Re: [Freesurfer] mri_normalize error
Hi Keyma! Could you send the command you used, and possibly more output? (say, the last 15 lines before the error message?) Thanks! On Mon, 26 Jul 2004, Chekema Nayasha Prince wrote: Hello, I'm trying to normalize an MPRAGE dataset and I received the following message from the mri_normalize: MRInormalize:could not find any valid peaks no such file or directory mri_normalize: normalization failed no such file or directory I tried to set control points ( 4 of them specifically) in the wm and tried to rerun the mri_normalize but I received the same error. my orig volume looks just like my other datasets that worked properly. Can you let me know what could be causing the error? -Keyma ___ Freesurfer mailing list [EMAIL PROTECTED] https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list [EMAIL PROTECTED] https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] edits not effective
Hi Kevin, Are you using Talairach co-ordinates? Is the talairach.xfm okay -- does it look reasonable? On Thu, 9 Sep 2004, Kevin DeSimone wrote: > i have a subject (who is not out of the ordinary) where the cerebellum > is sticking to one hemisphere. i make the usual edits on the > segmentation, and indicate the coordinates for the cutting planes to > rid myself o the cerebellum. i then save everything and re-run the > create surface program. nothing happens! > > literally nothing happens, my edits still appear in the wm volume, but > looking at the filled volume, it looks like nothing is even affected. > in addition, the surfaces don't seem to have been altered. what's > going on? > > ___ > Freesurfer mailing list > [EMAIL PROTECTED] > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > -- ___ Freesurfer mailing list [EMAIL PROTECTED] https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] thresh_zstat1.img
Hi If you are new to fMRI then it's likely you will be dissatisfied with the level of exchange on the freesurfer mailing list. Might we recommend several excellent online sources for NMR neophytes? This seems like a good one with links to some very active fMRI research centers: http://www.functionalmri.org Thanks, good luck! On Fri, 19 Nov 2004, Joongnam Yang wrote: > > Did you visually check the registration of the functional to the > structural? > > The registration using tkregister2 produces three files > func2struc.mat > func2struc.hdr > func2struc.img, > > I've tried to load func2struc.hdr in TkSurfer, but it crashes. > Again, I don't understand what you do when you "visual check" registration. > I am new to fMRI, please be more specific. > > Thanks. > Nam. > ___ > Freesurfer mailing list > [EMAIL PROTECTED] > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > -- ___ Freesurfer mailing list [EMAIL PROTECTED] https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] two questions
On Wed, 5 Jan 2005, Joongnam Yang wrote: > Hi, > > Sounds like trivial questions... > > (1) How do you check if the talairach.xfm is OK? You load the mri/orig in tkmedit as main volume, then: File--> Load Transform for Main Volume --> and select SUBJECTNAME/mri/transforms/talairach.xfm *or* talairach.lta now you should be able to toggle between the two volumes -- check to make sure the talairach is aligned properly (e.g. corpus callosum, anterior commissure, temporal lobes are roughly where they should be, the entire talairach transform should also be in the field of view) if one of them is good, then use that one if one of them is bad, rename it to talairach_xfm.bad of neither one is good, remake it by running: talairach_mgh SUBJECTNAME (should take about 20 minutes) 2) that depends on what you're using tkregister2 to register -- if you're using it for the talairach transform then you should use it as soon as possible in the process... what volumes are you registering? it can also be used after recon-all to register functional data of course, but this seems an obvious point so probably not what you meant > > (2) Either during the command-line option of recon-all -stage 1 thru 4, > when do you use tkregister2 for registeration? > > Thanks for the help. > > Nam. > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > -- ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] manual editting not implemented
