Freesurfer

freesurfer@nmr.mgh.harvard.edu

15 participants
30097 discussions

Re: [Freesurfer] nu.mgz intensity too dark
by aqureshi＠nmr.mgh.harvard.edu 08 Aug '13

08 Aug '13

When I looked at orig.mgz it is actually too bright. It's very hard to differentiate white and gray matter from how bright the image is. Maybe that is the root of the problem. I tried correcting it with mri_convert like this: cp orig.mgz holder_orig.mgz mri_convert --scale 3 holder_orig.mgz orig.mgz But scale 2-5 all increase the brightness further, which would probably worsen the problem. I wasn't able to find how to decrease brightness (or increase contrast) in mri_convert --help. How would I decrease the brightness? It does not take negative numbers (like -3). Thanks, Abid ------------------ maybe try scaling up the orig.mgz then? I never really understood why the nu darkens it sometime. Alternatively you could scale up the nu, but you will have already lost dynamic range ------------------ > The 001.mgz actually looks good in this case (in terms of intensity) so > I'm not sure if it makes sense to scale it up further. The problem is with > the nu.mgz being too dark. I'll try it out though if you think it will > also work in this case. > > - Abid > > > --------------- > > you could try using --scale <scale factor> to scale the intensities of the > 001.mgz up > > --------------- > >> Hi Dr. Fischl, >> >> I had a couple subjects that failed recon-all. Although the error log >> said >> recon-all failed at mri_watershed it looks like the root problem is a >> couple steps earlier, because the nu.mgz looks too dark. This was >> discussed in a previous thread from 2008. >> >> http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg07293.html. >> >> You wrote, "p.s. are the 001.mgz and 002.mgz dark? The orig.mgz? >> Sometimes >> nu_correct can create very dark images, and there are some switches you >> can loo through to correct them. Alternatively if it is the 001.mgz, >> mri_convert has a scale option you can use." >> >> On my subject 001.mgz looks good (there was no 002.mgz file). It is only >> nu.mgz that looks too dark. It looks like the solution you gave then was >> for a problematic 001.mgz file, but from your response it looks as if >> the >> problem was nu.mgz the solution would be different. What are the >> switches >> you can loop through to correct the nu.mgz. >> >> Thanks, >> Abid >> >> >

2 1

Re: [Freesurfer] error when using selxavg3-sess in retinotopy analysis
by Sepide Movaghati 08 Aug '13

08 Aug '13

I did the following preprocessing before making the analysis: preproc-sess -s session1 -surface self lhrh -fsd bold -mni305 –fwhm 5 % gives me an error: can not find register.dof6 , but it creates mask files inorm-sess -d $sepidDir/subjects/ZY -s session1 -mask -funcstem fmcpr I have attached the full terminal output after executing selxavg3-sess. Thanks ________________________________________ 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, August 08, 2013 1:21 PM To: freesurfer(a)nmr.mgh.harvard.edu Subject: Re: [Freesurfer] error when using selxavg3-sess in retinotopy analysis hmm, that is a little strange. It is trying to find the preprocessed time series data. If it does not find it, it should generate it. Can you send me the full terminal output? doug On 08/08/2013 01:15 PM, Sepide Movaghati wrote: > thank you for your respond. > I create the subjectname file like the following: > touch subjectname.txt > echo "ZY" > $sessionDir/subjectname.txt > > now I removed the ".txt", and now I am getting this new error: > > outtop = /export01/data/sepid/subjects/ZY > Extension format = nii.gz > Error using MRIread (line 76) > ERROR: cannot determine format of > /export01/data/sepid/subjects/ZY/session1/bold/003/fmcpr.sm5.self.lh (MRIread) > > > Error in flac_customize (line 87) > mri = MRIread(fstem,1); > > Error in fast_selxavg3 (line 65) > flac0 = flac_customize(flac0); > >>> ------------------------------------------ > ERROR: fast_selxavg3() failed\n > > ________________________________________ > 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: Wednesday, August 07, 2013 6:41 PM > To: freesurfer(a)nmr.mgh.harvard.edu > Subject: Re: [Freesurfer] error when using selxavg3-sess in retinotopy analysis > > It is having problems reading the subjectname file in the session > folder. Look in there to see if there is something obviously wrong. Did > you create it on a windows computer? > doug > > > On 08/07/2013 04:16 PM, Sepide Movaghati wrote: >> Hi, >> >> I followed the steps for doing the retinotopy analysis. At the end I >> made my analysis as follows: >> >> mkanalysis-sess -a Retinotopy_ZY -surface self lh -TR 2 -retinotopy >> 36-paradigm rtopy.par -fsd bold -fwhm 5 >> >> and then execute selxavg3-sess: >> selxavg3-sess –a Retinotopy_ZY –s session1 >> >> then I got this error which I do not how to solve it: >> >> outtop = /export01/data/sepid/subjects/ZY >> Extension format = nii.gz >> Error using fscanf >> Invalid file identifier. Use fopen to generate a valid file identifier. >> >> Error in flac_customize (line 47) >> flacnew.sourcesubject = fscanf(fp,'%s',1); >> >> Error in fast_selxavg3 (line 65) >> flac0 = flac_customize(flac0); >> >>>> ------------------------------------------ >> ERROR: fast_selxavg3() failed\n >> >> >> I would appreciate if you help me through this. >> Regards, >> Sepide >> >> - >> >> I >> >> >> I >> >> - >> >> >> >> >> >> a >> >> >> >> _______________________________________________ >> 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. > > > _______________________________________________ > 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

