[Freesurfer] license key
Hello, I received a license key by email, but cannot find where in the license it should go. Thanks, Margaret ___ Freesurfer mailing list [EMAIL PROTECTED] https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] inflated surface not appearing
Hi, I have run the process volume and create surface commands on a set of structural data, but when i go to edit segmentation, nothing comes up in the TkSurfer window. There are pictures in the TkEdit window, though. I have looked through my files and the surf folder has both lh and rh files in it so I was wondering if anyone had any idea why the inflated surface will not show up in TkSurfer. The only step I have omitted during processing is the Talairaching step. Thanks for your help, Margaret ___ Freesurfer mailing list [EMAIL PROTECTED] https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] Printing or saving TkSurfer image
Hello, Does anyone know how to print or save as an image, the infated brain surface as shown using TkSurfer? Thanks, Margaret ___ Freesurfer mailing list [EMAIL PROTECTED] https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] fsfast parfiles
Hello, When writing par files for each functional run, do you match the timing of the stimuli to the ideal timing (starting at zero), the ideal adjusted timing for the 10 seconds of dummy scans (starting at 10 s), or the timing from the log files from Presentation? How much does this timing affect the data? Thanks, Margaret ___ Freesurfer mailing list [EMAIL PROTECTED] https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] FsFast file conversion/preprocessing
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
Re: [Freesurfer] FsFast file conversion/preprocessing
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 ___ Freesurfer mailing list [EMAIL PROTECTED] https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] FsFast file conversion/preprocessing
hi, i am using bshort files. should i try bfloat? thanks, margaret On Thu, 4 Nov 2004, Doug Greve wrote: > > Hi Margaret, > > is the input volume bshort or bfloat? I've never been able to get the > AFNI 3dvolreg to work with floats. Could be my bfloat-AFNI converter. > > doug > > > Margaret Duff wrote: > > > > 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 > > > > ___ > > 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] FsFast file conversion/preprocessing
oh sorry, /space/troy/1/users/FREESURFER/SM2S1_fsfast/func/SM2S1 and i was trying to run it on the bold folder. could it have to do with my matlab startup? i thought i modified it correctly when i started using the program. but as i look back through my command window i see a warning that my startup.m file might be wrong. can you tell me everything that needs to be included in that file? thanks so much, margaret On Mon, 8 Nov 2004, Doug Greve wrote: > > No, bshort should work fine. Can you be more specific as to where the > data are? There are lots of possibilities under /space/troy ... > > doug > > > Margaret Duff wrote: > > > > hi, i am using bshort files. should i try bfloat? thanks, margaret > > > > On > > Thu, 4 Nov 2004, Doug Greve wrote: > > > > > > > > Hi Margaret, > > > > > > is the input volume bshort or bfloat? I've never been able to get the > > > AFNI 3dvolreg to work with floats. Could be my bfloat-AFNI converter. > > > > > > doug > > > > > > > > > Margaret Duff wrote: > > > > > > > > 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 > > > > > > > > ___ > > > > 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
[Freesurfer] fsfast stxgrinder-sess
hello, i was running the stxgrinder-sess command and in the fsfast tutorial manual the results of this command are supposed to be f, fsig, t, sig, minsig, and iminsig. i don't get any t or sig files, and noticed that bert's tutorial data does not have these either. are these files not used anymore? also, does anyone know if where i can find the fsfast manual, not just the tutorial manual? thanks, margaret duff ___ Freesurfer mailing list [EMAIL PROTECTED] https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] wmfill
Hi, I keep getting an error message after I run Create Surface. It is similar to questions found in the archive but those solutions did not work and this problem did not occur for the first 2 brains I reconstructed. I get an alert that the Images (filled): /subjectsdir/mri/filled/COR-001 not found. wmfill first. I thought the first step was to fill the wm so these files should have already been created. Thanks for any help, Margaret ___ Freesurfer mailing list [EMAIL PROTECTED] https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] wmfill
The log file is below. And at the end it says command finished, not that something went wrong. I am not sure about the cutting planes or how to specify them manually. Thanks for your help. Margaret /space/lyon/1/home/inverse/freesurfer_alpha/bin/Linux/mri_fill -lval 255 -rval 80 -ccmask -T 1 -L /space/troy/1/users/FREESURFER/SM2S4_freesurfer/mri/tmp/ponscall.dat /space/troy/1/users/FREESURFER/SM2S4_freesurfer/mri/wm /space/troy/1/users/FREESURFER/SM2S4_freesurfer/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 /space/troy/1/users/FREESURFER/SM2S4_freesurfer/mri/tmp/ponscall.dat... 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; updating initial cc seed to Tal vol (121.00, 151.00, 77.00) TAL (15.27, 0.28, -12.82) Looking for area (min, max) = (350, 1400) area[0] = 365 (min = 350, max = 1400), aspect = 1.27 (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. area[0] = 1210 (min = 350, max = 1400), aspect = 0.37 (min = 0.10, max = 0.75) corpus callosum seed point found at Tal vol: (121, 125, 162) TAL: (15.27, 85.28, 13.18) min_slice = -1, min_area = 65536 Looking for area (min, max) = (350, 1400) area[0] = 5435 (min = 350, max = 1400), aspect = 0.50 (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. area[0] = 488 (min = 350, max = 1400), aspect = 0.26 (min = 0.10, max = 0.75) corpus callosum seed point found at Tal vol: (127, 97, 124) TAL: (9.27, 47.28, 41.18) min_slice = -1, min_area = 65536 /space/lyon/1/home/inverse/freesurfer_alpha/bin/Linux/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 Command Finished On Tue, 30 Nov 2004, Bruce Fischl wrote: > Hi Margaret, > > we need more information than that. Can you send us log files from trying > to run mri_fill? Is it finding the cutting planes? Have you tried > specifying them manually? > > cheers, > Bruce > > On Tue, 30 Nov 2004, Margaret Duff wrote: > > > Hi, I keep getting an error message after I run Create Surface. It is > > similar to questions found in the archive but those solutions did not work > > and this problem did not occur for the first 2 brains I reconstructed. I > > get an alert that the Images (filled): /subjectsdir/mri/filled/COR-001 not > > found. wmfill first. I thought the first step was to fill the wm so > > these files should have already been created. Thanks for any help, > > Margaret > > > > ___ > > 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] wmfill
