Freesurfer May 2013

freesurfer@nmr.mgh.harvard.edu

174 participants
299 discussions

command not found
by clelia pellicano 23 May '13

23 May '13

Hi, I have run recon-all -s bert -all to try my installation and it worked. Now, when I try to use other command (and also again recon-all -s bert -all) I always get this: dyn1097-8:subjects cpellica$ tkmedit bert orig.mgz -bash: tkmedit: command not found dyn1097-8:subjects cpellica$ tkmedit -s bert orig.mgz -bash: tkmedit: command not found dyn1097-8:subjects cpellica$ tksurfer -s bert rh pial -bash: tksurfer: command not found dyn1097-8:subjects cpellica$ qdec -bash: qdec: command not found dyn1097-8:subjects cpellica$ recon-all help -bash: recon-all: command not found dyn1097-8:subjects cpellica$ recon-all -s bert -all -bash: recon-all: command not found I don't know how to do. Please, could you help me? Thanks Clelia

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qdec for .stats file
by stdp82＠virgilio.it 23 May '13

23 May '13

Hi list, how can I use qdec to investigate the difference among groups regarding the measures contained in .stats file (for example thalamic volume)? Thanks, Stefano

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Siemens dicom error on mri_convert
by Cat Chong 23 May '13

23 May '13

Hello Experts, I am trying to run the mri_convert command prior to the recon-all command on Siemens T1 dicoms (as suggested in the archives). I am using freesurfer version: freesurfer-Darwin-lion-stable-pub-v5.3.0, Mac OS X Lion 10.7.5 I am using the command below: mri_convert -it siemens_dicom -ot mgz 1002/IM-0001-0001.dcm 2001.mgz Below is the command line error I receive, it is a similar error I receive when I try to use the command recon-all on the Siemens dicoms. I have used freesurfer before on GE dicoms and never had a problem running recon-all. Is this error message particular to the Siemens dicoms, and would you be able to tell me how to proceed? Thank you very much for you help, Cat reading from 1002/IM-0001-0001.dcm... Getting Series No Scanning Directory INFO: Found 130 files in 1002 INFO: Scanning for Series Number 2 INFO: found 128 files in series INFO: loading series header info. INFO: sorting. RunNo = 1 WARNING: Run 1 appears to be truncated Files Found: 128, Files Expected (lRep+1): 1 FileName 1002/IM-0001-0001.dcm Identification NumarisVer syngo MR D11 ScannerModel Skyra PatientName RS-FMRI^RS-FMRI Date and time StudyDate 20130222 StudyTime 082109.140000 SeriesTime 082812.906000 AcqTime 082237.315000 Acquisition parameters PulseSeq *tfl3d1_16ns Protocol SAG MP Rage PhEncDir ROW EchoNo 1 FlipAngle 8 EchoTime 3.03 InversionTime 1000 RepetitionTime 2400 PhEncFOV 0 ReadoutFOV 0 Image information RunNo 1 SeriesNo 2 ImageNo 1 NImageRows 256 NImageCols 256 NFrames 128 SliceArraylSize 0 IsMosaic 1 ImgPos -78.6002 128.0000 93.1332 VolRes 1.0000 1.0000 1.2500 VolDim 0 0 0 Vc -0.0000 -1.0000 0.0000 Vr -0.0000 -0.0000 -1.0000 Vs 0.0000 0.0000 0.0000 VolCenter 0.0000 0.0000 0.0000 TransferSyntaxUID 1.2.840.10008.1.2.1 WARNING: file 1002/IM-0001-0001.dcm does not contain a Siemens ASCII header has this file been anonymized? ERROR: cannot unpack mosiacs without ASCII header

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3 recon-all errors: v5.0.0
by Sudhin A. Shah 23 May '13