2 2

QDEC error in asegstats2table
by Rando, Kenneth 08 Aug '13

08 Aug '13

Hello Experts, This QDEC error is one that appears in the archives, but I did not see a solution that solves my problem. The error (after some information about initialization of the program) is as follows: SUBJECTS_DIR : /home/freesurfer_ocd Parsing the .stats files ERROR: The stats file /home/freesurfer_ocd/tb0314 /stats/aseg.stats is not found or is too small to be a valid statsfile Use --skip flag to automatically skip bad stats files ERROR: In /usr/pubsw/packages/KWWidgets/CVS-vtk560/KWWidgets/vtkKWTkUtilities.cxx, line 230 vtkKWQdecApp (0x27a1f070): Script: vtkTemp2 GenerateStatsDataTables Returned Error on line 1: Uncaught exception: command failed: asegstats2table --common-segs --meas volume --tablefile /home/freesurfer_ocd/qdec/stats_tables/aseg.volume.stats.dat --statsfile=aseg.stats --subjects ta0743 ta0860 tb0168 tb0183 tb0195 tb0294 tb0314 tb0341 tb0529 tb0628 tb0728 tb0791 tb0817 tb0850 tb0861 tb0892 tb0901 tb1012 tb1043 tb1086 tb1450 tb1464 tb1646 tb1751 tb2002 tb2073 tr7582 tr7733 tr7825 tr7901 tr7932 tr7987 tr8167 tr8222 tr8240 tr8285 tr8345 tr8511 tr8529 tr8688 tr8740 tr8791 tr8860 tr9043 tr9124 tr9222 tr9332 tr9459 tr9515 tr9561 tr9707 tr9746 tr9765 tr9824 Stack trace: Uncaught exception: command failed: asegstats2table --common-segs --meas volume --tablefile /home/freesurfer_ocd/qdec/stats_tables/aseg.volume.stats.dat --statsfile=aseg.stats --subjects ta0743 ta0860 tb0168 tb0183 tb0195 tb0294 tb0314 tb0341 tb0529 tb0628 tb0728 tb0791 tb0817 tb0850 tb0861 tb0892 tb0901 tb1012 tb1043 tb1086 tb1450 tb1464 tb1646 tb1751 tb2002 tb2073 tr7582 tr7733 tr7825 tr7901 tr7932 tr7987 tr8167 tr8222 tr8240 tr8285 tr8345 tr8511 tr8529 tr8688 tr8740 tr8791 tr8860 tr9043 tr9124 tr9222 tr9332 tr9459 tr9515 tr9561 tr9707 tr9746 tr9765 tr9824 while executing "vtkTemp2 GenerateStatsDataTables" The error occurs at the seventh subject in the dataset, so it appears to be subject-specific. As recommended in previous posts, I have verified that the aseg.stats file exists for that subject. I am new to Freesurfer, but a comparison of this aseg.stats file to the previous subject's file and a few others reveals no obvious differences (e.g., missing lines, extreme or corrupt data values). One response to an earlier post asked the user to run asegstats2table -i aseg.stats -t test.dat in the stats directory of the file with the error. I followed that advice and it produces a file for this subject. There was, however, no follow-up posting, so I don't know what that indicates, and how I should follow-up. Thanks for your help. Ken Kenneth Rando Research Assistant 2 203-974-7731 Yale OCD Research Clinic Yale University School of Medicine Connecticut Mental Health Center 34 Park Street, Room W309 New Haven, CT 06519