So, even though it says it will substitute the identity matrix for the transform, I still need a transform or it won't work? Is the only way to create a transform with that separate MNI software? Thanks, Margaret On Wed, 1 Dec 2004, Yasunari Tosa wrote: > Hi, > > The log says that it could not find > $subject/mri/transforms/talairach.xfm for this volume. > > Tosa > > Margaret Duff wrote: > > >The log file is below. And at the end it says command finished, not that > >something went wrong. I am not sure about the cutting planes or how to > >specify them manually. Thanks for your help. Margaret > > > >/space/lyon/1/home/inverse/freesurfer_alpha/bin/Linux/mri_fill -lval 255 > >-rval 80 -ccmask -T 1 -L > >/space/troy/1/users/FREESURFER/SM2S4_freesurfer/mri/tmp/ponscall.dat > >/space/troy/1/users/FREESURFER/SM2S4_freesurfer/mri/wm > >/space/troy/1/users/FREESURFER/SM2S4_freesurfer/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 > >/space/troy/1/users/FREESURFER/SM2S4_freesurfer/mri/tmp/ponscall.dat... > >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; > >updating initial cc seed to Tal vol (121.00, 151.00, 77.00) TAL (15.27, > >0.28, -12.82) > >Looking for area (min, max) = (350, 1400) > >area[0] = 365 (min = 350, max = 1400), aspect = 1.27 (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. > >area[0] = 1210 (min = 350, max = 1400), aspect = 0.37 (min = 0.10, max = > >0.75) > >corpus callosum seed point found at Tal vol: (121, 125, 162) TAL: (15.27, > >85.28, 13.18) > >min_slice = -1, min_area = 65536 > >Looking for area (min, max) = (350, 1400) > >area[0] = 5435 (min = 350, max = 1400), aspect = 0.50 (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. > >area[0] = 488 (min = 350, max = 1400), aspect = 0.26 (min = 0.10, max = > >0.75) > >corpus callosum seed point found at Tal vol: (127, 97, 124) TAL: (9.27, > >47.28, 41.18) > >min_slice = -1, min_area = 65536 > >/space/lyon/1/home/inverse/freesurfer_alpha/bin/Linux/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 > > > >Command Finished > > > > > >On Tue, 30 Nov 2004, Bruce Fischl wrote: > > > > > > > >>Hi Margaret, > >> > >>we need more information than that. Can you send us log files from trying > >>to run mri_fill? Is it finding the cutting planes? Have you tried > >>specifying them manually? > >> > >>cheers, > >>Bruce > >> > >>On Tue, 30 Nov 2004, Margaret Duff wrote: > >> > >> > >> > >>>Hi, I keep getting an error message after I run Create Surface. It is > >>>similar to questions found in the archive but those solutions did not work > >>>and this problem did not occur for the first 2 brains I reconstructed. I > >>>get an alert that the Images (filled): /subjectsdir/mri/filled/COR-001 not > >>>found. wmfill first. I thought the first step was to fill the wm so > >>>these files should have already been created. Thanks for any help, > >>>Margaret > >>> > >>>___ > >>>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 > > > > > > > > > ___ Freesurfer mailing list [EMAIL PROTECTED] https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] wmfill
Hi, I tried to manually set the cutting planes, but I was unable to get the create surface to run. My subjects info is at /space/troy/1/users/FREESURFER/SM2S4_freesurfer and I tried to specify coordinates (121 90 139) for the CC and (131 159 118) for the pons. I used the manuals troubleshooting to guide me, but is still cannot find them. The logfile I got is below. Could something besides specifying these coordinates be going wrong? Thanks, Margaret /space/lyon/1/home/inverse/freesurfer_alpha/bin/Linux/mri_fill -lval 255 -rval 80 -P 131 159 118 -C 121 90 139 -ccmask -T 1 -L /space/troy/1/users/FREESURFER/SM2S4_freesurfer/mri/tmp/ponscall.dat /space/troy/1/users/FREESURFER/SM2S4_freesurfer/mri/wm /space/troy/1/users/FREESURFER/SM2S4_freesurfer/mri/filled using 255 as fill val for left hemisphere. using 80 as fill val for right hemisphere. using Talairach position (131, 159, 118) as pons seed point using Talairach position (121, 90, 139) as corpus callosum seed point not using corpus callosum to mask possible location of pons. logging cutting plane coordinates to /space/troy/1/users/FREESURFER/SM2S4_freesurfer/mri/tmp/ponscall.dat... 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; The seed point (121.00, 90.00, 139.00) is mapped to a voxel (15.27, -0.82. 166.72). Make sure that the seed point is given in talaraich position or use -CV option 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 Using the seed to calculate the cutting plane Verify whether the seed point is inside the volume first Command Finished On Wed, 1 Dec 2004, Bruce Fischl wrote: > Hi Margaret, > > if no talairach.xfm exists, then the fill may still find the cc and pons, > but it might not. You can always specify them manually be finding a > sagittal slice in which the cc is disconnected and a horizontal slice above > the cerebellar peduncles where the pons is disconnected. > > cheers, > Bruce > > On Wed, 1 Dec > 2004, Margaret Duff wrote: > > > The log file is below. And at the end it says command finished, not that > > something went wrong. I am not sure about the cutting planes or how to > > specify them manually. Thanks for your help. Margaret > > > > /space/lyon/1/home/inverse/freesurfer_alpha/bin/Linux/mri_fill -lval 255 > > -rval 80 -ccmask -T 1 -L > > /space/troy/1/users/FREESURFER/SM2S4_freesurfer/mri/tmp/ponscall.dat > > /space/troy/1/users/FREESURFER/SM2S4_freesurfer/mri/wm > > /space/troy/1/users/FREESURFER/SM2S4_freesurfer/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 > > /space/troy/1/users/FREESURFER/SM2S4_freesurfer/mri/tmp/ponscall.dat... > > 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; > > updating initial cc seed to Tal vol (121.00, 151.00, 77.00) TAL (15.27, > > 0.28, -12.82) > > Looking for area (min, max) = (350, 1400) > > area[0] = 365 (min = 350, max = 1400), aspect = 1.27 (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. > > area[0] = 1210 (min = 350, max = 1400), aspect = 0.37 (min = 0.10, max = > > 0.75) > > corpus callosum seed point found at Tal vol: (121, 125, 162) TAL: (15.27, > > 85.28, 13.18) > > min_slice = -1, min_area = 65536 > > Looking for area (min, max) = (350, 1400) > > area[0] = 5435 (min = 350, max = 1400), aspect = 0.50 (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. > > area[0] = 488 (min = 350, max = 1400), aspect = 0.26 (min = 0.10, max = > > 0.75) > > corpus callosum seed point found at Tal vol: (127, 97, 124) TAL: (9.27, > > 47.28, 41.18) > > min_slice = -1, min_area
