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skull-stripping hi-res monkey data
by florent segonne 16 Jun '05

16 Jun '05

Hello, mri_watershed was specifically designed for the skull-stripping of human brain data. Not surprisingly, it might fail on hi-res monkey data. However, here is a short watershed trouble shooting guide that might help you find a valid set of options to successfully skull-strip your images. Good Luck, Best, Florent ----------------------------------------------------------- WATERSHED TROUBLESHOUTING GUIDE: I am putting below some suggestions about how to find the correct set of parameters without spending too much time on it. I think that there are sufficient options to get a correct skull-stripping on almost every sca ns. Before getting into the details, you have to know that mri_watershed is a pipelined process, composed of two main steps. The first one ends with the first template smoothing and is composed of 3 substeps (watershed segmentation, post-processing and first template smoothing). The second step corresponds to a fine template deformation. HOW TO PROCEED TO OBTAIN A VALID SKULL-STRIPPING (when it fails with the default options): * If the skull-stripping fails, my first suggestion is to try to understand why it is failling. Rerun the mri_watershed program with the -surf_debug option, which writes out two surfaces into the output volume (first template smoothing and fine template deformation). V * Looking at the output, there are two possibilities: either the first step fails (this corresponds to the first template smoothing, which is the exterior surface into the output volume), or the second step fails (the fine template deformation = the interior surface). Let's analyze the two cases separately: 1) Failing of the first segmentation step. This first step is the result of 3 pipelined sub-steps: watershed segmentation, post-processing and first template smoothing. In order to fix the problem, there are a few choices about how to proceed. 1-1) "I-am-feeling-lucky" choice: you might want to go down this path, if the skull-stripping removed a few brain regions. The best option is probably to try to add seed points in the excluded brain regions (with the -s option), even though you could increase the preflooding height (-h option). In my experience, there is no point in trying thousand of values for the preflooding height. A couple of tries are sufficient. If it does not work for these, then, try with more seed points... 1-2) "what-is-failling" approach: since the program fails during the first step, it could come either from the watershed segmentation, or the post-processing step, or the first template smoothing. One way to find out is to first run the program with the option -wat and -n: this will stop the program right after the watershed segmentation before the post-processing. If the segmentation is already failing, try adding seed points with the option -s or play with the preflooding height -h. In my experience, the best way to quickly find the right set of parameters is to use seed points (potentially lots of them). In order to find the right set of parameters, just run the program with the options "-wat -n". This will be much faster. nce the right set of parameters have been found, run the program with the "-n" option, as the postprocessing step should be useless... If the program fails after the watershed processing, then this means that the post-processing is probably producing the errors. This is often resulting in too much tissue being included. Simply run the program with the "-n" option. 2) In case of failure during the second step (fine surface deformation), you have several option (most failures come from the first step). 2-1) if you think that the first step produced a correct segmentation, you can directly stop the segmentation at this point with the -wat+temp option. 2-2) you think that the first step produced a good intialization for the brain surface and that it needs to be refined a little: use the -first_temp option. 2-3) try the -atlas option that will incorporate shape information into the deformation process and should give some correct results! IN SUMMARY: 1) Try to understand what's happening with the option "-surf_debug" 2) Try the option "-atlas" if the program advises you to do so, or try it too if you have time for it (~10 minutes)! "I usually skip this step". 3) Depending on what you see with the surf_debug option, you may try to correct the watershed segmentation or the fine segmentation. * To correct the watershed segmentation, you can: - play with the preflooding height (use the -wat option to visualize the result quickly, without having to run all the program). - modify or suppress the post-watershed analysis mode (-n to suppress the post_watershed analysis, -t to change the threshold used in the merging of the basins). - use some (lots of) seed points... THIS IS WHAT WORKS BEST AND QUICKLY. IMPORTANT: In order to experiment with the options -n, -h, -s, don't forget to run the program with the option -wat. (no need to run all the program). SOME OTHER MODE ADVANCED TIPS: o You can set the global parameters manually, if you think that the ones found during the process are incorrect: this is the -man option. You would have to precise the csf max, the transition intensity, and the gray matter intensity. o The difference between -first_temp and -wat+temp is that the first option will use the first surface to compute the local intensity values at the border of the brain and then try to shrink it a bit. The second option -wat_temp will only use the first surface and immediately segment the brain out. PARTIAL LIST OF OPTIONS (command line: "mri_watershed -option") Option -wat : option that stops the algorithm after the initial watershed segmentation (the post-analyze segmentation is included). Option -h hpf , with hpf an integer: modification of the preflooding height used in the watershed segmentation. A typical value for hpf is 25 (corresponding to 25% of the maximal intensity); lower values tend to decrease the size of the main basin (which could be infirmed by the post-analyze process) and higher values increase its size. However, for any given image, the preflooding height hpf can be varied over a certain range without significantly changing the output. Option -n : the post-analyze is not used with this option. Option -t th, with th an integer: that option specifies the threshold used in the post-watershed analysis. The default value is 100 (100%, meaning that the threshold is exactly the cubic root of the size of the ambiguous basin). A value of 0 will result in a post-watershed analysis that will merge any ambiguous basin with the main one. Option -wat+temp : with this option, only the watershed segmentation and the first template deformation is used. This option could be typically used when the image contains a lot of artifacts, resulting in a fine surface segmentation that shaves some part of the cortex; in that extreme case, the watershed segmentation may still lead to successful results and the first template deformation to a valid brain segmentation. Options -less or -more: option designed to increase or decrease the transition threshold used in the fine surface. The result is respectively a shrunk or expanded surface compared to the typical surface. Option -surf_debug: this option will write out, into the output volume, the localization of the different surfaces used during the algorithm; it will enable the user to visualize the results of the different template deformations, and eventually to detect, understand and correct some errors. Option -s int_i int_j int_k : this option allows the user to add some new seed points for the watershed process. This option is very useful when the cerebellum is removed by the watershed segmentation, since a seed point inside the removed cerebellum may be added, leading to the merging of the corresponding basin with the main one. However, the atlas-based validation-correction step should be sufficient to correct the segmentation. Option -man int_CSF int_transition int_GM: this option allows the user to manually set the parameters used in the fine surface deformation. Option -surf surface_name: this option is used to generate tessellated surfaces of the brain, inner and outer skull, and outer scalp from the T1-weighted image. The brain surface is the one produced by the fine surface deformatio n described. The outer scalp surface is generated by another surface deformation. However, the MRI-based force is quite simple, since the scalp appears bright on T1-weighted images. The deformation is initialized with a radius set to include the whole head, and a series of iterative deformation matches the surface onto the head scalp-skin. The outer and inner skull surfaces are much harder to find, since the skull and the cerebrospinal fluid look the same in these type of images (dark intensity). Besides, the skull may contain some fat tissue that makes the border between the scalp and the outer skull difficult to localize. For these reasons, the two surfaces, outer skull and inner skull, are respectively interpolated from the outer scalp and brain surface. They are a smoothed version of the corresponding surface that has been respectively shrunk or expanded a few millimeters inwards or outwards (3 mm). Option -brainsurf surface_name: that option writes out the final tessellated brain surface. Option -shk_br_surf hshk surface_name: this option writes out the final tessellated brain surface that has been shrunk hshk mm inwards. Option -LABEL: this option enables the user to obtain a labeled volume into 5 classes: scalp, skull, csf, gray and white matter. First the whole algorithm is run and the surfaces corresponding to the brain, outer scalp, outer skull, inner skull are estimated. Based on the localization of these surfaces, we label the volume into brain, scalp, skull, and csf ; then, the brain segment is divided into gray an white matter based on the intensity statistics calculated during the template deformation process. Option -atlas: with that option, the program uses an atlas, compiled from successfully segmented brains, in order to detect the rightness of the surface, and to eventually correct it. That should solve some of the problems, especially those when the cerebellum is removed (or part of it!). Option -first_temp: with that option, the final deformation uses the first template deformation as a starting point. ------------------------------------- Florent Segonne PhD Candidate Stata Center 32-D430 CSAIL MIT 1 617 253 2986 http://people.csail.mit.edu/~fsegonne ------------------------------------- On Thu, 5 May 2005, Bruce Fischl wrote: > Hi Flo, > > could you send your watershed troubleshooting guide to the BWH folks (ccd) so > they can include it in the manual? > > thanks, > Bruce > >

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skullstripping hi-res monkey data
by Bell, Andrew (NIH/NIMH) 15 Jun '05