2 1

Corpus Callosum thickness
by Joao Pedro Battistella Nadas 08 Aug '13

08 Aug '13

Hi all, I need to perform segmentation of the whole Corpus Callosum but I don't really know how the determine which thickness should I use to extract all of it (or at least most of it). Does anyone know what would be typical thickness of CC (the distance along coronal axis) or if is there a way to determine this optimal thickness for a given volume? thank you, João Pedro Battistella Nadas

1 0

Re: [Freesurfer] hippo_subfields atlas
by Rajapillai Pillai 08 Aug '13

08 Aug '13

Okay--thanks for clearing that up. Two follow-up questions: 1. Can we get a full T1 weighted volume corresponding to imagedump.mgz reference volume that includes the entire brain? 2. Would it be possible to get the original T1 images and their manual labels from which the reference volume was constructed? Thank you very much for your patience, and for responding so promptly. Raja On Thu, Aug 8, 2013 at 4:47 PM, Juan Eugenio Iglesias < iglesias(a)nmr.mgh.harvard.edu> wrote: > PS I don't see why you would want to use any other mesh in the collection > other than the reference (index -1) > > > > > On 08/08/2013 04:35 PM, Rajapillai Pillai wrote: > > V > ery funny indeed...so, just for absolute clarification is there a > one-to-one correspondence between the order listed in the mesh collection > and the order in the lookup tables? i.e. does label 2 (CSF) correspond to > position -1 (reference)? Does label 8 (left subiculum) correspond to > position 9? > > Also, when I open a given rasterized file, it shows me a subfield view > of a particular area. If we wanted to register this with another image, how > would we do it--could we find bounding box coordinates? Or can we access > the entire t1 weighted image? > > Best regards, > Raja > > > > On Thu, Aug 8, 2013 at 4:23 PM, Juan Eugenio Iglesias < > iglesias(a)nmr.mgh.harvard.edu> wrote: > >> It's a funny coincidence that the number of meshes is equal to the >> number of labels... For each mesh, you can rasterize all labels, indexed as >> in the table. >> Cheers, >> /Eugenio >> >> >> >> On 08/08/2013 04:21 PM, Rajapillai Pillai wrote: >> >> Okay. I'm still a little unclear. So I'm looking at the compression >> lookup file (left in this case) and seeing this: >> >> 24 2 CSF 60 60 60 255 >> 2 0 Left-Cerebral-White-Matter 0 225 0 255 >> 3 1 Left-Cerebral-Cortex 205 62 78 255 <205%2062%2078%20255> >> 17 3 Left-Hippocampus 220 216 20 255 >> 550 5 left_CA2_3 17 85 136 255 >> 552 9 left_CA1 204 68 34 255 <204%2068%2034%20255> >> 553 4 left_fimbria 204 0 255 255 >> 554 7 left_presubiculum 221 187 17 255 >> 555 10 left_hippocampal_fissure 153 221 238 255 >> 556 6 left_CA4_DG 51 17 17 255 >> 557 8 left_subiculum 0 119 85 255 >> >> Then when I look at the CurrentMeshCollection, I am seeing Positions >> 0-9, and the reference position, which as you said is -1. What is the >> correspondence between these labels and meshes? Sorry if I'm being >> obtuse--I'm just having trouble piecing it all together. >> >> Best regards, >> Raja >> >> >> On Thu, Aug 8, 2013 at 1:49 PM, Juan Eugenio Iglesias < >> iglesias(a)nmr.mgh.harvard.edu> wrote: >> >>> Hi again, Raja. >>> Which labels and meshes to use depends on what you want to do. If you >>> extract all the priors corresponding to all the labels in the atlas (the >>> list is in $FREESURFER_HOME/data/GEMS/compressionLookupTable.txt), you >>> would have a volumetric version of the atlas (rather than a mesh). >>> Cheers, >>> /Eugenio >>> >>> >>> >>> On 08/07/2013 06:04 PM, Rajapillai Pillai wrote: >>> >>> Final question regarding this: what combinations of labels and meshes >>> should I use? Should I do all combinations between labels and