Re: [Freesurfer] wmfill
hi, just to clarify, running this from the command line will create talairach coordinates or do you need to download the additional mni software? and, is this step included in the process volume command when using the csurf interface? thanks, margaret On Mon, 6 Dec 2004, Yasunari Tosa wrote: > Hi, Margaret > > The head is tilted almost 10 degrees. This makes it difficult to cut > the brain into two. > You really need the talairach transform or any other transform to > straighten up the head to > find the cutting planes. > > I just copied your volume and ran recon-all -stage1 and "mri_fill" > created a very clean filled > volume. > > Tosa > > Margaret Duff wrote: > > >Hi, I tried to manually set the cutting planes, but I was unable to get > >the create surface to run. My subjects info is at > >/space/troy/1/users/FREESURFER/SM2S4_freesurfer and I tried to specify > >coordinates (121 90 139) for the CC and (131 159 118) for the pons. I > >used the manuals troubleshooting to guide me, but is still cannot find > >them. The logfile I got is below. Could something besides > >specifying these coordinates be going wrong? Thanks, Margaret > > > >/space/lyon/1/home/inverse/freesurfer_alpha/bin/Linux/mri_fill -lval 255 > >-rval 80 -P 131 159 118 -C 121 90 139 -ccmask -T 1 -L > >/space/troy/1/users/FREESURFER/SM2S4_freesurfer/mri/tmp/ponscall.dat > >/space/troy/1/users/FREESURFER/SM2S4_freesurfer/mri/wm > >/space/troy/1/users/FREESURFER/SM2S4_freesurfer/mri/filled > >using 255 as fill val for left hemisphere. > >using 80 as fill val for right hemisphere. > >using Talairach position (131, 159, 118) as pons seed point > >using Talairach position (121, 90, 139) as corpus callosum seed point > >not using corpus callosum to mask possible location of pons. > >logging cutting plane coordinates to > >/space/troy/1/users/FREESURFER/SM2S4_freesurfer/mri/tmp/ponscall.dat... > >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; > >The seed point (121.00, 90.00, 139.00) is mapped to a voxel (15.27, -0.82. > >166.72). > >Make sure that the seed point is given in talaraich position or use -CV > >option > >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 > >Using the seed to calculate the cutting plane > >Verify whether the seed point is inside the volume first > > > >Command Finished > > > > > > > > > >On Wed, 1 Dec 2004, > >Bruce Fischl wrote: > > > > > > > >>Hi Margaret, > >> > >>if no talairach.xfm exists, then the fill may still find the cc and pons, > >>but it might not. You can always specify them manually be finding a > >>sagittal slice in which the cc is disconnected and a horizontal slice above > >>the cerebellar peduncles where the pons is disconnected. > >> > >>cheers, > >>Bruce > >> > >>On Wed, 1 Dec > >>2004, Margaret Duff wrote: > >> > >> > >> > >>>The log file is below. And at the end it says command finished, not that > >>>something went wrong. I am not sure about the cutting planes or how to > >>>specify them manually. Thanks for your help. Margaret > >>> > >>>/space/lyon/1/home/inverse/freesurfer_alpha/bin/Linux/mri_fill -lval 255 > >>>-rval 80 -ccmask -T 1 -L > >>>/space/troy/1/users/FREESURFER/SM2S4_freesurfer/mri/tmp/ponscall.dat > >>>/space/troy/1/users/FREESURFER/SM2S4_freesurfer/mri/wm > >>>/space/troy/1/users/FREESURFER/SM2S4_freesurfer/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 > >>>/space/troy/1/users/FREESURFER/SM2S4_freesurfer/mri/tmp/ponscall.dat... > >>>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; > >>>updating initial cc seed to Tal vol (121.00, 151.00, 77.00) TAL (15.27, > >>>0.28, -12.82) > >>>Looking for area
Re: [Freesurfer] wmfill
in the manual it says if the talairach coordinates are not available, enter the x,y,z locations from the volume index in the cursor area. is this not true anymore? thanks, margaret On Mon, 6 Dec 2004, Bruce Fischl wrote: > Hi Margaret, > > the points need to be specified in talairach coords - it looks like you > are using voxels coords. > > Bruce > > On Mon, 6 Dec 2004, Margaret Duff wrote: > > > Hi, I tried to manually set the cutting planes, but I was unable to get > > the create surface to run. My subjects info is at > > /space/troy/1/users/FREESURFER/SM2S4_freesurfer and I tried to specify > > coordinates (121 90 139) for the CC and (131 159 118) for the pons. I > > used the manuals troubleshooting to guide me, but is still cannot find > > them. The logfile I got is below. Could something besides > > specifying these coordinates be going wrong? Thanks, Margaret > > > > /space/lyon/1/home/inverse/freesurfer_alpha/bin/Linux/mri_fill -lval 255 > > -rval 80 -P 131 159 118 -C 121 90 139 -ccmask -T 1 -L > > /space/troy/1/users/FREESURFER/SM2S4_freesurfer/mri/tmp/ponscall.dat > > /space/troy/1/users/FREESURFER/SM2S4_freesurfer/mri/wm > > /space/troy/1/users/FREESURFER/SM2S4_freesurfer/mri/filled > > using 255 as fill val for left hemisphere. > > using 80 as fill val for right hemisphere. > > using Talairach position (131, 159, 118) as pons seed point > > using Talairach position (121, 90, 139) as corpus callosum seed point > > not using corpus callosum to mask possible location of pons. > > logging cutting plane coordinates to > > /space/troy/1/users/FREESURFER/SM2S4_freesurfer/mri/tmp/ponscall.dat... > > 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; > > The seed point (121.00, 90.00, 139.00) is mapped to a voxel (15.27, -0.82. > > 166.72). > > Make sure that the seed point is given in talaraich position or use -CV > > option > > 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 > > Using the seed to calculate the cutting plane > > Verify whether the seed point is inside the volume first > > > > Command Finished > > > > > > > > > > On Wed, 1 Dec 2004, > > Bruce Fischl wrote: > > > >> Hi Margaret, > >> > >> if no talairach.xfm exists, then the fill may still find the cc and pons, > >> but it might not. You can always specify them manually be finding a > >> sagittal slice in which the cc is disconnected and a horizontal slice above > >> the cerebellar peduncles where the pons is disconnected. > >> > >> cheers, > >> Bruce > >> > >> On Wed, 1 Dec > >> 2004, Margaret Duff wrote: > >> > >>> The log file is below. And at the end it says command finished, not that > >>> something went wrong. I am not sure about the cutting planes or how to > >>> specify them manually. Thanks for your help. Margaret > >>> > >>> /space/lyon/1/home/inverse/freesurfer_alpha/bin/Linux/mri_fill -lval 255 > >>> -rval 80 -ccmask -T 1 -L > >>> /space/troy/1/users/FREESURFER/SM2S4_freesurfer/mri/tmp/ponscall.dat > >>> /space/troy/1/users/FREESURFER/SM2S4_freesurfer/mri/wm > >>> /space/troy/1/users/FREESURFER/SM2S4_freesurfer/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 > >>> /space/troy/1/users/FREESURFER/SM2S4_freesurfer/mri/tmp/ponscall.dat... > >>> 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; > >>> updating initial cc seed to Tal vol (121.00, 151.00, 77.00) TAL (15.27, > >>> 0.28, -12.82) > >>> Looking for area (min, max) = (350, 1400) > >>> area[0] = 365 (min = 350, max = 1400), aspect = 1.27 (min = 0.10, max = > >>> 0.75) > >>> need search nearby > >>> using +/- offset search region where offset is 3. > >>> using +/- offset search region where
