Freesurfer February 2010

freesurfer@nmr.mgh.harvard.edu

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153 discussions

Re: [Freesurfer] recon-all doesn't recon-all
by Janani Dhinakaran 22 Feb '10

22 Feb '10

On 22 February 2010 16:27, Janani Dhinakaran <janinthesky(a)gmail.com> wrote: > When I set SUBJECTS_DIR to /Desktop/..... I get this > > s0964091@CRIC-0012:~$ export > SUBJECTS_DIR=~/Desktop/Allimages/MRIscan/janani/CRIC-0014_5679.adb.DICOM/ > s0964091@CRIC-0012:~$ echo $SUBJECTS_DIR > /home/s0964091/Desktop/Allimages/MRIscan/janani/CRIC-0014_5679.adb.DICOM/ > > Which makes it part of home anyway. > > When I add home into the path I get a double- > > s0964091@CRIC-0012:~$ export > SUBJECTS_DIR=~/home/s0964091/Desktop/Allimages/MRIscan/janani/CRIC-0014_5679.adb.DICOM > s0964091@CRIC-0012:~$ echo $SUBJECTS_DIR > > /home/s0964091/home/s0964091/Desktop/Allimages/MRIscan/janani/CRIC-0014_5679.adb.DICOM > > And the Recon-all has errors too. > > > s0964091@CRIC-0012:~$ recon-all -i > /home/s0964091/Desktop/Allimages/MRIscan/janani/CRIC-0014_5679.adb.DICOM/Dhinakaran^Janani^-0002-0001-00001.dcm > -i > /home/s0964091/Desktop/Allimages/MRIscan/janani/CRIC-0014_5679.adb.DICOM/Dhinakaran^Janani^-0004-0001-00001.d > ERROR: cannot find > /home/s0964091/Desktop/Allimages/MRIscan/janani/CRIC-0014_5679.adb.DICOM/Dhinakaran^Janani^-0004-0001-00001.d > > Linux CRIC-0012 2.6.31-19-generic #56-Ubuntu SMP Thu Jan 28 02:39:34 UTC > 2010 x86_64 GNU/Linux > > recon-all exited with ERRORS at Mon Feb 22 16:24:46 GMT 2010 > > > It doesn't run recon at all. Unlike the previous command which did but > incompletely. > > Jan > > > > On 22 February 2010 16:21, Xue, Feng <xfgavin(a)gmail.com> wrote: > >> It seems that your problem is the recon-all script couldn't find your >> SUBJECTS_DIR, possibly because you didn't give it full path. So I >> suggest to try define SUBJECTS_DIR as >> /home/s0964091/Desktop/Allimages/MRIscan/janani/CRIC-0014_5679.adb.DICOM, >> then rerun your recon-all command as before. >> >> On Mon, Feb 22, 2010 at 10:44 PM, Janani Dhinakaran >> <janinthesky(a)gmail.com> wrote: >> > Is this what you meant: >> > >> > First I tried >> > s0964091@CRIC-0012:~$ recon-all >> > home/s0964091/Desktop/Allimages/MRIscan/janani/CRIC-0014_5679.adb.DICOM >> > ERROR: Flag >> > home/s0964091/Desktop/Allimages/MRIscan/janani/CRIC-0014_5679.adb.DICOM >> > unrecognized. >> > home/s0964091/Desktop/Allimages/MRIscan/janani/CRIC-0014_5679.adb.DICOM >> > Linux CRIC-0012 2.6.31-19-generic #56-Ubuntu SMP Thu Jan 28 02:39:34 UTC >> > 2010 x86_64 GNU/Linux >> > >> > recon-all exited with ERRORS at Mon Feb 22 14:39:27 GMT 2010 >> > >> > Then I tried putting full path in front of both file sets >> > >> > >> > s0964091@CRIC-0012:~$ recon-all -i >> > >> home/s0964091/Desktop/Allimages/MRIscan/janani/CRIC-0014_5679.adb.DICOM/Dhinakaran^Janani^-0002-0001-00001.dcm >> > -i >> > >> home/s0964091/Desktop/Allimages/MRIscan/janani/CRIC-0014_5679.adb.DICOM/Dhinakaran^Janani^-0004-0001-00001.dcm >> > -s subj001 >> > ERROR: cannot find >> > >> home/s0964091/Desktop/Allimages/MRIscan/janani/CRIC-0014_5679.adb.DICOM/Dhinakaran^Janani^-0002-0001-00001.dcm >> > Linux CRIC-0012 2.6.31-19-generic #56-Ubuntu SMP Thu Jan 28 02:39:34 UTC >> > 2010 x86_64 GNU/Linux >> > >> > recon-all exited with ERRORS at Mon Feb 22 14:41:36 GMT 2010 >> > >> > Jan >> > >> > >> > On 22 February 2010 14:30, Xue, Feng <xfgavin(a)gmail.com> wrote: >> >> >> >> Try with full path, e.g. >> >> >> /home/s0964091/Desktop/Allimages/MRIscan/janani/CRIC-0014_5679.adb.DICOM >> >> >> >> On Mon, Feb 22, 2010 at 7:36 PM, Janani Dhinakaran >> >> <janinthesky(a)gmail.com> wrote: >> >> > Hello, >> >> > I ran recon-all on Friday. It ran for around a minute instead of >> 30-48 >> >> > hours. Unfortunately, when I try tkmedit and other such commands, the >> >> > pictures don't visualise. >> >> > So today I first confirmed that the SUBJECTS_DIR was in Desktop path. >> >> > (Because over the weekend it had gone back to usr/local... path and >> so I >> >> > re-exported it just now.) >> >> > Then I tried running recon-all again. >> >> > >> >> > >> >> > >> >> > s0964091@CRIC-0012 >> :~/Desktop/Allimages/MRIscan/janani/CRIC-0014_5679.adb.DICOM$ >> >> > echo $SUBJECTS_DIR >> >> > Desktop/Allimages/MRIscan/janani/CRIC-0014_5679.adb.DICOM >> >> > >> >> > s0964091@CRIC-0012 >> :~/Desktop/Allimages/MRIscan/janani/CRIC-0014_5679.adb.DICOM$ >> >> > recon-all -i Dhinakaran^Janani^-0002-0001-00001.dcm -i >> >> > Dhinakaran^Janani^-0004-0001-00001.dcm -s subj001 >> >> > ERROR: SUBJECTS_DIR >> >> > Desktop/Allimages/MRIscan/janani/CRIC-0014_5679.adb.DICOM does not >> >> > exist. >> >> > >> >> > Can anyone help me understand what I can do? >> >> > Thanks >> >> > Jan >> >> > -- >> >> > I am the Sun, I know no darkness. >> >> > >> >> > _______________________________________________ >> >> > Freesurfer mailing list >> >> > Freesurfer(a)nmr.mgh.harvard.edu >> >> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> > >> >> >> >> >> >> >> >> -- >> >> Best Regards >> >> >> >> Xue, Feng Phd. candidate >> >> Major in Developmental Cognitive Neuroscience >> >> >> >> National Key Laboratory of Cognitive Neuroscience and Learning >> >> Beijing Normal University >> >> Beijing, China. 100875 >> >> Tel: +86-13810154455 >> >> web: http://psychbrain.bnu.edu.cn >> >> ============================================== >> >> Welcome to MuDuo JinSheng BBS @ Beijing Normal University >> >> telnet://bbs.mdjs.org >> >> http://bbs.mdjs.org >> > >> > >> > >> > -- >> > I am the Sun, I know no darkness. >> > >> >> >> >> -- >> Best Regards >> >> Xue, Feng Phd. candidate >> Major in Developmental Cognitive Neuroscience >> >> National Key Laboratory of Cognitive Neuroscience and Learning >> Beijing Normal University >> Beijing, China. 100875 >> Tel: +86-13810154455 >> web: http://psychbrain.bnu.edu.cn >> ============================================== >> Welcome to MuDuo JinSheng BBS @ Beijing Normal University >> telnet://bbs.mdjs.org >> http://bbs.mdjs.org >> > > > > -- > I am the Sun, I know no darkness. > -- I am the Sun, I know no darkness.