positions, >>> matching labels/positions only, etc? How can I tell which meshes correspond >>> to what labels/areas? >>> >>> Thanks for your time, >>> Raja >>> >>> >>> On Wed, Aug 7, 2013 at 4:26 PM, Rajapillai Pillai < >>> raja.i.pillai(a)gmail.com> wrote: >>> >>>> Thanks very much! >>>> >>>> >>>> On Wed, Aug 7, 2013 at 4:23 PM, Juan Eugenio Iglesias < >>>> iglesias(a)nmr.mgh.harvard.edu> wrote: >>>> >>>>> Shame on me; there's a way of doing this. You need a reference >>>>> volume; for the hippocampal subfield atlas: >>>>> $FREESURFER_HOME/data/GEMS/CurrentMeshCollection30.gz >>>>> the reference volume would be: >>>>> $FREESURFER_HOME/data/GEMS/imageDump.mgz >>>>> >>>>> The command would be: >>>>> >>>>> kvlRasterizeAtlasMesh CurrentMeshCollection30.gz imageDump.mgz >>>>> [labelNumber] [meshNumber] >>>>> >>>>> "meshNumber" is the index of the mesh to extract in the collection; >>>>> use -1 for the reference position. >>>>> labelNumber is the label whose probability map you want to rasterize ( >>>>> 0 = white matter, 1 = gray matter, 2 = CSF, 9 = CA1, etc; see >>>>> $FREESURFER_HOME/data/GEMS/compressionLookupTable.txt). >>>>> >>>>> From the volumetric rasterized prior probability map, you can easily >>>>> compute volumes, if you want. >>>>> >>>>> Cheers, and sorry again for the original wrong answer, >>>>> >>>>> /Eugenio >>>>> >>>>> >>>>> >>>>> >>>>> >>>>> On 08/07/2013 01:30 PM, Rajapillai Pillai wrote: >>>>> >>>>> Hi again! >>>>> >>>>> I have another question about the hippocampal subfields atlas--might >>>>> be a silly one. Is there a way to extract volumes from the mesh collection? >>>>> >>>>> Thanks a lot, >>>>> Raja >>>>> >>>>> >>>>> On Wed, Jul 31, 2013 at 5:06 PM, Juan Eugenio Iglesias < >>>>> iglesias(a)nmr.mgh.harvard.edu> wrote: >>>>> >>>>>> Sounds good, but please email the list, rather than only me ;-) >>>>>> /E >>>>>> >>>>>> >>>>>> On 07/31/2013 05:03 PM, Rajapillai Pillai wrote: >>>>>> >>>>>> Thanks a lot. I'll let you know if I have any more issues. >>>>>> >>>>>> Best regards, >>>>>> Raja >>>>>> >>>>>> >>>>>> On Wed, Jul 31, 2013 at 4:44 PM, Juan Eugenio Iglesias < >>>>>> iglesias(a)nmr.mgh.harvard.edu> wrote: >>>>>> >>>>>>> Did you run recon-all -subjid bert -hippo-subfields? If so, there >>>>>>> should be a log file with the output from the hippo-subfield code in >>>>>>> $SUBJECTS_DIR/bert/scripts/hippo-subfields.log. You can take a look at it >>>>>>> to get an idea of what happened. >>>>>>> Kind regards, >>>>>>> /Eugenio >>>>>>> >>>>>>> >>>>>>> On 07/31/2013 04:38 PM, Rajapillai Pillai wrote: >>>>>>> >>>>>>> Thanks very much for the prompt response. The command I ran was >>>>>>> >>>>>>> $ kvlQuantifyPosteriorProbabilityImages >>>>>>> /Applications/freesurfer/data/GEMS/compressionLookupTable.txt >>>>>>> posterior_right_* posterior_Right-Hippocampus.mgz >>>>>>> >>>>>>> in $SUBJECTS_DIR/bert/mri >>>>>>> >>>>>>> And yeah, it's not in the mri directory. Any idea what might have >>>>>>> gone wrong and how I can try and fix it? >>>>>>> >>>>>>> Thanks, >>>>>>> Raja >>>>>>> >>>>>>> >>>>>>> On Wed, Jul 31, 2013 at 4:29 PM, Juan Eugenio Iglesias < >>>>>>> iglesias(a)nmr.mgh.harvard.edu> wrote: >>>>>>> >>>>>>>> Hi Raja, >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> I'm have a question regarding the GEMS hippocampal segmentation. I >>>>>>>> saw on the wiki how to run -hippo_subfields, but how do I access the atlas >>>>>>>> itself? What file is it under. >>>>>>>> >>>>>>>> >>>>>>>> That would be >>>>>>>> $FREESURFER_HOME/data/GEMS/CurrentMeshCollection30.gz >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> Also, I'm not sure if I'm missing some files: whenever I try to >>>>>>>> do one of the individual commands using, for