Re: [Freesurfer] wmfill error
i had this problem recently. try using recon-all -stage one in a terminal window instead of process volume in csurf. or specify the corpus collosum and pons in the WMFill tab under Preferences->Expert Preferences in csurf. it probably cant find where to segment. you might want to check the archives for more detail on this problem. hope this helps, margaret On Wed, 22 Dec 2004, Joongnam Yang wrote: > Hi all, > > During "create surface" on csurf, > right after "fill white matter" is done, as soon as "tesselate RH white > matter" starts, > an error message comes up, which is > > images filled: > somedirectory/mri/filled/COR-001...not found, wmfill first. > > I checked the directory of /mri/filled, which did not have COR-00* files. > There was only one file, COR-.info. > It seems that the first process in "create surface" (fill white matter) is > supposed to create all those COR-00* files in the /mri/filled, but none is > created. > I changed permission on the directory, to no avail. > Would someone suggest something? > > 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] wmfill error
check out the free surfer manual, around page 31. they show pictures and an example. use talairach or volume scanner coordinates to specify them, not volume index as it might say in the manual. margaret On Thu, 23 Dec 2004, Joongnam Yang wrote: > Thanks Margaret, > > Is there a reference on how to specify the corpus collosum and pons in the > WMFill under Preferences->Expert Preferences in csurf? > > Nam. > > >>> Margaret Duff <[EMAIL PROTECTED]> 12/22/04 12:10 PM >>> > i had this problem recently. try using recon-all -stage one in a terminal > window instead of process volume in csurf. or specify the corpus collosum > and pons in the WMFill tab under Preferences->Expert Preferences in csurf. > it probably cant find where to segment. you might want to check the > archives for more detail on this problem. hope this helps, margaret > > > On Wed, 22 Dec > 2004, Joongnam Yang wrote: > > > Hi all, > > > > During "create surface" on csurf, > > right after "fill white matter" is done, as soon as "tesselate RH white > > matter" starts, > > an error message comes up, which is > > > > images filled: > > somedirectory/mri/filled/COR-001...not found, wmfill first. > > > > I checked the directory of /mri/filled, which did not have COR-00* files. > > There was only one file, COR-.info. > > It seems that the first process in "create surface" (fill white matter) is > > supposed to create all those COR-00* files in the /mri/filled, but none is > > created. > > I changed permission on the directory, to no avail. > > Would someone suggest something? > > > > 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
[Freesurfer] recon-all exiting with errors
Hello, I am trying to run recon-all but it seems to have some problems during nu_correct. I am using the command recon-all -subjid SM2C1tal -stage1, my subjectsdir is /space/troy/1/users/FREESURFER, and I am getting the error, Can't locate MNI/Startup.pm in @INC. then it says all the stuff @INC does contain, the says at /space/lyon/9/pubsw/Linux2/packages/mni/current/bin/nu_correct line 38. BEGIN failed--compilation aborted at /space/lyon/9/pubsw/Linux2/packages/mni/current/bin/nu_correct line 38. ERROR: nu_correct Does this have to do with the FS software or my settings or usage? Thanks, Margaret ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] Preproc-sess failed during smoothing
Hi, I was trying to preprocess some functional data using the command
preproc-sess -fwhm 6 -sf sessid -df sesspar. My subjects study directory
is located at /space/troy/1/users/FREESURFER/SM2C2_fsfast/study. The
command made it through motion correction, then during smoothing gave me
this error:
ERROR:: Environment variable FSLOUTPUTTYPE is not set!
Please make sure that the appropriate configuration file is sourced by
your shell (e.g. by putting it in .profile).
e.g. bash or sh users add the line ". ${FSLDIR}/etc/fslconf/fsl.sh"
e.g. tcsh or csh users add the line "source ${FSLDIR}/etc/fslconf/fsl.csh"
/tmp/ipfsl_23657
/space/lyon/1/home/inverse/freesurfer_alpha/fsl/bin/ip fmc fmcsm .1 -s
2.54237288135593220338
ERROR: ip failed
ERROR: ipfsl failed
ERROR: spatialsmooth-sess failed
I have never received this error before and am not sure if I should just
set the env. variable or where the .profile is. What is the recommended
course of action and is there any reason I got this error now, and never
before? Thanks! Margaret
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] averaging brains over two sessions
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
Re: [Freesurfer] averaging brains over two sessions
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
Hi, Both images are from here on the old bay 2 scanner, they just occurred 1 month apart. Could you describe a little for me how to use mri_motion_correct and how it differs from setup structural scans in csurf? I checked the wiki, but it did not have tons of info. Also, what are the major differences in using only one scan as opposed to two for the reconstruction? Thanks for your help, Margaret On Wed, 2 Feb 2005, Bruce Fischl wrote: > Hi Margaret, > > what are you using to align them? If they are from different sites, then > they may not be possible to really align, due to differences in shims, > read-out directions and bandwidth. Reconning with a single image is > certainly doable (we've done hundreds), but is more labor intensive. > > cheers, > Bruce > > 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] Volume /tmp/mritotal_5659/nu_8_dxyz.mnc cannot be found.