23 May '13

1) BEST FITNESS (M) is 984.24263 mri =0.000 curv = 4.318 unmri = -1001.515 ( f=0.00 , v=0.00 , c=4.32 , q= 8.64 ) ( f=0.00 , v=0.00 , c=4.32 , q= 8.64 ) 63 patches have been generated - 38 self-intersected max face = 36973(40653) - loop = 46 (73) - ntries = [27,14799] ERROR: _FindFacePath: could not find path! Linux sudhin-Precision-WorkStation-690 2.6.35-32-generic #67-Ubuntu SMP Mon Mar 5 19:39:49 UTC 2012 x86_64 GNU/Linux recon-all -s xtyzW exited with ERRORS at Tue May 21 05:48:38 EDT 2013 =============== 2)*************************WATERSHED************************** Sorting... mri_watershed Error: Problem in the COG calculation: T1.mgz may not contain properly normalized white-matter. Confirm that T1.mgz has enough white-matter voxels of value 110. If white-matter contains few if any voxels of value 110, try adding wm control-points to nu.mgz, and re-run recon-all. Linux sudhin-Precision-WorkStation-690 2.6.35-32-generic #67-Ubuntu SMP Mon Mar 5 19:39:49 UTC 2012 x86_64 GNU/Linux recon-all -s cbvfB exited with ERRORS at Fri May 17 17:45:23 EDT 2013 ============== 3)CORRECTING DEFECT 2 (vertices=30163, convex hull=6211) error in the retessellation normal vector of length zero at vertex 88778 with 0 faces vertex 88778 has 0 face No such file or directory Linux sudhin-Precision-WorkStation-690 2.6.35-32-generic #67-Ubuntu SMP Mon Mar 5 19:39:49 UTC 2012 x86_64 GNU/Linux recon-all -s ghjG exited with ERRORS at Thu May 16 05:11:49 EDT 2013

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Re: [Freesurfer] log transform of the mgh file
by Minjie Wu 23 May '13

23 May '13

Hello All, Is there any way in FreeSurfer to take the log transform of a .mgh file and save the output as .mgh file? Thank you. Minjie

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Re: [Freesurfer] Freesurfer Digest, Vol 111, Issue 30
by Yongxia Zhou 23 May '13

23 May '13

Hi, I have a question running fsfast in my Mac, The mkcontrast command gave the error of can not launch matlab. Could you please let me know how to solve this problem. Thank you very much Yongxia On Wednesday, May 22, 2013, 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 error (Yizhou Ma) > 2. Re: Still confused by group analysis.. (Tudor Popescu) > 3. Re: ERROR in long_mris_slope (Martin Reuter) > 4. Re: ERROR in long_mris_slope (Martin Reuter) > 5. temporal lobe left out in pial surface - edits on > brainmask.mgz or brain.finalsurfs.mgz? (Yizhou Ma) > 6. Re: temporal lobe left out in pial surface - edits on > brainmask.mgz or brain.finalsurfs.mgz? (Chris Watson) > 7. Re: temporal lobe left out in pial surface - edits on > brainmask.mgz or brain.finalsurfs.mgz? (Yizhou Ma) > 8. Re: temporal lobe left out in pial surface - edits on > brainmask.mgz or brain.finalsurfs.mgz? (Bruce Fischl) > 9. Re: temporal lobe left out in pial surface - edits on > brainmask.mgz or brain.finalsurfs.mgz? (Yizhou Ma) > 10. Re: temporal lobe left out in pial surface - edits on > brainmask.mgz or brain.finalsurfs.mgz? (Yizhou Ma) > 11. Re: ERROR: recon-all -subcortseg (Akio Yamamoto) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Wed, 22 May 2013 13:19:35 -0400 > From: Yizhou Ma <ym850(a)nyu.edu> > Subject: [Freesurfer] recon-all error > To: freesurfer <freesurfer(a)nmr.mgh.harvard.edu> > Message-ID: > < > CAHqJiV6t-fKQRWcfFg8r5O9gJrtZsTe+ZgKU0qVD2J7aoNSVHw(a)mail.gmail.com> > Content-Type: text/plain; charset="iso-8859-1" > > Dear FS experts, > > I have a recon-all error regarding one of my subjects. The scan suffers > from weakened signals at the lower part of the brain. Skullstrip stripped > most of the cerebellum at first, and we fixed it manually. After running > recon-all for the first time, large portions of the temporal lobes were > left out of the brain. Knowing that this may not be the correct way, we > still tried to fixed that by adding lots of control points. The second run > of recon-all, then, came back with the following error message:" > > Loading source data > Reading curvature file > /space/mdeh3/3/halgdev/projects/nyuproj/subjects/sub4422b/surf/rh.thickness > ERROR: number of vertices in > /space/mdeh3/3/halgdev/projects/nyuproj/subjects/sub4422b/surf/rh.thickness > does not match surface (192226,134773) > ERROR: reading curvature file > Linux mmil-compute-1-11.local 2.6.18-308.16.1.el5 #1 SMP Tue Oct 2 22:01:43 > EDT 2012 x86_64 x86_64 x86_64 GNU/Linux > recon-all -s sub4422b exited with ERRORS at Mon May 20 > " > > Any ideas for why it is, or how we can fix the problem at the temporal > lobes, will be really appreciated. > > Thanks, > Cherry >

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intersection of triangles from the reconstructed pial surface
by mcpiastra＠libero.it 23 May '13