example, >>>>>>>> posterior_Right_Hippocampus.mgz, it gives the following error: >>>>>>>> >>>>>>>> volumeInVoxels: >>>>>>>> terminate called after throwing an instance of >>>>>>>> 'itk::ExceptionObject' >>>>>>>> what(): itkMGHImageIO.cxx:216: >>>>>>>> itk::ERROR: MGHImageIO(0x56b5c0): Can't find/open file: >>>>>>>> posterior_Right-Hippocampus.mgz >>>>>>>> Abort trap >>>>>>>> >>>>>>>> >>>>>>>> What command is this? In any case, it's pretty clear that the file >>>>>>>> is missing.... >>>>>>>> >>>>>>>> >>>>>>>> Also, upon searching through my freesurfer directory, I cannot >>>>>>>> find any posterior_Right-Hippocamus.mgz or posterior_Left-Hippocampus.mgz >>>>>>>> files. >>>>>>>> >>>>>>>> It should be under the "mri" directory. If it isn't, there was >>>>>>>> some problem running the algorithms. >>>>>>>> >>>>>>>> Cheers, >>>>>>>> >>>>>>>> /Eugenio >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> Thanks very much for your time, >>>>>>>> Raja >>>>>>>> >>>>>>>> >>>>>>>> _______________________________________________ >>>>>>>> Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>>>>>>> >>>>>>>> >>>>>>>> -- >>>>>>>> ------------------------------------------------------------------------------------- >>>>>>>> Juan Eugenio Iglesias, PhDhttp://www.jeiglesias.comiglesias@nmr.mgh.harvard.edu >>>>>>>> Athinoula A. Martinos Center for Biomedical Imaging >>>>>>>> 149 Thirteenth Street, Suite 2301 >>>>>>>> Charlestown, Massachusetts 2129 >>>>>>>> U.S.A. >>>>>>>> >>>>>>>> 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. >>>>>>>> >>>>>>> >>>>>>> >>>>>>> -- >>>>>>> ------------------------------------------------------------------------------------- >>>>>>> Juan Eugenio Iglesias, PhDhttp://www.jeiglesias.comiglesias@nmr.mgh.harvard.edu >>>>>>> Athinoula A. Martinos Center for Biomedical Imaging >>>>>>> 149 Thirteenth Street, Suite 2301 >>>>>>> Charlestown, Massachusetts 2129 >>>>>>> U.S.A. >>>>>>> >>>>>>> >>>>>> >>>>>> -- >>>>>> ------------------------------------------------------------------------------------- >>>>>> Juan Eugenio Iglesias, PhDhttp://www.jeiglesias.comiglesias@nmr.mgh.harvard.edu >>>>>> Athinoula A. Martinos Center for Biomedical Imaging >>>>>> 149 Thirteenth Street, Suite 2301 >>>>>> Charlestown, Massachusetts 2129 >>>>>> U.S.A. >>>>>> >>>>>> >>>>> >>>>> >>>>> _______________________________________________ >>>>> Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>>>> >>>>> >>>>> -- >>>>> ------------------------------------------------------------------------------------- >>>>> Juan Eugenio Iglesias, PhDhttp://www.jeiglesias.comiglesias@nmr.mgh.harvard.edu >>>>> Athinoula A. Martinos Center for Biomedical Imaging >>>>> 149 Thirteenth Street, Suite 2301 >>>>> Charlestown, Massachusetts 2129 >>>>> U.S.A. >>>>> >>>>> >>>> >>> >>> -- >>> ------------------------------------------------------------------------------------- >>> Juan Eugenio Iglesias, PhDhttp://www.jeiglesias.comiglesias@nmr.mgh.harvard.edu >>> Athinoula A. Martinos Center for Biomedical Imaging >>> 149 Thirteenth Street, Suite 2301 >>> Charlestown, Massachusetts 2129 >>> U.S.A. >>> >>> >> >> -- >> ------------------------------------------------------------------------------------- >> Juan Eugenio Iglesias, PhDhttp://www.jeiglesias.comiglesias@nmr.mgh.harvard.edu >> Athinoula A. Martinos Center for Biomedical Imaging >> 149 Thirteenth Street, Suite 2301 >> Charlestown, Massachusetts 2129 >> U.S.A. >> >> > > -- > ------------------------------------------------------------------------------------- > Juan Eugenio Iglesias, PhDhttp://www.jeiglesias.comiglesias@nmr.mgh.harvard.edu > Athinoula A. Martinos Center for Biomedical Imaging > 149 Thirteenth Street, Suite 2301 > Charlestown, Massachusetts 2129 > U.S.A. > >