Hi, During running recon-all, I get this line INFO: Volume /tmp/mritotal_5659/nu_8_dxyz.mnc cannot be found. I looked in my /tmp folder and I have a mritotal_7563 folder but no mritotal_5659 folder. Will this affect my recon-all processing? This error also appears in my orig.euler files. I am running the line recon-all-nmr -stage3 -stage4a -stage4b -subjid t217c, my subjects directory is /space/troy/2/users/garysdata, and i am running this on the computer troy. Thanks, Margaret ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] -notalairach option not working
Hello, I am running the line recon-all-nmr -notalairach -stage1 -stage2 -subjid SM2C3 from SUBJECTS_DIR /space/troy/users/2/mikesfolder and in the std-env. The recon-all-nmr program is still creating a bad talairach transform that overwrites the good one I just made. So, the recon-all-nmr keeps exiting with errors because of the bad talairach. Is -notalairach still the correct option for not creating a transform during this step? Thanks, Margaret ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] ERROR: nu_correct
Hi, I have just recently gotten an error when running recon-all-nmr. I am on the computer troy and my command line is recon-all-nmr -stage1 -subjid SM2S2 and my SUBJECTS_DIR is /space/troy/1/users/FREESURFER. I tried resetting my LANG to C and en_US and neither made a difference. It seems like it can't find a start up file, which I found in /usr/lib/perl5/5.8.5/MNI, but this doesn't seem to be one of the paths its looking in. Is there anything I can do to prevent this error? I have attached the error file from the terminal window below. Thanks, Margaret (nmr-std-env) recon-all-nmr -stage1 -subjid SM2S2 program versions used $Id: recon-all-nmr,v 1.53 2004/12/08 20:45:06 greve Exp $ $Id: mri_motion_correct2,v 1.9 2004/12/14 03:37:42 greve Exp $ mri_convert --version stable2 minctracc.c $Id: talairach2,v 1.7 2004/08/31 18:07:37 tosa Exp $ mri_convert --version stable2 # $Id: mritotal.in,v 1.12 2004/02/12 05:55:18 rotor Exp $ # $Id: nu_estimate.in,v 1.1 2003/04/16 14:29:34 bert Exp $ stable2 stable2 stable2 stable2 stable2 stable2 stable2 stable2 stable2 stable2 stable2 stable2 stable2 stable2 stable2 stable2 ### INFO: SUBJECTS_DIR is /autofs/space/troy_001/users/FREESURFER WARNING: current FREESURFER_HOME does not match that of previous processing. Current: /usr/local/freesurfer/beta Previous: /usr/local/freesurfer/dev - MotionCor Fri Jun 17 16:16:50 EDT 2005 /autofs/space/troy_001/users/FREESURFER/SM2S2/mri/orig mri_motion_correct2 -o . -i 001 -i 002 tmpdir is ./tmp-mri_motion_correct2-27002 -- mri_motion_correct2 logfile is ./mri_motion_correct2.log -- - Converting 001 Fri Jun 17 16:16:54 EDT 2005 mri_convert 001 /autofs/space/troy_001/users/FREESURFER/SM2S2/mri/orig/tmp-mri_motion_correct2-27002/cor-1.mnc ^[[B^[[A^[[B^[[B^[[B^[[Breading from 001... TR=273.00, 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 /autofs/space/troy_001/users/FREESURFER/SM2S2/mri/orig/tmp-mri_motion_correct2-27002/cor-1.mnc... - Converting 002 Fri Jun 17 16:17:06 EDT 2005 mri_convert 002 /autofs/space/troy_001/users/FREESURFER/SM2S2/mri/orig/tmp-mri_motion_correct2-27002/cor-2.mnc reading from 002... TR=273.00, 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 /autofs/space/troy_001/users/FREESURFER/SM2S2/mri/orig/tmp-mri_motion_correct2-27002/cor-2.mnc... - Motion Correcting /autofs/space/troy_001/users/FREESURFER/SM2S2/mri/orig/tmp-mri_motion_correct2-27002/cor-2.mnc Fri Jun 17 16:17:17 EDT 2005 COG of v1: 4.496311 15.253652 -23.867643 COG of v2: 4.493972 15.296473 -24.011532 [trans] = -0.002339 0.042821 -0.143888 Initial objective function val = 0.01666989 Final objective function value = 0.01148322 successful write - Resampling /autofs/space/troy_001/users/FREESURFER/SM2S2/mri/orig/tmp-mri_motion_correct2-27002/cor-2.mnc Fri Jun 17 16:18:21 EDT 2005 Transforming slices:Done - Averaging Fri Jun 17 16:18:27 EDT 2005 Processing:Done - Converting Average to output Fri Jun 17 16:18:32 EDT 2005 mri_convert /autofs/space/troy_001/users/FREESURFER/SM2S2/mri/orig/tmp-mri_motion_correct2-27002/avgvol.mnc . -tr 2.73e+06 -te 0 -TI 0 -flip_angle 0 reading from /autofs/space/troy_001/users/FREESURFER/SM2S2/mri/orig/tmp-mri_motion_correct2-27002/avgvol.mnc... 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) Original Data has (1, 1, 1) mm size and (256, 256, 256) voxels. Data is conformed to 1 mm size and 256 voxels for all directions writing to Started at: Fri Jun 17 16:16:54 EDT 2005 Ended at: Fri Jun 17 16:18:41 EDT 2005 mri_motion_correct2: done - Nu Intensity Correction Fri Jun 17 16:18:41 EDT 2005 mri_convert orig nu0.mnc mri_convert orig nu0.mnc reading from orig... TR=273.00, 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 nu0.mnc...
