Freesurfer March 2010

freesurfer@nmr.mgh.harvard.edu

101 participants
153 discussions

Re: [Freesurfer] Freesurfer Digest, Vol 73, Issue 56
by Sebastian Moeller 22 Mar '10

22 Mar '10

Hi Janani, I seem to recall that newer distributions (and judging from your kernel it is a rather new distribution) come with libtiff.so.4 instead of libtiff.so.3. My solution to this problem so far just was to symlink libtiff.so.4 to libtiff.so.3. (Just go in the directory where the library lives (might be /usr/lib or /usr/lib64) and issued the following command: "ln -s ./libtiff.so.4 ./libbtiff.so.3", you might have to get root permissions first (or ask the system administrator for help)). While there might be differences between the two versions I did not run into problems with freesurfer yet... best Sebastian On Mar 22, 2010, at 9:00 AM, freesurfer-request(a)nmr.mgh.harvard.edu wrote: > Message: 2 > Date: Mon, 22 Mar 2010 09:18:11 -0400 (EDT) > From: Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> > Subject: Re: [Freesurfer] Recon runs longer than the previous time and > exits this time with errors > To: Janani Dhinakaran <janinthesky(a)gmail.com> > Cc: freesurfer(a)nmr.mgh.harvard.edu > Message-ID: > <Pine.LNX.4.62.1003220917180.30973(a)gate.nmr.mgh.harvard.edu> > Content-Type: TEXT/PLAIN; charset=US-ASCII; format=flowed > > Hi Janani, > > do you not have libtiff installed on your system? Maybe your > LD_LIBRARY_PATH is incorrect? You should talk to a local sysadmin about it. > > cheers > Bruce > > > > > On Mon, 22 Mar > 2010, Janani Dhinakaran wrote: > >> I was unable to extract parts of the cortex with the commands you had told >> me to try last time. I realised then that it was because recon hadn't >> finished running and I was using partially processed data. So I tried >> running it again. Here below is what I got. Since I'm using a partitioned >> machine space may be a problem but it doesn't seem to say so. >> Thanks in advance for the advice. >> >> #-------------------------------------------- >> #@# Cortical ribbon mask Sat Mar 20 07:17:29 GMT 2010 >> /home/s0964091/Desktop/jan/mri >> >> mris_volmask --label_left_white 2 --label_left_ribbon 3 --label_right_white >> 41 --label_right_ribbon 42 --save_ribbon --save_distance jan >> >> mris_volmask.bin: error while loading shared libraries: libtiff.so.3: cannot >> open shared object file: No such file or directory >> Linux CRIC-0012 2.6.31-20-generic #57-Ubuntu SMP Mon Feb 8 09:02:26 UTC 2010 >> x86_64 GNU/Linux >> >> recon-all exited with ERRORS at Sat Mar 20 07:17:29 GMT 2010 >> >> >> >

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Recon runs longer than the previous time and exits this time with errors
by Janani Dhinakaran 22 Mar '10

22 Mar '10

I was unable to extract parts of the cortex with the commands you had told me to try last time. I realised then that it was because recon hadn't finished running and I was using partially processed data. So I tried running it again. Here below is what I got. Since I'm using a partitioned machine space may be a problem but it doesn't seem to say so. Thanks in advance for the advice. #-------------------------------------------- #@# Cortical ribbon mask Sat Mar 20 07:17:29 GMT 2010 /home/s0964091/Desktop/jan/mri mris_volmask --label_left_white 2 --label_left_ribbon 3 --label_right_white 41 --label_right_ribbon 42 --save_ribbon --save_distance jan mris_volmask.bin: error while loading shared libraries: libtiff.so.3: cannot open shared object file: No such file or directory Linux CRIC-0012 2.6.31-20-generic #57-Ubuntu SMP Mon Feb 8 09:02:26 UTC 2010 x86_64 GNU/Linux recon-all exited with ERRORS at Sat Mar 20 07:17:29 GMT 2010 -- I am the Sun, I know no darkness.