2 1

Re: [Freesurfer] hippo_subfields atlas
by Rajapillai Pillai 08 Aug '13

08 Aug '13

Hi again! I have another question about the hippocampal subfields atlas--might be a silly one. Is there a way to extract volumes from the mesh collection? Thanks a lot, Raja On Wed, Jul 31, 2013 at 5:06 PM, Juan Eugenio Iglesias < iglesias(a)nmr.mgh.harvard.edu> wrote: > Sounds good, but please email the list, rather than only me ;-) > /E > > > On 07/31/2013 05:03 PM, Rajapillai Pillai wrote: > > Thanks a lot. I'll let you know if I have any more issues. > > Best regards, > Raja > > > On Wed, Jul 31, 2013 at 4:44 PM, Juan Eugenio Iglesias < > iglesias(a)nmr.mgh.harvard.edu> wrote: > >> Did you run recon-all -subjid bert -hippo-subfields? If so, there should >> be a log file with the output from the hippo-subfield code in >> $SUBJECTS_DIR/bert/scripts/hippo-subfields.log. You can take a look at it >> to get an idea of what happened. >> Kind regards, >> /Eugenio >> >> >> On 07/31/2013 04:38 PM, Rajapillai Pillai wrote: >> >> Thanks very much for the prompt response. The command I ran was >> >> $ kvlQuantifyPosteriorProbabilityImages >> /Applications/freesurfer/data/GEMS/compressionLookupTable.txt >> posterior_right_* posterior_Right-Hippocampus.mgz >> >> in $SUBJECTS_DIR/bert/mri >> >> And yeah, it's not in the mri directory. Any idea what might have gone >> wrong and how I can try and fix it? >> >> Thanks, >> Raja >> >> >> On Wed, Jul 31, 2013 at 4:29 PM, Juan Eugenio Iglesias < >> iglesias(a)nmr.mgh.harvard.edu> wrote: >> >>> Hi Raja, >>> >>> >>> >>> I'm have a question regarding the GEMS hippocampal segmentation. I saw >>> on the wiki how to run -hippo_subfields, but how do I access the atlas >>> itself? What file is it under. >>> >>> >>> That would be $FREESURFER_HOME/data/GEMS/CurrentMeshCollection30.gz >>> >>> >>> >>> Also, I'm not sure if I'm missing some files: whenever I try to do one >>> of the individual commands using, for example, >>> posterior_Right_Hippocampus.mgz, it gives the following error: >>> >>> volumeInVoxels: >>> terminate called after throwing an instance of 'itk::ExceptionObject' >>> what(): itkMGHImageIO.cxx:216: >>> itk::ERROR: MGHImageIO(0x56b5c0): Can't find/open file: >>> posterior_Right-Hippocampus.mgz >>> Abort trap >>> >>> >>> What command is this? In any case, it's pretty clear that the file is >>> missing.... >>> >>> >>> Also, upon searching through my freesurfer directory, I cannot find >>> any posterior_Right-Hippocamus.mgz or posterior_Left-Hippocampus.mgz files. >>> >>> It should be under the "mri" directory. If it isn't, there was some >>> problem running the algorithms. >>> >>> Cheers, >>> >>> /Eugenio >>> >>> >>> >>> >>> >>> Thanks very much for your time, >>> Raja >>> >>> >>> _______________________________________________ >>> Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>> >>> >>> -- >>> ------------------------------------------------------------------------------------- >>> Juan Eugenio Iglesias, PhDhttp://www.jeiglesias.comiglesias@nmr.mgh.harvard.edu >>> Athinoula A. Martinos Center for Biomedical Imaging >>> 149 Thirteenth Street, Suite 2301 >>> Charlestown, Massachusetts 2129 >>> U.S.A. >>> >>> 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. >>> >> >> >> -- >> ------------------------------------------------------------------------------------- >> Juan Eugenio Iglesias, PhDhttp://www.jeiglesias.comiglesias@nmr.mgh.harvard.edu >> Athinoula A. Martinos Center for Biomedical Imaging >> 149 Thirteenth Street, Suite 2301 >> Charlestown, Massachusetts 2129 >> U.S.A. >> >> > > -- > ------------------------------------------------------------------------------------- > Juan Eugenio Iglesias, PhDhttp://www.jeiglesias.comiglesias@nmr.mgh.harvard.edu > Athinoula A. Martinos Center for Biomedical Imaging > 149 Thirteenth Street, Suite 2301 > Charlestown, Massachusetts 2129 > U.S.A. > >

