouse vertex index shows 83914. This number does not change, regardless of the position of the mouse. It is not a latency issue, as even after a full minute, nothing has registered. Note that the cursor vertex still shows "none". Now I left-click with the mouse. The cursor index shows 83914, and a blue star appears on the image at that location REGARDLESS of mouse position when I click. I move the mouse, and click with the mouse, but the mouse and cursor vertexes do not change. If I manually edit the cursor vertex index, I can move the blue star. Oddly, if I right-click on the image, it re-draws. So at some level mouse events are getting through. Also, tkmedit seems to work, at least the mouse and cursor values update as I scroll around the image. setup: RH9, tk/tcl 8.3, modern machine (2.6 gh pentium 4, 1.5 gigs ram, intel video-on-motherboard) /usr/lib/libtk8.3.so /usr/lib/libtcl8.3.so /usr/lib/libtcl.so /usr/lib/libtclstub8.3.a Ideas, anyone? +glenn -- I want to go farther, farther! A. E. L. > Glenn Lawyer < > Instituttgruppe for psykiatri < > Postboks 1130 Blindern < > 0318 Oslo < < http://folk.uio.no/davidgl > <><><><><><><><><><><><><><><><><:) -- I want to go farther, farther! A. E. L. > Glenn Lawyer < > Instituttgruppe for psykiatri < > Postboks 1130 Blindern < > 0318 Oslo < < http://folk.uio.no/davidgl > <><><><><><><><><><><><><><><><><:)

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help
by aleontie＠meded-mail.ucsd.edu 03 Nov '04

03 Nov '04

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Re: [Freesurfer] tkregister2
by George Papadimitriou 01 Nov '04