Re: [Freesurfer] ERROR: nu_correct
ok, it is working now. thanks! margaret On Fri, 17 Jun 2005, Nick Schmansky wrote: Try it now. I have recently rebuilt the MINC toolkit, but it seems I overlooked its dependencies, and just now reverted the path back to where it was (and will leave it that way). Sorry for the hassle. On Fri, 2005-06-17 at 16:32 -0400, Margaret Duff wrote: Hi, I have just recently gotten an error when running recon-all-nmr. I am on the computer troy and my command line is recon-all-nmr -stage1 -subjid SM2S2 and my SUBJECTS_DIR is /space/troy/1/users/FREESURFER. I tried resetting my LANG to C and en_US and neither made a difference. It seems like it can't find a start up file, which I found in /usr/lib/perl5/5.8.5/MNI, but this doesn't seem to be one of the paths its looking in. Is there anything I can do to prevent this error? I have attached the error file from the terminal window below. Thanks, Margaret (nmr-std-env) recon-all-nmr -stage1 -subjid SM2S2 program versions used $Id: recon-all-nmr,v 1.53 2004/12/08 20:45:06 greve Exp $ $Id: mri_motion_correct2,v 1.9 2004/12/14 03:37:42 greve Exp $ mri_convert --version stable2 minctracc.c $Id: talairach2,v 1.7 2004/08/31 18:07:37 tosa Exp $ mri_convert --version stable2 # $Id: mritotal.in,v 1.12 2004/02/12 05:55:18 rotor Exp $ # $Id: nu_estimate.in,v 1.1 2003/04/16 14:29:34 bert Exp $ stable2 stable2 stable2 stable2 stable2 stable2 stable2 stable2 stable2 stable2 stable2 stable2 stable2 stable2 stable2 stable2 ### INFO: SUBJECTS_DIR is /autofs/space/troy_001/users/FREESURFER WARNING: current FREESURFER_HOME does not match that of previous processing. Current: /usr/local/freesurfer/beta Previous: /usr/local/freesurfer/dev - MotionCor Fri Jun 17 16:16:50 EDT 2005 /autofs/space/troy_001/users/FREESURFER/SM2S2/mri/orig mri_motion_correct2 -o . -i 001 -i 002 tmpdir is ./tmp-mri_motion_correct2-27002 -- mri_motion_correct2 logfile is ./mri_motion_correct2.log -- - Converting 001 Fri Jun 17 16:16:54 EDT 2005 mri_convert 001 /autofs/space/troy_001/users/FREESURFER/SM2S2/mri/orig/tmp-mri_motion_correct2-27002/cor-1.mnc ^[[B^[[A^[[B^[[B^[[B^[[Breading from 001... TR=273.00, 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 /autofs/space/troy_001/users/FREESURFER/SM2S2/mri/orig/tmp-mri_motion_correct2-27002/cor-1.mnc... - Converting 002 Fri Jun 17 16:17:06 EDT 2005 mri_convert 002 /autofs/space/troy_001/users/FREESURFER/SM2S2/mri/orig/tmp-mri_motion_correct2-27002/cor-2.mnc reading from 002... TR=273.00, 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 /autofs/space/troy_001/users/FREESURFER/SM2S2/mri/orig/tmp-mri_motion_correct2-27002/cor-2.mnc... - Motion Correcting /autofs/space/troy_001/users/FREESURFER/SM2S2/mri/orig/tmp-mri_motion_correct2-27002/cor-2.mnc Fri Jun 17 16:17:17 EDT 2005 COG of v1: 4.496311 15.253652 -23.867643 COG of v2: 4.493972 15.296473 -24.011532 [trans] = -0.002339 0.042821 -0.143888 Initial objective function val = 0.01666989 Final objective function value = 0.01148322 successful write - Resampling /autofs/space/troy_001/users/FREESURFER/SM2S2/mri/orig/tmp-mri_motion_correct2-27002/cor-2.mnc Fri Jun 17 16:18:21 EDT 2005 Transforming slices:Done - Averaging Fri Jun 17 16:18:27 EDT 2005 Processing:Done - Converting Average to output Fri Jun 17 16:18:32 EDT 2005 mri_convert /autofs/space/troy_001/users/FREESURFER/SM2S2/mri/orig/tmp-mri_motion_correct2-27002/avgvol.mnc . -tr 2.73e+06 -te 0 -TI 0 -flip_angle 0 reading from /autofs/space/troy_001/users/FREESURFER/SM2S2/mri/orig/tmp-mri_motion_correct2-27002/avgvol.mnc... 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) Original Data has (1, 1, 1) mm size and (256, 256, 256) voxels. Data is conformed to 1 mm size and 256 voxels for all directions writing to Started at: Fri Jun 17 16:16:54 EDT 2005 Ended at: Fri Jun 17 16
Re: [Freesurfer] defining labels
You have to use the aparc.annot file that is in your label folder in your subjects folder. That would be $SUBJECTS_DIR/subjid/label. It is made during recon-all-nmr -stage4b. Hope this helps, margaret On Thu, 23 Jun 2005, Kirk, Gregory wrote: Hello, I remember a message from Bruce to use mris_anotomical_stats -l label to generate statistics for a region, but unfortunatly I cannot find how to define a label, docs do not seem to tell, a quick start tip please. G. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] defining labels
oh sorry, i was think of the -a file. not sure about the label file. margaret On Thu, 23 Jun 2005, Margaret Duff wrote: You have to use the aparc.annot file that is in your label folder in your subjects folder. That would be $SUBJECTS_DIR/subjid/label. It is made during recon-all-nmr -stage4b. Hope this helps, margaret On Thu, 23 Jun 2005, Kirk, Gregory wrote: Hello, I remember a message from Bruce to use mris_anotomical_stats -l label to generate statistics for a region, but unfortunatly I cannot find how to define a label, docs do not seem to tell, a quick start tip please. G. ___ 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] segmentation fault during mri_convert
Hi, Is mri_convert setup yet to convert to mgz format? I have been trying it in both the std and dev environment from dicom format and spm format and i keep getting a segmentation fault. it still converts to cor format fine but i thought we were trying to get away from that. i dont know exactly whats causing it, but here is my command line and the running information. troy:mduff[84] mri_convert -ot mgz -it dicom 33749275 $SUBJECTS_DIR/SM2C1_autoreconall/mri/orig/002 mri_convert -ot mgz -it dicom 33749275 /space/troy/1/users/FREESURFER/SM2C1_autoreconall/mri/orig/002 reading from 33749275... Getting Series No Scanning Directory INFO: Found 131 files in /autofs/space/troy_002/users/fmridata/sm2c1_041118/3danat/dicom/028 INFO: Scanning for Series Number 28 INFO: found 128 files in series INFO: loading series header info. INFO: sorting. RunNo = 27 INFO: (256 256 128), nframes = 1, ismosaic=0 FileName /autofs/space/troy_002/users/fmridata/sm2c1_041118/3danat/dicom/028/33747925 Identification NumarisVersyngo MR 2004V 4VB11D ScannerModel Avanto PatientName sm2c1 Date and time StudyDate 20041118 StudyTime 180537.015000 SeriesTime190942.968000 AcqTime 190056.292500 Acquisition parameters PulseSeq tfl3d1_ns Protocol T1_MPRAGE_sag PhEncDir ROW EchoNo0 FlipAngle 7 EchoTime 3.31 InversionTime 1000 RepetitionTime2730 PhEncFOV 256 ReadoutFOV256 Image information RunNo 27 SeriesNo 28 ImageNo 1 NImageRows256 NImageCols256 NFrames 1 SliceArraylSize 1 IsMosaic 0 ImgPos 71.7733 130.0894 131.5385 VolRes 1. 