2 9

CUDA binaries
by Jordi Delgado 08 Aug '13

08 Aug '13

Dear freesurfers, I'm trying to exploit CUDA capabilities by using recon-all with -use-gpu. On the freesurfer wiki I found an approximate speedups for the main CUDA implementations in Freesurfer ( http://ftp.nmr.mgh.harvard.edu/fswiki/CUDADevelopersGuide) But I can't found mri_watershed_cuda and mri_ca_label_cuda on my freesurfer5.3/bin folder, and neither on previous versions. Are these implementations available? I tried to found the CUDA binaries on ( ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/) without luck. I know that CUDA support is no longer offered but it seems interesting to enable all the -cuda binaries executions to measure the improvement. And finally I would know if the cuda binaries offered in 5.3 version are compiled for a Fermi or Tesla? I hope that you are enjoying the summer! Kind regards,

2 1

error when using selxavg3-sess in retinotopy analysis
by Sepide Movaghati 08 Aug '13

08 Aug '13

thank you for your respond. I create the subjectname file like the following: touch subjectname.txt echo "ZY" > $sessionDir/subjectname.txt now I removed the ".txt", and now I am getting this new error: outtop = /export01/data/sepid/subjects/ZY Extension format = nii.gz Error using MRIread (line 76) ERROR: cannot determine format of /export01/data/sepid/subjects/ZY/session1/bold/003/fmcpr.sm5.self.lh (MRIread) Error in flac_customize (line 87) mri = MRIread(fstem,1); Error in fast_selxavg3 (line 65) flac0 = flac_customize(flac0); >> ------------------------------------------ ERROR: fast_selxavg3() failed\n ________________________________________ 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: Wednesday, August 07, 2013 6:41 PM To: freesurfer(a)nmr.mgh.harvard.edu Subject: Re: [Freesurfer] error when using selxavg3-sess in retinotopy analysis It is having problems reading the subjectname file in the session folder. Look in there to see if there is something obviously wrong. Did you create it on a windows computer? doug On 08/07/2013 04:16 PM, Sepide Movaghati wrote: > Hi, > > I followed the steps for doing the retinotopy analysis. At the end I > made my analysis as follows: > > mkanalysis-sess -a Retinotopy_ZY -surface self lh -TR 2 -retinotopy > 36-paradigm rtopy.par -fsd bold -fwhm 5 > > and then execute selxavg3-sess: > selxavg3-sess –a Retinotopy_ZY –s session1 > > then I got this error which I do not how to solve it: > > outtop = /export01/data/sepid/subjects/ZY > Extension format = nii.gz > Error using fscanf > Invalid file identifier. Use fopen to generate a valid file identifier. > > Error in flac_customize (line 47) > flacnew.sourcesubject = fscanf(fp,'%s',1); > > Error in fast_selxavg3 (line 65) > flac0 = flac_customize(flac0); > > >> ------------------------------------------ > ERROR: fast_selxavg3() failed\n > > > I would appreciate if you help me through this. > Regards, > Sepide > > - > > I > > > I > > - > > > > > > a > > > > _______________________________________________ > 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.