15 Jun '05

Greetings Fellow FreeSurfers, I've been having some trouble skull stripping some hi-res monkey data and was wondering if anyone had some tips for a newbie: The data is 256*256*256, 0.5mm3 I've normalized using the following: mri_normalize -no1d -f ../tmp/control.dat -n 1 orig T1 and it yields a very nice set of brain images (good contrast between wm and gm). there is some very intense areas outside the brain (muscles) - i don't know whether that has an effect. When I try "mri_watershed T1 brain", it runs (and takes a LONG time) to completion but the images are essentially untouched from the T1 images. There are several warnings (e.g., mean intensity may be too low) which it looks like it tries to adjust for but again... no success. Any help is greatly appreciated!!! Andy Andrew H. Bell, PhD Laboratory of Brain and Cognition National Institute of Mental Health Bethesda Maryland USA

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RE: [Freesurfer] recon-all stage3
by Fornito, Alexander 15 Jun '05

15 Jun '05

I'll keep an eye one it. As an aside, I tried to run freesurfer on an image acquired at 3T (I converted it to 8 bit first), and got an error during stage1 of recon-all. I've included the relevant bits below. Any ideas? Transforming slices:...............................................................................................................Done Not implemented yet in cache_volume_range_has_changed() Not implemented yet in cache_volume_range_has_changed() Transforming slices:..........................................................................................................................................................................................................................................................................................................................................Done mri_convert nu/nu4.mnc nu mri_convert nu/nu4.mnc nu reading from nu/nu4.mnc... DimSizes: 3, 330, 330, 330, 1 DataType: 1 MINC Linear Transform -1.0000 0.0000 0.0000 165.0000 0.0000 0.0000 1.0000 -165.0000 0.0000 -1.0000 0.0000 165.0000 0.0000 0.0000 0.0000 1.0000 Done reading minc 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 (330, 330, 330) voxels. Data is conformed to 1 mm size and 330 voxels for all directions writing to nu... non-standard value for imnr1 (330, usually 256) in volume structure non-standard value for width (330, usually 256) in volume structure non-standard value for height (330, usually 256) in volume structure ... #it then seems to proceed as normal until I get this: --------------------------------------------- Tessellate rh Tue Jun 14 18:34:47 EST 2005 mri_tessellate /data/flanders/work/alex/freesurfer/subjects/mw_3T/mri/filled 127 /data/flanders/work/alex/freesurfer/subjects/mw_3T/surf/rh.orig /data/flanders/work/alex/freesurfer/subjects/mw_3T/scripts warning: non-standard value for imnr1 (330, usually 256) in file /data/flanders/work/alex/freesurfer/subjects/mw_3T/mri/filled/COR-.info warning: non-standard value for x (330, usually 256) in file /data/flanders/work/alex/freesurfer/subjects/mw_3T/mri/filled/COR-.info warning: non-standard value for y (330, usually 256) in file /data/flanders/work/alex/freesurfer/subjects/mw_3T/mri/filled/COR-.info slice 80: 25 vertices, 35 faces slice 90: 2235 vertices, 2414 faces slice 100: 7950 vertices, 8225 faces slice 110: 14980 vertices, 15343 faces slice 120: 24760 vertices, 25210 faces slice 130: 35948 vertices, 36485 faces slice 140: 47251 vertices, 47791 faces slice 150: 59398 vertices, 59994 faces slice 160: 69840 vertices, 70396 faces slice 170: 79968 vertices, 80513 faces slice 180: 89126 vertices, 89647 faces slice 190: 97517 vertices, 98045 faces slice 200: 104180 vertices, 104653 faces slice 210: 110417 vertices, 110849 faces slice 220: 115639 vertices, 116067 faces slice 230: 120291 vertices, 120699 faces slice 240: 123600 vertices, 123982 faces slice 250: 125319 vertices, 125574 faces slice 260: 125319 vertices, 125574 faces slice 270: 125319 vertices, 125574 faces slice 280: 125319 vertices, 125574 faces slice 290: 125319 vertices, 125574 faces slice 300: 125319 vertices, 125574 faces slice 310: 125319 vertices, 125574 faces slice 320: 125319 vertices, 125574 faces slice 330: 125319 vertices, 125574 faces using the conformed surface RAS to save vertex points... writing /data/flanders/work/alex/freesurfer/subjects/mw_3T/surf/rh.orig --------------------------------------------- Smooth1 rh Tue Jun 14 18:35:32 EST 2005 mris_smooth /data/flanders/work/alex/freesurfer/subjects/mw_3T/surf/rh.orig /data/flanders/work/alex/freesurfer/subjects/mw_3T/surf/rh.smoothwm /data/flanders/work/alex/freesurfer/subjects/mw_3T/scripts Segmentation fault ------------------------------------------ Filesystem 1k-blocks Used Available Use% Mounted on /dev/hda9 130282400 12524220 111140208 11% /data/flanders ------------------------------------------ recon-all exited with errors at Tue Jun 14 18:35:33 EST 2005 -----Original Message----- From: Bruce Fischl [mailto:fischl@nmr.mgh.harvard.edu] Sent: Wed 6/15/2005 12:33 PM To: Fornito, Alexander Cc: freesurfer(a)nmr.mgh.harvard.edu Subject: RE: [Freesurfer] recon-all stage3 then you should just run the rest of the analysis I guess and see if it works. In general all the surfaces of a hemisphere should have the same # of edges/faces/vertices *except* the ?h.qsphere surface. They should have all have an euler number of 2. cheers, Bruce On Wed, 15 Jun 2005, Fornito, Alexander wrote: > > Hi Bruce, > I ran the topology fixer again and it seemed to work. Unfortunately, silly me just wrote over the original files, so all I have is the euler number from the orig surface that is output in the recon-all log. > > > Euler Number lh Sat Jun 11 04:20:04 EST 2005 > /data/flanders/work/alex/freesurfer/subjects/1000192 > mris_euler_number /data/flanders/work/alex/freesurfer/subjects/1000192/surf/lh.orig > euler # = v-e+f = 2g-2: 179761 - 539277 + 359518 = 2 --> 0 holes > F =2V-4: 359518 = 359522-4 (0) > 2E=3F: 1078554 = 1078554 (0) > > total defect index = 0 > Euler: NHoles = 0 > > > > -----Original Message----- > From: Bruce Fischl [mailto:fischl@nmr.mgh.harvard.edu] > Sent: Tue 6/14/2005 10:12 PM > To: Fornito, Alexander > Cc: freesurfer(a)nmr.mgh.harvard.edu > Subject: Re: [Freesurfer] recon-all stage3 > Hi Alex, > > that's a starnge one. Did the partition run out of space? Can you do an ls > -l in the surf dir and send it along? Also, run mris_euler_number on > lh.orig, lh.smoothwm, lh.inflated and lh.qsphere. > > > > On Tue, 14 Jun 2005, Fornito, > Alexander wrote: > >> Hi, >> I got an error when running recon-all -stage3.I've included the relevant part of the log below. Any ideas as to what went wrong? >> Thanks, >> alex >> >> writing spherical brain to /data/flanders/work/alex/freesurfer/subjects/1000192/surf/lh.qsphere >> spherical transformation took 0.91 hours >> navgs=32 and tol=1.000e-01 >> integrating with navgs=32 and tol=1.000e-01 >> integrating with navgs=8 and tol=1.000e-01 >> taking momentum steps... >> integrating with navgs=8 and tol=1.000e-01 >> integrating with navgs=8 and tol=1.000e-01 >> integrating with navgs=2 and tol=1.000e-01 >> taking momentum steps... >> integrating with navgs=2 and tol=1.000e-01 >> integrating with navgs=2 and tol=1.000e-01 >> integrating with navgs=0 and tol=1.000e-01 >> pass 1 complete, delta sse/iter = 0.16/60 = 0.00 >> final distance error %31.34 >> optimization complete. >> unfolding took 0.81 hours >> --------------------------------------------- >> Fix Topology lh Sat Jun 11 04:24:54 EST 2005 >> /data/flanders/work/alex/freesurfer/subjects/1000192/scripts >> mris_fix_topology 1000192 lh >> reading input surface /data/flanders/work/alex/freesurfer/subjects/1000192/surf/lh.qsphere... >> before topology correction, eno=-301 (nv=188932, nf=378516, ne=567749, g=151) >> mrisReadTriangleFile(/data/flanders/work/alex/freesurfer/subjects/1000192/surf/lh.orig): surface doesn't match /data/flanders/work/alex/freesurfer/subjects/1000192/surf/lh.qsphere >> >> No such file or directory >> mrisReadTriangleFile failed. >> >> No such file or directory >> MRISreadOriginalProperties: could not read surface file orig >> No such file or directory >> mris_fix_topology: could not read original surface orig >> No such file or directory >> reading T1 volume from T1... >> reading wm segmentation from wm... >> >> recon-all exited with errors at Sat Jun 11 04:24:58 EST 2005 >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer(a)nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> > > > >

