Freesurfer

freesurfer@nmr.mgh.harvard.edu

19 participants
30088 discussions

OpenMP and non-OpenMP output is different at mri_ca_register
by Chris Adamson 07 Mar '14

07 Mar '14

I was trying to compile Freesurfer (in a Centos 6.5 VM) with a later gcc to see if the performance improved and noticed that the output gcc 4.4 vs. 4.8 was slightly different. I later compiled with gcc 4.4 *without* openmp support and this version produced the same output as the gcc 4.8 version, as expected. I have attached the recon-all log files, they first differ at line 1664, at iteration 451 of mri_ca_register; after that the differences accumulate. I feel that this shouldn't happen and the outputs should be equivalent. As a side note, I am unable to compile GEMS and dmri_poistats or any of the GUI programs due to vtk undefined symbols errors. Similar to this http://www.vtk.org/pipermail/vtkusers/2010-September/062426.html. This is apparently a known issue with vtk 5.6. How is this resolved? PS. The gcc 4.8 binaries were slower than the 4.4 binaries. Thanks in advance, Chris. Dr Chris Adamson Research Officer, Developmental Imaging, Murdoch Childrens Research Institute Murdoch Childrens Research Institute Royal Children's Hospital Flemington Road, Parkville, Victoria 3052, Australia www.mcri.edu.au<http://www.mcri.edu.au/> E chris.adamson(a)mcri.edu.au T 03 9936 6780 ______________________________________________________________________ This email has been scanned by the Symantec Email Security.cloud service. For more information please visit http://www.symanteccloud.com ______________________________________________________________________

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Convert expert segmentation to FreeSurfer space
by Mohamed Oualid Benkarim 07 Mar '14

07 Mar '14

Hi all, I've performed FS subcortical segmentation and my purpose is to use these segmentations as seeds to another method. As FS uses GCA atlas to perform subcortical segmentation, I want to know if the *aseg.mgz* output is in GCA atlas space, or in original space except that the dimensions are 256x256x256, 1mm. On the other hand, I also need to convert expert segmentations in native space to GCA atlas space, that is, the inverse of the process explained in http://surfer.nmr.mgh.harvard.edu/fswiki/FsAnat-to-NativeAnat. I don't know if there is a command to do so, or we have to use a transformation matrix. In the latter case, FreeSurfer creates several tranformation matrices: talairach.lta, talairach.xfm, talairach.m3z....but it's is not clear which one I should use. Thank you in advance!!

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Longitudinal analysis - the effect of FS release?
by Kivisaari Sasa 07 Mar '14

07 Mar '14

Hi, we have a longitudinal data set and have processed all of the baseline data using FS v5.1.0. We are now about to start preprocessing follow-up brains. Can you please give your opinion on whether we had better stick with v5.1.0 for the follow-up data as well or whether it would be safe to switch to v5.3.0? Do you have any updates on the potential time frame of the v6.0 (?) release? Many thanks in advance! Best wishes, Sasa

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Re: [Freesurfer] Surface area in aparc stats
by Douglas Greve 07 Mar '14

07 Mar '14

Hi Zhuangming, please remember to post to the list. Thanks! I don't understand your question. What do you mean by the exterior, anterior, posterior, etc, surfaces? On 3/5/14 11:56 PM, 沈庄明 wrote: > Hi Doug, > Thank you for your prompting response. Do you mean the computation > only calculate exterior surface of the cortical region ? The other > five surface (i.e. anterior, posterior, left, right, interior) are > excluded ? > Thanks! > > Zhuangming > > > -----原始邮件----- > *发件人:* "Douglas Greve" <greve(a)nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu>> > *发送时间:* 2014年3月6日星期四 > *收件人:* freesurfer(a)nmr.mgh.harvard.edu > <mailto:freesurfer@nmr.mgh.harvard.edu> > *抄送:* > *主题:* Re: [Freesurfer] Surface area in aparc stats > > > By default, the surface area is computed from the white surface > (ie, boundary between WM and GM). It is possible to compute it > from the pial surface (ie, boundary between GM and background) > doug > > > On 3/5/14 9:14 PM, 沈庄明 wrote: >> Hi all, >> I need to know how is the SurfArea in ?h.aparc.stats calculated >> by FreeSurfer? Since each cortical parcellation has its own >> thickness in 3D space, does the surface area computation consider >> both the exterior surface (i.e. the surface separating the gray >> matter and the background) and the interior surface (i.e. the >> surface separating the gray matter and the white matter)? >> Thanks! >> >> Zhuangming Shen >> >> >> >> >> >> >> >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer(a)nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > >

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Large areas of white matter ignored, even with control points
by Andrea Grant 06 Mar '14

06 Mar '14

Hello, I'm working with T1 weighted scans obtained at 7T and have a problem with a subject. I preprocess the images to deal with the B1 inhomogeneity (normalize to PD and mask noisy pixels), and have successfully segmented about 20 scans. I often need to use control points, but they normally work just as I expect. However, I have one subject where large areas of the brain are completely excluded from the segmentation (basically the entire occipital lobe). I added control points and re-ran, to no effect. I'm attaching a screenshot of the brainmask with surfaces, my control points, and the white matter mask. Clearly, the skull stripping wasn't very successful (I adjusted the watershed threshold manually, but at one value I got the current result and at a single integer lower I lost half the brain). I have successfully segmented other subjects with equally poor skull strips, though, so I don't believe this has any bearing on the current issue. Is editing the white matter mask the only way to fix this? If so, do I need to carefully fill in on every slice, or can I just brush in here and there to sort of "goose" the white matter into that region? I can do the slice by slice fix, but if there's a way to avoid the several hours it will take me, I would love to know! Thanks, Andrea ----- Andrea Grant Visual Neuroimaging Technologist Center for Magnetic Resonance Research, University of Minnesota 2021 6th St. SE, Minneapolis, MN 55455, 612-626-4948 gran0260(a)umn.edu umn.edu/~gran0260 <http://umn.edu/%7Egran0260>

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Re: [Freesurfer] DICOM input format and structure
by Douglas N Greve 06 Mar '14