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volume segmentation corrections
by Roser Sala 22 Mar '10

22 Mar '10

Hello, We are running FreeSurfer in order to obtain Callosal volumes from pathologic brain. Segmentation volumes (aseg.mgz) seem 'not bad', but specially in the Callossum there are some misclassifications (attached image with an example). Which would be the best way to correct this? Do you recommend us to add some control points? we are not sure if adding control points will affect only the surface reconstruction, or will help aslo to correct segmentation, which is our purpose. Many thanks in advance - Roser -

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White matter volumes of different lobes?
by Gergely Orsi 22 Mar '10

22 Mar '10

Hi all. Is there any fast method to get the total (R+L) white matter volumes of different lobes? I need the: average ratio of temporal lobe wm to total white matter average ratio of parietal lobe wm to total white matter average ratio of frontal lobe wm to total white matter average ratio of occipital lobe wm to total white matter in our 100 normal healthy population. Autorecon 1-2-3 (and qcache) is already done. Anyone can help in this? Thank you. Gergely Orsi

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Re: [Freesurfer] Freesurfer Digest, Vol 73, Issue 52
by Sebastian Moeller 19 Mar '10

19 Mar '10

Hi Paige, I ran into a similar problem a few months ago. Freesurfer 3.0.5 could not read data from a TIM trio with numaris B17. I solved this by transplanting (copying) a number of files from freesurfer 4.4.0 (the recent one at the time) into 3.0.5. unpacsdcmdir, mri_convert and a few more, that worked okay, but I since switched to freesurfer 4.5.0 for good. If you have to stick to 3.0.3 I can try to look up which files I had to replace in 3.0.5. Or alternatively you can install v4.5.0 parallel to 3.0.3 and only use it to import the DICOM data... best regards Sebastian On Mar 19, 2010, at 12:37 PM, freesurfer-request(a)nmr.mgh.harvard.edu wrote: > Message: 7 > Date: Fri, 19 Mar 2010 14:37:24 -0500 > From: Paige Scalf <pscalf(a)gmail.com> > Subject: [Freesurfer] trio dicom files and mri_convert > To: freesurfer(a)nmr.mgh.harvard.edu > Message-ID: > <1113e70c1003191237y6f5723aeha927124dd30b593e(a)mail.gmail.com> > Content-Type: text/plain; charset="iso-8859-1" > > Hello, > > I've been trying to use mri_convert > (freesurfer-Darwin-tiger-stable-pub-v3.0.3) to reconstruct images from our > Siemens Magnetom Trio. When I type: > > mri_convert -it siemens_dicom -ot analyze4d DB_A0A1_318.MR.BECK-PAIGE_ > A0A1_INHABITION.0003.0001.2010.03.18.16.34.50.500000.21615932.IMA Block1.img > > > DB*.IMA and Block1.img are the input and output files respectively, I get > the output detailed below (the salient error seems to be that mri_convert > can't find a useful transformation matrix). > > Can you tell me what I can do to correct this problem? > Many thanks in advance, > > Paige Scalf > > > mri_convert -it siemens_dicom -ot analyze4d > DB_A0A1_318.MR.BECK-PAIGE_A0A1_INHABITION.0003.0001.2010.03.18.16.34.50.500000.21615932.IMA > Block1.img > reading from > DB_A0A1_318.MR.BECK-PAIGE_A0A1_INHABITION.0003.0001.2010.03.18.16.34.50.500000.21615932.IMA... > Getting Series No > Scanning Directory > INFO: Found 111 files in /Volumes/dubois/A0A1inhibition/DB_A0A1_318/Block1 > INFO: Scanning for Series Number 3 > INFO: found 107 files in series > INFO: loading series header info. > > INFO: sorting. > RunNo = 2 > INFO: (120 110 50), nframes = 107, ismosaic=1 > ERROR: incorreclty formatted version string syngo MR B17 > found in dicom tag 18,1020 (len = 3 != 6) > Numaris Version: syngo MR B17 Maj = 0, Min=-1073775504, MinMin = 0 > mojo:/Volumes/dubois/A0A1inhibition/DB_A0A1_318/Block1 paige$ mri_convert > -it dicom -ot analyze4d > DB_A0A1_318.MR.BECK-PAIGE_A0A1_INHABITION.0003.0001.2010.03.18.16.34.50.500000.21615932.IMA > Block1.img > mri_convert -it dicom -ot analyze4d > DB_A0A1_318.MR.BECK-PAIGE_A0A1_INHABITION.0003.0001.2010.03.18.16.34.50.500000.21615932.IMA > Block1.img > reading from > DB_A0A1_318.MR.BECK-PAIGE_A0A1_INHABITION.0003.0001.2010.03.18.16.34.50.500000.21615932.IMA... > Getting Series No > Scanning Directory > INFO: Found 111 files in /Volumes/dubois/A0A1inhibition/DB_A0A1_318/Block1 > INFO: Scanning for Series Number 3 > INFO: found 107 files in series > INFO: loading series header info. > > INFO: sorting. > RunNo = 2 > INFO: (120 110 50), nframes = 107, ismosaic=1 > ERROR: incorreclty formatted version string syngo MR B17 > found in dicom tag 18,1020 (len = 3 != 6) > Numaris Version: syngo MR B17 Maj = -1073770984, Min=22021328, MinMin = > -1610546680 > 107 DICOM 3.0 files in list > Found 107 DICOM Files > WARNING: NumberOfFrames 0 != Found Count of slices 107. > reading DICOM image... > ------------------------------------------------- > DICOM meta-header > > file name > /Volumes/dubois/A0A1inhibition/DB_A0A1_318/Block1/DB_A0A1_318.MR.BECK-PAIGE_A0A1_INHABITION.0003.0001.2010.03.18.16.34.50.500000.21615932.IMA > Date and time > study date 20100318 > study time 160300.312000 > series time 162802.453000 > acquisition time 162802.453000 > Identification > patient name DB_A0A1_318 > manufacturer SIEMENS > Dimensions > number of rows 880 > number of columns 960 > number of frames 107 > pixel width 2.13333 > pixel height 2.13333 > slice thickness 2.1 > field of view 1877.33 > image number 1 (might be not reliable) > transfer syntax UID 1.2.840.10008.1.2.1 > Acquisition parameters > echo time 25 > repetition time 3000 > inversion time not found > echo number 1 > flip angle 1.5708 > bits allocated 16 > Spatial information > first image position -1027.46 -12.1727 952.833 > last image position -1027.46 -12.1727 952.833 > image orientation 1 0 0 0 -0.00174528 -0.999998 > ------------------------------------------------- > > TR=3000.00, TE=25.00, TI=0.00, flip angle=90.00 > i_ras = (-1, -0, 0) > j_ras = (-0, 0.00174528, -0.999999) > k_ras = (nan, nan, nan) > Reslicing using trilinear interpolation > MRIresample(): error inverting matrix; determinant is nan, matrix is: > -2.133 -0.000 nan nan; > -0.000 0.004 nan nan; > 0.000 -2.133 nan nan; > 0.000 0.000 0.000 1.000; >