It isn't useless but being a GUI it is less stable, and the command line outputs a recon-all.log, at least the tail line of which you should include with any enquiries to the freesurfer list, otherwise it is sometimes difficult to say what caused an undesirable freesurfer result. On Fri, 14 Jan 2005, Joongnam Yang wrote: > Thanks Brian, > Does that mean csurf interface is useless for "creating surfaces" to > implement > the editting of major topological defects? > > Nam. > > >>> "Brian T. Quinn" <[EMAIL PROTECTED]> 01/14/05 3:22 PM >>> > hi Nam- > > please refrain from using the csurf interface to create surfaces. > instead, run through the command line: > recon-all -stage2 -subjid > > this will create a log > file($SUBJECTS_DIR/subject_name/scripts/recon-all.log) > > include this with your email so we can better assist you with your > difficulties. > > thanks, > brian > > On Fri, 14 Jan 2005, Joongnam Yang wrote: > > > Hi, > > > > I did manual editting for lateral ventricles, fornix, basal ganglia, optic > > nerve, > > as illustrated in the cortical reconstruction tutorial, for both left and > > right hemispheres, and DID save them in the "wm" volume. > > Then I ran "create surface", but nothing is changed. > > > > What could have been wrong? > > > > Comments are appreciated. > > Nam. > > ___ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > -- ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] how to seed points
Hi Wan, Looks like it had difficulty automatically finding the corpus callosum cutting plane, so you'll have to give it the coordinates manually. To do so: Load the WM volume, and click in the dead center of the corpus callosum, in coronal view. Then switch to a sagittal plane. You should find a slice where the corp. cal. is detached from the rest of the cortical white matter. You may have to scroll around a slice or two to find that. Now, note the talairach coordinates displayed in the TkMedit tools dialog box. For example, let's say those coordinates read: 2.3 4.5 6.7 and the subject id is wan_subject. Those are the coordinates you'll manually specify when you rerun the step that separates the two hemispheres and creates their surfaces. So, run this from the command line: recon-all -stage2 -cc-xyz 2.3 4.5 6.7 -subjid wan_subject Let us know if this did not fix the problem. Note: This fix assumes that the talairach transform (wan_subject/mri/transforms/talairach.*) looks good. Good luck! On Tue, 25 Jan 2005, Wan Park wrote: > when i try to create the surface, i receive this message: > > > /usr/local/freesurfer_package/freesurfer/bin/Darwin/mri_fill -lval 255 > -rval 80 -ccmask -T 1 -L > /usr/local/freesurfer_package/freesurfer/subjects/23963/mri/tmp/ > ponscall.dat > /usr/local/freesurfer_package/freesurfer/subjects/23963/mri/wm > /usr/local/freesurfer_package/freesurfer/subjects/23963/mri/filled > using 255 as fill val for left hemisphere. > using 80 as fill val for right hemisphere. > not using corpus callosum to mask possible location of pons. > logging cutting plane coordinates to > /usr/local/freesurfer_package/freesurfer/subjects/23963/mri/tmp/ > ponscall.dat... > reading input volume...done. > searching for cutting planes...voxel to talairach voxel transform > 1.000 0.000 0.000 0.000; > 0.000 1.000 0.000 0.000; > 0.000 0.000 1.000 0.000; > 0.000 0.000 0.000 1.000; > /usr/local/freesurfer_package/freesurfer/bin/Darwin/mri_fill: could not > find valid seed for the cc > No such file or directory > Looking for area (min, max) = (350, 1400) > area[0] = 2435 (min = 350, max = 1400), aspect = 0.88 (min = 0.10, max > = 0.75) > 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. > Looking for area (min, max) = (350, 1400) > area[0] = 2001 (min = 350, max = 1400), aspect = 0.99 (min = 0.10, max > = 0.75) > 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. > /usr/local/freesurfer_package/freesurfer/bin/Darwin/mri_fill: could not > find corpus callosum > 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... > > > could you please teach me how to solve the problem? thanks, > > wan park -- ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] averaging brains over two sessions
Hi Margaret, How does the talairach transform look? On Wed, 2 Feb 2005, Margaret Duff wrote: > Hello, I am trying to reconstruct brains of patients who had one > structural scan during each of 2 visits, a month apart. I averaged the > two images together, but since they are from different visits, they look > very badly lined up. It looks like there is one image and another image > overlaid and shifted by a cm or so. These are clearly wrong and will not > work but I was wondering if it was OK to run freesurfer with only one of > the images, or if there was a way to line these two images up better so > they can be combined? Thanks, Margaret > > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > -- ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] averaging brains over two sessions