06 Mar '14

Hi Sravan , please post to the list and not to us personally. Thanks! This is just a list of what you (or whoever you are working with acquired), so I don't know what is in there. Probably #2 is what you want, less sure about #4 doug On 03/06/2014 03:34 PM, Mattevada, Sravan wrote: > Hello Doug, > > I ran the dcmunpac command and below is what I got. > Sorry I am new to freesurfer, Linux and MRI Images as well. > > Are no. 2 and no. 4 the T1s ? which one do I need to pass to the recon-all ? > Thank you very much for your response. It helps a lot. > > [freesurfer@localhost freesurfer]# dcmunpack -src /home/freesurfer/Documents/Sub_9884/DICOM > > cd /home/freesurfer > /usr/local/freesurfer/bin/dcmunpack -src /home/freesurfer/Documents/Sub_9884/DICOM > > -rwxr-xr-x. 1 root root 23416 May 13 2013 /usr/local/freesurfer/bin/dcmunpack > --------------------------------------- > --------------------------------------- > Searching for matching files > Thu Mar 6 14:22:14 CST 2014 > Thu Mar 6 14:22:14 CST 2014 > Found 229 total files. > Interrogating each and every one of them. > Be patient. > If you have collected the data in the Martinos center, this > will run faster if you kill this job and re-run with -martinos > Found 9 unique series: 1 2 3 4 5 6 7 8 9 > Subject 9884^9884^^^ > Date 20131203 > Time 082101.937000 > Institution RADIOLOGY ASSOCIATES-CDI > 1 LOCALIZER3PLANE 5 20 40 0.546875 ROW 180 /home/freesurfer/Documents/Sub_9884/DICOM/PA000000/ST000000/SE000000/IM000003 > 2 T1SESAG 8 345 90 0.8984375 ROW 140 /home/freesurfer/Documents/Sub_9884/DICOM/PA000000/ST000000/SE000001/IM000011 > 3 T2TSEAX 85 4010 180 0.8984375 ROW 110 /home/freesurfer/Documents/Sub_9884/DICOM/PA000000/ST000000/SE000002/IM000011 > 4 T1SEAX 8 500 90 0.8984375 ROW 140 /home/freesurfer/Documents/Sub_9884/DICOM/PA000000/ST000000/SE000003/IM000011 > 5 T2FLAIRAX 117 9000 180 0.8984375 ROW 130 /home/freesurfer/Documents/Sub_9884/DICOM/PA000000/ST000000/SE000004/IM000011 > 6 T2AXHEMO 27 1220 25 0.44921875 ROW 195 /home/freesurfer/Documents/Sub_9884/DICOM/PA000000/ST000000/SE000005/IM000011 > 7 AXep2d_diff_2scan_trace 98 4100 90 1.796875\1.796875 COL 1260 /home/freesurfer/Documents/Sub_9884/DICOM/PA000000/ST000000/SE000006/IM000011 > 8 AXep2d_diff_2scan_trace_ADC 98 4100 90 1.796875\1.796875 COL 1260 /home/freesurfer/Documents/Sub_9884/DICOM/PA000000/ST000000/SE000007/IM000011 > 9 T2TSECOROBL 87 4260 180 0.4296875 ROW 110 /home/freesurfer/Documents/Sub_9884/DICOM/PA000000/ST000000/SE000008/IM000011 > > > Thu Mar 6 14:22:43 CST 2014 > dcmunpack done > > > -Sravan > > > ________________________________________ > From: freesurfer-bounces(a)nmr.mgh.harvard.edu [freesurfer-bounces(a)nmr.mgh.harvard.edu] on behalf of Douglas N Greve [greve(a)nmr.mgh.harvard.edu] > Sent: Thursday, March 06, 2014 1:15 PM > To: freesurfer(a)nmr.mgh.harvard.edu > Subject: Re: [Freesurfer] DICOM input format and structure > > They do not have to have a dcm extension. The 180 files represent many > slices from a single volume (or multiple volumes). You need to find out > which ones are which. One way to do this is to run > > dcmunpack -src path-to-dicom folder > > this will look through all the folders and files under path-to-dicom and > sort them into acqusitions. It will print out a list of each volume and > a single dicom file