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Re: [Freesurfer] merging rh and lh surfaces
by Raghav Puranmalka 19 Mar '10

19 Mar '10

Hi all - I was trying to merge rh and lh surfaces. I succeeded after reading the mailing list archives from March 2009 found at http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg09665.html. I following this guide: you can get something like what you want with cd $SUBJECTS_DIR/subject mri_binarize --i mri/ribbon.mgz --min .0001 --o mri/tmp.mgh mri_tessellate mri/tmp.mgh 1 surf/lh.both mris_smooth -nw surf/lh.both surf/lh.smboth tksurfer subject lh smboth Note that eventhough you call it "lh" it has both hemis. "lh" is just to fool freesurfer into thinking it is a hemi. The issue I run into is that I try to get matlab to read the surface through read_surf, I find that the magic number is not recognized. Has anyone experienced this before? Any thoughts about navigating through this? Best, Raghav

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mri_surfcluster
by Kelly Silva 19 Mar '10

19 Mar '10

Hello, I would like to know if the output coordinates from the "mri_surfcluster" command is on the MNI space or on the Talairach. Thanks in advance. Best, Kelly ________________________________ Veja quais são os assuntos do momento no Yahoo! + Buscados: Top 10 - Celebridades - Música - Esportes ____________________________________________________________________________________ Veja quais são os assuntos do momento no Yahoo! +Buscados http://br.maisbuscados.yahoo.com _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.

