The command line is
recon-all -all -i <dicom1> -i <dicom2> -s <subjID> Sita. On Mon, 22 Feb 2010, Janani Dhinakaran wrote: > 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- > > s0964...@cric-0012:~$ echo $SUBJECTS_DIR > /home/s0964091/Desktop/Allimages/MRIscan/janani/CRIC-0014_5679.adb.DICOM/ > s0964...@cric-0012:~$ 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.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 <s...@nmr.mgh.harvard.edu> >> To: Janani Dhinakaran <janinthe...@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 >> s0964...@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 >> >> >> s0964...@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-requ...@nmr.mgh.harvard.edu> wrote: >>> Send Freesurfer mailing list submissions to >>> freesurfer@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-requ...@nmr.mgh.harvard.edu >>> >>> You can reach the person managing the list at >>> freesurfer-ow...@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 <janinthe...@gmail.com> >>> To: freesurfer@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. >>> >>> >>> s0964...@cric-0012:~/Desktop/Allimages/MRIscan/janani/CRIC-0014_5679.adb.DICOM$ >> echo $SUBJECTS_DIR >>> Desktop/Allimages/MRIscan/janani/CRIC-0014_5679.adb.DICOM >>> s0964...@cric-0012:~/Desktop/Allimages/MRIscan/janani/CRIC-0014_5679.adb.DICOM$ >> 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 <janinthe...@gmail.com> >>> To: "Xue, Feng" <xfga...@gmail.com>, freesurfer@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 >>> s0964...@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 >>> >>> >>> s0964...@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 <xfga...@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 >>>> <janinthe...@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. >>>>> >>>>> >>>>> s0964...@cric-0012 >> :~/Desktop/Allimages/MRIscan/janani/CRIC-0014_5679.adb.DICOM$ >>>>> echo $SUBJECTS_DIR >>>>> Desktop/Allimages/MRIscan/janani/CRIC-0014_5679.adb.DICOM >>>>> s0964...@cric-0012 >> :~/Desktop/Allimages/MRIscan/janani/CRIC-0014_5679.adb.DICOM$ >>>>> 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@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.elmora...@student.tudelft.nl> >>> To: <freesurfer@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 <s...@nmr.mgh.harvard.edu> >>> To: Janani Dhinakaran <janinthe...@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 >>>> s0964...@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 >>>> >>>> >>>> s0964...@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 <xfga...@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 >>>>> <janinthe...@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. >>>>>> >>>>>> >>>>>> s0964...@cric-0012 >>>>> >>>>> :~/Desktop/Allimages/MRIscan/janani/CRIC-0014_5679.adb.DICOM$ >>>>>> >>>>>> echo $SUBJECTS_DIR >>>>>> Desktop/Allimages/MRIscan/janani/CRIC-0014_5679.adb.DICOM >>>>>> s0964...@cric-0012 >>>>> >>>>> :~/Desktop/Allimages/MRIscan/janani/CRIC-0014_5679.adb.DICOM$ >>>>>> >>>>>> 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@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 <joon...@umich.edu> >>> To: Douglas N Greve <gr...@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 >>> <gr...@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@nmr.mgh.harvard.edu >>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>>>> >>>>> >>>>> >>>> >>>> -- >>>> Douglas N. Greve, Ph.D. >>>> MGH-NMR Center >>>> gr...@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@nmr.mgh.harvard.edu >>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>> >> > > > > _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