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RE: [Freesurfer] recon-all stage3
by Fornito, Alexander 14 Jun '05

14 Jun '05

Hi Bruce, I ran the topology fixer again and it seemed to work. Unfortunately, silly me just wrote over the original files, so all I have is the euler number from the orig surface that is output in the recon-all log. Euler Number lh Sat Jun 11 04:20:04 EST 2005 /data/flanders/work/alex/freesurfer/subjects/1000192 mris_euler_number /data/flanders/work/alex/freesurfer/subjects/1000192/surf/lh.orig euler # = v-e+f = 2g-2: 179761 - 539277 + 359518 = 2 --> 0 holes F =2V-4: 359518 = 359522-4 (0) 2E=3F: 1078554 = 1078554 (0) total defect index = 0 Euler: NHoles = 0 -----Original Message----- From: Bruce Fischl [mailto:fischl@nmr.mgh.harvard.edu] Sent: Tue 6/14/2005 10:12 PM To: Fornito, Alexander Cc: freesurfer(a)nmr.mgh.harvard.edu Subject: Re: [Freesurfer] recon-all stage3 Hi Alex, that's a starnge one. Did the partition run out of space? Can you do an ls -l in the surf dir and send it along? Also, run mris_euler_number on lh.orig, lh.smoothwm, lh.inflated and lh.qsphere. On Tue, 14 Jun 2005, Fornito, Alexander wrote: > Hi, > I got an error when running recon-all -stage3.I've included the relevant part of the log below. Any ideas as to what went wrong? > Thanks, > alex > > writing spherical brain to /data/flanders/work/alex/freesurfer/subjects/1000192/surf/lh.qsphere > spherical transformation took 0.91 hours > navgs=32 and tol=1.000e-01 > integrating with navgs=32 and tol=1.000e-01 > integrating with navgs=8 and tol=1.000e-01 > taking momentum steps... > integrating with navgs=8 and tol=1.000e-01 > integrating with navgs=8 and tol=1.000e-01 > integrating with navgs=2 and tol=1.000e-01 > taking momentum steps... > integrating with navgs=2 and tol=1.000e-01 > integrating with navgs=2 and tol=1.000e-01 > integrating with navgs=0 and tol=1.000e-01 > pass 1 complete, delta sse/iter = 0.16/60 = 0.00 > final distance error %31.34 > optimization complete. > unfolding took 0.81 hours > --------------------------------------------- > Fix Topology lh Sat Jun 11 04:24:54 EST 2005 > /data/flanders/work/alex/freesurfer/subjects/1000192/scripts > mris_fix_topology 1000192 lh > reading input surface /data/flanders/work/alex/freesurfer/subjects/1000192/surf/lh.qsphere... > before topology correction, eno=-301 (nv=188932, nf=378516, ne=567749, g=151) > mrisReadTriangleFile(/data/flanders/work/alex/freesurfer/subjects/1000192/surf/lh.orig): surface doesn't match /data/flanders/work/alex/freesurfer/subjects/1000192/surf/lh.qsphere > > No such file or directory > mrisReadTriangleFile failed. > > No such file or directory > MRISreadOriginalProperties: could not read surface file orig > No such file or directory > mris_fix_topology: could not read original surface orig > No such file or directory > reading T1 volume from T1... > reading wm segmentation from wm... > > recon-all exited with errors at Sat Jun 11 04:24:58 EST 2005 > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >

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Problem with tkmedit Tools/fMRI/Select Contiguous Voxels by Threshold
by Tommi Raij 14 Jun '05

14 Jun '05

Hi guys, I use tkmedit (current MGH beta release) to manually select my ROIs. I overlay the functional contrast, move the cursor inside the cluster of interest, and then go Tools/fMRI/Select contiguous voxels by threshold (after setting the threshold for a proper value of course). Works great, the volume turns green, and can be saved as a label. But only for positive contrast values. When I point the cursor inside a negative cluster and Select Contiguous Voxels by Threshold, nothing will turn green. Saving the label will result in a file with contents zero. Reversing values in "Configure functional overlay" does not help. Same problem with the alpha release. However, selecting with "Select contiguous voxels by Func Value" can pick also negative clusters. But then it is more difficult to control the threshold of course - I would prefer to use the Threshold. Any suggested ways around this? Or am I just doing something plain wrong? Thanks, Tommi --- Tommi Raij, M.D., Ph.D. MGH/MIT/HMS Athinoula A. Martinos Center for Biomedical Imaging Bldg 149, 13th St Charlestown, MA 02129

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Problem with the parcellation
by Wan Park 14 Jun '05

14 Jun '05

Hello, I have been running freesurfer in G5 Macs with Panther. I was able to parcellate and retrieve data of the different areas. However, recently we changed the OS from Panther to Tiger. Since then, I have the following problem: When I do mris_anatomical_stats: [ogden:freesurfer_package/freesurfer/subjects] wpark% mris_anatomical_stats -b -a 14649/label/rh.aparc.annot 14649 rh computing statistics for each annotation in 14649/label/rh.aparc.annot. reading volume /usr/local/freesurfer_package/freesurfer/subjects/14649/mri/wm... reading input surface /usr/local/freesurfer_package/freesurfer/subjects/14649/surf/ rh.white... INFO: Volume /tmp/mritotal_2576/orig_8_dxyz.mnc cannot be found. INFO: found the orig volume (mri/orig) to get c_(ras) information for src INFO: added info to the surface. done. computing second fundamental form...reading colortable from annotation file... colortable with 0 entries read (originally ) done. total white matter volume = 509402 mm^3 table columns are: number of vertices total surface area (mm^2) total gray matter volume (mm^3) average cortical thickness +- standard error (mm) integrated rectified mean curvature integrated rectified Gaussian curvature folding index intrinsic curvature index structure name 3758 2149 4165 1.950 +- 0.579 0.199 0.067 75.676 9.502 ** annotation 003c148c 2251 1174 3233 2.652 +- 0.702 0.200 0.081 67.771 6.118 ** annotation 00b43cb4 1285 731 1674 2.284 +- 0.590 0.179 0.065 25.068 2.573 ** annotation 003cdc14 1282 792 1629 2.076 +- 0.523 0.170 0.041 14.336 1.902 ** annotation 00dc3c65 1304 794 1569 2.005 +- 0.501 0.190 0.044 19.070 2.299 ** annotation 008c1415 306 137 291 2.137 +- 0.534 0.147 0.025 3.083 0.471 ** annotation 00b43c15 1604 935 1722 1.840 +- 0.477 0.203 0.070 34.702 3.964 ** annotation 001414b4 2363 1479 3196 2.165 +- 0.602 0.160 0.035 27.198 3.101 ** annotation 00b46465 2602 1659 3292 1.968 +- 0.729 0.189 0.052 47.088 5.998 ** annotation 00b4b43f 2299 1339 3348 2.510 +- 0.575 0.192 0.051 50.159 4.279 ** annotation 00dcb4dc 548 309 766 2.469 +- 0.454 0.165 0.043 5.623 0.997 ** annotation 00c8c80a 1015 591 1455 2.481 +- 0.499 0.196 0.056 24.732 1.704 ** annotation 0064dc8c .......... Instead of having the name of different areas, I receive "annotation..." Curiously, this does not happen if I do mris_anatomical_stats in previously parcellated brains (before the new installation). This happens when I parcellate_subject and then I try to get the info of the areas. This is what I got when I parcellate: [ogden:freesurfer_package/freesurfer/subjects] wpark% parcellate_subject 14649 reading atlas from /usr/local/freesurfer_package/freesurfer/average/ lh.atlas2002_simple.gcs... reading color table from GCSA file.... reading color table from GCSA file.... input 1: CURVATURE FILE, flags 0, avgs 0, name sulc input 0: MEAN CURVATURE, flags 0, avgs 5, name mean_curvature labeling surface... relabeling using gibbs priors... 000: 9935 changed, 137093 examined... 001: 2397 changed, 37088 examined... 002: 731 changed, 12222 examined... 003: 340 changed, 4117 examined... 004: 155 changed, 1818 examined... 005: 88 changed, 871 examined... 006: 47 changed, 459 examined... 007: 28 changed, 255 examined... 008: 19 changed, 160 examined... 009: 12 changed, 97 examined... 010: 10 changed, 64 examined... 011: 5 changed, 64 examined... 012: 3 changed, 27 examined... 013: 2 changed, 19 examined... 014: 1 changed, 9 examined... 015: 0 changed, 6 examined... 000: 340 total segments, 238 labels (3015 vertices) changed 001: 123 total segments, 23 labels (316 vertices) changed 002: 104 total segments, 4 labels (20 vertices) changed 003: 100 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 164 changed) writing output to /usr/local/freesurfer_package/freesurfer/subjects/14649/label/ lh.aparc.annot... writing colortable into annotation file... classification took 3 minutes and 42 seconds. reading atlas from /usr/local/freesurfer_package/freesurfer/average/ rh.atlas2002_simple.gcs... reading color table from GCSA file.... reading color table from GCSA file.... input 1: CURVATURE FILE, flags 0, avgs 0, name sulc input 0: MEAN CURVATURE, flags 0, avgs 5, name mean_curvature labeling surface... relabeling using gibbs priors... 000: 9869 changed, 137521 examined... 001: 2399 changed, 36932 examined... 002: 698 changed, 12235 examined... 003: 282 changed, 3952 examined... 004: 150 changed, 1565 examined... 005: 81 changed, 821 examined... 006: 58 changed, 453 examined... 007: 30 changed, 299 examined... 008: 10 changed, 170 examined... 009: 4 changed, 54 examined... 010: 4 changed, 26 examined... 011: 3 changed, 22 examined... 012: 2 changed, 17 examined... 013: 2 changed, 14 examined... 014: 1 changed, 8 examined... 015: 0 changed, 10 examined... 000: 303 total segments, 200 labels (2164 vertices) changed 001: 114 total segments, 14 labels (62 vertices) changed 002: 100 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 127 changed) writing output to /usr/local/freesurfer_package/freesurfer/subjects/14649/label/ rh.aparc.annot... writing colortable into annotation file... classification took 3 minutes and 38 seconds. [ogden:freesurfer_package/freesurfer/subjects] wpark% Anybody please could help me? I am a little desperate... Wan Park