that belongs to that volume. When you find the T1 > that you want to run thru FS, pass that single dicom file to recon-all > with the -i flag > > duog > > > On 03/06/2014 12:57 PM, Mattevada, Sravan wrote: >> Hello, >> >> I am new to freesurfer. I went through the Wiki and >> FAQ's but couldn't find information on >> the format of the input for recon-all. I understand >> that one of the input files must have a ".dcm" extension. >> >> I have a CD which has MRI scanned images. >> >> The folder structure is E:\DICOM\PA000000\ST000000 >> >> under ST000000 there are 8 folders SE000000, >> SE000001,... SE000008 >> Each SE00000* folder has files IM000000, >> IM000001, ... >> >> There are about 180 files all together in the 8 >> folders. >> >> At first there were no extentions to any of the >> image files, so, I add an extension ".dcm" to all of the files. >> >> I ran recon-all got an error. >> >> the error.log file has "MRIresample(): source >> matrix has zero determinant; matrix is:" >> >> Am I on the right path ? or am I missing something ? >> So I need to convert the images before running >> the recon ? >> I see that only 8 files in the first folder in >> the series are being read, Do I need to input the files in a different >> structure ? >> >> I am trying to do a proof of concept with our data before buying a >> machine for running Linux CentOS for freesurfer. >> >> >> recon-all command generates the following >> >> [freesurfer@localhost freesurfer]# recon-all -i >> Documents/Sub_9884/SE000000/IM000000.dcm -subject test -all >> Subject Stamp: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 >> Current Stamp: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 >> INFO: SUBJECTS_DIR is /usr/local/freesurfer/subjects >> Actual FREESURFER_HOME /usr/local/freesurfer >> Linux localhost.localdomain 2.6.32-431.el6.x86_64 #1 SMP Fri Nov 22 >> 03:15:09 UTC 2013 x86_64 x86_64 x86_64 GNU/Linux >> /usr/local/freesurfer/subjects/test >> >> mri_convert /home/freesurfer/Documents/Sub_9884/SE000000/IM000000.dcm >> /usr/local/freesurfer/subjects/test/mri/orig/001.mgz >> >> mri_convert /home/freesurfer/Documents/Sub_9884/SE000000/IM000000.dcm >> /usr/local/freesurfer/subjects/test/mri/orig/001.mgz >> $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ >> reading from /home/freesurfer/Documents/Sub_9884/SE000000/IM000000.dcm... >> Getting Series No >> INFO: Found 8 files in /home/freesurfer/Documents/Sub_9884/SE000000 >> INFO: Scanning for Series Number 1 >> Scanning Directory >> INFO: found 6 files in series >> INFO: loading series header info. >> >> RunNo = 0 >> INFO: sorting. >> INFO: (512 512 6), 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/freesurfer/Documents/Sub_9884/SE000000/IM000004.dcm >> Identification >> NumarisVer syngo MR A35 4VA35A >> ScannerModel Symphony >> PatientName 9884^9884^^^ >> Date and time >> StudyDate 20131203 >> StudyTime 082101.937000 >> SeriesTime 082131.093000 >> AcqTime 082138.020010 >> Acquisition parameters >> PulseSeq *fl2d1 >> Protocol LOCALIZER 3 PLANE >> PhEncDir ROW >> EchoNo 0 >> FlipAngle 40 >> EchoTime 5 >> InversionTime -1 >> RepetitionTime 20 >> PhEncFOV 280 >> ReadoutFOV 280 >> Image information >> RunNo 0 >> SeriesNo 1 >> ImageNo 3 >> NImageRows 512 >> NImageCols 512 >> NFrames 1 >> SliceArraylSize 6 >> IsMosaic 0 >> ImgPos 140.0000 