Hi again, If the shadowing/rimming effect appears to be because of an artifact in one of the scans, then you might be better off to exclude that acquisition. But if each of the individual scans looks okay, then it does sound like improving your lousy average is dependent upon getting a better talairach transform. You can do this by trying various talairach scripts or even registering it manually. On Wed, 2 Feb 2005, Margaret Duff wrote: > The one using the orig is really horrible looking, very distorted and > rotated. I tried using the brain volume, and it looks better, but also > has a rimming/shadowing effect. > > On Wed, 2 Feb 2005, Evelina Busa wrote: > > > > > Hi Margaret, > > > > How does the talairach transform look? > > > > On Wed, 2 Feb 2005, Margaret Duff wrote: > > > > > Hello, I am trying to reconstruct brains of patients who had one > > > structural scan during each of 2 visits, a month apart. I averaged the > > > two images together, but since they are from different visits, they look > > > very badly lined up. It looks like there is one image and another image > > > overlaid and shifted by a cm or so. These are clearly wrong and will not > > > work but I was wondering if it was OK to run freesurfer with only one of > > > the images, or if there was a way to line these two images up better so > > > they can be combined? Thanks, Margaret > > > > > > ___ > > > Freesurfer mailing list > > > Freesurfer@nmr.mgh.harvard.edu > > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > > > > -- ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] averaging brains over two sessions
On Wed, 2 Feb 2005, Brian T. Quinn wrote: > i would not advise averaging data from two separate visits. > use one or the other. The auto-align feature aims to offer a fair degree of consistency between session scans, but if this was not the case (and it often isn't, because you cannot control for the position of the coil, etc.), then definitely be prepared to ditch the worse scan. Unfortunately! > On Wed, 2 Feb 2005, Evelina Busa wrote: > > > Hi again, > > > > If the shadowing/rimming effect appears to be because of an artifact in > > one of the scans, then you might be better off to exclude that > > acquisition. But if each of the individual scans looks okay, then it does > > sound like improving your lousy average is dependent upon getting a better > > talairach transform. You can do this by trying various talairach scripts > > or even registering it manually. > > > > > > > > On Wed, 2 Feb 2005, Margaret Duff wrote: > > > >> The one using the orig is really horrible looking, very distorted and > >> rotated. I tried using the brain volume, and it looks better, but also > >> has a rimming/shadowing effect. > >> > >> On Wed, 2 Feb 2005, Evelina Busa wrote: > >> > >>> > >>> Hi Margaret, > >>> > >>> How does the talairach transform look? > >>> > >>> On Wed, 2 Feb 2005, Margaret Duff wrote: > >>> > >>>> Hello, I am trying to reconstruct brains of patients who had one > >>>> structural scan during each of 2 visits, a month apart. I averaged the > >>>> two images together, but since they are from different visits, they look > >>>> very badly lined up. It looks like there is one image and another image > >>>> overlaid and shifted by a cm or so. These are clearly wrong and will not > >>>> work but I was wondering if it was OK to run freesurfer with only one of > >>>> the images, or if there was a way to line these two images up better so > >>>> they can be combined? Thanks, Margaret > >>>> > >>>> ___ > >>>> Freesurfer mailing list > >>>> Freesurfer@nmr.mgh.harvard.edu > >>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > >>>> > >>> > >>> > >> > > > > -- > > > > > > ___ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > -- ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] averaging brains over two sessions
Before you give up you could try running distortion correction on each of those volumes before you try averaging/motion correction again... On Wed, 2 Feb 2005, Margaret Duff wrote: > The one using the orig is really horrible looking, very distorted and > rotated. I tried using the brain volume, and it looks better, but also > has a rimming/shadowing effect. > > On Wed, 2 Feb 2005, Evelina Busa wrote: > > > > > Hi Margaret, > > > > How does the talairach transform look? > > > > On Wed, 2 Feb 2005, Margaret Duff wrote: > > > > > Hello, I am trying to reconstruct brains of patients who had one > > > structural scan during each of 2 visits, a month apart. I averaged the > > > two images together, but since they are from different visits, they look > > > very badly lined up. It looks like there is one image and another image > > > overlaid and shifted by a cm or so. These are clearly wrong and will not > > > work but I was wondering if it was OK to run freesurfer with only one of > > > the images, or if there was a way to line these two images up better so > > > they can be combined? Thanks, Margaret > > > > > > ___ > > > Freesurfer mailing list > > > Freesurfer@nmr.mgh.harvard.edu > > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > > > > -- ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Getting the resolution out