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recon-all stage3
by Fornito, Alexander 14 Jun '05

14 Jun '05

Hi, I got an error when running recon-all -stage3.I've included the relevant part of the log below. Any ideas as to what went wrong? Thanks, alex writing spherical brain to /data/flanders/work/alex/freesurfer/subjects/1000192/surf/lh.qsphere spherical transformation took 0.91 hours navgs=32 and tol=1.000e-01 integrating with navgs=32 and tol=1.000e-01 integrating with navgs=8 and tol=1.000e-01 taking momentum steps... integrating with navgs=8 and tol=1.000e-01 integrating with navgs=8 and tol=1.000e-01 integrating with navgs=2 and tol=1.000e-01 taking momentum steps... integrating with navgs=2 and tol=1.000e-01 integrating with navgs=2 and tol=1.000e-01 integrating with navgs=0 and tol=1.000e-01 pass 1 complete, delta sse/iter = 0.16/60 = 0.00 final distance error %31.34 optimization complete. unfolding took 0.81 hours --------------------------------------------- Fix Topology lh Sat Jun 11 04:24:54 EST 2005 /data/flanders/work/alex/freesurfer/subjects/1000192/scripts mris_fix_topology 1000192 lh reading input surface /data/flanders/work/alex/freesurfer/subjects/1000192/surf/lh.qsphere... before topology correction, eno=-301 (nv=188932, nf=378516, ne=567749, g=151) mrisReadTriangleFile(/data/flanders/work/alex/freesurfer/subjects/1000192/surf/lh.orig): surface doesn't match /data/flanders/work/alex/freesurfer/subjects/1000192/surf/lh.qsphere No such file or directory mrisReadTriangleFile failed. No such file or directory MRISreadOriginalProperties: could not read surface file orig No such file or directory mris_fix_topology: could not read original surface orig No such file or directory reading T1 volume from T1... reading wm segmentation from wm... recon-all exited with errors at Sat Jun 11 04:24:58 EST 2005

2 1

Problems in pial surface?
by Fornito, Alexander 14 Jun '05

14 Jun '05

Hi, I've been using freesurfer with only one run (image) pers subject and have generally been obtaining good results. I've just noticed a few quirks in the estimation of the pial surface that I was seeking some clarification. 1 - the algorithm consistently misses portions of grey matter in the medial temporal lobes (amygdala/hippocampus). I've noticed that this "missed" area becomes part of the "medial wall" region when parcellate_subject is run. Does the algorithm intentionally avoid estimatiung the grey/csf surface in the medial temporal lobes? 2 - Sometimes a portion of the other hemisphere gets included in estimates of the pial surface. Any tips for dealing with this? I was thinking of manually deleting a thin line of voxels through the midline of the T1 to emphasise the medial surface in areas where the algorithm has trouble? As an aside, where can I find the average7? I thought it would be in /usr/local/freesurfer/average/, but all I have is .gcs, .tif, and .txt files. Thanks as always, Alex