6.0000 140.0000 >> VolRes 0.5469 0.5469 12.0000 >> VolDim 512 512 6 >> Vc -1.0000 -0.0000 0.0000 >> Vr -0.0000 -0.0000 -1.0000 >> Vs -1.0000 -0.0000 0.0000 >> VolCenter -36.0000 6.0000 0.0000 >> TransferSyntaxUID 1.2.840.10008.1.2.1 >> UseSliceScaleFactor 0 (slice 0: 1) >> INFO: no Siemens slice order reversal detected (good!). >> TR=20.00, TE=5.00, TI=-1.00, flip angle=40.00 >> warning: input volume axes are not orthogonal:i_dot_j = 0.000000, >> i_dot_k = 1.000000, j_dot_k = 0.000000 >> i_ras = (-1, -0, 0) >> j_ras = (-0, -0, -1) >> k_ras = (-1, -0, 0) >> warning: output volume axes are not orthogonal:i_dot_j = 0.000000, >> i_dot_k = 1.000000, j_dot_k = 0.000000 >> i_ras = (-1, -0, 0) >> j_ras = (-0, -0, -1) >> k_ras = (-1, -0, 0) >> writing to /usr/local/freesurfer/subjects/test/mri/orig/001.mgz... >> #-------------------------------------------- >> #@# MotionCor Thu Mar 6 11:02:35 CST 2014 >> Found 1 runs >> /usr/local/freesurfer/subjects/test/mri/orig/001.mgz >> Checking for (invalid) multi-frame inputs... >> WARNING: only one run found. This is OK, but motion >> correction cannot be performed on one run, so I'll >> copy the run to rawavg and continue. >> >> cp /usr/local/freesurfer/subjects/test/mri/orig/001.mgz >> /usr/local/freesurfer/subjects/test/mri/rawavg.mgz >> >> /usr/local/freesurfer/subjects/test >> >> mri_convert /usr/local/freesurfer/subjects/test/mri/rawavg.mgz >> /usr/local/freesurfer/subjects/test/mri/orig.mgz --conform >> >> mri_convert /usr/local/freesurfer/subjects/test/mri/rawavg.mgz >> /usr/local/freesurfer/subjects/test/mri/orig.mgz --conform >> MRIresample(): source matrix has zero determinant; matrix is: >> $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ >> reading from /usr/local/freesurfer/subjects/test/mri/rawavg.mgz... >> TR=20.00, TE=5.00, TI=-1.00, flip angle=40.00 >> warning: input volume axes are not orthogonal:i_dot_j = 0.000000, >> i_dot_k = 1.000000, j_dot_k = 0.000000 >> i_ras = (-1, -0, 0) >> j_ras = (-0, -0, -1) >> k_ras = (-1, -0, 0) >> Original Data has (0.546875, 0.546875, 12) mm size and (512, 512, 6) >> voxels. >> Data is conformed to 1 mm size and 256 voxels for all directions >> changing data type from short to uchar (noscale = 0)... >> MRIchangeType: Building histogram >> Reslicing using trilinear interpolation >> -0.547 -0.000 -12.000 140.000; >> -0.000 -0.000 -0.000 6.000; >> 0.000 -0.547 0.000 140.000; >> 0.000 0.000 0.000 1.000; >> Linux localhost.localdomain 2.6.32-431.el6.x86_64 #1 SMP Fri Nov 22 >> 03:15:09 UTC 2013 x86_64 x86_64 x86_64 GNU/Linux >> >> recon-all -s test exited with ERRORS at Thu Mar 6 11:02:38 CST 2014 >> >> For more details, see the log file >> /usr/local/freesurfer/subjects/test/scripts/recon-all.log >> To report a problem, see >> http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting >> >> >> >> >> >> >> _______________________________________________ >> 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: https://gate.nmr.mgh.harvard.edu/filedrop2 > www.nmr.mgh.harvard.edu/facility/filedrop/index.html > Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > > _______________________________________________ > 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. > > > -- 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: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