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Re: [Freesurfer] Freesurfer Digest, Vol 72, Issue 70
by Janani Dhinakaran 22 Feb '10

22 Feb '10

Thank you. I ran it correctly. It took less than a minute. Somethings not right. Here is a paste of everything past checking the SUBJECTS_DIR location with echo- s0964091@CRIC-0012:~$ echo $SUBJECTS_DIR /home/s0964091/Desktop/Allimages/MRIscan/janani/CRIC-0014_5679.adb.DICOM/ s0964091@CRIC-0012:~$ recon-all -i /home/s0964091/Desktop/Allimages/MRIscan/janani/CRIC-0014_5679.adb.DICOM/Dhinakaran^Janani^-0002-0001-00001.dcm -i /home/s0964091/Desktop/Allimages/MRIscan/janani/CRIC-0014_5679.adb.DICOM/Dhinakaran^Janani^-0004-0001-00001.dcm -s subj001 Subject Stamp: freesurfer-Linux-centos4_x86_64-stable-pub-v4.5.0 Current Stamp: freesurfer-Linux-centos4_x86_64-stable-pub-v4.5.0 INFO: SUBJECTS_DIR is /home/s0964091/Desktop/Allimages/MRIscan/janani/CRIC-0014_5679.adb.DICOM Actual FREESURFER_HOME /usr/local/freesurfer Linux CRIC-0012 2.6.31-19-generic #56-Ubuntu SMP Thu Jan 28 02:39:34 UTC 2010 x86_64 GNU/Linux /home/s0964091/Desktop/Allimages/MRIscan/janani/CRIC-0014_5679.adb.DICOM/subj001 mri_convert /home/s0964091/Desktop/Allimages/MRIscan/janani/CRIC-0014_5679.adb.DICOM/Dhinakaran^Janani^-0002-0001-00001.dcm /home/s0964091/Desktop/Allimages/MRIscan/janani/CRIC-0014_5679.adb.DICOM/subj001/mri/orig/001.mgz mri_convert /home/s0964091/Desktop/Allimages/MRIscan/janani/CRIC-0014_5679.adb.DICOM/Dhinakaran^Janani^-0002-0001-00001.dcm /home/s0964091/Desktop/Allimages/MRIscan/janani/CRIC-0014_5679.adb.DICOM/subj001/mri/orig/001.mgz $Id: mri_convert.c,v 1.146.2.5 2009/04/08 18:40:23 nicks Exp $ reading from /home/s0964091/Desktop/Allimages/MRIscan/janani/CRIC-0014_5679.adb.DICOM/Dhinakaran^Janani^-0002-0001-00001.dcm... Getting Series No INFO: Found 751 files in /home/s0964091/Desktop/Allimages/MRIscan/janani/CRIC-0014_5679.adb.DICOM INFO: Scanning for Series Number 2 Scanning Directory INFO: found 176 files in series INFO: loading series header info. RunNo = 1 INFO: sorting. INFO: (512 512 176), nframes = 1, ismosaic=0 PE Dir ROW ROW AutoAlign matrix detected AutoAlign Matrix --------------------- 1.000 0.000 0.000 0.000; 0.000 1.000 0.000 0.000; 0.000 0.000 1.000 0.000; 0.000 0.000 0.000 1.000; FileName /home/s0964091/Desktop/Allimages/MRIscan/janani/CRIC-0014_5679.adb.DICOM/Dhinakaran^Janani^-0002-0001-00001.dcm Identification NumarisVer syngo MR B17 ScannerModel Verio PatientName Dhinakaran^Janani^ Date and time StudyDate 20100126 StudyTime 141335.671000 SeriesTime 142623.875000 AcqTime 142155.855000 Acquisition parameters PulseSeq tfl3d1_ns Protocol t1_mpr_ns_sag_p2_iso PhEncDir ROW EchoNo 1 FlipAngle 9 EchoTime 2.48 InversionTime 900 RepetitionTime 1900 PhEncFOV 250 ReadoutFOV 250 Image information RunNo 1 SeriesNo 2 ImageNo 1 NImageRows 512 NImageCols 512 NFrames 1 SliceArraylSize 1 IsMosaic 0 ImgPos 90.3776 114.4676 105.9606 VolRes 0.4883 0.4883 1.0000 VolDim 512 512 176 Vc -0.0244 -0.9997 -0.0000 Vr -0.0170 0.0004 -0.9999 Vs -0.9996 0.0244 0.0170 VolCenter -2.7567 -8.2942 -17.5285 TransferSyntaxUID 1.2.840.10008.1.2.1 INFO: no Siemens slice order reversal detected (good!). TR=1900.00, TE=2.48, TI=900.00, flip angle=9.00 i_ras = (-0.0244253, -0.999702, -2.75516e-09) j_ras = (-0.0169601, 0.000414383, -0.999856) k_ras = (-0.999558, 0.0244218, 0.0169652) writing to /home/s0964091/Desktop/Allimages/MRIscan/janani/CRIC-0014_5679.adb.DICOM/subj001/mri/orig/001.mgz... /home/s0964091/Desktop/Allimages/MRIscan/janani/CRIC-0014_5679.adb.DICOM/subj001 mri_convert /home/s0964091/Desktop/Allimages/MRIscan/janani/CRIC-0014_5679.adb.DICOM/Dhinakaran^Janani^-0004-0001-00001.dcm /home/s0964091/Desktop/Allimages/MRIscan/janani/CRIC-0014_5679.adb.DICOM/subj001/mri/orig/002.mgz mri_convert /home/s0964091/Desktop/Allimages/MRIscan/janani/CRIC-0014_5679.adb.DICOM/Dhinakaran^Janani^-0004-0001-00001.dcm /home/s0964091/Desktop/Allimages/MRIscan/janani/CRIC-0014_5679.adb.DICOM/subj001/mri/orig/002.mgz $Id: mri_convert.c,v 1.146.2.5 2009/04/08 18:40:23 nicks Exp $ reading from /home/s0964091/Desktop/Allimages/MRIscan/janani/CRIC-0014_5679.adb.DICOM/Dhinakaran^Janani^-0004-0001-00001.dcm... Getting Series No INFO: Found 751 files in /home/s0964091/Desktop/Allimages/MRIscan/janani/CRIC-0014_5679.adb.DICOM INFO: Scanning for Series Number 4 Scanning Directory INFO: found 176 files in series INFO: loading series header info. RunNo = 3 INFO: sorting. INFO: (512 512 176), nframes = 