Hi Daniel, Is it possible to get the original dicom data? You said the data were already processed by Freesurfer when they got to you, so maybe whoever gave them to you can point you to the whereabouts of the raw dicom files? Ev On Tue, 20 Sep 2005, Daniel Goldenholz wrote: Hi Bruce I am not sure that I have the original dicom files. I did find a file called COR-.info in mri/orig/ This is the filedump... Perhaps this has the answer? imnr0 1 imnr1 256 ptype 2 x 256 y 256 fov 0.256000 thick 0.001000 psiz 0.001000 locatn 0.00 strtx -0.128000 endx 0.128000 strty -0.128000 endy 0.128000 strtz -0.128000 endz 0.128000 tr 0.00 te 0.00 ti 0.00 xform /local_mount/space/linus/7/users/sms/MRI/ips015c/mri/transforms/talairach.xfm ras_good_flag 1 x_ras -1.00 0.00 0.00 y_ras 0.00 0.00 -1.00 z_ras 0.00 1.00 0.00 c_ras -10.110786 29.012054 -11.469879 Bruce Fischl wrote: Hi Daniel, you need to look at your original data (e.g. dicom files). You can mri_info to tell you. Bruce On Tue, 20 Sep 2005, Daniel Goldenholz wrote: Hi. I was handed some data analyzed with freesurfer, and I would like to know what is the exact resolution of the T1 mri, i.e. 1.25mm x 3mm x 2mm for example. Where can I look in the freesurfer folder to find out? Thanks -- ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] recalculating surfaces
Hi Dahlia Since it seems unclear whether or not you edited the WM volume of this second subject whose surface files were overwritten, it might be helpful for you to first look at the recon-all.log text files in that subject's scripts/ directory, to see what commands you ran. Probably what happened is that you recreated the surfaces unnecessarily, if the WM volume is correct. The files in mri/wm are from Sep12th, but the mri/filled volume files are new. So back to the subject you *want* to edit/create surfaces for -- just make sure you likes its WM volume, and proceed with stages 3 & 4, if you haven't already. I guess the main caveat here is that you're using the same version to recon all these subjects. okay! On Thu, 27 Oct 2005, Dahlia Sharon wrote: Hi, I overwrote several surface files (.inflated, .sulc, .curv, .smoothwm, .orig) by mistake while editing another subject. The volume in mri/wm/ is still the correct one. I should be able to run some of the recon steps again to get the correct surfaces back, but I don't want to do this without guidance so as not to make mistakes and start stepping over other files. Can you tell me which commands to run to regenerate these surfaces correctly? Thanks!!! Dahlia. PS - the subject is ~dahlia/structurals/subj21_bay2 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] recalculating surfaces
Hi again, Yes, assuming you are using the same version of FreeSurfer and since the WM volume is the same, the new surfaces you created should be similar to the September ones. okay! On Thu, 27 Oct 2005, Dahlia Sharon wrote: Hi Ev, recon-all.log says I ran recon-all stage 2 on Saturday, overwriting the good files from September. The subject I had really WANTED to edit at the time is already edited and fixed etc. My problem is with the overwritten files of the older subject. For this older subject, if I simply rerun stage2 and then stages 3&4, will that recalculate the correct surfaces from the (currently correct) mri/wm? Thanks! Dahlia. On Thu, 27 Oct 2005, Evelina Busa wrote: Hi Dahlia Since it seems unclear whether or not you edited the WM volume of this second subject whose surface files were overwritten, it might be helpful for you to first look at the recon-all.log text files in that subject's scripts/ directory, to see what commands you ran. Probably what happened is that you recreated the surfaces unnecessarily, if the WM volume is correct. The files in mri/wm are from Sep12th, but the mri/filled volume files are new. So back to the subject you *want* to edit/create surfaces for -- just make sure you likes its WM volume, and proceed with stages 3 & 4, if you haven't already. I guess the main caveat here is that you're using the same version to recon all these subjects. okay! On Thu, 27 Oct 2005, Dahlia Sharon wrote: Hi, I overwrote several surface files (.inflated, .sulc, .curv, .smoothwm, .orig) by mistake while editing another subject. The volume in mri/wm/ is still the correct one. I should be able to run some of the recon steps again to get the correct surfaces back, but I don't want to do this without guidance so as not to make mistakes and start stepping over other files. Can you tell me which commands to run to regenerate these surfaces correctly? Thanks!!! Dahlia. PS - the subject is ~dahlia/structurals/subj21_bay2 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] recalculating surfaces