23 May '13

Dear Bruce, we have the same problem as Yasheng's so we would like to know how to solve it. To answer what you ask Yasheng: it intersects two faces, but what do you meant with "native (binary) format"? Thank you a lot. Best regards, Maria Carla e Gabriele Hi Yasheng, hmmm, there is triangle/triangle intersection code that is supposed to prevent this from happening. Does this happen if you use the native (binary) format? How many faces intersect? Bruce On Mon, 8 Mar 2010 yasheng_chen at med.unc.edu wrote: > Hi all, > > I am using tetgen to construct a tetrahedral mesh with the extracted pial surface in subject 004 from the tutorial datasets. But I got an error message from tetgen to say that some triangles are intersecting each other. I am not sure whether anyone has found this before. The file I tested was 004/lh.pial. I first transferred it to asc format with mris_convert, and then make a straightforward transfer to .off (used by tetgen and geomview). I loaded the .off file with geomview and it looks right. Then I run tetgen with the .off file and got an error message like below, which means that there are intersections among the facets. > Error: Invalid PLC. > Two subfaces (219028, 5283, 5282) and (219054, 5300, 5283) > are found intersecting each other. > Hint: Use -d switch to find all intersecting facets. > > This is a little strange to me since the topology issue has been handled in the reconstructed surface, does any one have any clue? > > Thank you very much! > > Yasheng > >

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Re: [Freesurfer] ERROR in long_mris_slope
by Martin Reuter 23 May '13

