Freesurfer June 2005

freesurfer@nmr.mgh.harvard.edu

35 participants
66 discussions

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

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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

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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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Re: [Freesurfer] dlcompat binaries needed.
by Nick Schmansky 13 Jun '05

13 Jun '05

Mark, Creating empty directories for the subjects and fsl/bin was the right solution to the warning messages you were seeing. I need to add stub directories with READMEs to the directory structure. The FreeSurferEnv.csh file (which I am guessing you 'source' in your .cshrc file) has some text on the environment variables it references, including SUBJECTS_DIR and FSL_DIR, which pertain to your question (remember to set these before sourcing FreeSurferEnv.csh). Here's a snippet from that file: ############################################################################# # Name: FreeSurferEnv.csh # Purpose: sets up the environment to run FreeSurfer and FS-FAST # Usage: # 1. Create an environment variable called FREESURFER_HOME and set it # to the directory in which FreeSurfer is installed. # 2. From a csh or tcsh shell or (.login): # source FreeSurferEnv.csh # 3. There are environment variables that should point to locations # of software or data used by FreeSurfer. If set prior # to sourcing, they will not be changed, but will otherwise be # set to default locations: # FSFAST_HOME # SUBJECTS_DIR # MINC_BIN_DIR # MINC_LIB_DIR # FSL_DIR # 4. If NO_MINC is set (to anything), then all the MINC stuff is ignored. # 5. If NO_FSFAST is set (to anything), then the startup.m stuff is # ignored # 6. The script will print the final settings for the above variables # as well as any warnings about missing directories. If # FS_FREESURFERENV_NO_OUTPUT is set, then no normal output will # be made (only error messages). # # The most convenient way to use this script is to write another # script that sets FREESURFER_HOME and possibly SUBJECTS_DIR for # your set-up, as well as NO_MINC, NO_FSFAST, or # FS_FREESURFERENV_NO_OUTPUT as appropriate, and then source this # script. Nick On Sat, 2005-06-11 at 00:21 -0400, Mark Pinsk wrote: > Hi Nick, > > Thanks for the Tiger installation. I just installed it on my ibook > just to see if it worked, and so far so good. I was able to get the > csurf GUI to pop up, so I'll have to run thru a subject on my G5 > desktop in the next few weeks after I get back from HBM. > > 1 question: > When I sourced my .cshrc file it could not find a 'subjects' directory > and a 'fsl/bin' directory within the freesurfer folder. > I went ahead and just created empty folders with those names so that > it wouldn't complain. > But for future reference, where can I define the location of my > subjects folder and of my FSL installation if they aren't within the > freesurfer folder? > > Thanks ! > Mark > > > On 6/10/05, Nick Schmansky <nicks(a)nmr.mgh.harvard.edu> wrote: > > Mark, > > > > I don't think dlcompat is required to run freesurfer. I am able to run it > > on a tiger machine without it. > > > > There is a new freesurfer build for Tiger just posted on the ftp site. Its > > a .dmg file, which is a compressed installation package. After download, a > > .mpkg file will appear, and clicking on that will begin the installation. > > > > The 'full' installation includes freesurfer binaries, support libraries and > > the MINC toolkit, all newly created on tiger from source. All install in > > /usr/pubsw/packages, thus Administrator access is required. The install > > location is not relocatable, as freesurfer depends on some fixed paths. A > > Fink installation is not necessary, as the support-libs packages includes > > everything freesurfer needs: jpeg, tiff, glut, tcl/tk, tix, blt and gsl. > > > > The full install file is at: > > > > ftp://surfer.nmr.mgh.harvard.edu > > and the file is called freesurfer-Darwin-tiger-full.dmg > > > > > > This is a work-in-progress, so I'd appreciate any comments, especially if > > it works for you. > > > > Nick > > > > > > > > On Fri, 2005-06-10 at 16:11 -0400, Mark Pinsk wrote: > > > > > > Hi, I just tried a fresh installation of freesurfer on a new OS X Tiger > > machine. > > > > Turns out that Fink is not longer offering the dlcompat library for > > download. > > > > Can anyone wrap those binaries up and send them to me, or post them > > for download by any chance? > > > > thanks so much! > > Mark > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer(a)nmr.mgh.harvard.edu > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > >

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Re: [Freesurfer] (MNI tools)
by Arvind Gururajan 10 Jun '05

10 Jun '05

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 >

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dlcompat binaries needed.
by Mark Pinsk 10 Jun '05

10 Jun '05

Hi, I just tried a fresh installation of freesurfer on a new OS X Tiger machine. Turns out that Fink is not longer offering the dlcompat library for download. Can anyone wrap those binaries up and send them to me, or post them for download by any chance? thanks so much! Mark

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Freesurfer June 2005