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trio dicom files and mri_convert
by Paige Scalf 19 Mar '10

19 Mar '10

Hello, I've been trying to use mri_convert (freesurfer-Darwin-tiger-stable-pub-v3.0.3) to reconstruct images from our Siemens Magnetom Trio. When I type: mri_convert -it siemens_dicom -ot analyze4d DB_A0A1_318.MR.BECK-PAIGE_ A0A1_INHABITION.0003.0001.2010.03.18.16.34.50.500000.21615932.IMA Block1.img DB*.IMA and Block1.img are the input and output files respectively, I get the output detailed below (the salient error seems to be that mri_convert can't find a useful transformation matrix). Can you tell me what I can do to correct this problem? Many thanks in advance, Paige Scalf mri_convert -it siemens_dicom -ot analyze4d DB_A0A1_318.MR.BECK-PAIGE_A0A1_INHABITION.0003.0001.2010.03.18.16.34.50.500000.21615932.IMA Block1.img reading from DB_A0A1_318.MR.BECK-PAIGE_A0A1_INHABITION.0003.0001.2010.03.18.16.34.50.500000.21615932.IMA... Getting Series No Scanning Directory INFO: Found 111 files in /Volumes/dubois/A0A1inhibition/DB_A0A1_318/Block1 INFO: Scanning for Series Number 3 INFO: found 107 files in series INFO: loading series header info. INFO: sorting. RunNo = 2 INFO: (120 110 50), nframes = 107, ismosaic=1 ERROR: incorreclty formatted version string syngo MR B17 found in dicom tag 18,1020 (len = 3 != 6) Numaris Version: syngo MR B17 Maj = 0, Min=-1073775504, MinMin = 0 mojo:/Volumes/dubois/A0A1inhibition/DB_A0A1_318/Block1 paige$ mri_convert -it dicom -ot analyze4d DB_A0A1_318.MR.BECK-PAIGE_A0A1_INHABITION.0003.0001.2010.03.18.16.34.50.500000.21615932.IMA Block1.img mri_convert -it dicom -ot analyze4d DB_A0A1_318.MR.BECK-PAIGE_A0A1_INHABITION.0003.0001.2010.03.18.16.34.50.500000.21615932.IMA Block1.img reading from DB_A0A1_318.MR.BECK-PAIGE_A0A1_INHABITION.0003.0001.2010.03.18.16.34.50.500000.21615932.IMA... Getting Series No Scanning Directory INFO: Found 111 files in /Volumes/dubois/A0A1inhibition/DB_A0A1_318/Block1 INFO: Scanning for Series Number 3 INFO: found 107 files in series INFO: loading series header info. INFO: sorting. RunNo = 2 INFO: (120 110 50), nframes = 107, ismosaic=1 ERROR: incorreclty formatted version string syngo MR B17 found in dicom tag 18,1020 (len = 3 != 6) Numaris Version: syngo MR B17 Maj = -1073770984, Min=22021328, MinMin = -1610546680 107 DICOM 3.0 files in list Found 107 DICOM Files WARNING: NumberOfFrames 0 != Found Count of slices 107. reading DICOM image... ------------------------------------------------- DICOM meta-header file name /Volumes/dubois/A0A1inhibition/DB_A0A1_318/Block1/DB_A0A1_318.MR.BECK-PAIGE_A0A1_INHABITION.0003.0001.2010.03.18.16.34.50.500000.21615932.IMA Date and time study date 20100318 study time 160300.312000 series time 162802.453000 acquisition time 162802.453000 Identification patient name DB_A0A1_318 manufacturer SIEMENS Dimensions number of rows 880 number of columns 960 number of frames 107 pixel width 2.13333 pixel height 2.13333 slice thickness 2.1 field of view 1877.33 image number 1 (might be not reliable) transfer syntax UID 1.2.840.10008.1.2.1 Acquisition parameters echo time 25 repetition time 3000 inversion time not found echo number 1 flip angle 1.5708 bits allocated 16 Spatial information first image position -1027.46 -12.1727 952.833 last image position -1027.46 -12.1727 952.833 image orientation 1 0 0 0 -0.00174528 -0.999998 ------------------------------------------------- TR=3000.00, TE=25.00, TI=0.00, flip angle=90.00 i_ras = (-1, -0, 0) j_ras = (-0, 0.00174528, -0.999999) k_ras = (nan, nan, nan) Reslicing using trilinear interpolation MRIresample(): error inverting matrix; determinant is nan, matrix is: -2.133 -0.000 nan nan; -0.000 0.004 nan nan; 0.000 -2.133 nan nan; 0.000 0.000 0.000 1.000;