1, ismosaic=0 PE Dir ROW ROW AutoAlign matrix detected AutoAlign Matrix --------------------- 1.000 0.000 0.000 0.000; 0.000 1.000 0.000 0.000; 0.000 0.000 1.000 0.000; 0.000 0.000 0.000 1.000; FileName /home/s0964091/Desktop/Allimages/MRIscan/janani/CRIC-0014_5679.adb.DICOM/Dhinakaran^Janani^-0004-0001-00001.dcm Identification NumarisVer syngo MR B17 ScannerModel Verio PatientName Dhinakaran^Janani^ Date and time StudyDate 20100126 StudyTime 141335.671000 SeriesTime 144205.640000 AcqTime 143536.830000 Acquisition parameters PulseSeq tfl3d1_ns Protocol t1_mpr_ns_sag_p2_iso PhEncDir ROW EchoNo 1 FlipAngle 9 EchoTime 2.64 InversionTime 900 RepetitionTime 1900 PhEncFOV 192 ReadoutFOV 192 Image information RunNo 3 SeriesNo 4 ImageNo 1 NImageRows 512 NImageCols 512 NFrames 1 SliceArraylSize 1 IsMosaic 0 ImgPos 72.1091 90.1873 96.0943 VolRes 0.3750 0.3750 0.8000 VolDim 512 512 176 Vc -0.0244 -0.9997 -0.0000 Vr -0.0170 0.0004 -0.9999 Vs -0.9996 0.0244 0.0170 VolCenter -2.2327 -4.0250 1.3025 TransferSyntaxUID 1.2.840.10008.1.2.1 INFO: no Siemens slice order reversal detected (good!). TR=1900.00, TE=2.64, TI=900.00, flip angle=9.00 i_ras = (-0.0244253, -0.999702, -2.75516e-09) j_ras = (-0.0169601, 0.000414383, -0.999856) k_ras = (-0.999558, 0.0244218, 0.0169652) writing to /home/s0964091/Desktop/Allimages/MRIscan/janani/CRIC-0014_5679.adb.DICOM/subj001/mri/orig/002.mgz... #------------------------------------------ recon-all finished without error at Mon Feb 22 16:08:03 GMT 2010 done It didn't recon ALL. Anyone know what I'm doing wrong? Thanks Jan On 22 February 2010 15:48, Justin Ales <justin.ales(a)gmail.com> wrote: > I think you're missing the leading / in your full path > > home/s0964091/Desktop/Allimages/MRIscan/janani/CRIC-0014_5679.adb.DICOM/ > > should be: > > /home/s0964091/Desktop/Allimages/MRIscan/janani/CRIC-0014_5679.adb.DICOM/ > > and the export line should be: > > export SUBJECTS_DIR=~/Desktop/Allimages/MRIscan/ > > > SUBJECTS_DIR is the directory which contains ALL subjects _not_ the > current subject. > > > Justin Ales > > > From: Sita Kakunoori <sita(a)nmr.mgh.harvard.edu> > To: Janani Dhinakaran <janinthesky(a)gmail.com> > Date: Mon, 22 Feb 2010 10:26:50 -0500 (EST) > Subject: Re: [Freesurfer] recon-all doesn't recon-all > > Hi Jan, > > Please try rerunning recon-all after removing the spaces or special > characters (if there are any) in the dicom files. > > Sita. > > > > On Mon, 22 Feb 2010, Janani Dhinakaran wrote: > > Is this what you meant: > > First I tried > s0964091@CRIC-0012:~$ recon-all > home/s0964091/Desktop/Allimages/MRIscan/janani/CRIC-0014_5679.adb.DICOM > ERROR: Flag > home/s0964091/Desktop/Allimages/MRIscan/janani/CRIC-0014_5679.adb.DICOM > unrecognized. > home/s0964091/Desktop/Allimages/MRIscan/janani/CRIC-0014_5679.adb.DICOM > Linux CRIC-0012 2.6.31-19-generic #56-Ubuntu SMP Thu Jan 28 02:39:34 UTC > 2010 x86_64 GNU/Linux > > recon-all exited with ERRORS at Mon Feb 22 14:39:27 GMT 2010 > > Then I tried putting full path in front of both file sets > > > s0964091@CRIC-0012:~$ recon-all -i > > home/s0964091/Desktop/Allimages/MRIscan/janani/CRIC-0014_5679.adb.DICOM/Dhinakaran^Janani^-0002-0001-00001.dcm > -i > > home/s0964091/Desktop/Allimages/MRIscan/janani/CRIC-0014_5679.adb.DICOM/Dhinakaran^Janani^-0004-0001-00001.dcm > -s subj001 > ERROR: cannot find > > home/s0964091/Desktop/Allimages/MRIscan/janani/CRIC-0014_5679.adb.DICOM/Dhinakaran^Janani^-0002-0001-00001.dcm > Linux CRIC-0012 2.6.31-19-generic #56-Ubuntu SMP Thu Jan 28 02:39:34 UTC > 2010 x86_64 GNU/Linux > > recon-all exited with ERRORS at Mon Feb 22 14:41:36 GMT 2010 > > Jan > > On Mon, Feb 22, 2010 at 7:36 AM, > <freesurfer-request(a)nmr.mgh.harvard.edu> wrote: > > Send Freesurfer mailing list submissions to > > freesurfer(a)nmr.mgh.harvard.edu > > > > To subscribe or unsubscribe via the World Wide Web, visit > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > or, via email, send a message with subject or body 'help' to > > freesurfer-request(a)nmr.mgh.harvard.edu > > > > You can reach the person managing the list at > > freesurfer-owner(a)nmr.mgh.harvard.edu > > > > When replying, please edit your Subject line so it is more specific > > than "Re: Contents of Freesurfer digest..." > > > > Today's Topics: > > > > 1. recon-all doesn't recon-all (Janani Dhinakaran) > > 2. Re: recon-all doesn't recon-all (Janani Dhinakaran) > > 3. Difference between aparc+aseg and aparc.a2009s+aseg > > (Mohammed el