1 0

Re: [Freesurfer] (MNI tools)
by Arvind Gururajan 13 Jun '05

13 Jun '05

Nick, Thanks. Yes, I used 'cd packages' and did the installation. After setting the environment and the subjit it works without errors. One more question, can I do a similar conversion for one .orig file having both hemisphere data points and generate one inflated surface or would have to use lh and rh.orig files seperately? Thanks, Arvind Gururajan On 13 Jun 2005, Nick Schmansky wrote: > Arvind, > > You are right, the MINC installation instructions are mistaken. A 'cd > packages' is missing: > > mkdir -p packages > cd packages <<<<< missing statement > tar xvfz mni.$OS.tar.gz > > As for the ZM error, is this the name of a subject? If so, preface it > with -subjid, like this: > > recon-all -smooth1 -subjid ZM > > The -smooth1 argument is not one normally used outright, but it will > work, once certain variables are set, namely these: > > setenv DoCANormalize 0 > setenv DoCAReg 0 > setenv DoCALabel 0 > setenv EditWMwithASeg 0 > > Nick > > On Mon, 2005-06-13 at 12:58 -0500, Arvind Gururajan wrote: > > > > Nick, > > > > Thanks for the clear description. I repeated the exact installation and got > > the same errors. I noticed that the 'current' directory was wrongly placed > > in this path. /usr/pubsw/mni/current. Repeated the same steps again, but > > now installed in the right directory. Getting the following errors: > > > > [root@node1 noarch]# ./recon-all -smooth1 ZM > > ######################################## > > program versions used > > $Id: recon-all-nmr,v 1.37 2004/01/06 22:21:48 tosa Exp $ > > $Id: mri_motion_correct2,v 1.7 2004/01/16 20:25:10 tosa Exp $ > > mri_convert --version > > $ > > $Header: /software/source/minc/cvsroot/minc/progs/rawtominc/rawtominc.c,v > > 6.3 1999/10/19 14:45:31 neelin Exp $ > > minctracc.c > > $Header: > > /software/source/registration/mni_autoreg/minctracc/Main/minctracc.c,v 96.3 > > 2000/03/15 08:42:41 stever Exp $ > > $Header: > > /software/source/minc/cvsroot/minc/progs/mincresample/mincresample.c,v 6.2 > > 1999/10/19 14:45:27 neelin Exp $ > > $Header: > > /software/source/minc/cvsroot/minc/progs/mincaverage/mincaverage.c,v 6.1 > > 1999/10/19 14:45:18 neelin Exp $ > > $Id: talairach2,v 1.5 2003/08/28 21:45:48 tosa Exp $ > > mri_convert --version > > $ > > # $Id: mritotal.in,v 1.10 2000/06/14 12:55:01 louis Exp $ > > # $Id: nu_estimate.in,v 1.15 1999/08/10 18:05:42 jgsled Exp $ > > $ > > $ > > $ > > $ > > $ > > $ > > $ > > $ > > $ > > $ > > $ > > $ > > $ > > $ > > $ > > $ > > ####################################### > > ERROR: Flag ZM unrecognized. > > -smooth1 ZM > > > > Your feedback will be appreciated. > > > > Thanks, > > Arvind > > > > On 10 Jun 2005, Nick Schmansky wrote: > > > > > > --=-yST7vkqiza7BNyzh64R8 > > > Content-Type: text/plain > > > Content-Transfer-Encoding: 7bit > > > > > > Arvind > > > > > > I'm suspect that our instructions may be a bit confusing. The files to > > > download are not the netcdf and minc files from the MNI distribution > > > site, but rather the file mni.Linux.tar.gz from our site (where it says > > > 'Download MNI binaries for Linux and/or SunOS.', click on Linux). > > > Following the instructions, this will result in an installation of files > > > in the directory /usr/pubsw/packages/mni/current. Then, the line: > > > > > > source $FREESURFER_HOME/FreeSurferEnv.csh > > > > > > will add MINC_BIN_DIR to the path. > > > > > > Also, where the instructions say to type: > > > > > > ln -s `which perl` perl > > > > > > be sure you are using the ` key, which is the far upper left corner key > > > on the keyboard (not to be confused with the ' key). > > > > > > The important thing is to have perl in the /usr/pubsw/bin directory. If > > > its already there, then no need to create a link. > > > > > > Hope this helps. > > > > > > Nick > > > > > > > > > > > > On Fri, 2005-06-10 at 16:51 -0500, Arvind Gururajan wrote: > > > > > > > Hi Nick, > > > > > > > > I am running it on Linux platform. I followed the same instruction > > > > described here. > > > > http://surfer.nmr.mgh.harvard.edu/freesurfer/minc-download.html > > > > and downloaded these two files: NetCDF 3.5.0 and MINC 1.0 > > > > > > > > I am not sure, if I created the symbolic link correctly. > > > > ln -s 5.8.0 perl - > > > > ln: `perl': File exists [ Same output even the first time] > > > > > > > > Also, there are no tools in the path, I manually created current/bin > > and > > > > current/lib. Is there a way to fix this, can I moved all the tools to > > these > > > > two directories? > > > > > > > > Your help is really appreciated. > > > > > > > > Arvind Gururajan > > > > > > > > > > > > > > > > On 10 Jun 2005, Nick Schmansky wrote: > > > > > Arvind, > > > > > > > > > > Hi. On what platform are you running? Linux? > > > > > > > > > > Did you follow the special installation instructions, involving > > making > > > > > the symbolic links? Lastly, are the tools in your path? > > > > > > > > > > If you are feeling brave, an alternative to installing the binaries > > is > > > > > to compile the MNI package from source on your platform, and install > > > > > those binaries. Instructions to do this are here: > > > > > > > > > > ftp://surfer.nmr.mgh.harvard.edu/pub/dist/mni.srcbuild.README > > > > > > > > > > and the gzip file is here: > > > > > > > > > > ftp://surfer.nmr.mgh.harvard.edu/pub/dist/mni.srcbuild.tar.gz > > > > > > > > > > > > > > > Nick > > > > > > > > > > > > > > > > > > > > On Fri, 2005-06-10 at 12:20 -0500, Arvind Gururajan wrote: > > > > > > > > > > > Hi, > > > > > > > > > > > > I downloaded the entire MNI package. Although I see all these MNI > > > > files, I > > > > > > still get the same error, file not found. Any clues why this might > > be? > > > > > > > > > > > > > > > > > > Thanks, > > > > > > > > > > > > Arvind Gururajan > > > > > > > > > > > > On 9 Jun 2005, Bruce Fischl wrote: > > > > > > > just download and install the whole MNI package. Much easier than > > > > trying > > > > > > > to install various pieces.... > > > > > > > > > > > > > > On Thu, 9 Jun 2005, Arvind Gururajan wrote: > > > > > > > > > > > > > > > Hello, > > > > > > > > > > > > > > > > I am very new to Freesurfer. Could anybody please tell me which > > > > > > specific > > > > > > > > MNI tool, I need to install? > > > > > > > > > > > > > > > > > > > > > > > >> > > > > > > > >> I tried the following command. > > > > > > > >> > > > > > > > >> ./recon-all -smooth1 ZM > > > > > > > >> ######################################## > > > > > > > >> program versions used > > > > > > > >> $Id: recon-all-nmr,v 1.37 2004/01/06 22:21:48 tosa Exp $ > > > > > > > >> $Id: mri_motion_correct2,v 1.7 2004/01/16 20:25:10 tosa Exp > > $fire > > > > > > > >> mri_convert --version > > > > > > > >> $ > > > > > > > >> strings: rawtominc:: No such file or directory > > > > > > > >> strings: Command: No such file or directory > > > > > > > >> strings: not: No such file or directory > > > > > > > >> strings: found.: No such file or directory > > > > > > > >> strings: minctracc:: No such file or directory > > > > > > > >> strings: Command: No such file or directory > > > > > > > >> strings: not: No such file or directory > > > > > > > >> strings: found.: No such file or directory > > > > > > > >> strings: mincresample:: No such file or directory > > > > > > > >> strings: Command: No such file or directory > > > > > > > >> strings: not: No such file or directory > > > > > > > >> strings: found.: No such file or directory > > > > > > > >> strings: mincaverage:: No such file or directory > > > > > > > >> strings: Command: No such file or directory > > > > > > > >> strings: not: No such file or directory > > > > > > > >> strings: found.: No such file or directory > > > > > > > >> $Id: talairach2,v 1.5 2003/08/28 21:45:48 tosa Exp $ > > > > > > > >> mri_convert --version > > > > > > > >> $ > > > > > > > >> strings: mritotal:: No such file or directory > > > > > > > >> strings: Command: No such file or directory > > > > > > > >> strings: not: No such file or directory > > > > > > > >> strings: found.: No such file or directory > > > > > > > >> strings: nu_correct:: No such file or directory > > > > > > > >> strings: Command: No such file or directory > > > > > > > >> strings: not: No such file or directory > > > > > > > >> strings: found.: No such file or directory > > > > > > > >> $ > > > > > > > >> $ > > > > > > > >> $ > > > > > > > >> $ > > > > > > > >> $ > > > > > > > >> $ > > > > > > > >> $ > > > > > > > >> $ > > > > > > > >> $ > > > > > > > >> $ > > > > > > > >> $ > > > > > > > >> $ > > > > > > > >> $ > > > > > > > >> $ > > > > > > > >> $ > > > > > > > >> $ > > > > > > > >> ####################################### > > > > > > > >> ERROR: Flag ZM unrecognized. > > > > > > > >> -smooth1 ZM > > > > > > > >> > > > > > > > >> > > > > > > > >> The folder ZM has only one orig file in the surf directory. > > There > > > > are > > > > > > no > > > > > > > >> raw data(.COR files). Please let me know your feedback. > > > > > > > >> > > > > > > > >> Sincerely, > > > > > > > >> > > > > > > > >> Arvind Gururajan > > > > > > > > > > > > > > > > _______________________________________________ > > > > > > > > Freesurfer mailing list > > > > > > > > Freesurfer(a)nmr.mgh.harvard.edu > > > > > > > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > > > > > > > > > > > _______________________________________________ > > > > > > > Freesurfer mailing list > > > > > > > Freesurfer(a)nmr.mgh.harvard.edu > > > > > > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > > > > > > > > > > > > > > > > > > > > > _______________________________________________ > > > > > > Freesurfer mailing list > > > > > > Freesurfer(a)nmr.mgh.harvard.edu > > > > > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > > > > > > > > > > > > > _______________________________________________ > > > > Freesurfer mailing list > > > > Freesurfer(a)nmr.mgh.harvard.edu > > > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > > --=-yST7vkqiza7BNyzh64R8 > > > Content-Type: text/html; charset=utf-8 > > > Content-Transfer-Encoding: 7bit > > > > > > <!