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mris_anatomical_stats question
by Bruehl, Hannah 19 Mar '10

19 Mar '10

Hi there, I have got 2 questions: 1) is there way to use mris_anatomical_stats to map back the label I have created onto all the subjects in my directory simultaneously? I know there is the "--subject" option but how do I then specify the directory for each individual subject? 2) I tried to do this for an individual subject and got the following error message: [LOE5145MAC:~] bruehh01% mris_anatomical_stats -l lh.CingulateKGvsPTSD.label -t lh.thickness -b -f 66/stats/lh.CingulateKGvsPTSD.stats 66 lh limiting computations to label lh.CingulateKGvsPTSD.label. using thickness file lh.thickness. reading volume /Users/bruehh01/Borderline_2/subjects/66/mri/wm.mgz... reading input surface /Users/bruehh01/Borderline_2/subjects/66/surf/lh.white... reading input pial surface /Users/bruehh01/Borderline_2/subjects/66/surf/lh.pial... reading input white surface /Users/bruehh01/Borderline_2/subjects/66/surf/lh.white... /Users/bruehh01/Borderline_2/subjects/66/label/lh.CingulateKGvsPTSD.label /Users/bruehh01/Borderline_2/subjects/66/label/lh.CingulateKGvsPTSD.label table columns are: number of vertices total surface area (mm^2) total gray matter volume (mm^3) average cortical thickness +- standard deviation (mm) integrated rectified mean curvature integrated rectified Gaussian curvature folding index intrinsic curvature index structure name Bus error Can anyone help? Thanks and greetz, hannah

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mri_aparc2aseg problems
by Alex Fornito 19 Mar '10

19 Mar '10

Hi all, Sorry if this is a re-post, but I¹m not sure if the first one got through. I¹m really stuck on a problem I was hoping to get help with. I¹m having trouble determining the correspondence between ROIs in a surface-based annotation and those in a volume-based annotation generated using mri_aparc2aseg. I have some custom-generated surface annotations and have been using a recently updated binary of mri_aparc2aseg which adds 10,000 to the values of left hemi annotation labels and 20.000 to the right hemi labels in the converted volume, to help distinguish the two hemisphere¹s rois. To check the correspondence between the surface and volume, I chose an roi 10386 from the volume. To check it on the surface I did the following in matlab: [v,l,ct]=read_anntotation('lh.fsavg_500_compact.aparc.annot'); new=zeros(size(v)); new(find(l==ct.table(386,5)))=1; % note the roi index should be 10,000 less that of the volume. F=write_wfile('386.w',new,v); I did this for both the fsaverage surface and a single subject surface, and compared it with the volume representation for the same single subject. The attached pic called vol386 shows the roi in blue, overlaid on the volume parcellation in greyscale. It is located in the left inferior temporal lobe. The attached surf386 pic however, indicates this region is in the retrosplenial cortex for both the single subject (left) and fsaverage (right). Am I missing something here? Have I misunderstood the correspondence between surface and volume rois? Thanks for your help, Alex ------------------------------------------ Alex Fornito CJ Martin Post-Doctoral Fellow Brain Mapping Unit Department of Psychiatry University of Cambridge Downing Site Downing St, Cambridge UK CB2 3EB Email: af397(a)cam.ac.uk Phone: +44 (0) 1223 764670 Fax: +44 (0) 1223 336581 Australian Details: Melbourne Neuropsychiatry Centre National Neuroscience Facility Levels 1 & 2, Alan Gilbert Building 161 Barry St Carlton South 3053 Victoria, Australia Email: fornitoa(a)unimelb.edu.au Phone: +61 3 8344 1861 Fax: +61 3 9348 0469

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Freesurfer March 2010