Morabit) > > 4. Re: recon-all doesn't recon-all (Sita Kakunoori) > > 5. Re: mri_vol2surf resulting in different dimensions for two > > different images in the same space (Joonkoo Park) > > > > > > ---------- Forwarded message ---------- > > From: Janani Dhinakaran <janinthesky(a)gmail.com> > > To: freesurfer(a)nmr.mgh.harvard.edu > > Date: Mon, 22 Feb 2010 11:36:48 +0000 > > Subject: [Freesurfer] recon-all doesn't recon-all > > Hello, > > I ran recon-all on Friday. It ran for around a minute instead of 30-48 > hours. Unfortunately, when I try tkmedit and other such commands, the > pictures don't visualise. > > So today I first confirmed that the SUBJECTS_DIR was in Desktop path. > (Because over the weekend it had gone back to usr/local... path and so I > re-exported it just now.) > > Then I tried running recon-all again. > > > > > > s0964091@CRIC-0012:~/Desktop/Allimages/MRIscan/janani/CRIC-0014_5679.adb.DICOM$ > echo $SUBJECTS_DIR > > Desktop/Allimages/MRIscan/janani/CRIC-0014_5679.adb.DICOM > > s0964091@CRIC-0012:~/Desktop/Allimages/MRIscan/janani/CRIC-0014_5679.adb.DICOM$ > recon-all -i Dhinakaran^Janani^-0002-0001-00001.dcm -i > Dhinakaran^Janani^-0004-0001-00001.dcm -s subj001 > > ERROR: SUBJECTS_DIR > Desktop/Allimages/MRIscan/janani/CRIC-0014_5679.adb.DICOM does not exist. > > > > Can anyone help me understand what I can do? > > Thanks > > Jan > > -- > > I am the Sun, I know no darkness. > > > > > > ---------- Forwarded message ---------- > > From: Janani Dhinakaran <janinthesky(a)gmail.com> > > To: "Xue, Feng" <xfgavin(a)gmail.com>, freesurfer(a)nmr.mgh.harvard.edu > > Date: Mon, 22 Feb 2010 14:44:58 +0000 > > Subject: Re: [Freesurfer] recon-all doesn't recon-all > > Is this what you meant: > > > > First I tried > > s0964091@CRIC-0012:~$ recon-all > home/s0964091/Desktop/Allimages/MRIscan/janani/CRIC-0014_5679.adb.DICOM > > ERROR: Flag > home/s0964091/Desktop/Allimages/MRIscan/janani/CRIC-0014_5679.adb.DICOM > unrecognized. > > home/s0964091/Desktop/Allimages/MRIscan/janani/CRIC-0014_5679.adb.DICOM > > Linux CRIC-0012 2.6.31-19-generic #56-Ubuntu SMP Thu Jan 28 02:39:34 UTC > 2010 x86_64 GNU/Linux > > > > recon-all exited with ERRORS at Mon Feb 22 14:39:27 GMT 2010 > > > > Then I tried putting full path in front of both file sets > > > > > > s0964091@CRIC-0012:~$ recon-all -i > home/s0964091/Desktop/Allimages/MRIscan/janani/CRIC-0014_5679.adb.DICOM/Dhinakaran^Janani^-0002-0001-00001.dcm > -i > home/s0964091/Desktop/Allimages/MRIscan/janani/CRIC-0014_5679.adb.DICOM/Dhinakaran^Janani^-0004-0001-00001.dcm > -s subj001 > > ERROR: cannot find > home/s0964091/Desktop/Allimages/MRIscan/janani/CRIC-0014_5679.adb.DICOM/Dhinakaran^Janani^-0002-0001-00001.dcm > > Linux CRIC-0012 2.6.31-19-generic #56-Ubuntu SMP Thu Jan 28 02:39:34 UTC > 2010 x86_64 GNU/Linux > > > > recon-all exited with ERRORS at Mon Feb 22 14:41:36 GMT 2010 > > > > Jan > > > > > > On 22 February 2010 14:30, Xue, Feng <xfgavin(a)gmail.com> wrote: > >> > >> Try with full path, e.g. > >> /home/s0964091/Desktop/Allimages/MRIscan/janani/CRIC-0014_5679.adb.DICOM > >> > >> On Mon, Feb 22, 2010 at 7:36 PM, Janani Dhinakaran > >> <janinthesky(a)gmail.com> wrote: > >> > Hello, > >> > I ran recon-all on Friday. It ran for around a minute instead of 30-48 > >> > hours. Unfortunately, when I try tkmedit and other such commands, the > >> > pictures don't visualise. > >> > So today I first confirmed that the SUBJECTS_DIR was in Desktop path. > >> > (Because over the weekend it had gone back to usr/local... path and so > I > >> > re-exported it just now.) > >> > Then I tried running recon-all again. > >> > > >> > > >> > s0964091@CRIC-0012 > :~/Desktop/Allimages/MRIscan/janani/CRIC-0014_5679.adb.DICOM$ > >> > echo $SUBJECTS_DIR > >> > Desktop/Allimages/MRIscan/janani/CRIC-0014_5679.adb.DICOM > >> > s0964091@CRIC-0012 > :~/Desktop/Allimages/MRIscan/janani/CRIC-0014_5679.adb.DICOM$ > >> > recon-all -i Dhinakaran^Janani^-0002-0001-00001.dcm -i > >> > Dhinakaran^Janani^-0004-0001-00001.dcm -s subj001 > >> > ERROR: SUBJECTS_DIR > >> > Desktop/Allimages/MRIscan/janani/CRIC-0014_5679.adb.DICOM does not > exist. > >> > > >> > Can anyone help me understand what I can do? > >> > Thanks > >> > Jan > >> > -- > >> > I am the Sun, I know no darkness. > >> > > >> > _______________________________________________ > >> > Freesurfer mailing list > >> > Freesurfer(a)nmr.mgh.harvard.edu > >> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > >> > > >> > >> > >> > >> -- > >> Best Regards > >> > >> Xue, Feng Phd. candidate > >> Major in Developmental Cognitive Neuroscience > >> > >> National Key Laboratory of Cognitive Neuroscience and Learning > >> Beijing Normal University > >> Beijing, China. 