Hi ARe you talking about the inflated surfaces as viewed in tksurfer? I don't see why they wouldn't be identical for the old subject, since your subject's mri/wm/* are still dated Sep11th: [EMAIL PROTECTED] structurals]$ ls -l subj21_bay2/mri/wm total 17412 -rwxrwxrwx 1 dahlia meganal 65536 Sep 11 14:13 COR-001 -rwxrwxrwx 1 dahlia meganal 65536 Sep 11 14:13 COR-002 ...etc ...and all you ran was: Sat Oct 22 14:26:20 EDT 2005 /autofs/space/mirabai_003/users/dahlia/structurals/subj21_bay2 /usr/local/freesurfer/dev/bin//recon-all -subjid subj21_bay2 -stage2 -hemi rh which should not have affected the wm volume anyway. But looking at this subject's scripts/recon-all.log, it seems you used different versions: Fri Sep 9 20:10:10 EDT 2005 /usr/local/freesurfer/beta/bin//recon-all vs. Sat Oct 22 14:26:20 EDT 2005 /autofs/space/mirabai_003/users/dahlia/structurals/subj21_bay2 /usr/local/freesurfer/dev/bin//recon-all -subjid subj21_bay2 -stage2 - So probably you could just try rerunning stages 3 onward using your beta version that you used in September for this subject. okay! On Thu, 27 Oct 2005, Dahlia Sharon wrote: Hey Ev, The problem is that the new surfaces don't currently look like the September ones - they look precisely like the new subject's surfaces before I did the final manual edits on Saturday. So I'm trying to find the way to get back the old surfaces. If I now rerun stages2-4, assuming the mri/wm/ volume is still correct, will I now get the correct old surfaces? Thanks! Dahlia. On Thu, 27 Oct 2005, Evelina Busa wrote: Hi again, Yes, assuming you are using the same version of FreeSurfer and since the WM volume is the same, the new surfaces you created should be similar to the September ones. okay! On Thu, 27 Oct 2005, Dahlia Sharon wrote: Hi Ev, recon-all.log says I ran recon-all stage 2 on Saturday, overwriting the good files from September. The subject I had really WANTED to edit at the time is already edited and fixed etc. My problem is with the overwritten files of the older subject. For this older subject, if I simply rerun stage2 and then stages 3&4, will that recalculate the correct surfaces from the (currently correct) mri/wm? Thanks! Dahlia. On Thu, 27 Oct 2005, Evelina Busa wrote: Hi Dahlia Since it seems unclear whether or not you edited the WM volume of this second subject whose surface files were overwritten, it might be helpful for you to first look at the recon-all.log text files in that subject's scripts/ directory, to see what commands you ran. Probably what happened is that you recreated the surfaces unnecessarily, if the WM volume is correct. The files in mri/wm are from Sep12th, but the mri/filled volume files are new. So back to the subject you *want* to edit/create surfaces for -- just make sure you likes its WM volume, and proceed with stages 3 & 4, if you haven't already. I guess the main caveat here is that you're using the same version to recon all these subjects. okay! On Thu, 27 Oct 2005, Dahlia Sharon wrote: Hi, I overwrote several surface files (.inflated, .sulc, .curv, .smoothwm, .orig) by mistake while editing another subject. The volume in mri/wm/ is still the correct one. I should be able to run some of the recon steps again to get the correct surfaces back, but I don't want to do this without guidance so as not to make mistakes and start stepping over other files. Can you tell me which commands to run to regenerate these surfaces correctly? Thanks!!! Dahlia. PS - the subject is ~dahlia/structurals/subj21_bay2 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] (no subject)
Hi Aaron, First, is it something simple and annoying like that your script doesn't look for an orig.mgz volume (vs. the 'orig' which was standard until fairly recently)? I have needed to edit my scripts to accommodate for this. okay! On Wed, 2 Nov 2005, Goldman, Aaron (NIH/NIMH) wrote: Hi, I have a script that basically opens up tksurfer and tkmedit for manual editing, and then runs recon-all stage2 once you're done editing. We recently tried to run the script on a different computer with the same freesurfer distribution, and got an error I'm not used to seeing. It says: WARNING: Couldn't not load orig volume from ///surf/../mri/orig.mgz Talairach coords will be incorrect. (the '' was edited in by me) I was just wondering if this error will create problems, either with correct manual editing or with running stage2. Thanks, -Aaron- Aaron L. Goldman Post-Bacc IRTA Genes, Cognition and Psychosis Program, NIMH Building 10, Room 3C108 Phone: (301) 435-0944 Email: [EMAIL PROTECTED] -- ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