01 Nov '04

tkregister2 was used to overlay (i.e. co-register) volume s to volume f. This actually succeeded; you can see results with: % tkregister2 --targ f_000.bfloat --mov s_000.bfloat --reg \ register1.dat Now, I want to actually create an actual new volume (e.g. s_to_f) that is in register with f, using the information contained in register1.dat. For this purpose I used mri_vol2vol, but ended up initially with a "zero volume" and then with a stretched out of version of s that is not in register with f. Does this make sense? Please, let me know if you need me to provide additional info. Thanks a lot! George P. On Mon, 1 Nov 2004, Doug Greve wrote: > > That's what I though, but I still don't know what you're tring to do. > Are you trying to make the f volume overlay onto the s volume or the > other way around? > > > George Papadimitriou wrote: >> >> Hi Doug, >> >> I tried running mri_vol2vol again (after you made the changes); the good >> news is that as you said the output is not zero, but at the same time the >> output volume is definitely not correct (the brain appears stretched, and >> not in register with the template). From what I can gather, you also >> tried this in: >> >> /space/friday/users/dtuch/tkregister2/s_to_f-dng >> >> I also tried a suggestion that Bruce had made earlier (i.e. specifying the >> output to be a bfloat volume, instead of COR), but it yielded the same >> result (output appears stretched and not in register). >> >> I would really appreciate your help resolving this issue. >> >> Thanks, >> George P. >> >> On Mon, 1 Nov 2004, Doug Greve wrote: >> >>> >>> OK, mri_vol2vol should give non-zero output now. I have not looked at it >>> closely enough to tell whether your actually doing what you want to do. >>> >>> doug >>> >>> >>> George Papadimitriou wrote: >>>> >>>> OK, I changed the permissions. I am trying to co-register s to f. >>>> >>>> George P. >>>> >>>> On Mon, 1 Nov 2004, Doug Greve wrote: >>>> >>>>> >>>>> Can you chmod those files? I don't have read perms to all of it. >>>>> >>>>> What are you trying to do? Resample f to s or s to f? >>>>> >>>>> doug >>>>> >>>>> >>>>> George Papadimitriou wrote: >>>>>> >>>>>> You are correct, my input is bfloat. Can you please offer a workaround to >>>>>> this issue? >>>>>> >>>>>> Should I convert my two inputs to unsigned characters before I proceed? >>>>>> >>>>>> Thanks, >>>>>> George P. >>>>>> >>>>>> On Mon, 1 Nov 2004, Bruce Fischl wrote: >>>>>> >>>>>>> Hi George, >>>>>>> >>>>>>> what is the range of values in your input (bfloat) volume? Note that COR is >>>>>>> an 8 bit format, so if you input is floating point and <1 it will be set to >>>>>>> 0. >>>>>>> >>>>>>> cheers, >>>>>>> Bruce >>>>>>> >>>>>>> On Mon, 1 Nov 2004, George Papadimitriou wrote: >>>>>>> >>>>>>>> Hi all, >>>>>>>> >>>>>>>> I'd really appreciate it if I can get some input on the issue below. I >>>>>>>> need to come up with an answer this week. >>>>>>>> >>>>>>>> I am having some trouble with manual co-registration using tkregister2. I >>>>>>>> have placed the data in: >>>>>>>> >>>>>>>> /space/friday/users/dtuch/tkregister2 >>>>>>>> >>>>>>>> Here is the info: >>>>>>>> >>>>>>>> f prefix --> template >>>>>>>> s prefix --> subject to be co-registered with template >>>>>>>> s_to_f/ --> contains the co-registered result (COR) >>>>>>>> >>>>>>>> I did the co-registration using the following command: >>>>>>>> >>>>>>>> % tkregister2 --targ f_000.bfloat --mov s_000.bfloat --reg \ >>>>>>>> register1.dat >>>>>>>> >>>>>>>> It worked pretty well; the only trick was that I had to click in the image >>>>>>>> window and hit 'i' to turn on the automatic intensity normalization. This >>>>>>>> process saved a new transformation matrix to the register1.dat file. >>>>>>>> >>>>>>>> The register1.dat file was used to transform the input volume by using the >>>>>>>> mri_vol2vol command: >>>>>>>> >>>>>>>> % mri_vol2vol --in f_000.bfloat --out s_to_f/. --interp \ >>>>>>>> trilin --temp f_000.bfloat --xfm register1.dat --invxfm >>>>>>>> >>>>>>>> The problem is that when I try to load the result in tkmedit (or >>>>>>>> tkregister2): >>>>>>>> >>>>>>>> tkmedit -f s_to_f >>>>>>>> >>>>>>>> I don't see an output volume (every voxel seems to be zero) >>>>>>>> >>>>>>>> Can you please take a look at the data when you get a chance? Please, let >>>>>>>> me know if you need me to provide additional info. >>>>>>>> >>>>>>>> Thanks a lot! >>>>>>>> George P. >>>>>>>> >>>>>>>> PS After you evaluate this case, if you also think I need to email the >>>>>>>> freesurfer list, just let me know. >>>>>>>> >>>>>>>> On Wed, 27 Oct 2004, David Tuch wrote: >>>>>>>> >>>>>>>>> >>>>>>>>> Hi George, >>>>>>>>> >>>>>>>>> can you direct me to avg_000.bfloat ? >>>>>>>>> >>>>>>>>> tnx, >>>>>>>>> D >>>>>>>>> >>>>>>>>> >>>>>>>>> On Wed, 27 Oct 2004, George Papadimitriou wrote: >>>>>>>>> >>>>>>>>>> Hi Dave, >>>>>>>>>> >>>>>>>>>> Have you run into the issue described below? >>>>>>>>>> >>>>>>>>>> Thanks a lot! >>>>>>>>>> George P. >>>>>>>>>> >>>>>>>>>> ---------- Forwarded message ---------- >>>>>>>>>> Date: Wed, 27 Oct 2004 11:53:07 -0400 (EDT) >>>>>>>>>> From: George Papadimitriou <georgep(a)nmr.mgh.harvard.edu> >>>>>>>>>> To: freesurfer(a)nmr.mgh.harvard.edu >>>>>>>>>> Subject: tkregister2 question >>>>>>>>>> >>>>>>>>>> I am trying to register a lowb volume to an average volume. >>>>>>>>>> >>>>>>>>>> In this particular case, I'm trying to use tkregister2: >>>>>>>>>> >>>>>>>>>> % tkregister2 --targ avg_000.bfloat --mov indivsubj_000.bfloat --reg \ >>>>>>>>>> register.dat >>>>>>>>>> >>>>>>>>>> I am having a problem with the brightness of the TARG volume. It >>>>>>>>>> seems to be set near ~1, and using the fmov option only adjusts the >>>>>>>>>> brightness on the MOV volume. It is kind of hard to align them, when >>>>>>>>>> the target volume looks like a binary mask (appears all white). Have >>>>>>>>>> you seen this before? >>>>>>>>>> >>>>>>>>>> Changing the contrast doesn't seem to help. >>>>>>>>>> >>>>>>>>>> Thanks, >>>>>>>>>> George P. >>>>>>>>>> >>>>>>>>> >>>>>>>> _______________________________________________ >>>>>>>> Freesurfer mailing list >>>>>>>> Freesurfer(a)nmr.mgh.harvard.edu >>>>>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>>>>>>> >>>>>>> >>>>>> _______________________________________________ >>>>>> Freesurfer mailing list >>>>>> Freesurfer(a)nmr.mgh.harvard.edu >>>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>>>> >>>>> -- >>>>> Douglas N. Greve, Ph.D. >>>>> MGH-NMR Center >>>>> greve(a)nmr.mgh.harvard.edu >>>>> Phone Number: 617-724-2358 >>>>> Fax: 617-726-7422 >>>>> >>> >>> -- >>> Douglas N. Greve, Ph.D. >>> MGH-NMR Center >>> greve(a)nmr.mgh.harvard.edu >>> Phone Number: 617-724-2358 >>> Fax: 617-726-7422 >>> > > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > greve(a)nmr.mgh.harvard.edu > Phone Number: 617-724-2358 > Fax: 617-726-7422 >