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 TRANSITIONAL//EN"> > > > <HTML> > > > <HEAD> > > > <META HTTP-EQUIV="Content-Type" CONTENT="text/html; CHARSET=UTF-8"> > > > <META NAME="GENERATOR" CONTENT="GtkHTML/3.3.2"> > > > </head> > > > <BODY> > > > Arvind > > > > > > I'm suspect that our instructions may be a bit confusing. The files to > > > download are not the netcdf and minc files from the MNI distribution > > site, > > > but rather the file mni.Linux.tar.gz from our site (where it says > > 'Download > > > MNI binaries for <A > > > > > HREF="ftp://surfer.nmr.mgh.harvard.edu/pub/dist/mni.Linux.tar.gz">Linux</a> > > > and/or <A > > > > > HREF="ftp://surfer.nmr.mgh.harvard.edu/pub/dist/mni.SunOS5.tar.gz">SunOS</a > > >. > > > ', > > > click on Linux). Following the instructions, this will result in an > > > installation of files in the directory /usr/pubsw/packages/mni/current. > > > Then, the line: > > > > > > source $FREESURFER_HOME/FreeSurferEnv.csh > > > > > > will add MINC_BIN_DIR to the path. > > > > > > Also, where the instructions say to type: > > > > > > ln -s `which perl` perl > > > > > > be sure you are using the ` key, which is the far upper left corner key > > on > > > the keyboard (not to be confused with the ' key). > > > > > > The important thing is to have perl in the /usr/pubsw/bin directory. If > > > its already there, then no need to create a link. > > > > > > Hope this helps. > > > > > > Nick > > > > > > > > > > > > On Fri, 2005-06-10 at 16:51 -0500, Arvind Gururajan wrote: > > > <BLOCKQUOTE TYPE=CITE> > > > <PRE> > > > Hi Nick, > > > > > > I am running it on Linux platform. I followed the > > same > > > instruction > > > described here. > > > <A > > > > > HREF="http://surfer.nmr.mgh.harvard.edu/freesurfer/minc-download.html">http > > :/ > > > /surfer.nmr.mgh.harvard.edu/freesurfer/minc-download.html</a> > > > and downloaded these two files: NetCDF 3.5.0 and > > MINC > > > 1.0 > > > > > > I am not sure, if I created the symbolic link > > > correctly. > > > ln -s 5.8.0 perl - > > > ln: `perl': File exists [ Same output even the > > first > > > time] > > > > > > Also, there are no tools in the path, I manually > > > created current/bin and > > > current/lib. Is there a way to fix this, can I > > moved > > > all the tools to these > > > two directories? > > > > > > Your help is really appreciated. > > > > > > Arvind Gururajan > > > > > > > > > > > > On 10 Jun 2005, Nick Schmansky wrote: > > > > Arvind, > > > > > > > > Hi. On what platform are you running? Linux? > > > > > > > > > > > Did you follow the special installation > > > instructions, involving making > > > > the symbolic links? Lastly, are the tools in > > your > > > path? > > > > > > > > If you are feeling brave, an alternative to > > > installing the binaries is > > > > to compile the MNI package from source on your > > > platform, and install > > > > those binaries. Instructions to do this are > > > here: > > > > > > > > <A > > > > > HREF="ftp://surfer.nmr.mgh.harvard.edu/pub/dist/mni.srcbuild.README">ftp:// > > su > > > rfer.nmr.mgh.harvard.edu/pub/dist/mni.srcbuild.README</a> > > > > > > > > and the gzip file is here: > > > > > > > > <A > > > > > HREF="ftp://surfer.nmr.mgh.harvard.edu/pub/dist/mni.srcbuild.tar.gz">ftp:// > > su > > > rfer.nmr.mgh.harvard.edu/pub/dist/mni.srcbuild.tar.gz</a> > > > > > > > > > > > > Nick > > > > > > > > > > > > > > > > On Fri, 2005-06-10 at 12:20 -0500, Arvind > > > Gururajan wrote: > > > > > > > > > Hi, > > > > > > > > > > I downloaded the entire MNI package. Although > > > I see all these MNI > > > files, I > > > > > still get the same error, file not found. Any > > > clues why this might be? > > > > > > > > > > > > > > > Thanks, > > > > > > > > > > Arvind Gururajan > > > > > > > > > > On 9 Jun 2005, Bruce Fischl wrote: > > > > > > just download and install the whole MNI > > > package. Much easier than > > > trying > > > > > > to install various pieces.... > > > > > > > > > > > > On Thu, 9 Jun 2005, Arvind Gururajan > > > wrote: > > > > > > > > > > > > > Hello, > > > > > > > > > > > > > > I am very new to Freesurfer. Could > > > anybody please tell me which > > > > > specific > > > > > > > MNI tool, I need to install? > > > > > > > > > > > > > > > > > > > > >> > > > > > > >> I tried the following > > > command. > > > > > > >> > > > > > > >> ./recon-all -smooth1 ZM > > > > > > >> > > > ######################################## > > > > > > >> program versions used > > > > > > >> $Id: recon-all-nmr,v 1.37 > > > 2004/01/06 22:21:48 tosa Exp $ > > > > > > >> $Id: mri_motion_correct2,v 1.7 > > > 2004/01/16 20:25:10 tosa Exp $fire > > > > > > >> mri_convert --version > > > > > > >> $ > > > > > > >> strings: rawtominc:: No such > > > file or directory > > > > > > >> strings: Command: No such file > > > or directory > > > > > > >> strings: not: No such file or > > > directory > > > > > > >> strings: found.: No such file > > > or directory > > > > > > >> strings: minctracc:: No such > > > file or directory > > > > > > >> strings: Command: No such file > > > or directory > > > > > > >> strings: not: No such file or > > > directory > > > > > > >> strings: found.: No such file > > > or directory > > > > > > >> strings: mincresample:: No such > > > file or directory > > > > > > >> strings: Command: No such file > > > or directory > > > > > > >> strings: not: No such file or > > > directory > > > > > > >> strings: found.: No such file > > > or directory > > > > > > >> strings: mincaverage:: No such > > > file or directory > > > > > > >> strings: Command: No such file > > > or directory > > > > > > >> strings: not: No such file or > > > directory > > > > > > >> strings: found.: No such file > > > or directory > > > > > > >> $Id: talairach2,v 1.5 > > > 2003/08/28 21:45:48 tosa Exp $ > > > > > > >> mri_convert --version > > > > > > >> $ > > > > > > >> strings: mritotal:: No such > > > file or directory > > > > > > >> strings: Command: No such file > > > or directory > > > > > > >> strings: not: No such file or > > > directory > > > > > > >> strings: found.: No such file > > > or directory > > > > > > >> strings: nu_correct:: No such > > > file or directory > > > > > > >> strings: Command: No such file > > > or directory > > > > > > >> strings: not: No such file or > > > directory > > > > > > >> strings: found.: No such file > > > or directory > > > > > > >> $ > > > > > > >> $ > > > > > > >> $ > > > > > > >> $ > > > > > > >> $ > > > > > > >> $ > > > > > > >> $ > > > > > > >> $ > > > > > > >> $ > > > > > > >> $ > > > > > > >> $ > > > > > > >> $ > > > > > > >> $ > > > > > > >> $ > > > > > > >> $ > > > > > > >> $ > > > > > > >> > > > ####################################### > > > > > > >> ERROR: Flag ZM > > > unrecognized. > > > > > > >> -smooth1 ZM > > > > > > >> > > > > > > >> > > > > > > >> The folder ZM has only one orig > > > file in the surf directory. There > > > are > > > > > no > > > > > > >> raw data(.COR files). Please > > > let me know your feedback. > > > > > > >> > > > > > > >> Sincerely, > > > > > > >> > > > > > > >> Arvind Gururajan > > > > > > > > > > > > > > > > > _______________________________________________ > > > > > > > Freesurfer mailing list > > > > > > > <A > > > > > HREF="mailto:Freesurfer@nmr.mgh.harvard.edu">Freesurfer(a)nmr.mgh.harvard.edu > > </ > > > A> > > > > > > > <A > > > > > HREF="https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer">https:/ > > /m > > > ail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer</a> > > > > > > > > > > > > > > > > _______________________________________________ > > > > > > Freesurfer mailing list > > > > > > <A > > > > > HREF="mailto:Freesurfer@nmr.mgh.harvard.edu">Freesurfer(a)nmr.mgh.harvard.edu > > </ > > > A> > > > > > > <A > > > > > HREF="https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer">https:/ > > /m > > > ail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer</a> > > > > > > > > > > > > > > > > > > > > > > > > _______________________________________________ > > > > > Freesurfer mailing list > > > > > <A > > > > > HREF="mailto:Freesurfer@nmr.mgh.harvard.edu">Freesurfer(a)nmr.mgh.harvard.edu > > </ > > > A> > > > > > <A > > > > > HREF="https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer">https:/ > > /m > > > ail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer</a> > > > > > > > > > > > > > > COLOR="#000000">_______________________________________________ > > > Freesurfer mailing list > > > <A > > > > > HREF="mailto:Freesurfer@nmr.mgh.harvard.edu">Freesurfer(a)nmr.mgh.harvard.edu > > </ > > > A> > > > <A > > > > > HREF="https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer">https:/ > > /m > > > ail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer</a> > > > </pre> > > > </blockquote> > > > </body> > > > </html> > > > > > > --=-yST7vkqiza7BNyzh64R8-- > > > > > > > > > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer(a)nmr.mgh.harvard.edu > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >

