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

03 Nov '04

2 1

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 >

3 3

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.

1 0

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 >

1 0

FsFast file conversion/preprocessing
by Margaret Duff 01 Nov '04

01 Nov '04

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

2 1

tkregister2
by George Papadimitriou 01 Nov '04

01 Nov '04

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. >> >

3 5

filling the white matter
by Wan Park 01 Nov '04

01 Nov '04

when I run recon-all -s uf1 -talairach (uf1 is the subject) I receive this message: $ ####################################### INFO: SUBJECTS_DIR is /Volumes/stem/freesurfer/subjects --------------------------------------------- Talairach Fri Oct 29 17:23:19 ADT 2004 /Volumes/stem/freesurfer/subjects/um1/mri talairach2 um1 INFO: registering um1 Fri Oct 29 17:23:19 ADT 2004 -------------------------------------------- mri_convert orig orig/orig.mnc mri_convert orig orig/orig.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 orig/orig.mnc... -------------------------------------------- mritotal -verbose -debug -clobber -protocol icbm orig/orig.mnc transforms/talairach.xfm -------------------------------------------- mri_add_xform_to_header /Volumes/stem/freesurfer/subjects/um1/mri/transforms/talairach.xfm /Volumes/s m/freesurfer/subjects/um1/mri/orig /Volumes/stem/freesurfer/subjects/um1/mri/orig Fri Oct 29 17:25:26 ADT 2004 INFO: starting per-hemisphere operations ----- Starting Hemisphere rh -------- ----- Starting Hemisphere lh -------- ------------------------------------------- recon-all finished without error at Fri Oct 29 17:25:26 ADT 2004 done but when I return to csurf and I try to create the surface, I receive this message when it is filling the white matter: area[0] = 2 (min = 350, max = 790), aspect = 2.00 (min = 0.60, max = 1.20) need search nearby using +/- offset search region where offset is 3..... using +/- offset search region where offset is 6..... using +/- offset search region where offset is 9..... using +/- offset search region where offset is 12..... using +/- offset search region where offset is 15..... using +/- offset search region where offset is 18..... using +/- offset search region where offset is 21..... using +/- offset search region where offset is 24..... using +/- offset search region where offset is 27..... using +/- offset search region where offset is 30..... using +/- offset search region where offset is 33..... using +/- offset search region where offset is 36..... using +/- offset search region where offset is 39..... using +/- offset search region where offset is 42..... using +/- offset search region where offset is 45..... using +/- offset search region where offset is 48..... /Users/wanpark/Desktop/FreeSurfer/freesurfer/bin/Darwin/mri_fill: could not find pons No such file or directory INFO: volume does not have linear_transform set nor lta is given by option.-xform. INFO: use identity matrix as the talairach transform. INFO: use src volume parameters for the talairach volume. INFO: Modifying dst c_(r,a,s), using the transform dst find_cutting_plane:seed point not in structure! Searching neighborhood... INFO: Modifying dst c_(r,a,s), using the transform dst talairach cc position changed to (2.00, 29.00, -8.00) INFO: Modifying dst c_(r,a,s), using the transform dst find_cutting_plane:seed point not in structure! Searching neighborhood... Command Finished Could you tell me what to do? Thanks Wan

3 2

what the qsurfer can show
by Joongnam Yang 31 Oct '04

31 Oct '04

I ran qsurfer -stat thresh_zstat1 -subject ID -hemi lh -old and got the image displayed. But the image is structural image only. I thought that the above command shows the anatomical and functional data overlaid. Am I wrong? Or how can I see the two data overlaid in one image? Thanks in advance Nam.

1 0

Re: [Freesurfer] MNI auto talairaching
by Joongnam Yang 29 Oct '04

29 Oct '04

I've got an error message when I was running "mri_vol2surf" file mri/transforms/talairach.xfm not found I guesss I need to do talairach transform, Could someone please tell me how to do it? Nam.

3 2

Re: [Freesurfer] MNI auto talairaching
by Joongnam Yang 29 Oct '04

29 Oct '04

>>> Doug Greve <greve(a)nmr.mgh.harvard.edu> 10/29/04 2:16 PM >>> In general, you should not need a talairach transform to run mri_vol2surf, but I can't tell what you're trying to do -- no command-line :(. If you need to talairach, then you can run: recon-all -s subjectid -talairach Joongnam Yang wrote: > > I've got an error message when I was running "mri_vol2surf" > > file > mri/transforms/talairach.xfm > not found > > I guesss I need to do talairach transform, Could someone please tell me how > to do it? > > Nam. > _______________________________________________ > 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

1 0

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