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Re: mri_vol2surf error
by Joongnam Yang 01 Nov '04

01 Nov '04

Thanks Doug, I am having trouble doing functional overlay with structural, either with GUI or command-line. On GUI, I open "structural" and "functional" directories in "csurf", but the overlay option under "File" doesn't show the overlay. I chose *.w file for the overlay data. Question1: Should "functional" directory in "csurf" be set to a *.feat directory which is the output of FEAT of FSL? Question 2: When the functional overlay is complete, how does it look? Of course, it depends on the functional data, but in general. I guess that the structural brain overlaied with functional data in COLOR? right? Take care Nam.

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Re: [Freesurfer] tkregister2
by George Papadimitriou 01 Nov '04

01 Nov '04

Hi Doug, I tried running mri_vol2vol again (after you made the changes); the good news is that as you said the output is not zero, but at the same time the output volume is definitely not correct (the brain appears stretched, and not in register with the template). From what I can gather, you also tried this in: /space/friday/users/dtuch/tkregister2/s_to_f-dng I also tried a suggestion that Bruce had made earlier (i.e. specifying the output to be a bfloat volume, instead of COR), but it yielded the same result (output appears stretched and not in register). I would really appreciate your help resolving this issue. Thanks, George P. On Mon, 1 Nov 2004, Doug Greve wrote: > > OK, mri_vol2vol should give non-zero output now. I have not looked at it > closely enough to tell whether your actually doing what you want to do. > > doug > > > George Papadimitriou wrote: >> >> OK, I changed the permissions. I am trying to co-register s to f. >> >> George P. >> >> On Mon, 1 Nov 2004, Doug Greve wrote: >> >>> >>> Can you chmod those files? I don't have read perms to all of it. >>> >>> What are you trying to do? Resample f to s or s to f? >>> >>> doug >>> >>> >>> George Papadimitriou wrote: >>>> >>>> You are correct, my input is bfloat. Can you please offer a workaround to >>>> this issue? >>>> >>>> Should I convert my two inputs to unsigned characters before I proceed? >>>> >>>> Thanks, >>>> George P. >>>> >>>> On Mon, 1 Nov 2004, Bruce Fischl wrote: >>>> >>>>> Hi George, >>>>> >>>>> what is the range of values in your input (bfloat) volume? Note that COR is >>>>> an 8 bit format, so if you input is floating point and <1 it will be set to >>>>> 0. >>>>> >>>>> cheers, >>>>> Bruce >>>>> >>>>> On Mon, 1 Nov 2004, George Papadimitriou wrote: >>>>> >>>>>> Hi all, >>>>>> >>>>>> I'd really appreciate it if I can get some input on the issue below. I >>>>>> need to come up with an answer this week. >>>>>> >>>>>> I am having some trouble with manual co-registration using tkregister2. I >>>>>> have placed the data in: >>>>>> >>>>>> /space/friday/users/dtuch/tkregister2 >>>>>> >>>>>> Here is the info: >>>>>> >>>>>> f prefix --> template >>>>>> s prefix --> subject to be co-registered with template >>>>>> s_to_f/ --> contains the co-registered result (COR) >>>>>> >>>>>> I did the co-registration using the following command: >>>>>> >>>>>> % tkregister2 --targ f_000.bfloat --mov s_000.bfloat --reg \ >>>>>> register1.dat >>>>>> >>>>>> It worked pretty well; the only trick was that I had to click in the image >>>>>> window and hit 'i' to turn on the automatic intensity normalization. This >>>>>> process saved a new transformation matrix to the register1.dat file. >>>>>> >>>>>> The register1.dat file was used to transform the input volume by using the >>>>>> mri_vol2vol command: >>>>>> >>>>>> % mri_vol2vol --in f_000.bfloat --out s_to_f/. --interp \ >>>>>> trilin --temp f_000.bfloat --xfm register1.dat --invxfm >>>>>> >>>>>> The problem is that when I try to load the result in tkmedit (or >>>>>> tkregister2): >>>>>> >>>>>> tkmedit -f s_to_f >>>>>> >>>>>> I don't see an output volume (every voxel seems to be zero) >>>>>> >>>>>> Can you please take a look at the data when you get a chance? Please, let >>>>>> me know if you need me to provide additional info. >>>>>> >>>>>> Thanks a lot! >>>>>> George P. >>>>>> >>>>>> PS After you evaluate this case, if you also think I need to email the >>>>>> freesurfer list, just let me know. >>>>>> >>>>>> On Wed, 27 Oct 2004, David Tuch wrote: >>>>>> >>>>>>> >>>>>>> Hi George, >>>>>>> >>>>>>> can you direct me to avg_000.bfloat ? >>>>>>> >>>>>>> tnx, >>>>>>> D >>>>>>> >>>>>>> >>>>>>> On Wed, 27 Oct 2004, George Papadimitriou wrote: >>>>>>> >>>>>>>> Hi Dave, >>>>>>>> >>>>>>>> Have you run into the issue described below? >>>>>>>> >>>>>>>> Thanks a lot! >>>>>>>> George P. >>>>>>>> >>>>>>>> ---------- Forwarded message ---------- >>>>>>>> Date: Wed, 27 Oct 2004 11:53:07 -0400 (EDT) >>>>>>>> From: George Papadimitriou <georgep(a)nmr.mgh.harvard.edu> >>>>>>>> To: freesurfer(a)nmr.mgh.harvard.edu >>>>>>>> Subject: tkregister2 question >>>>>>>> >>>>>>>> I am trying to register a lowb volume to an average volume. >>>>>>>> >>>>>>>> In this particular case, I'm trying to use tkregister2: >>>>>>>> >>>>>>>> % tkregister2 --targ avg_000.bfloat --mov indivsubj_000.bfloat --reg \ >>>>>>>> register.dat >>>>>>>> >>>>>>>> I am having a problem with the brightness of the TARG volume. It >>>>>>>> seems to be set near ~1, and using the fmov option only adjusts the >>>>>>>> brightness on the MOV volume. It is kind of hard to align them, when >>>>>>>> the target volume looks like a binary mask (appears all white). Have >>>>>>>> you seen this before? >>>>>>>> >>>>>>>> Changing the contrast doesn't seem to help. >>>>>>>> >>>>>>>> Thanks, >>>>>>>> George P. >>>>>>>> >>>>>>> >>>>>> _______________________________________________ >>>>>> Freesurfer mailing list >>>>>> Freesurfer(a)nmr.mgh.harvard.edu >>>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>>>>> >>>>> >>>> _______________________________________________ >>>> Freesurfer mailing list >>>> Freesurfer(a)nmr.mgh.harvard.edu >>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>> >>> -- >>> Douglas N. Greve, Ph.D. >>> MGH-NMR Center >>> greve(a)nmr.mgh.harvard.edu >>> Phone Number: 617-724-2358 >>> Fax: 617-726-7422 >>> > > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > greve(a)nmr.mgh.harvard.edu > Phone Number: 617-724-2358 > Fax: 617-726-7422 >

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Freesurfer November 2004