2 1

Re: [Freesurfer] (MNI tools)
by Arvind Gururajan 13 Jun '05

13 Jun '05

Nick, Thanks for the clear description. I repeated the exact installation and got the same errors. I noticed that the 'current' directory was wrongly placed in this path. /usr/pubsw/mni/current. Repeated the same steps again, but now installed in the right directory. Getting the following errors: [root@node1 noarch]# ./recon-all -smooth1 ZM ######################################## program versions used $Id: recon-all-nmr,v 1.37 2004/01/06 22:21:48 tosa Exp $ $Id: mri_motion_correct2,v 1.7 2004/01/16 20:25:10 tosa Exp $ mri_convert --version $ $Header: /software/source/minc/cvsroot/minc/progs/rawtominc/rawtominc.c,v 6.3 1999/10/19 14:45:31 neelin Exp $ minctracc.c $Header: /software/source/registration/mni_autoreg/minctracc/Main/minctracc.c,v 96.3 2000/03/15 08:42:41 stever Exp $ $Header: /software/source/minc/cvsroot/minc/progs/mincresample/mincresample.c,v 6.2 1999/10/19 14:45:27 neelin Exp $ $Header: /software/source/minc/cvsroot/minc/progs/mincaverage/mincaverage.c,v 6.1 1999/10/19 14:45:18 neelin Exp $ $Id: talairach2,v 1.5 2003/08/28 21:45:48 tosa Exp $ mri_convert --version $ # $Id: mritotal.in,v 1.10 2000/06/14 12:55:01 louis Exp $ # $Id: nu_estimate.in,v 1.15 1999/08/10 18:05:42 jgsled Exp $ $ $ $ $ $ $ $ $ $ $ $ $ $ $ $ $ ####################################### ERROR: Flag ZM unrecognized. -smooth1 ZM Your feedback will be appreciated. Thanks, Arvind On 10 Jun 2005, Nick Schmansky wrote: > > --=-yST7vkqiza7BNyzh64R8 > Content-Type: text/plain > Content-Transfer-Encoding: 7bit > > Arvind > > I'm suspect that our instructions may be a bit confusing. The files to > download are not the netcdf and minc files from the MNI distribution > site, but rather the file mni.Linux.tar.gz from our site (where it says > 'Download MNI binaries for Linux and/or SunOS.', click on Linux). > Following the instructions, this will result in an installation of files > in the directory /usr/pubsw/packages/mni/current. Then, the line: > > source $FREESURFER_HOME/FreeSurferEnv.csh > > will add MINC_BIN_DIR to the path. > > Also, where the instructions say to type: > > ln -s `which perl` perl > > be sure you are using the ` key, which is the far upper left corner key > on the keyboard (not to be confused with the ' key). > > The important thing is to have perl in the /usr/pubsw/bin directory. If > its already there, then no need to create a link. > > Hope this helps. > > Nick > > > > On Fri, 2005-06-10 at 16:51 -0500, Arvind Gururajan wrote: > > > Hi Nick, > > > > I am running it on Linux platform. I followed the same instruction > > described here. > > http://surfer.nmr.mgh.harvard.edu/freesurfer/minc-download.html > > and downloaded these two files: NetCDF 3.5.0 and MINC 1.0 > > > > I am not sure, if I created the symbolic link correctly. > > ln -s 5.8.0 perl - > > ln: `perl': File exists [ Same output even the first time] > > > > Also, there are no tools in the path, I manually created current/bin and > > current/lib. Is there a way to fix this, can I moved all the tools to these > > two directories? > > > > Your help is really appreciated. > > > > Arvind Gururajan > > > > > > > > On 10 Jun 2005, Nick Schmansky wrote: > > > Arvind, > > > > > > Hi. On what platform are you running? Linux? > > > > > > Did you follow the special installation instructions, involving making > > > the symbolic links? Lastly, are the tools in your path? > > > > > > If you are feeling brave, an alternative to installing the binaries is > > > to compile the MNI package from source on your platform, and install > > > those binaries. Instructions to do this are here: > > > > > > ftp://surfer.nmr.mgh.harvard.edu/pub/dist/mni.srcbuild.README > > > > > > and the gzip file is here: > > > > > > ftp://surfer.nmr.mgh.harvard.edu/pub/dist/mni.srcbuild.tar.gz > > > > > > > > > Nick > > > > > > > > > > > > On Fri, 2005-06-10 at 12:20 -0500, Arvind Gururajan wrote: > > > > > > > Hi, > > > > > > > > I downloaded the entire MNI package. Although I see all these MNI > > files, I > > > > still get the same error, file not found. Any clues why this might be? > > > > > > > > > > > > Thanks, > > > > > > > > Arvind Gururajan > > > > > > > > On 9 Jun 2005, Bruce Fischl wrote: > > > > > just download and install the whole MNI package. Much easier than > > trying > > > > > to install various pieces.... > > > > > > > > > > On Thu, 9 Jun 2005, Arvind Gururajan wrote: > > > > > > > > > > > Hello, > > > > > > > > > > > > I am very new to Freesurfer. Could anybody please tell me which > > > > specific > > > > > > MNI tool, I need to install? > > > > > > > > > > > > > > > > > >> > > > > > >> I tried the following command. > > > > > >> > > > > > >> ./recon-all -smooth1 ZM > > > > > >> ######################################## > > > > > >> program versions used > > > > > >> $Id: recon-all-nmr,v 1.37 2004/01/06 22:21:48 tosa Exp $ > > > > > >> $Id: mri_motion_correct2,v 1.7 2004/01/16 20:25:10 tosa Exp $fire > > > > > >> mri_convert --version > > > > > >> $ > > > > > >> strings: rawtominc:: No such file or directory > > > > > >> strings: Command: No such file or directory > > > > > >> strings: not: No such file or directory > > > > > >> strings: found.: No such file or directory > > > > > >> strings: minctracc:: No such file or directory > > > > > >> strings: Command: No such file or directory > > > > > >> strings: not: No such file or directory > > > > > >> strings: found.: No such file or directory > > > > > >> strings: mincresample:: No such file or directory > > > > > >> strings: Command: No such file or directory > > > > > >> strings: not: No such file or directory > > > > > >> strings: found.: No such file or directory > > > > > >> strings: mincaverage:: No such file or directory > > > > > >> strings: Command: No such file or directory > > > > > >> strings: not: No such file or directory > > > > > >> strings: found.: No such file or directory > > > > > >> $Id: talairach2,v 1.5 2003/08/28 21:45:48 tosa Exp $ > > > > > >> mri_convert --version > > > > > >> $ > > > > > >> strings: mritotal:: No such file or directory > > > > > >> strings: Command: No such file or directory > > > > > >> strings: not: No such file or directory > > > > > >> strings: found.: No such file or directory > > > > > >> strings: nu_correct:: No such file or directory > > > > > >> strings: Command: No such file or directory > > > > > >> strings: not: No such file or directory > > > > > >> strings: found.: No such file or directory > > > > > >> $ > > > > > >> $ > > > > > >> $ > > > > > >> $ > > > > > >> $ > > > > > >> $ > > > > > >> $ > > > > > >> $ > > > > > >> $ > > > > > >> $ > > > > > >> $ > > > > > >> $ > > > > > >> $ > > > > > >> $ > > > > > >> $ > > > > > >> $ > > > > > >> ####################################### > > > > > >> ERROR: Flag ZM unrecognized. > > > > > >> -smooth1 ZM > > > > > >> > > > > > >> > > > > > >> The folder ZM has only one orig file in the surf directory. There > > are > > > > no > > > > > >> raw data(.COR files). Please let me know your feedback. > > > > > >> > > > > > >> Sincerely, > > > > > >> > > > > > >> Arvind Gururajan > > > > > > > > > > > > _______________________________________________ > > > > > > Freesurfer mailing list > > > > > > Freesurfer(a)nmr.mgh.harvard.edu > > > > > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > > > > > > > _______________________________________________ > > > > > Freesurfer mailing list > > > > > Freesurfer(a)nmr.mgh.harvard.edu > > > > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > > > > > > > > > > > > > _______________________________________________ > > > > Freesurfer mailing list > > > > Freesurfer(a)nmr.mgh.harvard.edu > > > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer(a)nmr.mgh.harvard.edu > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > --=-yST7vkqiza7BNyzh64R8 > Content-Type: text/html; charset=utf-8 > Content-Transfer-Encoding: 7bit > > <!