100875 > >> Tel: +86-13810154455 > >> web: http://psychbrain.bnu.edu.cn > >> ============================================== > >> Welcome to MuDuo JinSheng BBS @ Beijing Normal University > >> telnet://bbs.mdjs.org > >> http://bbs.mdjs.org > > > > > > > > -- > > I am the Sun, I know no darkness. > > > > > > ---------- Forwarded message ---------- > > From: "Mohammed el Morabit" <M.elMorabit(a)student.TUDelft.NL> > > To: <freesurfer(a)nmr.mgh.harvard.edu> > > Date: Mon, 22 Feb 2010 16:05:53 +0100 > > Subject: [Freesurfer] Difference between aparc+aseg and aparc.a2009s+aseg > > > > Dear all, > > > > I am using freesurfer to generate a parcellation on the cortex. The > regions of this demarced cortex serve as ROIs in further research. My > question is... what is the difference between aparc+aseg and > aparc.a2009s+aseg? And which one should I use? > > > > Thanx in advance > > > > Morabit. > > > > ---------- Forwarded message ---------- > > From: Sita Kakunoori <sita(a)nmr.mgh.harvard.edu> > > To: Janani Dhinakaran <janinthesky(a)gmail.com> > > Date: Mon, 22 Feb 2010 10:26:50 -0500 (EST) > > Subject: Re: [Freesurfer] recon-all doesn't recon-all > > > > Hi Jan, > > > > Please try rerunning recon-all after removing the spaces or special > characters (if there are any) in the dicom files. > > > > Sita. > > > > > > > > On Mon, 22 Feb 2010, Janani Dhinakaran wrote: > > > >> Is this what you meant: > >> > >> First I tried > >> s0964091@CRIC-0012:~$ recon-all > >> home/s0964091/Desktop/Allimages/MRIscan/janani/CRIC-0014_5679.adb.DICOM > >> ERROR: Flag > >> home/s0964091/Desktop/Allimages/MRIscan/janani/CRIC-0014_5679.adb.DICOM > >> unrecognized. > >> home/s0964091/Desktop/Allimages/MRIscan/janani/CRIC-0014_5679.adb.DICOM > >> Linux CRIC-0012 2.6.31-19-generic #56-Ubuntu SMP Thu Jan 28 02:39:34 UTC > >> 2010 x86_64 GNU/Linux > >> > >> recon-all exited with ERRORS at Mon Feb 22 14:39:27 GMT 2010 > >> > >> Then I tried putting full path in front of both file sets > >> > >> > >> s0964091@CRIC-0012:~$ recon-all -i > >> > home/s0964091/Desktop/Allimages/MRIscan/janani/CRIC-0014_5679.adb.DICOM/Dhinakaran^Janani^-0002-0001-00001.dcm > >> -i > >> > home/s0964091/Desktop/Allimages/MRIscan/janani/CRIC-0014_5679.adb.DICOM/Dhinakaran^Janani^-0004-0001-00001.dcm > >> -s subj001 > >> ERROR: cannot find > >> > home/s0964091/Desktop/Allimages/MRIscan/janani/CRIC-0014_5679.adb.DICOM/Dhinakaran^Janani^-0002-0001-00001.dcm > >> Linux CRIC-0012 2.6.31-19-generic #56-Ubuntu SMP Thu Jan 28 02:39:34 UTC > >> 2010 x86_64 GNU/Linux > >> > >> recon-all exited with ERRORS at Mon Feb 22 14:41:36 GMT 2010 > >> > >> Jan > >> > >> > >> On 22 February 2010 14:30, Xue, Feng <xfgavin(a)gmail.com> wrote: > >> > >>> Try with full path, e.g. > >>> > /home/s0964091/Desktop/Allimages/MRIscan/janani/CRIC-0014_5679.adb.DICOM > >>> > >>> On Mon, Feb 22, 2010 at 7:36 PM, Janani Dhinakaran > >>> <janinthesky(a)gmail.com> wrote: > >>>> > >>>> Hello, > >>>> I ran recon-all on Friday. It ran for around a minute instead of 30-48 > >>>> hours. Unfortunately, when I try tkmedit and other such commands, the > >>>> pictures don't visualise. > >>>> So today I first confirmed that the SUBJECTS_DIR was in Desktop path. > >>>> (Because over the weekend it had gone back to usr/local... path and so > I > >>>> re-exported it just now.) > >>>> Then I tried running recon-all again. > >>>> > >>>> > >>>> s0964091@CRIC-0012 > >>> > >>> :~/Desktop/Allimages/MRIscan/janani/CRIC-0014_5679.adb.DICOM$ > >>>> > >>>> echo $SUBJECTS_DIR > >>>> Desktop/Allimages/MRIscan/janani/CRIC-0014_5679.adb.DICOM > >>>> s0964091@CRIC-0012 > >>> > >>> :~/Desktop/Allimages/MRIscan/janani/CRIC-0014_5679.adb.DICOM$ > >>>> > >>>> recon-all -i Dhinakaran^Janani^-0002-0001-00001.dcm -i > >>>> Dhinakaran^Janani^-0004-0001-00001.dcm -s subj001 > >>>> ERROR: SUBJECTS_DIR > >>>> Desktop/Allimages/MRIscan/janani/CRIC-0014_5679.adb.DICOM does not > exist. > >>>> > >>>> Can anyone help me understand what I can do? > >>>> Thanks > >>>> Jan > >>>> -- > >>>> I am the Sun, I know no darkness. > >>>> > >>>> _______________________________________________ > >>>> Freesurfer mailing list > >>>> Freesurfer(a)nmr.mgh.harvard.edu > >>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > >>>> > >>> > >>> > >>> > >>> -- > >>> Best Regards > >>> > >>> Xue, Feng Phd. candidate > >>> Major in Developmental Cognitive Neuroscience > >>> > >>> National Key Laboratory of Cognitive Neuroscience and Learning > >>> Beijing Normal University > >>> Beijing, China. 