2 1

Re: [Freesurfer] Different results in surface and volume analyses
by Emily Boeke 08 Aug '13

08 Aug '13

Hi Doug, Thanks for the response. Is this masking out of the cortical regions in the volume analysis a newer aspect of the processing stream? Previously I have seen this activation in the volume. It would be great if you could let me know the flags to see the full volume analysis. Thanks! Emily Message: 41 Date: Wed, 07 Aug 2013 19:29:33 -0400 From: Douglas N Greve <greve(a)nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] Different results in surface and volume analyses To: freesurfer(a)nmr.mgh.harvard.edu Message-ID: <5202D85D.1090808(a)nmr.mgh.harvard.edu> Content-Type: text/plain; charset=ISO-8859-1; format=flowed Hi Emily, the processing stream is designed to mask out cortical regions from the volume analysis. The volume analysis is used for subcortical structures. To make sure that the same voxels are not analyzed twice, the cortical surface is masked out of the mni305 analysis. doug ps. If you really want to see the full volume analysis, then there are some flags that will do this. Message: 14 Date: Wed, 7 Aug 2013 13:15:37 -0400 From: Emily Boeke <eboeke01(a)nmr.mgh.harvard.edu> Subject: [Freesurfer] Different results in surface and volume analyses To: freesurfer(a)nmr.mgh.harvard.edu Message-ID: <948E8FDF-754A-4AE0-A0C9-86D848F1438A(a)nmr.mgh.harvard.edu> Content-Type: text/plain; charset=us-ascii Hello everyone, I am looking at a visual stimulus vs fixation contrast in my individual subjects' data to make sure we are seeing normal activation there. If I look at the surface data in tksurfer, I see activation in the occipital cortex, but in the mni305 analysis, there is no activation in this region. These are the preprocess , mkanalysis, and selxavg commands I used for the surface vs. mni305: preproc-sess -s amur_dss -df sesspar -per-run -fwhm 5 -sliceorder down -surface fsaverage lhrh -mni305-2mm -fsd cond mkanalysis-sess -fsd cond -surface fsaverage lh -fwhm 5 -paradigm Fear_Gen_Cond.par -event-related -TR 3 -nconditions 3 -polyfit 4 -spmhrf 0 -refeventdur 6 -analysis cond.sm05.lh -per-run -nskip 4 -stc down mkanalysis-sess -fsd cond -surface fsaverage rh -fwhm 5 -paradigm Fear_Gen_Cond.par -event-related -TR 3 -nconditions 3 -polyfit 4 -spmhrf 0 -refeventdur 6 -analysis cond.sm05.rh -per-run -nskip 4 -stc down mkanalysis-sess -fsd cond -mni305 2 -fwhm 5 -paradigm Fear_Gen_Cond.par -event-related -TR 3 -nconditions 3 -polyfit 4 -spmhrf 0 -refeventdur 6 -analysis cond.sm05.mni305 -per-run -nskip 4 -stc down selxavg3-sess -s amur_dss -df sesspar -analysis cond.sm.lh selxavg3-sess -s amur_dss -df sesspar -analysis cond.sm.rh selxavg3-sess -s amur_dss -df sesspar -analysis cond.sm.mni305 Why might we be seeing this activation on the surface map but not the volume one? Thanks! Emily

2 1

(no subject)
by aqureshi＠nmr.mgh.harvard.edu 08 Aug '13

08 Aug '13

Hi Dr. Fischl, I had a couple subjects that failed recon-all. Although the error log said recon-all failed at mri_watershed it looks like the root problem is a couple steps earlier, because the nu.mgz looks too dark. This was discussed in a previous thread from 2008. http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg07293.html. You wrote, "p.s. are the 001.mgz and 002.mgz dark? The orig.mgz? Sometimes nu_correct can create very dark images, and there are some switches you can loo through to correct them. Alternatively if it is the 001.mgz, mri_convert has a scale option you can use." On my subject 001.mgz looks good (there was no 002.mgz file). It is only nu.mgz that looks too dark. It looks like the solution you gave then was for a problematic 001.mgz file, but from your response it looks as if the problem was nu.mgz the solution would be different. What are the switches you can loop through to correct the nu.mgz. Thanks, Abid

3 4

Jump to page:

2026

2025

2024

2023

2022

2021

2020

2019

2018

2017

2016

2015

2014

2013

2012

2011

2010

2009

2008

2007

2006

2005

2004

Freesurfer