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 TRANSITIONAL//EN"> > <HTML> > <HEAD> > <META HTTP-EQUIV="Content-Type" CONTENT="text/html; CHARSET=UTF-8"> > <META NAME="GENERATOR" CONTENT="GtkHTML/3.3.2"> > </head> > <BODY> > Arvind > > I'm suspect that our instructions may be a bit confusing. The files to > download are not the netcdf and minc files from the MNI distribution site, > but rather the file mni.Linux.tar.gz from our site (where it says 'Download > MNI binaries for <A > HREF="ftp://surfer.nmr.mgh.harvard.edu/pub/dist/mni.Linux.tar.gz">Linux</a> > and/or <A > HREF="ftp://surfer.nmr.mgh.harvard.edu/pub/dist/mni.SunOS5.tar.gz">SunOS</a >. > ', > click on Linux). Following the instructions, this will result in an > installation of files in the directory /usr/pubsw/packages/mni/current. > Then, the line: > > source $FREESURFER_HOME/FreeSurferEnv.csh > > will add MINC_BIN_DIR to the path. > > Also, where the instructions say to type: > > ln -s `which perl` perl > > be sure you are using the ` key, which is the far upper left corner key on > the keyboard (not to be confused with the ' key). > > The important thing is to have perl in the /usr/pubsw/bin directory. If > its already there, then no need to create a link. > > Hope this helps. > > Nick > > > > On Fri, 2005-06-10 at 16:51 -0500, Arvind Gururajan wrote: > <BLOCKQUOTE TYPE=CITE> > <PRE> > Hi Nick, > > I am running it on Linux platform. I followed the same > instruction > described here. > <A > HREF="http://surfer.nmr.mgh.harvard.edu/freesurfer/minc-download.html">http :/ > /surfer.nmr.mgh.harvard.edu/freesurfer/minc-download.html</a> > and downloaded these two files: NetCDF 3.5.0 and MINC > 1.0 > > I am not sure, if I created the symbolic link > correctly. > ln -s 5.8.0 perl - > ln: `perl': File exists [ Same output even the first > time] > > Also, there are no tools in the path, I manually > created current/bin and > current/lib. Is there a way to fix this, can I moved > all the tools to these > two directories? > > Your help is really appreciated. > > Arvind Gururajan > > > > On 10 Jun 2005, Nick Schmansky wrote: > > Arvind, > > > > Hi. On what platform are you running? Linux? > > > > > Did you follow the special installation > instructions, involving making > > the symbolic links? Lastly, are the tools in your > path? > > > > If you are feeling brave, an alternative to > installing the binaries is > > to compile the MNI package from source on your > platform, and install > > those binaries. Instructions to do this are > here: > > > > <A > HREF="ftp://surfer.nmr.mgh.harvard.edu/pub/dist/mni.srcbuild.README">ftp:// su > rfer.nmr.mgh.harvard.edu/pub/dist/mni.srcbuild.README</a> > > > > and the gzip file is here: > > > > <A > HREF="ftp://surfer.nmr.mgh.harvard.edu/pub/dist/mni.srcbuild.tar.gz">ftp:// su > rfer.nmr.mgh.harvard.edu/pub/dist/mni.srcbuild.tar.gz</a> > > > > > > Nick > > > > > > > > On Fri, 2005-06-10 at 12:20 -0500, Arvind > Gururajan wrote: > > > > > Hi, > > > > > > I downloaded the entire MNI package. Although > I see all these MNI > files, I > > > still get the same error, file not found. Any > clues why this might be? > > > > > > > > > Thanks, > > > > > > Arvind Gururajan > > > > > > On 9 Jun 2005, Bruce Fischl wrote: > > > > just download and install the whole MNI > package. Much easier than > trying > > > > to install various pieces.... > > > > > > > > On Thu, 9 Jun 2005, Arvind Gururajan > wrote: > > > > > > > > > Hello, > > > > > > > > > > I am very new to Freesurfer. Could > anybody please tell me which > > > specific > > > > > MNI tool, I need to install? > > > > > > > > > > > > > > >> > > > > >> I tried the following > command. > > > > >> > > > > >> ./recon-all -smooth1 ZM > > > > >> > ######################################## > > > > >> program versions used > > > > >> $Id: recon-all-nmr,v 1.37 > 2004/01/06 22:21:48 tosa Exp $ > > > > >> $Id: mri_motion_correct2,v 1.7 > 2004/01/16 20:25:10 tosa Exp $fire > > > > >> mri_convert --version > > > > >> $ > > > > >> strings: rawtominc:: No such > file or directory > > > > >> strings: Command: No such file > or directory > > > > >> strings: not: No such file or > directory > > > > >> strings: found.: No such file > or directory > > > > >> strings: minctracc:: No such > file or directory > > > > >> strings: Command: No such file > or directory > > > > >> strings: not: No such file or > directory > > > > >> strings: found.: No such file > or directory > > > > >> strings: mincresample:: No such > file or directory > > > > >> strings: Command: No such file > or directory > > > > >> strings: not: No such file or > directory > > > > >> strings: found.: No such file > or directory > > > > >> strings: mincaverage:: No such > file or directory > > > > >> strings: Command: No such file > or directory > > > > >> strings: not: No such file or > directory > > > > >> strings: found.: No such file > or directory > > > > >> $Id: talairach2,v 1.5 > 2003/08/28 21:45:48 tosa Exp $ > > > > >> mri_convert --version > > > > >> $ > > > > >> strings: mritotal:: No such > file or directory > > > > >> strings: Command: No such file > or directory > > > > >> strings: not: No such file or > directory > > > > >> strings: found.: No such file > or directory > > > > >> strings: nu_correct:: No such > file or directory > > > > >> strings: Command: No such file > or directory > > > > >> strings: not: No such file or > directory > > > > >> strings: found.: No such file > or directory > > > > >> $ > > > > >> $ > > > > >> $ > > > > >> $ > > > > >> $ > > > > >> $ > > > > >> $ > > > > >> $ > > > > >> $ > > > > >> $ > > > > >> $ > > > > >> $ > > > > >> $ > > > > >> $ > > > > >> $ > > > > >> $ > > > > >> > ####################################### > > > > >> ERROR: Flag ZM > unrecognized. > > > > >> -smooth1 ZM > > > > >> > > > > >> > > > > >> The folder ZM has only one orig > file in the surf directory. There > are > > > no > > > > >> raw data(.COR files). Please > let me know your feedback. > > > > >> > > > > >> Sincerely, > > > > >> > > > > >> Arvind Gururajan > > > > > > > > > > > _______________________________________________ > > > > > Freesurfer mailing list > > > > > <A > HREF="mailto:Freesurfer@nmr.mgh.harvard.edu">Freesurfer(a)nmr.mgh.harvard.edu </ > A> > > > > > <A > HREF="https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer">https:/ /m > ail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer</a> > > > > > > > > > > _______________________________________________ > > > > Freesurfer mailing list > > > > <A > HREF="mailto:Freesurfer@nmr.mgh.harvard.edu">Freesurfer(a)nmr.mgh.harvard.edu </ > A> > > > > <A > HREF="https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer">https:/ /m > ail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer</a> > > > > > > > > > > > > > > _______________________________________________ > > > Freesurfer mailing list > > > <A > HREF="mailto:Freesurfer@nmr.mgh.harvard.edu">Freesurfer(a)nmr.mgh.harvard.edu </ > A> > > > <A > HREF="https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer">https:/ /m > ail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer</a> > > > > > _______________________________________________ > Freesurfer mailing list > <A > HREF="mailto:Freesurfer@nmr.mgh.harvard.edu">Freesurfer(a)nmr.mgh.harvard.edu </ > A> > <A > HREF="https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer">https:/ /m > ail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer</a> > </pre> > </blockquote> > </body> > </html> > > --=-yST7vkqiza7BNyzh64R8-- > >

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