1. 1.3300 VolDim256 256 128 Vc 0.1238 -0.9687 -0.2150 Vr -0.0454 0.2110 -0.9764 Vs -0.9913 -0.1306 0.0178 VolCenter -2.5670 21.9742 -19.4516 TransferSyntaxUID 1.2.840.10008.1.2.1 INFO: no Siemens slice order reversal detected (good!). 128 DICOM 3.0 files in list Found 128 DICOM Files WARNING: NumberOfFrames 0 != Found Count of slices 128. reading DICOM image... - DICOM meta-header file name /autofs/space/troy_002/users/fmridata/sm2c1_041118/3danat/dicom/028/33747925 Date and time study date 20041118 study time 180537.015000 series time 190942.968000 acquisition time190942.968000 Identification patient namesm2c1 manufacturerSIEMENS Dimensions number of rows 256 number of columns 256 number of frames128 pixel width 1 pixel height1 slice thickness 1.33 field of view 256 image number1 (might be not reliable) transfer syntax UID 1.2.840.10008.1.2.1 Acquisition parameters echo time 3.31 repetition time 2730 inversion time 1000 echo number 0 flip angle 0.122173 bits allocated 16 Spatial information first image position-71.7733 -130.089 131.539 last image position 95.662 -108.024 134.554 image orientation -0.123794 0.968728 -0.215038 0.0453834 -0.210951 -0.976442 - TR=2730.00, TE=3.31, TI=1000.00, flip angle=7.00 i_ras = (0.123794, -0.968728, -0.215038) j_ras = (-0.0453834, 0.210951, -0.976442) k_ras = (-0.99127, -0.130637, 0.0178497) writing to /space/troy/1/users/FREESURFER/SM2C1_autoreconall/mri/orig/002... Segmentation fault i saw a couple other problems on the list but nothing exactly like this. thanks for the help. margaret ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] segmentation fault during mri_convert
yes, this worked. thanks so much, margaret On Fri, 19 Aug 2005, Nick Schmansky wrote: Margaret, The specified output filename needs to have .mgz at the end. In your case, it would be: $SUBJECTS_DIR/SM2C1_autoreconall/mri/orig/002.mgz I noticed that $SUBJECTS_DIR/SM2C1_autoreconall/mri/orig/002 is a directory, which might be the source of the segfault (which, of course, shouldn't happen, and I will investigate this). So adding .mgz to your output file should work (I just tried it myself with your specified dicom file and it worked). Nick On Fri, 2005-08-19 at 12:42 -0400, Margaret Duff wrote: Hi, Is mri_convert setup yet to convert to mgz format? I have been trying it in both the std and dev environment from dicom format and spm format and i keep getting a segmentation fault. it still converts to cor format fine but i thought we were trying to get away from that. i dont know exactly whats causing it, but here is my command line and the running information. troy:mduff[84] mri_convert -ot mgz -it dicom 33749275 $SUBJECTS_DIR/SM2C1_autoreconall/mri/orig/002 mri_convert -ot mgz -it dicom 33749275 /space/troy/1/users/FREESURFER/SM2C1_autoreconall/mri/orig/002 reading from 33749275... Getting Series No Scanning Directory INFO: Found 131 files in /autofs/space/troy_002/users/fmridata/sm2c1_041118/3danat/dicom/028 INFO: Scanning for Series Number 28 INFO: found 128 files in series INFO: loading series header info. INFO: sorting. RunNo = 27 INFO: (256 256 128), nframes = 1, ismosaic=0 FileName /autofs/space/troy_002/users/fmridata/sm2c1_041118/3danat/dicom/028/33747925 Identification NumarisVersyngo MR 2004V 4VB11D ScannerModel Avanto PatientName sm2c1 Date and time StudyDate 20041118 StudyTime 180537.015000 SeriesTime190942.968000 AcqTime 190056.292500 Acquisition parameters PulseSeq tfl3d1_ns Protocol T1_MPRAGE_sag PhEncDir ROW EchoNo0 FlipAngle 7 EchoTime 3.31 InversionTime 1000 RepetitionTime2730 PhEncFOV 256 ReadoutFOV256 Image information RunNo 27 SeriesNo 28 ImageNo 1 NImageRows256 NImageCols256 NFrames 1 SliceArraylSize 1 IsMosaic 0 ImgPos 71.7733 130.0894 131.5385 VolRes 1. 1. 1.3300 VolDim256 256 128 Vc 0.1238 -0.9687 -0.2150 Vr -0.0454 0.2110 -0.9764 Vs -0.9913 -0.1306 0.0178 VolCenter -2.5670 21.9742 -19.4516 TransferSyntaxUID 1.2.840.10008.1.2.1 INFO: no Siemens slice order reversal detected (good!). 128 DICOM 3.0 files in list Found 128 DICOM Files WARNING: NumberOfFrames 0 != Found Count of slices 128. reading DICOM image... - DICOM meta-header file name /autofs/space/troy_002/users/fmridata/sm2c1_041118/3danat/dicom/028/33747925 Date and time study date 20041118 study time 180537.015000 series time 190942.968000 acquisition time190942.968000 Identification patient namesm2c1 manufacturerSIEMENS Dimensions number of rows 256 number of columns 256 number of frames128 pixel width 1 pixel height1 slice thickness 1.33 field of view 256 image number1 (might be not reliable) transfer syntax UID 1.2.840.10008.1.2.1 Acquisition parameters echo time 3.31 repetition time 2730 inversion time 1000 echo number 0 flip angle 0.122173 bits allocated 16 Spatial information first image position-71.7733 -130.089 131.539 last image position 95.662 -108.024 134.554 image orientation -0.123794 0.968728 -0.215038 0.0453834 -0.210951 -0.976442 - TR=2730.00, TE=3.31, TI=1000.00, flip angle=7.00 i_ras = (0.123794, -0.968728, -0.215038) j_ras = (-0.0453834, 0.210951, -0.976442) k_ras = (-0.99127, -0.130637, 0.0178497) writing to /space/troy/1/users/FREESURFER/SM2C1_autoreconall/mri/orig/002... Segmentation fault i saw a couple other problems on the list but nothing exactly like this. thanks for the help. margaret ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/lis
[Freesurfer] ERROR:nu_correct