100875 > >>> Tel: +86-13810154455 > >>> web: http://psychbrain.bnu.edu.cn > >>> ============================================== > >>> Welcome to MuDuo JinSheng BBS @ Beijing Normal University > >>> telnet://bbs.mdjs.org > >>> http://bbs.mdjs.org > >>> > >> > >> > >> > >> > > > > > > > > ---------- Forwarded message ---------- > > From: Joonkoo Park <joonkoo(a)umich.edu> > > To: Douglas N Greve <greve(a)nmr.mgh.harvard.edu> > > Date: Mon, 22 Feb 2010 10:36:51 -0500 > > Subject: Re: [Freesurfer] mri_vol2surf resulting in different dimensions > for two different images in the same space > > Thanks Doug, > > > > Where can I find the surface annotation for the fsaverage (or any > > other template) data? > > I will need to import the data into matlab eventually, so I'm thinking > > that the surface annotation file should be readable using load_mgh.m > > (and writable using save_mgh.m). I'm very new to FreeSurfer so I'd > > really appreciate if you can describe each step for me. > > > > Thank you. > > > > Joon > > > > > > > > On Fri, Feb 19, 2010 at 11:47 AM, Douglas N Greve > > <greve(a)nmr.mgh.harvard.edu> wrote: > >> You're better off loading in the surface annotation directly rather than > >> dealing with aparc+aseg. To make surf2surf output the right dimensions, > add > >> --noreshape. > >> > >> doug > >> > >> Joonkoo Park wrote: > >>> > >>> Dear Surfers, > >>> > >>> I (successfully) resampled a functional data on the surface map using > >>> mri_vol2surf: > >>> > >>> > >>>> > >>>> mri_vol2surf --mov func.nii --reg register.dat --projfrac 0.5 --interp > >>>> nearest --hemi lh --o lh.func.mgh > >>>> > >>> > >>> Then, I normalized this image to a standard space (fsaverage) using > >>> mri_surf2surf: > >>> > >>> > >>>> > >>>> mri_surf2surf --srcsubject sub1 --trgsubject fsaverage --sval > >>>> sub1/lh.func.mgh --tval sub1/lh.func.norm.mgh --fwhm 5 --cortex --hemi > lh > >>>> > >>> > >>> The dimension of the output file, lh.func.norm.mgh, was 163842 x 1 x 1 > >>> (identified from mri_info). This file can be opened from Matlab, and I > >>> can successfully get access to 163842 vertices. What I want now is to > >>> take the aparc+aseg information from the average brain (fsaverage) and > >>> be able identify which vertex falls under which ROI label. I decided > >>> to resample aparc+aseg.mgz in fsaverage on the surface map, hoping to > >>> get label information at the dimension of 163842 x 1 x 1. So I ran: > >>> > >>> > >>>> > >>>> mri_vol2surf --mov fsaverage/mri/aparc+aseg.mgz --regheader fsaverage > >>>> --projfrac 0.5 --interp nearest --hemi lh --o > fsaverage/surf/lh.roi.mgh > >>>> mri_vol2surf --mov fsaverage/mri/aparc+aseg.mgz --regheader fsaverage > >>>> --projfrac 0.5 --interp nearest --hemi rh --o > fsaverage/surf/rh.roi.mgh > >>>> > >>> > >>> The resulting mgh files, however, had a dimension of 23406 x 1 x 7. > >>> > >>> 1. As I said, I wanted to get label information (roi number from the > >>> FreeSurferColorLUT) for each vertex of the surface image in the > >>> fsaverage space. Is this the right approach? And did I do this > >>> correctly (I'm concerned about many options above)? > >>> > >>> 2. If so, why is the resulting dimension different from the other one? > >>> I assume that it's probably a reshape issue, but how I can reshape the > >>> dimension to match 163842 x 1 x 1? > >>> > >>> Thanks in advance. > >>> > >>> Joon > >>> > >>> -- > >>> Joonkoo Park > >>> Ph.D. Candidate, Cognition & Cognitive Neuroscience > >>> Department of Psychology, University of Michigan > >>> _______________________________________________ > >>> Freesurfer mailing list > >>> Freesurfer(a)nmr.mgh.harvard.edu > >>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > >>> > >>> > >>> > >> > >> -- > >> Douglas N. Greve, Ph.D. > >> MGH-NMR Center > >> greve(a)nmr.mgh.harvard.edu > >> Phone Number: 617-724-2358 Fax: 617-726-7422 > >> > >> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > >> FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html > >> > >> > > > > > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer(a)nmr.mgh.harvard.edu > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > -- I am the Sun, I know no darkness.