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DICOM input format and structure
by Mattevada, Sravan 06 Mar '14

06 Mar '14

Hello, I am new to freesurfer. I went through the Wiki and FAQ's but couldn't find information on the format of the input for recon-all. I understand that one of the input files must have a ".dcm" extension. I have a CD which has MRI scanned images. The folder structure is E:\DICOM\PA000000\ST000000 under ST000000 there are 8 folders SE000000, SE000001,... SE000008 Each SE00000* folder has files IM000000, IM000001, ... There are about 180 files all together in the 8 folders. At first there were no extentions to any of the image files, so, I add an extension ".dcm" to all of the files. I ran recon-all got an error. the error.log file has "MRIresample(): source matrix has zero determinant; matrix is:" Am I on the right path ? or am I missing something ? So I need to convert the images before running the recon ? I see that only 8 files in the first folder in the series are being read, Do I need to input the files in a different structure ? I am trying to do a proof of concept with our data before buying a machine for running Linux CentOS for freesurfer. recon-all command generates the following [freesurfer@localhost freesurfer]# recon-all -i Documents/Sub_9884/SE000000/IM000000.dcm -subject test -all Subject Stamp: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 Current Stamp: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 INFO: SUBJECTS_DIR is /usr/local/freesurfer/subjects Actual FREESURFER_HOME /usr/local/freesurfer Linux localhost.localdomain 2.6.32-431.el6.x86_64 #1 SMP Fri Nov 22 03:15:09 UTC 2013 x86_64 x86_64 x86_64 GNU/Linux /usr/local/freesurfer/subjects/test mri_convert /home/freesurfer/Documents/Sub_9884/SE000000/IM000000.dcm /usr/local/freesurfer/subjects/test/mri/orig/001.mgz mri_convert /home/freesurfer/Documents/Sub_9884/SE000000/IM000000.dcm /usr/local/freesurfer/subjects/test/mri/orig/001.mgz $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from /home/freesurfer/Documents/Sub_9884/SE000000/IM000000.dcm... Getting Series No INFO: Found 8 files in /home/freesurfer/Documents/Sub_9884/SE000000 INFO: Scanning for Series Number 1 Scanning Directory INFO: found 6 files in series INFO: loading series header info. RunNo = 0 INFO: sorting. INFO: (512 512 6), 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/freesurfer/Documents/Sub_9884/SE000000/IM000004.dcm Identification NumarisVer syngo MR A35 4VA35A ScannerModel Symphony PatientName 9884^9884^^^ Date and time StudyDate 20131203 StudyTime 082101.937000 SeriesTime 082131.093000 AcqTime 082138.020010 Acquisition parameters PulseSeq *fl2d1 Protocol LOCALIZER 3 PLANE PhEncDir ROW EchoNo 0 FlipAngle 40 EchoTime 5 InversionTime -1 RepetitionTime 20 PhEncFOV 280 ReadoutFOV 280 Image information RunNo 0 SeriesNo 1 ImageNo 3 NImageRows 512 NImageCols 512 NFrames 1 SliceArraylSize 6 IsMosaic 0 ImgPos 140.0000 6.0000 140.0000 VolRes 0.5469 0.5469 12.0000 VolDim 512 512 6 Vc -1.0000 -0.0000 0.0000 Vr -0.0000 -0.0000 -1.0000 Vs -1.0000 -0.0000 0.0000 VolCenter -36.0000 6.0000 0.0000 TransferSyntaxUID 1.2.840.10008.1.2.1 UseSliceScaleFactor 0 (slice 0: 1) INFO: no Siemens slice order reversal detected (good!). TR=20.00, TE=5.00, TI=-1.00, flip angle=40.00 warning: input volume axes are not orthogonal:i_dot_j = 0.000000, i_dot_k = 1.000000, j_dot_k = 0.000000 i_ras = (-1, -0, 0) j_ras = (-0, -0, -1) k_ras = (-1, -0, 0) warning: output volume axes are not orthogonal:i_dot_j = 0.000000, i_dot_k = 1.000000, j_dot_k = 0.000000 i_ras = (-1, -0, 0) j_ras = (-0, -0, -1) k_ras = (-1, -0, 0) writing to /usr/local/freesurfer/subjects/test/mri/orig/001.mgz... #-------------------------------------------- #@# MotionCor Thu Mar 6 11:02:35 CST 2014 Found 1 runs /usr/local/freesurfer/subjects/test/mri/orig/001.mgz Checking for (invalid) multi-frame inputs... WARNING: only one run found. This is OK, but motion correction cannot be performed on one run, so I'll copy the run to rawavg and continue. cp /usr/local/freesurfer/subjects/test/mri/orig/001.mgz /usr/local/freesurfer/subjects/test/mri/rawavg.mgz /usr/local/freesurfer/subjects/test mri_convert /usr/local/freesurfer/subjects/test/mri/rawavg.mgz /usr/local/freesurfer/subjects/test/mri/orig.mgz --conform mri_convert /usr/local/freesurfer/subjects/test/mri/rawavg.mgz /usr/local/freesurfer/subjects/test/mri/orig.mgz --conform MRIresample(): source matrix has zero determinant; matrix is: $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from /usr/local/freesurfer/subjects/test/mri/rawavg.mgz... TR=20.00, TE=5.00, TI=-1.00, flip angle=40.00 warning: input volume axes are not orthogonal:i_dot_j = 0.000000, i_dot_k = 1.000000, j_dot_k = 0.000000 i_ras = (-1, -0, 0) j_ras = (-0, -0, -1) k_ras = (-1, -0, 0) Original Data has (0.546875, 0.546875, 12) mm size and (512, 512, 6) voxels. Data is conformed to 1 mm size and 256 voxels for all directions changing data type from short to uchar (noscale = 0)... MRIchangeType: Building histogram Reslicing using trilinear interpolation -0.547 -0.000 -12.000 140.000; -0.000 -0.000 -0.000 6.000; 0.000 -0.547 0.000 140.000; 0.000 0.000 0.000 1.000; Linux localhost.localdomain 2.6.32-431.el6.x86_64 #1 SMP Fri Nov 22 03:15:09 UTC 2013 x86_64 x86_64 x86_64 GNU/Linux recon-all -s test exited with ERRORS at Thu Mar 6 11:02:38 CST 2014 For more details, see the log file /usr/local/freesurfer/subjects/test/scripts/recon-all.log To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting

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Re: [Freesurfer] QDEC bad fd number
by dgw 06 Mar '14

06 Mar '14

Please be sure to 'reply all' so everyone may participate. Yes, You need to set the SUBJECTS_DIR before using freesurfer tools. HTH D On Tue, Mar 4, 2014 at 2:02 PM, Mihaela Stefan <mikaelastephan(a)gmail.com> wrote: > It says "No such file or directory" > The environment for SUBJECTS_DIR was set as /usr/local/freesurfer/subjects > but I have my working folder in a different location. Could that be the > problem? > > > On Tue, Mar 4, 2014 at 1:34 PM, dgw <dgwakeman(a)gmail.com> wrote: >> >> Are those subjects in your SUBJECTS_DIR? >> >> What is the output of >> ls $SUBJECTS_DIR >> ? >> >> On Tue, Mar 4, 2014 at 1:10 PM, Mihaela Stefan <mikaelastephan(a)gmail.com> >> wrote: >> > Hello, >> > I am re-posting this since I haven't got an answer yet. >> > >> > Thanks! >> > Mihaela >> > >> > >> > On Fri, Feb 21, 2014 at 3:55 PM, Mihaela Stefan >> > <mikaelastephan(a)gmail.com> >> > wrote: >> >> >> >> Hi freesurfers, >> >> >> >> I get this error when I load qdec.table.dat. Is it something wrong or >> >> should I ignore it? >> >> Verifying subject data.sh: 1: Syntax error: Bad fd number >> >> ERROR: QdecProject::VerifySubjects: Couldn't find subject '6027' in >> >> SUBJECTS_DIR >> >> .sh: 1: Syntax error: Bad fd number >> >> ERROR: QdecProject::VerifySubjects: Couldn't find subject '6209' in >> >> SUBJECTS_DIR >> >> .sh: 1: Syntax error: Bad fd number >> >> ERROR: QdecProject::VerifySubjects: Couldn't find subject '6243' in >> >> SUBJECTS_DIR >> >> . >> >> . >> >> . >> >> ERROR: QdecProject::VerifySubjects: Couldn't find subject '6052' in >> >> SUBJECTS_DIR >> >> Too many subjects not found! >> >> >> >> >> >> Someone else complained about the same problem but there was no reply: >> >> >> >> http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg08288.html >> >> >> >> My qdec.table looks like this: >> >> fsid diagnosis Cage >> >> 6027 ABN -1.39 >> >> 6209 ABN 2.61 >> >> . >> >> . >> >> >> >> Thanks! >> >> Mihaela >> >> >> > >> > >> > _______________________________________________ >> > 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. >> > > >

3 2

extract pial_lgi from v1.thresh labels
by krista kelly 06 Mar '14

06 Mar '14

Hello, I would like to extract the pial_lgi data from Freesurfer's V1.thresh labels but can't quite figure it out. I've tried adapting the commands from the LGI Freesurfer tutorial as such: mri_segstats --label-thresh BV20 lh V1.thresh.label --i $SUBJECTS_DIR/BV20/surf/lh.pial_lgi --sum lh.V1.thresh.label.stats I've also tried mris_anatomical_stats -l lh.V1.thresh.label -f BV20/stats/lh.V1.thresh.label.stats BV20 lh pial_lgi but I've had no luck with either. I would appreciate any help! Thanks, Krista

2 15

Difference in Volumetric measure of Hippocampus Segmentation
by Saurabh Thakur 06 Mar '14

06 Mar '14

Hello Freesurfer Expert, I am working on volumetric analysis of Hippocampus. When i am find the no of voxel's for left Hippocampus (17) and Right Hippocampus(53) using command i m getting some what diffrence. I just want to know which command should be used for the volumetric analysis: Lh Hippo Rh Hippo *Command used * *17* *53* asegstats2table 4563 4502 EstimatedTotalIntraCranialVol 1594882.91136 mri_label_volume 4645 4545 eTIV volume (1594796) Thanks for timely reply. cheers Saurabh Thakur,

2 1

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