Hello, I am running the command: recon-all -subjid SM2S12_autoreconall -autorecon1 -notalairach on troy and getting the following error message: - Nu Intensity Correction Thu Aug 25 12:11:42 EDT 2005 mri_convert orig.mgz nu0.mnc mri_convert orig.mgz nu0.mnc reading from orig.mgz... TR=2730.00, TE=3.31, TI=1000.00, flip angle=7.00 i_ras = (-1, -1.01845e-10, -1.20596e-09) j_ras = (-1.65567e-09, 6.42749e-09, -1) k_ras = (-2.65927e-10, 1, 9.43205e-09) writing to nu0.mnc... nu_correct -clobber nu0.mnc nu1.mnc [EMAIL PROTECTED]:/autofs/space/troy_001/users/FREESURFER/SM2S12_autoreconall/mri/] [2005-08-25 12:11:52] running: /usr/pubsw/packages/mni/current/bin/nu_estimate_np_and_em -parzen -log -sharpen 0.15 0.01 -iterations 50 -stop 0.001 -shrink 4 -auto_mask -nonotify -b_spline 1 -distance 200 -quiet -execute -clobber -nokeeptmp -tmpdir /usr/tmp/nu_correct_27529/ nu0.mnc nu1.imp /usr/pubsw/packages/mni/current/bin/volume_stats: error while loading shared libraries: libstdc++.so.6: cannot open shared object file: No such file or directory nu_estimate_np_and_em: crashed while running volume_stats (termination status=32512) nu_correct: crashed while running nu_estimate_np_and_em (termination status=32512) ERROR: nu_correct recon-all exited with errors at Thu Aug 25 12:11:53 EDT 2005 This command was working yesterday, so I am not sure what has changed over night. Thanks for your help, Margaret ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] ERROR:nu_correct
hi, it seems to be working now. at least its getting further than it was before. thanks! margaret On Thu, 25 Aug 2005, Nick Schmansky wrote: Margaret, The volume_stats tool should work for you now. The reason for the difference is that the MNI tools were upgraded to a newer version (to v1.4, from 1.0.4), and I hadn't fully tested against all the binary/platform/machine dependencies, which can be quite complicated and exasperating! Let me know how things work. Sorry for the delay. Nick On Thu, 2005-08-25 at 12:14 -0400, Margaret Duff wrote: Hello, I am running the command: recon-all -subjid SM2S12_autoreconall -autorecon1 -notalairach on troy and getting the following error message: - Nu Intensity Correction Thu Aug 25 12:11:42 EDT 2005 mri_convert orig.mgz nu0.mnc mri_convert orig.mgz nu0.mnc reading from orig.mgz... TR=2730.00, TE=3.31, TI=1000.00, flip angle=7.00 i_ras = (-1, -1.01845e-10, -1.20596e-09) j_ras = (-1.65567e-09, 6.42749e-09, -1) k_ras = (-2.65927e-10, 1, 9.43205e-09) writing to nu0.mnc... nu_correct -clobber nu0.mnc nu1.mnc [EMAIL PROTECTED]:/autofs/space/troy_001/users/FREESURFER/SM2S12_autoreconall/mri/] [2005-08-25 12:11:52] running: /usr/pubsw/packages/mni/current/bin/nu_estimate_np_and_em -parzen -log -sharpen 0.15 0.01 -iterations 50 -stop 0.001 -shrink 4 -auto_mask -nonotify -b_spline 1 -distance 200 -quiet -execute -clobber -nokeeptmp -tmpdir /usr/tmp/nu_correct_27529/ nu0.mnc nu1.imp /usr/pubsw/packages/mni/current/bin/volume_stats: error while loading shared libraries: libstdc++.so.6: cannot open shared object file: No such file or directory nu_estimate_np_and_em: crashed while running volume_stats (termination status=32512) nu_correct: crashed while running nu_estimate_np_and_em (termination status=32512) ERROR: nu_correct recon-all exited with errors at Thu Aug 25 12:11:53 EDT 2005 This command was working yesterday, so I am not sure what has changed over night. Thanks for your help, 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] mris_euler_number
Hi, I am running the command recon-all -subjid SM2C4_autoreconall -autorecon2 on troy, with subjects directory being /space/troy/1/users/FREESURFER. I just got this error message, which I have never gotten before: - Euler Number rh Fri Sep 9 02:03:07 EDT 2005 /autofs/space/troy_001/users/FREESURFER/SM2C4_autoreconall /autofs/space/troy_001/users/FREESURFER/SM2C4_autoreconall/scripts /autofs/space/troy_001/users/FREESURFER/SM2C4_autoreconall/scripts /autofs/space/troy_001/users/FREESURFER/SM2C4_autoreconall/scripts /autofs/space/troy_001/users/FREESURFER/SM2C4_autoreconall/scripts /autofs/space/troy_001/users/FREESURFER/SM2C4_autoreconall/scripts /autofs/space/troy_001/users/FREESURFER/SM2C4_autoreconall/mri /autofs/space/troy_001/users/FREESURFER/SM2C4_autoreconall/scripts /autofs/space/troy_001/users/FREESURFER/SM2C4_autoreconall/scripts /autofs/space/troy_001/users/FREESURFER/SM2C4_autoreconall/scripts /autofs/space/troy_001/users/FREESURFER/SM2C4_autoreconall /autofs/space/troy_001/users/FREESURFER/SM2C4_autoreconall/scripts /autofs/space/troy_001/users/FREESURFER/SM2C4_autoreconall/scripts /autofs/space/troy_001/users/FREESURFER/SM2C4_autoreconall/scripts /autofs/space/troy_001/users/FREESURFER/SM2C4_autoreconall/scripts /autofs/space/troy_001/users/FREESURFER/SM2C4_autoreconall/scripts /autofs/space/troy_001/users/FREESURFER/SM2C4_autoreconall/mri /autofs/space/troy_001/users/FREESURFER/SM2C4_autoreconall/mri /autofs/space/troy_001/users/FREESURFER/SM2C4_autoreconall/mri /autofs/space/troy_001/users/FREESURFER/SM2C4_autoreconall/mri /autofs/space/troy_001/users/FREESURFER/SM2C4_autoreconall /autofs/space/troy_001/users/FREESURFER/SM2C4_autoreconall/mri /autofs/space/troy_001/users/FREESURFER/SM2C4_autoreconall/mri /autofs/space/troy_001/users/FREESURFER/SM2C4_autoreconall/mri /autofs/space/troy_001/users/FREESURFER/SM2C4_autoreconall/mri /autofs/space/troy_001/users/FREESURFER/SM2C4_autoreconall /autofs/space/troy_001/users/FREESURFER/SM2C4_autoreconall mris_euler_number /autofs/space/troy_001/users/FREESURFER/SM2C4_autoreconall/surf/rh.orig mris_euler_number: Command not found. ERROR: mris_euler_number exited with non-zero status Linux troy 2.6.6-1.436.2.3smp #1 SMP Fri Jul 9 15:27:18 EDT 2004 i686 i686 i386 GNU/Linux recon-all exited with errors at Fri Sep 9 02:03:08 EDT 2005 Why is the command all of a sudden not found? Thanks, Margaret ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] slight head wrapping using tkregister2
Hi, When I am looking at a brain using tkregister2 to see how well the talairach lines up, it seems like the brain is leaving the viewing window and gets cut off. This is especially apparent using the sagittal view and additionally, a white rounded blob(maybe the nose) appears behind the brain. However, when looking at the brain using tkmedit, all the slices are present and the brain looks centered and not cut off. Will how the brain looks in tkregister2 affect any subsequent analyses? My subjects dir is /space/troy/1/users/FREESURFER and the command i am using is tkregister2 --s SM2S4_autoreconall --fstal. The only thing funny I noticed was the tal transform had a 71 for one of the translation directions where mine usually dont go that high. Thanks, Margaret ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