2 1

Difference between aparc+aseg and aparc.a2009s+aseg
by Mohammed el Morabit 22 Feb '10

22 Feb '10

Dear all, I am using freesurfer to generate a parcellation on the cortex. The regions of this demarced cortex serve as ROIs in further research. My question is... what is the difference between aparc+aseg and aparc.a2009s+aseg? And which one should I use? Thanx in advance Morabit.

2 1

Re: [Freesurfer] recon-all doesn't recon-all
by Janani Dhinakaran 22 Feb '10

22 Feb '10

Is this what you meant: First I tried s0964091@CRIC-0012:~$ recon-all home/s0964091/Desktop/Allimages/MRIscan/janani/CRIC-0014_5679.adb.DICOM ERROR: Flag home/s0964091/Desktop/Allimages/MRIscan/janani/CRIC-0014_5679.adb.DICOM unrecognized. home/s0964091/Desktop/Allimages/MRIscan/janani/CRIC-0014_5679.adb.DICOM Linux CRIC-0012 2.6.31-19-generic #56-Ubuntu SMP Thu Jan 28 02:39:34 UTC 2010 x86_64 GNU/Linux recon-all exited with ERRORS at Mon Feb 22 14:39:27 GMT 2010 Then I tried putting full path in front of both file sets s0964091@CRIC-0012:~$ recon-all -i home/s0964091/Desktop/Allimages/MRIscan/janani/CRIC-0014_5679.adb.DICOM/Dhinakaran^Janani^-0002-0001-00001.dcm -i home/s0964091/Desktop/Allimages/MRIscan/janani/CRIC-0014_5679.adb.DICOM/Dhinakaran^Janani^-0004-0001-00001.dcm -s subj001 ERROR: cannot find home/s0964091/Desktop/Allimages/MRIscan/janani/CRIC-0014_5679.adb.DICOM/Dhinakaran^Janani^-0002-0001-00001.dcm Linux CRIC-0012 2.6.31-19-generic #56-Ubuntu SMP Thu Jan 28 02:39:34 UTC 2010 x86_64 GNU/Linux recon-all exited with ERRORS at Mon Feb 22 14:41:36 GMT 2010 Jan On 22 February 2010 14:30, Xue, Feng <xfgavin(a)gmail.com> wrote: > Try with full path, e.g. > /home/s0964091/Desktop/Allimages/MRIscan/janani/CRIC-0014_5679.adb.DICOM > > On Mon, Feb 22, 2010 at 7:36 PM, Janani Dhinakaran > <janinthesky(a)gmail.com> wrote: > > Hello, > > I ran recon-all on Friday. It ran for around a minute instead of 30-48 > > hours. Unfortunately, when I try tkmedit and other such commands, the > > pictures don't visualise. > > So today I first confirmed that the SUBJECTS_DIR was in Desktop path. > > (Because over the weekend it had gone back to usr/local... path and so I > > re-exported it just now.) > > Then I tried running recon-all again. > > > > > > s0964091@CRIC-0012 > :~/Desktop/Allimages/MRIscan/janani/CRIC-0014_5679.adb.DICOM$ > > echo $SUBJECTS_DIR > > Desktop/Allimages/MRIscan/janani/CRIC-0014_5679.adb.DICOM > > s0964091@CRIC-0012 > :~/Desktop/Allimages/MRIscan/janani/CRIC-0014_5679.adb.DICOM$ > > recon-all -i Dhinakaran^Janani^-0002-0001-00001.dcm -i > > Dhinakaran^Janani^-0004-0001-00001.dcm -s subj001 > > ERROR: SUBJECTS_DIR > > Desktop/Allimages/MRIscan/janani/CRIC-0014_5679.adb.DICOM does not exist. > > > > Can anyone help me understand what I can do? > > Thanks > > Jan > > -- > > I am the Sun, I know no darkness. > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer(a)nmr.mgh.harvard.edu > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > > -- > Best Regards > > Xue, Feng Phd. candidate > Major in Developmental Cognitive Neuroscience > > National Key Laboratory of Cognitive Neuroscience and Learning > Beijing Normal University > Beijing, China. 100875 > Tel: +86-13810154455 > web: http://psychbrain.bnu.edu.cn > ============================================== > Welcome to MuDuo JinSheng BBS @ Beijing Normal University > telnet://bbs.mdjs.org > http://bbs.mdjs.org > -- I am the Sun, I know no darkness.