23 May '13

Hi Cathy, please cc the freesurfer list when replying, so that other people can profit from or contribute to the discussion. (Maybe someone else can comment on the transfer of edits in cross processing between versions 5.0.....5.3 ??) So your cross data is processed with a mix of version 5 and 5.1? or is all processed with 5.1? Within a study you should never mix versions, ie. process some subjects with one versions others with a different version. It is OK to mix some FS versions between the cross and long processing, if it is done for all subjects the same way. I think you have these options: 1. keep 5.1 cross sectional data (assuming all is 5.1) and run base and long with 5.3. Then start processing base and long (qual check the base and edit if necessary). It should also work if all cross data is in 5.0. 2. reprocess the cross sectionals with 5.3 keeping the edits. Check if edits got transferred correctly, maybe edit more (or remove edits). Then start the base and long (again qual check base and edit if necessary). Obviously 1. would be less work. If you have mixed versions in your cross data, I'd rather recommend 2. Best, Martin On 05/23/2013 05:16 AM, Catherine Bois wrote: > Great, > > Thank you very much. I was also hoping to ask for some advice in terms > of large dataset handling; I have a dataset of ca 500 scans, with > several individuals having only one timepoint. The editing to the > -cross runs has been done on version 5 and version 5.1, however we now > want to move on to longitudinal processing(I am only completing a > "trial" run now). In terms of data management and the laborious task > of editing these scans, what to you would be the most time efficient? > I would like to, if possible, recon everything again with version 5.3 > (as it can handle individuals with only 1 tp) but I would also like to > maintain the edits done in version 5 and version 5.1, even thoguh I > want to reprocess all the longitudinal runs etc with version 5.3 to > maintain consistency. What would be the best plan of action form your > point of view/how would you organize this task? > > Thank you so much for your help, it would be greatly appreciated. > > Best Wishes, > > Cathy > > > Quoting Martin Reuter <mreuter(a)nmr.mgh.harvard.edu> on Wed, 22 May > 2013 14:33:08 -0400: > >> Hi Cathy, >> >> I think the problem is when there are tabs AND spaces. Only spaces >> should also work. I can write some code (when I have time) that >> checks these things, maybe for the next release. >> >> Best, Martin >> >> On 05/22/2013 02:21 PM, Catherine Bois wrote: >>> Hi, >>> >>> Thank you for your reply. I finally got it working today.thanks for >>> your help=)! You say the qdec table should have only spaces; however >>> they only seem to work when they are completely tab separated and >>> not a single space? If there is accidently a space it will suddenly >>> not work. Is there a way that can solve this problem that you can >>> think of? It is very time consuming because suddenly it will jsut >>> stop working and I need to start from scratch! >>> >>> >>> Quoting Martin Reuter <mreuter(a)nmr.mgh.harvard.edu> on Wed, 22 May >>> 2013 14:08:44 -0400: >>> >>>> Hi Cathy, >>>> >>>> it must be something else (I think). The mris_calc command looks >>>> weird ("--label " looks like the label is not passed, but a space >>>> instead, it then thinks 'mul' is a file). >>>> >>>> qdecfinal is your qdec table? Make sure it contains only spaces to >>>> separate the fields. It should have at least these columns >>>> fsid fsid-base time >>>> >>>> also in your command below, why are there "?" before do-label and >>>> time? >>>> >>>> Unless you want to use the stack (within subject stack of thickness >>>> values), I would drop the --do-stack (maybe also drop do-avg or >>>> whatever else you don't need). >>>> >>>> For debugging, I would create a directory, place a single subject >>>> there, create a new qdec table with only that subject and try again >>>> there. If it still happens , let me know. >>>> >>>> Best, Martin >>>> >>>> >>>> On 05/20/2013 10:25 AM, Catherine Bois wrote: >>>>> Dear Freesurfer experts, >>>>> >>>>> I am trying to conduct the long_mris_slopes --qdec qdecfinal --meas >>>>> thickness --hemi lh --do-avg --do-rate --do-pc1 --do-spc --do-stack >>>>> ?do-label ?time time --qcache fsaverage command for my longitudinal >>>>> processing. However I keep getting the error message: >>>>> >>>>> mris_calc -o /directory/baseX/surf/lh.long.thickness-spc.fwhm0.mgh >>>>> --label /directory/baseX/surf/lh.long.thickness-spc.fwhm0.mgh mul 100 >>>>> >>>>> >>>>> mris_calc: >>>>> Sorry, but I seem to have encountered an error. >>>>> While accessing file 'mul', >>>>> >>>>> I read online that this was due to a bug encountered in version 5.1, >>>>> however I recently upgraded to version 5.3 and the error message >>>>> persists. As my Long and base runs have been done in version 5.1 >>>>> still, I was wondering whether in order to fix this problem the long >>>>> and base runs need to be rerun with version 5.3, or whether the error >>>>> I am encountering has another solution/ is caused by another problem >>>>> entirely? >>>>> >>>>> Thank you for your help, >>>>> >>>>> Best Wishes, >>>>> >>>>> Cathy >>>>> >>>> >>>> -- >>>> Martin Reuter, Ph.D. >>>> Assistant in Neuroscience - Massachusetts General Hospital >>>> Instructor in Neurology - Harvard Medical School >>>> MGH / HMS / MIT >>>> >>>> A.A.Martinos Center for Biomedical Imaging >>>> 149 Thirteenth Street, Suite 2301 >>>> Charlestown, MA 02129 >>>> >>>> Phone: +1-617-724-5652 >>>> Email: >>>> mreuter(a)nmr.mgh.harvard.edu >>>> reuter(a)mit.edu >>>> Web : http://reuter.mit.edu >>>> >>>> >>>> >>>> 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. >>>> >>>> >>>> >>> >>> >>> >> >> -- >> Martin Reuter, Ph.D. >> Assistant in Neuroscience - Massachusetts General Hospital >> Instructor in Neurology - Harvard Medical School >> MGH / HMS / MIT >> >> A.A.Martinos Center for Biomedical Imaging >> 149 Thirteenth Street, Suite 2301 >> Charlestown, MA 02129 >> >> Phone: +1-617-724-5652 >> Email: >> mreuter(a)nmr.mgh.harvard.edu >> reuter(a)mit.edu >> Web : http://reuter.mit.edu >> >> >> > > > -- Martin Reuter, Ph.D. Assistant in Neuroscience - Massachusetts General Hospital Instructor in Neurology - Harvard Medical School MGH / HMS / MIT A.A.Martinos Center for Biomedical Imaging 149 Thirteenth Street, Suite 2301 Charlestown, MA 02129 Phone: +1-617-724-5652 Email: mreuter(a)nmr.mgh.harvard.edu reuter(a)mit.edu Web : http://reuter.mit.edu

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Merging labels for multiple data sets
by Anupa AV 23 May '13

23 May '13

Dear All, I am having a total of 100 subjects for my analysis. My aim is to seperate DLPFC by making coronal cuts. I know the procedure to do for single subjects. Can anyone help me with the command line for mutiple data sets..? Any help will be greatly appreciated..

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temporal lobe left out in pial surface - edits on brainmask.mgz or brain.finalsurfs.mgz?
by Yizhou Ma 22 May '13

22 May '13

Dear FS experts, I have a subject where large portions of temporal lobe is not included in the pial surface. A member in my lab has suggested edits on brain.finalsurfs.mgz. However, in the following page it is indicated that edits on brain.finalsurfs.mgz is only intended for cases regarding inclusion of cerebellum. Can anyone please let me know which volume I should be working on in this case? http://ftp.nmr.mgh.harvard.edu/fswiki/FsTutorial/PialEdits Thanks, Cherry

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Freesurfer May 2013