3 2

recon-all doesn't recon-all
by Janani Dhinakaran 22 Feb '10

22 Feb '10

Hello, I ran recon-all on Friday. It ran for around a minute instead of 30-48 hours. Unfortunately, when I try tkmedit and other such commands, the pictures don't visualise. So today I first confirmed that the SUBJECTS_DIR was in Desktop path. (Because over the weekend it had gone back to usr/local... path and so I re-exported it just now.) Then I tried running recon-all again. s0964091@CRIC-0012:~/Desktop/Allimages/MRIscan/janani/CRIC-0014_5679.adb.DICOM$ echo $SUBJECTS_DIR Desktop/Allimages/MRIscan/janani/CRIC-0014_5679.adb.DICOM s0964091@CRIC-0012:~/Desktop/Allimages/MRIscan/janani/CRIC-0014_5679.adb.DICOM$ recon-all -i Dhinakaran^Janani^-0002-0001-00001.dcm -i Dhinakaran^Janani^-0004-0001-00001.dcm -s subj001 ERROR: SUBJECTS_DIR Desktop/Allimages/MRIscan/janani/CRIC-0014_5679.adb.DICOM does not exist. Can anyone help me understand what I can do? Thanks Jan -- I am the Sun, I know no darkness.

1 0

Text field input error in tkmeidt
by SG KIM 21 Feb '10

21 Feb '10

Hi all, I use Ubuntu 9.10 i386, and ran tkmedit to rotate orig.mgz from Analyze format. The problem is that I can't type anything into text fields. It gets mouse actions and works fine though. Should I use CentOS instead? What can I try before that?

1 0

ERROR: comparison in expression
by Xue, Feng 20 Feb '10

20 Feb '10

Dear experts, We are running freesurfer with Sun GridEngine. Currently, we repeatedly got this error in SGE's job error log file on some data when doing recon_all: $ cat recon_xf.e437 (standard_in) 2: Error: comparison in expression $ cat recon_xf.e431 (standard_in) 2: comparison in expression I also checked the recon-all-status.log file, but not error was found. Has anyone met this problem? Is it critical? Thanks in advance. -- Best Regards Xue, Feng Phd. candidate Major in Developmental Cognitive Neuroscience National Key Laboratory of Cognitive Neuroscience and Learning Beijing Normal University Beijing, China. 100875 Tel: +86-13810154455 web: http://psychbrain.bnu.edu.cn ============================================== Welcome to MuDuo JinSheng BBS @ Beijing Normal University telnet://bbs.mdjs.org http://bbs.mdjs.org

1 0

Re: [Freesurfer] Freesurfer Digest, Vol 72, Issue 66
by Sebastian Moeller 20 Feb '10

20 Feb '10

Hi Jonathan, On Feb 20, 2010, at 10:15 AM, freesurfer-request(a)nmr.mgh.harvard.edu wrote: > Message: 2 > Date: Fri, 19 Feb 2010 17:08:06 -0500 > From: Jonathan Winkle <jwink(a)mit.edu> > Subject: [Freesurfer] Distorted images > To: freesurfer(a)nmr.mgh.harvard.edu > Message-ID: <4B7F0BC6.3020207(a)mit.edu> > Content-Type: text/plain; charset="iso-8859-1" > > Hi! > > I'm new to freesurfer and I am trying to reconstruct some recent scans > of a rhesus macaque. The dicoms appear to be fine, but after converting > to cor files the images appear distorted. I have attached a screenshot > as an example of what the images look like. For converting the dicoms to > cor I used: > > "mri_convert $path/1500-4-1.dcm $path/001 -ot COR -nc -sc 0.5" > > I am using freesurfer 3 on ubuntu. > > Any help you can give is much appreciated! Have a look at the attached tar.gz, it contains the scripts I use to process rhesus data. Especially myscripts_anat might be helpful (and unpack_CIT.csh for how to import DICOM data). For me it works to go from macaque anatomical scans to reconstructed surfaces (but I never actually used the recons for morphometry so the thickness values might be completely off). I am sure there are other people on this list who can give more experienced advise regarding monkey processing, but until they comment have a look at my scripts :). What I do not know is, is whether the scripts in the attachement will reach the list... Oh, there is also a somewhat old copy of my "myscripts_anat" folder on the freesurfer wiki (http://surfer.nmr.mgh.harvard.edu/fswiki/MonkeyData) but I would rather try the attached ones... (Oh well, these scripts were never meant to be distributed so they are full of typos and comments are often actually about older versions of the scripts, but hey better than nothing...) Best Sebastian

1 0

Local GI - euler number and compute_lgi
by Lena Palaniyappan 20 Feb '10

20 Feb '10

Hi all I am running recon-all localGI One subjects image is not getting processed and crashes repeatedly with message that there may be a topological defect in a particular vertex. It asks me to check euler number. The wiki indicates that this crash is a known issue and restrating _mris_compute_lgi must solve this. My questions are 1. how to check the euler number and how to interpret this number in terms of topological defects? 2. mris_compute_lgi does not find lh.pial surface when I TRY TO RESTART - what should I do? I used mris_compute_lgi subjid/surf/lh.pial Many thanks in advance Lena _______________________________________________________ Lena Palaniyappan Clinical Lecturer & Honorary StR | Division of Psychiatry ( University of Nottingham) South Block 'A' floor| Queens Medical Centre | Nottingham | NG7 2UH This message has been checked for viruses but the contents of an attachment may still contain software viruses which could damage your computer system: you are advised to perform your own checks. Email communications with the University of Nottingham may be monitored as permitted by UK legislation.

3 2

Distorted images
by Jonathan Winkle 19 Feb '10

19 Feb '10

Hi! I'm new to freesurfer and I am trying to reconstruct some recent scans of a rhesus macaque. The dicoms appear to be fine, but after converting to cor files the images appear distorted. I have attached a screenshot as an example of what the images look like. For converting the dicoms to cor I used: "mri_convert $path/1500-4-1.dcm $path/001 -ot COR -nc -sc 0.5" I am using freesurfer 3 on ubuntu. Any help you can give is much appreciated!

1 0

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Freesurfer February 2010